publications

Porubsky D, Dashnow H, Sasani TA, Logsdon GA, Hallast P, Noyes MD, Kronenberg ZN, Mokveld T, Koundinya N, Nolan C, Steely CJ, Guarracino A, Dolzhenko E, Harvey WT, Rowell WJ, Grigorev K, Nicholas TJ, Goldberg ME, Oshima KK, Lin J, Ebert P, Watkins WS, Leung TY, Hanlon VCT, McGee S, Pedersen BS, Happ HC, Jeong H, Munson KM, Hoekzema K, Chan DD, Wang Y, Knuth J, Garcia GH, Fanslow C, Lambert C, Lee C, Smith JD, Levy S, Mason CE, Garrison E, Lansdorp PM, Neklason DW, Jorde LB, Quinlan AR, Eberle MA, Eichler EE. (2025). Human de novo mutation rates from a four-generation pedigree reference. Nature Apr 23. doi: 10.1038/s41586-025-08922-2. Online ahead of print.

Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O’Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. (2024). Complete sequencing of ape genomes. Nature Apr 9. doi: 10.1038/s41586-025-08816-3. Online ahead of print.

Dubocanin D, Hartley GA, Sedeño Cortés AE, Mao Y, Hedouin S, Ranchalis J, Agarwal A, Logsdon GA, Munson KM, Real T, Mallory BJ, Eichler EE, Biggins S, O’Neill RJ, Stergachis AB. (2025). Conservation of dichromatin organization along regional centromeres. Cell Genom Apr 9;5(4):100819.

Haberman M, Kamyshinsky R, Reznik N, Yeshaya N, Khmelnitsky L, Plender EG, Eichler EE, Fass D. (2025). MUC5AC filaments illuminate the structural diversification of respiratory and intestinal mucins. Proc Natl Acad Sci U S A Mar 11;122(10):e2419717122.

Zhang S, Xu N, Fu L, Yang X, Ma K, Li Y, Yang Z, Li Z, Feng Y, Jiang X, Han J, Hu R, Zhang L, Lian D, de Gennaro L, Paparella A, Ryabov F, Meng D, He Y, Wu D, Yang C, Mao Y, Bian X, Lu Y, Antonacci F, Ventura M, Shepelev VA, Miga KH, Alexandrov IA, Logsdon GA, Phillippy AM, Su B, Zhang G, Eichler EE, Lu Q, Shi Y, Sun Q, Mao Y. (2025). Integrated analysis of the complete sequence of a macaque genome. Nature Apr;640(8059):714-721.

Jeong H, Dishuck PC, Yoo D, Harvey WT, Munson KM, Lewis AP, Kordosky J, Garcia GH; Human Genome Structural Variation Consortium (HGSVC); Yilmaz F, Hallast P, Lee C, Pastinen T, Eichler EE. (2025). Structural polymorphism and diversity of human segmental duplications. Nat Genet Feb;57(2):390–401.

Rea HM, Webb SJ, Kurtz-Nelson EC, Hudac CM, Bernier RA, Miles C, Earl R, Whiting A, Eayrs C, Johansson M, Wang T, Eichler EE, Neuhaus E. (2025). Characterizing executive functioning and associated behaviors in individuals with dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) syndrome. Front Neurosci Jan 7;18:1485499.

Li C, Bonder MJ, Syed S, Jensen M; Human Genome Structural Variation Consortium (HGSVC); HGSVC Functional Analysis Working Group; Gerstein MB, Zody MC, Chaisson MJP, Talkowski ME, Marschall T, Korbel JO, Eichler EE, Lee C, Shi X. (2024). An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Genome Res Dec 23;34(12):2304-2318.

Micale L, Vourlia A, Fusco C, Pracella R, Karagiannis DC, Nardella G, Vaccaro L, Leone MP, Gramazio A, Dentici ML, Aiello C, Novelli A, Xenou L, Sui Y, Eichler EE, Cacchiarelli D, Mavrothalassitis G, Castori M. (2024). Heterozygous variants disrupting the interaction of ERF with activated ERK1/2 cause microcephaly, developmental delay, and skeletal anomalies. Eur J Hum Genet Dec 12. doi: 10.1038/s41431-024-01721-9. Online ahead of print.

Mastrorosa FK, Oshima KK, Rozanski AN, Harvey WT, Eichler EE, Logsdon GA. (2024). Identification and annotation of centromeric hypomethylated regions with CDR-Finder. Bioinformatics Nov 28;40(12):btae733. doi: 10.1093/bioinformatics/btae733.

Guitart X, Porubsky D, Yoo D, Dougherty ML, Dishuck PC, Munson KM, Lewis AP, Hoekzema K, Knuth J, Chang S, Pastinen T, Eichler EE. (2024). Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans. Genome Res Nov 20;34(11):1798-1810.

Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson ZB, Storz SH, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves CE, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal C, Zakarian C, Goodwin S, Jensen TD, Robb E; 1000 Genomes ONT Sequencing Consortium; University of Washington Center for Rare Disease Research (UW-CRDR); Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium; McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. (2024). High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. Genome Res Nov 20;34(11):2061-2073.

Duan W, Huang G, Sui Y, Wang K, Yu Y, Chu X, Cao X, Chen L, Liu J, Eichler EE, Xiong B. (2024). Deficiency of DDX3X results in neurogenesis defects and abnormal behaviors via dysfunction of the Notch signaling. Proc Natl Acad Sci U S A Nov 5;121(45):e2404173121. doi: 10.1073/pnas.2404173121. Epub 2024 Oct 29.

Zalusky MP, Gustafson JA, Bohaczuk SC, Mallory B, Reed P, Wenger T, Beckman E, Chang IJ, Paschal CR, Buchan JG, Lockwood CM, Puia-Dumitrescu M, Garalde DR, Guillory J, Markham AJ, Bamshad MJ, Eichler EE, Stergachis AB, Miller DE. (2024). 3-hour genome sequencing and targeted analysis to rapidly assess genetic risk. Genet Med 2024;2:101833. doi: 10.1016/j.gimo.2024.101833. Epub 2024 Feb 24.

Henglin M, Ghareghani M, Harvey WT, Porubsky D, Koren S, Eichler EE, Ebert P, Marschall T. (2024). Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing. Genome Biol Oct 10;25(1):265.

Fornezza S, Delvecchio VS, Harvey WT, Dishuck PC, Eichler EE, Giannuzzi G. (2024). AGAP duplicons associate with structural diversity at Chromosome 10q11.22. Genome Res Oct 29;34(10):1487–1499.

Blackburn PR, Ebstein F, Hsieh TC, Motta M, Radio FC, Herkert JC, Rinne T, Thiffault I, Rapp M, Alders M, Maas S, Gerard B, Smol T, Vincent-Delorme C, Cogné B, Isidor B, Vincent M, Bachmann-Gagescu R, Rauch A, Joset P, Ferrero GB, Ciolfi A, Husson T, Guerrot AM, Bacino C, Macmurdo C, Thompson SS, Rosenfeld JA, Faivre L, Mau-Them FT, Deb W, Vignard V, Agrawal PB, Madden JA, Goldenberg A, Lecoquierre F, Zech M, Prokisch H, Necpál J, Jech R, Winkelmann J, Koprušáková MT, Konstantopoulou V, Younce JR, Shinawi M, Mighton C, Fung C, Morel CF, Lerner-Ellis J, DiTroia S, Barth M, Bonneau D, Krapels I, Stegmann APA, van der Schoot V, Brunet T, Bußmann C, Mignot C, Zampino G, Wortmann SB, Mayr JA, Feichtinger RG, Courtin T, Ravelli C, Keren B, Ziegler A, Hasadsri L, Pichurin PN, Klee EW, Grand K, Sanchez-Lara PA, Krüger E, Bézieau S, Klinkhammer H, Krawitz PM, Eichler EE, Tartaglia M, Küry S, Wang T. (2024). Loss-of-function variants in CUL3 cause a syndromic neurodevelopmental disorder. Ann Neurol Sep 20. doi: 10.1002/ana.27077. Online ahead of print.

Plender EG, Prodanov T, Hsieh P, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, O’Neal WK, Valdmanis PN, Marschall T, Bloom JD, Eichler EE. (2024). Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B. Am J Hum Genet Aug 8;111(8):1700-1716.

Hudac CM, Dommer K, Mahony M, DesChamps TD, Cairney B, Earl R, Kurtz-Nelson EC, Bradshaw J, Bernier RA, Eichler EE, Neuhaus E, Webb SJ, Shic F. (2024). Visual and auditory attention in individuals with DYRK1A and SCN2A disruptive variants. Autism Res Jul 30. doi: 10.1002/aur.3202. Online ahead of print.

van der Sluijs PJ, Gösgens M, Dingemans AJM, Striano P, Riva A, Mignot C, Faudet A, Vasileiou G, Walther M, Schrier Vergano SA, Alders M, Alkuraya FS, Alorainy I, Alsaif HS, Anderlid B, Bache I, van Beek I, Blanluet M, van Bon BW, Brunet T, Brunner H, Carriero ML, Charles P, Chatron N, Coccia E, Dubourg C, Earl RK, Eichler EE, Faivre L, Foulds N, Graziano C, Guerrot AM, Hashem MO, Heide S, Heron D, Hickey SE, Hopman SMJ, Kattentidt-Mouravieva A, Kerkhof J, Klein Wassink-Ruiter JS, Kurtz-Nelson EC, Kušíková K, Kvarnung M, Lecoquierre F, Leszinski GS, Loberti L, Magoulas PL, Mari F, Maystadt I, Merla G, Milunsky JM, Moortgat S, Nicolas G, Leary MO’, Odent S, Ozmore JR, Parbhoo K, Pfundt R, Piccione M, Pinto AM, Popp B, Putoux A, Rehm HL, Reis A, Renieri A, Rosenfeld JA, Rossi M, Salzano E, Saugier-Veber P, Seri M, Severi G, Sonmez FM, Strobl-Wildemann G, Stuurman KE, Uctepe E, Van Esch H, Vitetta G, de Vries BBA, Wahl D, Wang T, Zacher P, Heitink KR, Ropers FG, Steenbeek D, Rybak T, Santen GWE. (2024). ARID1B-related disorder in 87 adults: Natural history and self-sustainability. Genet Med Open Jul 23;2:101873.

Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bornberg-Bauer E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Pond SLK, LaPolice TM, Lee C, Lewis AP, Loh YE, Masterson P, McGarvey KM, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler EE, Phillippy AM. (2024). The complete sequence and comparative analysis of ape sex chromosomes. Nature Jun;630(8016):401-411.

Benavidez HR, Johansson M, Jones E, Rea H, Kurtz-Nelson EC, Miles C, Whiting A, Eayrs C, Earl R, Bernier RA, Eichler EE, Neuhaus E. (2024). Predicting Intervention Use in Youth with Rare Variants in Autism-Associated Genes. J Autism Dev Disord May 29. doi: 10.1007/s10803-024-06414-2. Online ahead of print.

Courchesne E, Taluja V, Nazari S, Aamodt CM, Pierce K, Duan K, Stophaeros S, Lopez L, Barnes CC, Troxel J, Campbell K, Wang T, Hoekzema K, Eichler EE, Nani JV, Pontes W, Sanchez SS, Lombardo MV, de Souza JS, Hayashi MAF, Muotri AR. (2024). Embryonic origin of two ASD subtypes of social symptom severity: the larger the brain cortical organoid size, the more severe the social symptoms. Mol Autism May 25;15(1):22.

Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Catacchio CR, Porubsky D, Mao Y, Yoo D, Rautiainen M, Koren S, Nurk S, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, Ventura M, Alexandrov IA, Eichler EE. (2024). The variation and evolution of complete human centromeres. Nature May;629(8010):136-145.

Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen HE, McNulty B, Porubsky D, Montague TG, Lucas JK, Condon C, Eizenga JM, Juul S, McKenzie SK, Simmonds SE, Park J, Asri M, Koren S, Eichler EE, Axel R, Martin B, Carnevali P, Miga KH, Paten B. (2024). Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Res Apr 25;34(3):454-468.

Neuhaus E, Rea H, Jones E, Benavidez H, Miles C, Whiting A, Johansson M, Eayrs C, Kurtz-Nelson EC, Earl R, Bernier RA, Eichler EE. (2024). Shared and divergent mental health characteristics of ADNP-, CHD8- and DYRK1A-related neurodevelopmental conditions. J Neurodev Disord Apr 15;16(1):15.

Porubsky D, Eichler EE. (2024). A 25-year odyssey of genomic technology advances and structural variant discovery. Cell Feb 29;187(5):1024-1037.

Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. (2024). Structurally divergent and recurrently mutated regions of primate genomes. Cell Mar 14;187(6):1547-1562.e13.

Schwartz CE, Aylsworth AS, Allanson J, Battaglia A, Carey JC, Curry CJ, Davies KE, Eichler EE, Graham JM Jr, Hall B, Hall JG, Holmes LB, Hoyme HE, Hunter A, Innis J, Johnson J, Keppler-Noreuil KM, Leroy JG, Moore C, Nelson DL, Neri G, Opitz JM, Picketts D, Raymond FL, Shalev SA, Stevenson RE, Stumpel CTRM, Sutherland G, Viskochil DH, Weaver DD, Zackai EH. (2024). Personal journeys to and in human genetics and dysmorphology. Am J Med Genet A Jun;194(6):e63514. doi: 10.1002/ajmg.a.63514. Epub 2024 Feb 8.

Goldberg ME, Noyes MD, Eichler EE, Quinlan AR, Harris K. (2024). Effects of parental age and polymer composition on short tandem repeat de novo mutation rates. Genetics Apr 3;226(4):iyae013.

Mahmoud M, Huang Y, Garimella K, Audano PA, Wan W, Prasad N, Handsaker RE, Hall S, Pionzio A, Schatz MC, Talkowski ME, Eichler EE, Levy SE, Sedlazeck FJ. (2024). Utility of long-read sequencing for All of Us. Nat Commun Jan 29;15(1):837.

Hudac CM, Friedman NR, Ward VR, Estreicher RE, Dorsey GC, Bernier RA, Kurtz-Nelson EC, Earl RK, Eichler EE, Neuhaus E. (2024). Characterizing sensory phenotypes of subgroups with a known genetic etiology pertaining to diagnoses of autism spectrum disorder and intellectual disability. J Autism Dev Disord Jun;54(6):2386-2401. doi: 10.1007/s10803-023-05897-9. Epub 2023 Apr 8.

Harvey WT, Ebert P, Ebler J, Audano PA, Munson KM, Hoekzema K, Porubsky D, Beck CR, Marschall T, Garimella K, Eichler EE. (2023). Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall. Genome Res Dec 27;33(12):2029-2040.

Harris RA, Raveendran M, Warren W, LaDeana HW, Tomlinson C, Graves-Lindsay T, Green RE, Schmidt JK, Colwell JC, Makulec AT, Cole SA, Cheeseman IH, Ross CN, Capuano S 3rd, Eichler EE, Levine JE, Rogers J. (2023). Whole Genome Analysis of SNV and Indel Polymorphism in Common Marmosets (Callithrix jacchus). Genes (Basel) Dec 7;14(12):2185.

Okhovat M, VanCampen J, Nevonen KA, Harshman L, Li W, Layman CE, Ward S, Herrera J, Wells J, Sheng RR, Mao Y, Ndjamen B, Lima AC, Vigh-Conrad KA, Stendahl AM, Yang R, Fedorov L, Matthews IR, Easow SA, Chan DK, Jan TA, Eichler EE, Rugonyi S, Conrad DF, Ahituv N, Carbone L. (2023). TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function. Nat Commun Dec 7;14(1):8111.

Morgan MAJ, Mohammad Parast S, Iwanaszko M, Aoi Y, Yoo D, Dumar ZJ, Howard BC, Helmin KA, Liu Q, Thakur WR, Zeidner JM, Singer BD, Eichler EE, Shilatifard A. (2023). ELOA3: A primate-specific RNA polymerase II elongation factor encoded by a tandem repeat gene cluster. Sci Adv Nov 24;9(47):eadj1261.

Garza R, Atacho DAM, Adami A, Gerdes P, Vinod M, Hsieh P, Karlsson O, Horvath V, Johansson PA, Pandiloski N, Matas-Fuentes J, Quaegebeur A, Kouli A, Sharma Y, Jönsson ME, Monni E, Englund E, Eichler EE, Gale Hammell M, Barker RA, Kokaia Z, Douse CH, Jakobsson J. (2023). LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification. Sci Adv Nov 3;9(44):eadh9543.

Miga KH, Eichler EE. (2023). Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes. Am J Hum Genet Nov 2;110(11):1832-1840. Review.

Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. (2023). Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci Dec 14;7(3):361-381.

Paparella A, L’Abbate A, Palmisano D, Chirico G, Porubsky D, Catacchio CR, Ventura M, Eichler EE, Maggiolini FAM, Antonacci F. (2023). Structural Variation Evolution at the 15q11-q13 Disease-Associated Locus. Int J Mol Sci Oct 31;24(21):15818.

Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O’Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. (2023). The complete sequence of a human Y chromosome. Nature Sep;621(7978):344-354.

Hallast P, Ebert P, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Höps W, Kim K, Li C, Hoyt SJ, Dishuck PC, Porubsky D, Tsetsos F, Kwon JY, Zhu Q, Munson KM, Hasenfeld P, Harvey WT, Lewis AP, Kordosky J, Hoekzema K; Human Genome Structural Variation Consortium (HGSVC); O’Neill RJ, Korbel JO, Tyler-Smith C, Eichler EE, Shi X, Beck CR, Marschall T, Konkel MK, Lee C. (2023). Assembly of 43 human Y chromosomes reveals extensive complexity and variation. Nature Sep;621(7978):355-364.

Yang X, Mao Y, Wang XK, Ma DN, Xu Z, Gong N, Henning B, Zhang X, He G, Shi YY, Eichler EE, Li ZQ, Takahashi E, Li WD. (2023). Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing. Zool Res Sep 18;44(5):837-847.

Kurtz-Nelson EC, Rea HM, Petriceks AC, Hudac CM, Wang T, Earl RK, Bernier RA, Eichler EE, Neuhaus E. (2023). Characterizing the autism spectrum phenotype in DYRK1A-related syndrome. Autism Res Aug;16(8):1488-1500.

Eichler EE. (2023). Sampling a wide swathe of primate genetic diversity. Cell Genom Jul 12;3(7):100358.

Yang X, Wang X, Zou Y, Zhang S, Xia M, Fu L, Vollger MR, Chen NC, Taylor DJ, Harvey WT, Logsdon GA, Meng D, Shi J, McCoy RC, Schatz MC, Li W, Eichler EE, Lu Q, Mao Y. (2023). Characterization of large-scale genomic differences in the first complete human genome. Genome Biol Jul 4;24(1):157.

Mastrorosa FK, Miller DE, Eichler EE. (2023). Applications of long-read sequencing to Mendelian genetics. Genome Med Jun 14;15(1):42.Review.

Ebstein F, Küry S, Most V, Rosenfelt C, Scott-Boyer MP, van Woerden GM, Besnard T, Papendorf JJ, Studencka-Turski M, Wang T, Hsieh TC, Golnik R, Baldridge D, Forster C, de Konink C, Teurlings SMW, Vignard V, van Jaarsveld RH, Ades L, Cogné B, Mignot C, Deb W, Jongmans MCJ, Cole FS, van den Boogaard MH, Wambach JA, Wegner DJ, Yang S, Hannig V, Brault JA, Zadeh N, Bennetts B, Keren B, Gélineau AC, Powis Z, Towne M, Bachman K, Seeley A, Beck AE, Morrison J, Westman R, Averill K, Brunet T, Haasters J, Carter MT, Osmond M, Wheeler PG, Forzano F, Mohammed S, Trakadis Y, Accogli A, Harrison R, Guo Y, Hakonarson H, Rondeau S, Baujat G, Barcia G, Feichtinger RG, Mayr JA, Preisel M, Laumonnier F, Kallinich T, Knaus A, Isidor B, Krawitz P, Völker U, Hammer E, Droit A, Eichler EE, Elgersma Y, Hildebrand PW, Bolduc F, Krüger E, Bézieau S. (2023). PSMC3 proteasome subunit variants are associated with neurodevelopmental delay and type I interferon production. Sci Transl Med May 31;15(698):eabo3189.

Ferraj A, Audano PA, Balachandran P, Czechanski A, Flores JI, Radecki AA, Mosur V, Gordon DS, Walawalkar IA, Eichler EE, Reinholdt LG, Beck CR. (2023). Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements. Cell Genom Apr 5;3(5):100291.

Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C; Human Pangenome Reference Consortium; Korbel JO, Paten B, Marschall T, Eichler EE. (2023). Gaps and complex structurally variant loci in phased genome assemblies. Genome Res Apr;33(4):496-510.

Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M; Human Pangenome Reference Consortium; Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE. (2023). Increased mutation and gene conversion within human segmental duplications. Nature May;617(7960):325-334.

Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, Paten B. (2023). A draft human pangenome reference. Nature May;617(7960):312-324.

Porubsky D, Harvey WT, Rozanski AN, Ebler J, Höps W, Ashraf H, Hasenfeld P; Human Pangenome Reference Consortium (HPRC); Human Genome Structural Variation Consortium (HGSVC); Paten B, Sanders AD, Marschall T, Korbel JO, Eichler EE. (2023). Inversion polymorphism in a complete human genome assembly. Genome Biol Apr 30;24(1):100.

Ding Z, Huang G, Wang T, Duan W, Li H, Wang Y, Jia H, Yang Z, Wang K, Chu X, Kurtz-Nelson EC, Ahlers K, Earl RK, Han Y, Feliciano P, Chung WK, Eichler EE, Jiang M, Xiong B. (2023). Genetic ablation of GIGYF1, associated with autism, causes behavioral and neurodevelopmental defects in zebrafish and mice. Biol Psychiatry Nov 15;94(10):769-779.

Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. (2023). Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat Biotechnol Oct;41(10):1474-1482.

Dishuck PC, Rozanski AN, Logsdon GA, Porubsky D, Eichler EE. (2023). GAVISUNK: Genome assembly validation via inter-SUNK distances in Oxford Nanopore reads. Bioinformatics Jan 1;39(1):btac714.

Bao B, Zahiri J, Gazestani VH, Lopez L, Xiao Y, Kim R, Wen TH, Chiang AWT, Nalabolu S, Pierce K, Robasky K, Wang T, Hoekzema K, Eichler EE, Lewis NE, Courchesne E. (2023). A predictive ensemble classifier for the gene expression diagnosis of ASD at ages 1 to 4 years. Mol Psychiatry Feb;28(2):822-833.
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Logsdon GA, Eichler EE. (2022). The Dynamic Structure and Rapid Evolution of Human Centromeric Satellite DNA. Genes (Basel) Dec 28;14(1):92. Review.

Gibson WS, Rodriguez OL, Shields K, Silver CA, Dorgham A, Emery M, Deikus G, Sebra R, Eichler EE, Bashir A, Smith ML, Watson CT. (2022). Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes Immun Feb;24(1):21-31. Epub 2022 Dec 21.

Gillentine MA, Wang T, Eichler EE. (2022). Estimating the Prevalence of De Novo Monogenic Neurodevelopmental Disorders from Large Cohort Studies. Biomedicines Nov 9;10(11):2865.

Wang T, Kim CN, Bakken TE, Gillentine MA, Henning B, Mao Y, Gilissen C; SPARK Consortium, Nowakowski TJ, Eichler EE. (2022). Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders. Proc Natl Acad Sci U S A Nov 15;119(46):e2203491119.

Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton RS, Fulton LL, Garg S, Gerton JL, Ghurye J, Granat A, Green RE, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger EB, Jain M, Kirsche M, Kolmogorov M, Korbel JO, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell MW, McDaniel J, Nie F, Olsen HE, Olson ND, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg SL, Sanders AD, Schatz MC, Schmitt A, Schneider VA, Selvaraj S, Shafin K, Shumate A, Stitziel NO, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin AV, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook JM, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH; Human Pangenome Reference Consortium. (2022). Semi-automated assembly of high-quality diploid human reference genomes. Nature Nov;611(7936):519-531.

Dingemans AJM, Truijen KMG, van de Ven S, Bernier R, Bongers EMHF, Bouman A, de Graaff-Herder L, Eichler EE, Gerkes EH, De Geus CM, van Hagen JM, Jansen PR, Kerkhof J, Kievit AJA, Kleefstra T, Maas SM, de Man SA, McConkey H, Patterson WG, Dobson AT, Prijoles EJ, Sadikovic B, Relator R, Stevenson RE, Stumpel CTRM, Heijligers M, Stuurman KE, Löhner K, Zeidler S, Lee JA, Lindy A, Zou F, Tedder ML, Vissers LELM, de Vries BBA. (2022). The phenotypic spectrum and genotype-phenotype correlations in 106 patients with variants in major autism gene CHD8. Transl Psychiatry Oct 1;12(1):421.

Zhou X, Feliciano P, Shu C, Wang T, Astrovskaya I, Hall JB, Obiajulu JU, Wright JR, Murali SC, Xu SX, Brueggeman L, Thomas TR, Marchenko O, Fleisch C, Barns SD, Snyder LG, Han B, Chang TS, Turner TN, Harvey WT, Nishida A, O’Roak BJ, Geschwind DH; SPARK Consortium, Michaelson JJ, Volfovsky N, Eichler EE, Shen Y, Chung WK. (2022). Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nat Genet Sep;54(9):1305-1319.

Jia X, Zhang S, Tan S, Du B, He M, Qin H, Chen J, Duan X, Luo J, Chen F, Ouyang L, Wang J, Chen G, Yu B, Zhang G, Zhang Z, Lyu Y, Huang Y, Jiao J, Chen JYH, Swoboda KJ, Agolini E, Novelli A, Leoni C, Zampino G, Cappuccio G, Brunetti-Pierri N, Gerard B, Ginglinger E, Richer J, McMillan H, White-Brown A, Hoekzema K, Bernier RA, Kurtz-Nelson EC, Earl RK, Meddens C, Alders M, Fuchs M, Caumes R, Brunelle P, Smol T, Kuehl R, Day-Salvatore DL, Monaghan KG, Morrow MM, Eichler EE, Hu Z, Yuan L, Tan J, Xia K, Shen Y, Guo H. (2022). De novo variants in genes regulating stress granule assembly associate with neurodevelopmental disorders. Sci Adv Aug 19;8(33):eabo7112.

van der Sluijs PJ, Joosten M, Alby C, Attié-Bitach T, Gilmore K, Dubourg C, Fradin M, Wang T, Kurtz-Nelson EC, Ahlers KP, Arts P, Barnett CP, Ashfaq M, Baban A, van den Born M, Borrie S, Busa T, Byrne A, Carriero M, Cesario C, Chong K, Cueto-González AM, Dempsey JC, Diderich KEM, Doherty D, Farholt S, Gerkes EH, Gorokhova S, Govaerts LCP, Gregersen PA, Hickey SE, Lefebvre M, Mari F, Martinovic J, Northrup H, O’Leary M, Parbhoo K, Patrier S, Popp B, Santos-Simarro F, Stoltenburg C, Thauvin-Robinet C, Thompson E, Vulto-van Silfhout AT, Zahir FR, Scott HS, Earl RK, Eichler EE, Vora NL, Wilnai Y, Giordano JL, Wapner RJ, Rosenfeld JA, Haak MC, Santen GWE. (2022). Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort. Genet Med Aug;24(8):1753-1760.

Chen G, Yu B, Tan S, Tan J, Jia X, Zhang Q, Zhang X, Jiang Q, Hua Y, Han Y, Luo S, Hoekzema K, Bernier RA, Earl RK, Kurtz-Nelson EC, Idleburg MJ, Khetarpal SM, Clark R, Sebastian J, Fernandez-Jaen A, Alvarez S, King SD, Ramos LL, Santos MLS, Martin DM, Brooks D, Symonds JD, Cutcutache I, Pan Q, Hu Z, Yuan L, Eichler EE, Xia K, Guo H. (2022). GIGYF1 disruption associates with autism and impaired IGF-1R signaling. J Clin Invest Oct 3;132(19):e159806.

Miller DE, Hanna P, Galey M, Reyes M, Linglart A, Eichler EE, Jüppner H. (2022). Targeted long-read sequencing identifies a retrotransposon insertion as a cause of altered GNAS exon A/B methylation in a family with autosomal dominant pseudohypoparathyroidism type 1b (PHP1B). J Bone Miner Res Sep;37(9):1711-1719.

Giannuzzi G, Chatron N, Mannik K, Auwerx C, Pradervand S, Willemin G, Hoekzema K, Nuttle X, Chrast J, Sadler MC, Porcu E; 16p11.2 Consortium, Herault Y, Isidor B, Gilbert-Dussardier B, Eichler EE, Kutalik Z, Reymond A. (2022). Possible association of 16p11.2 copy number variation with altered lymphocyte and neutrophil counts. NPJ Genom Med Jun 17;7(1):38.

Gaik M, Kojic M, Stegeman MR, Öncü-Öner T, Kościelniak A, Jones A, Mohamed A, Chau PYS, Sharmin S, Chramiec-Głąbik A, Indyka P, Rawski M, Biela A, Dobosz D, Millar A, Chau V, Ünalp A, Piper M, Bellingham MC, Eichler EE, Nickerson DA, Güleryüz H, Abbassi NEH, Jazgar K, Davis MJ, Mercimek-Andrews S, Cingöz S, Wainwright BJ, Glatt S. (2022). Functional divergence of the two Elongator subcomplexes during neurodevelopment. EMBO Mol Med Jul 7;14(7):e15608.

Miller DE, Lee L, Galey M, Kandhaya-Pillai R, Tischkowitz M, Amalnath D, Vithlani A, Yokote K, Kato H, Maezawa Y, Takada-Watanabe A, Takemoto M, Martin GM, Eichler EE, Hisama FM, Oshima J. (2022). Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases. J Med Genet May 9;59(11):1087-1094.

Porubsky D, Höps W, Ashraf H, Hsieh P, Rodriguez-Martin B, Yilmaz F, Ebler J, Hallast P, Maria Maggiolini FA, Harvey WT, Henning B, Audano PA, Gordon DS, Ebert P, Hasenfeld P, Benito E, Zhu Q; Human Genome Structural Variation Consortium (HGSVC), Lee C, Antonacci F, Steinrücken M, Beck CR, Sanders AD, Marschall T, Eichler EE, Korbel JO. (2022). Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell May 26;185(11):1986-2005.e26.

Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison NA, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D; Human Pangenome Reference Consortium. (2022). The Human Pangenome Project: a global resource to map genomic diversity. Nature Apr;604(7906):437-446. Review.

Cingoz S, Soydemir D, Oner TO, Karaca E, Ozden B, Kurul SH, Bayram E; University of Washington Center for Mendelian Genomics Study Group, Coe BP, Nickerson DA, Eichler EE. (2022). Novel biallelic variants affecting the OTU domain of the gene OTUD6B associate with severe intellectual disability syndrome and molecular dynamics simulations. Eur J Med Genet Jun;65(6):104497.

Wang T, Zhao PA, Eichler EE. (2022). Rare variants and the oligogenic architecture of autism. Trends Genet Sep;38(9):895-903. Review.

Ebler J, Ebert P, Clarke WE, Rausch T, Audano PA, Houwaart T, Mao Y, Korbel JO, Eichler EE, Zody MC, Dilthey AT, Marschall T. (2022). Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. Nat Genet Apr;54(4):518-525.

Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. (2022). The complete sequence of a human genome. Science Apr;376(6588):44-53.

Vollger MR, Guitart X, Dishuck PC, Mercuri L, Harvey WT, Gershman A, Diekhans M, Sulovari A, Munson KM, Lewis AP, Hoekzema K, Porubsky D, Li R, Nurk S, Koren S, Miga KH, Phillippy AM, Timp W, Ventura M, Eichler EE. (2022). Segmental duplications and their variation in a complete human genome. Science Apr;376(6588):eabj6965.

Gershman A, Sauria MEG, Guitart X, Vollger MR, Hook PW, Hoyt SJ, Jain M, Shumate A, Razaghi R, Koren S, Altemose N, Caldas GV, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O’Neill RJ, Phillippy AM, Miga KH, Timp W. (2022). Epigenetic patterns in a complete human genome. Science Apr;376(6588):eabj5089.

Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O’Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. (2022). Complete genomic and epigenetic maps of human centromeres. Science Apr;376(6588):eabl4178.

Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O’Neill RJ. (2022). From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science Apr;376(6588):eabk3112.

Noyes MD, Harvey WT, Porubsky D, Sulovari A, Li R, Rose NR, Audano PA, Munson KM, Lewis AP, Hoekzema K, Mantere T, Graves-Lindsay TA, Sanders AD, Goodwin S, Kramer M, Mokrab Y, Zody MC, Hoischen A, Korbel JO, McCombie WR, Eichler EE. (2022). Familial long-read sequencing increases yield of de novo mutations. Am J Hum Genet Apr 7;109(4):631-646.

Jacquemont S, Huguet G, Klein M, Chawner SJRA, Donald KA, van den Bree MBM, Sebat J, Ledbetter DH, Constantino JN, Earl RK, McDonald-McGinn DM, van Amelsvoort T, Swillen A, O’Donnell-Luria AH, Glahn DC, Almasy L, Eichler EE, Scherer SW, Robinson E, Bassett AS, Martin CL, Finucane B, Vorstman JAS, Bearden CE, Gur RE; Genes to Mental Health Network. (2022). Genes To Mental Health (G2MH): A framework to map the combined effects of rare and common variants on dimensions of cognition and psychopathology. Am J Psychiatry Mar;179(3):189-203. Review.

Gofin Y, Wang T, Gillentine MA, Scott TM, Berry AM, Azamian MS, Genetti C, Agrawal PB, Picker J, Wojcik MH, Delgado MR, Lynch SA, Scherer SW, Howe JL, Bacino CA, DiTroia S, VanNoy GE, O’Donnell-Luria A, Lalani SR, Graf WD, Rosenfeld JA, Eichler EE, Earl RK, Scott DA. (2022). Delineation of a novel neurodevelopmental syndrome associated with PAX5 haploinsufficiency. Hum Mutat Apr;43(4):461-470.

Vollger MR, Kerpedjiev P, Phillippy AM, Eichler EE. (2022). StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps. Bioinformatics Apr 1;38(7):2049–51.

Fanjul-Fernández M, Brown NJ, Hickey P, Diakumis P, Rafehi H, Bozaoglu K, Green CC, Rattray A, Young S, Alhuzaimi D, Mountford HS, Gillies G, Lukic V, Vick T, Finlay K, Coe BP, Eichler EE, Delatycki MB, Wilson SJ, Bahlo M, Scheffer IE, Lockhart PJ. (2022). A family study implicates GBE1 in the etiology of autism spectrum disorder. Hum Mutat Jan;43(1):16-29.

Ahring PK, Liao VWY, Gardella E, Johannesen KM, Krey I, Selmer KK, Stadheim BF, Davis H, Peinhardt C, Koko M, Coorg RK, Syrbe S, Bertsche A, Santiago-Sim T, Diemer T, Fenger CD, Platzer K, Eichler EE, Lerche H, Lemke JR, Chebib M, Møller RS. (2022). Gain-of-function variants in GABRD reveal a novel pathway for neurodevelopmental disorders and epilepsy. Brain May 24;145(4):1299-1309.

Johansson PA, Brattås PL, Douse CH, Hsieh P, Adami A, Pontis J, Grassi D, Garza R, Sozzi E, Cataldo R, Jönsson ME, Atacho DAM, Pircs K, Eren F, Sharma Y, Johansson J, Fiorenzano A, Parmar M, Fex M, Trono D, Eichler EE, Jakobsson J. (2022). A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development. Cell Stem Cell Jan 6;29(1):52-69.e8.

Lin J, Yang X, Kosters W, Xu T, Jia Y, Wang S, Zhu Q, Ryan M, Guo L, Zhang C, Lee C, Devine SE, Eichler EE, Ye K; Human Genome Structural Variation Consortium. (2022). Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants. Genomics Proteomics Bioinformatics Feb;20(1):205-218. Epub 2021 Jul 3.

Mouakkad-Montoya L, Murata MM, Sulovari A, Suzuki R, Osia B, Malkova A, Katsumata M, Giuliano AE, Eichler EE, Tanaka H. (2021). Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA. Proc Natl Acad Sci U S A Nov 23;118(47):e2102842118.

Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D, Bogdanoff D, Kreimer A, Pollard KS, Ament SA, Eichler EE, Ahituv N, Nowakowski TJ. (2021). Single-cell epigenomics reveals mechanisms of human cortical development. Nature Oct;598(7879):205-213.

Giannuzzi G, Logsdon GA, Chatron N, Miller DE, Reversat J, Munson KM, Hoekzema K, Bonnet-Dupeyron MN, Rollat-Farnier PA, Baker CA, Sanlaville D, Eichler EE, Schluth-Bolard C, Reymond A. (2021). Alpha satellite insertion close to an ancestral centromeric region. Mol Biol Evol Dec 9;38(12):5576-5587.

Hsieh P, Dang V, Vollger MR, Mao Y, Huang TH, Dishuck PC, Baker C, Cantsilieris S, Lewis AP, Munson KM, Sorensen M, Welch AE, Underwood JG, Eichler EE. (2021). Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans. Nat Commun Aug 25;12(1):5118.

Wilfert AB, Turner TN, Murali SC, Hsieh P, Sulovari A, Wang T, Coe BP, Guo H, Hoekzema K, Bakken TE, Winterkorn LH, Evani US, Byrska-Bishop M, Earl RK, Bernier RA; SPARK Consortium, Zody MC, Eichler EE. (2021). Recent ultra-rare inherited variants implicate new autism candidate risk genes. Nat Genet Aug;53(8):1125-1134.

Goldmann JM, Hampstead JE, Wong WSW, Wilfert AB, Turner TN, Jonker MA, Bernier R, Huynen MA, Eichler EE, Veltman JA, Maxwell GL, Gilissen C. (2021). Differences in the number of de novo mutations between individuals are due to small family-specific effects and stochasticity. Genome Res Sep;31(9):1513-1518.

Course MM, Sulovari A, Gudsnuk K, Eichler EE, Valdmanis PN. (2021). Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats. Genome Res Aug;31(8):1313-1324.

Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Alikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS, University of Washington for Mendelian Genomics, King MC, Cherry T, Chong J, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. (2021). Targeted long-read sequencing identifies missing disease-causing variation. AJHG Aug 5;108(8):1436-1449.

Cousin MA, Creighton BA, Breau KA, Spillmann RC, Torti E, Dontu S, Tripathi S, Ajit D, Edwards RJ, Afriyie S, Bay JC, Harper KM, Beltran AA, Munoz LJ, Falcon Rodriguez L, Stankewich MC, Person RE, Si Y, Normand EA, Blevins A, May AS, Bier L, Aggarwal V, Mancini GMS, van Slegtenhorst MA, Cremer K, Becker J, Engels H, Aretz S, MacKenzie JJ, Brilstra E, van Gassen KLI, van Jaarsveld RH, Oegema R, Parsons GM, Mark P, Helbig I, McKeown SE, Stratton R, Cogne B, Isidor B, Cacheiro P, Smedley D, Firth HV, Bierhals T, Kloth K, Weiss D, Fairley C, Shieh JT, Kritzer A, Jayakar P, Kurtz-Nelson E, Bernier RA, Wang T, Eichler EE, van de Laar IMBH, McConkie-Rosell A, McDonald MT, Kemppainen J, Lanpher BC, Schultz-Rogers LE, Gunderson LB, Pichurin PN, Yoon G, Zech M, Jech R, Winkelmann J; Undiagnosed Diseases Network; Genomics England Research Consortium, Beltran AS, Zimmermann MT, Temple B, Moy SS, Klee EW, Tan QK, Lorenzo DN. (2021). Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome. Nat Genet Jul;53(7):1006-1021.

Arnett AB, Wang T, Eichler EE, Bernier RA. (2021). Reflections on the genetics-first approach to advancements in molecular genetic and neurobiological research on neurodevelopmental disorders. J Neurodev Disord Jun 21;13(1):24.

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Earl RK, Ward T, Gerdts J, Eichler EE, Bernier RA, Hudac CM. (2021). Sleep Problems in Children with ASD and Gene Disrupting Mutations. J Genet Psychol Sep-Oct;182(5):317-334.

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Kurtz-Nelson EC, Tham SW, Ahlers K, Cho D, Wallace AS, Eichler EE, Bernier RA, Earl RK. (2021). Brief Report: Associations Between Self-injurious Behaviors and Abdominal Pain Among Individuals with ASD-Associated Disruptive Mutations. J Autism Dev Disord Sep;51(9):3365-3373. doi: 10.1007/s10803-020-04774-z. Epub 2020 Nov 11.

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Maggiolini FAM, Sanders AD, Shew CJ, Sulovari A, Mao Y, Puig M, Catacchio CR, Dellino M, Palmisano D, Mercuri L, Bitonto M, Porubský D, Cáceres M, Eichler EE, Ventura M, Dennis MY, Korbel JO, Antonacci F. (2020). Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution. Genome Res Nov;30(11):1680-1693.

Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M, Deikus G, Auckland K, Eichler EE, Marasco WA, Sebra R, Sharp AJ, Smith ML, Bashir A, Watson CT. (2020). A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus. Front Immunol Sep 23;11:2136.

Wang T, Hoekzema K, Vecchio D, Wu H, Sulovari A, Coe BP, Gillentine MA, Wilfert AB, Perez-Jurado LA, Kvarnung M, Sleyp Y, Earl RK, Rosenfeld JA, Geisheker MR, Han L, Du B, Barnett C, Thompson E, Shaw M, Carroll R, Friend K, Catford R, Palmer EE, Zou X, Ou J, Li H, Guo H, Gerdts J, Avola E, Calabrese G, Elia M, Greco D, Lindstrand A, Nordgren A, Anderlid BM, Vandeweyer G, Van Dijck A, Van der Aa N, McKenna B, Hancarova M, Bendova S, Havlovicova M, Malerba G, Bernardina BD, Muglia P, van Haeringen A, Hoffer MJV, Franke B, Cappuccio G, Delatycki M, Lockhart PJ, Manning MA, Liu P, Scheffer IE, Brunetti-Pierri N, Rommelse N, Amaral DG, Santen GWE, Trabetti E, Sedláček Z, Michaelson JJ, Pierce K, Courchesne E, Kooy RF; SPARK Consortium, Nordenskjöld M, Romano C, Peeters H, Bernier RA, Gecz J, Xia K, Eichler EE. (2020). Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders. Nat Commun Oct 1;11(1):4932.

Arnett AB, Beighley JS, Kurtz-Nelson EC, Hoekzema K, Wang T, Bernier RA, Eichler EE. (2020). Developmental Predictors of Cognitive and Adaptive Outcomes in Genetic Subtypes of Autism Spectrum Disorder. Autism Res Oct;13(10):1659-1669.

Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. (2020). HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res Sep;30(9):1291-1305.

Cantsilieris S, Sunkin SM, Johnson ME, Anaclerio F, Huddleston J, Baker C, Dougherty ML, Underwood JG, Sulovari A, Hsieh P, Mao Y, Catacchio CR, Malig M, Welch AE, Sorensen M, Munson KM, Jiang W, Girirajan S, Ventura M, Lamb BT, Conlon RA, Eichler EE. (2020). An evolutionary driver of interspersed segmental duplications in primates. Genome Biol Aug 10;21(1):202.

Course MM, Gudsnuk K, Smukowski SN, Winston K, Desai N, Ross JP, Sulovari A, Bourassa CV, Spiegelman D, Couthouis J, Yu CE, Tsuang DW, Jayadev S, Kay MA, Gitler AD, Dupre N, Eichler EE, Dion PA, Rouleau GA, Valdmanis PN. (2020). Evolution of a Human-Specific Tandem Repeat Associated with ALS. Am J Hum Genet Sep 3;107(3):445-460.

Cappuccio G, Sayou C, Tanno PL, Tisserant E, Bruel AL, Kennani SE, Sá J, Low KJ, Dias C, Havlovicová M, Hancarova M, Eichler EE, Devillard F, Moutton S, Van-Gils J, Dubourg C, Odent S, Gerard B, Piton A, Yamamoto T, Okamoto N, Firth H, Metcalfe K, Moh A, Chapman KA, Aref-Eshghi E, Kerkhof J, Torella A, Nigro V, Perrin L, Piard J, Le Guyader G, Jouan T, Thauvin-Robinet C, Duffourd Y, George-Abraham JK, Buchanan CA, Williams D, Kini U, Wilson K; Telethon Undiagnosed Diseases Program, Sousa SB, Hennekam RCM, Sadikovic B, Thevenon J, Govin J, Vitobello A, Brunetti-Pierri N. (2020). De novo SMARCA2 variants clustered outside the helicase domain cause a new recognizable syndrome with intellectual disability and blepharophimosis distinct from Nicolaides-Baraitser syndrome. Genet Med Nov;22(11):1838-1850.

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Hudac CM, Bove J, Barber S, Duyzend M, Wallace A, Martin CL, Ledbetter DH, Hanson E, Goin-Kochel RP, Green-Snyder L, Chung WK, Eichler EE, Bernier RA. (2020). Evaluating heterogeneity in ASD symptomatology, cognitive ability, and adaptive functioning among 16p11.2 CNV carriers. Autism Res Aug;13(8):1300-1310.

Porubsky D, Sanders AD, Hops W, Hsieh P, Sulovari A, Li R, Mercuri L, Sorensen M, Murali SC, Gordon D, Cantsilieris S, Pollen AA, Ventura M, Antonacci F, Marschall T, Korbel JO, Eichler EE. (2020). Recurrent inversion toggling and great ape genome evolution. Nat Genet Aug;52(8):849-858.

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Myers SM, Challman TD, Bernier R, Bourgeron T, Chung WK, Constantino JN, Eichler EE, Jacquemont S, Miller DT, Mitchell KJ, Zoghbi HY, Martin CL, Ledbetter DH. (2020). Insufficient Evidence for “Autism-Specific” Genes. Am J Hum Genet May 7;106(5):587-595.

Zhang QJ, Li W, Li K, Nan H, Shi C, Zhang Y, Dai ZY, Lin YL, Yang XL, Tong Y, Zhang D, Lu C, Feng LY, Wang CF, Liu XX, Huang JA, Jiang WK, Wang XH, Zhang XC, Eichler EE, Liu ZH, Gao LZ. (2020). The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons to Drive Genome Size Evolution. Mol Plant Jul 6;13(7):935-938.

Maggiolini FAM, Mercuri L, Antonacci F, Anaclerio F, Calabrese FM, Lorusso N, L’Abbate A, Sorensen M, Giannuzzi G, Eichler EE, Catacchio CR, Ventura M. (2020). Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates. Genes Feb 18;11(2). pii: E213.

Nakamori M, Panigrahi GB, Lanni S, Gall-Duncan T, Hayakawa H, Tanaka H, Luo J, Otabe T, Li J, Sakata A, Caron MC, Joshi N, Prasolava T, Chiang K, Masson JY, Wold MS, Wang X, Lee MYWT, Huddleston J, Munson KM, Davidson S, Layeghifard M, Edward LM, Gallon R, Santibanez-Koref M, Murata A, Takahashi MP, Eichler EE, Shlien A, Nakatani K, Mochizuki H, Pearson CE. (2020). A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo. Nat Genet Feb;52(2):146-159.

Scott TM, Guo H, Eichler EE, Rosenfeld JA, Pang K, Liu Z, Lalani S, Bi W, Yang Y, Bacino CA, Streff H, Lewis AM, Koenig MK, Thiffault I, Bellomo A, Everman DB, Jones JR, Stevenson RE, Bernier R, Gilissen C, Pfundt R, Hiatt SM, Cooper GM, Holder JL, Scott DA. (2020). BAZ2B haploinsufficiency as a cause of developmental delay, intellectual disability, and autism spectrum disorder. Hum Mutat May;41(5):921-925.

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Liu J, Shi C, Shi CC, Li W, Zhang QJ, Zhang Y, Li K, Lu HF, Shi C, Zhu ST, Xiao ZY, Nan H, Yue Y, Zhu XG, Wu Y, Hong XN, Fan GY, Tong Y, Zhang D, Mao CL, Liu YL, Hao SJ, Liu WQ, Lv MQ, Zhang HB, Liu Y, Hu-Tang GR, Wang JP, Wang JH, Sun YH, Ni SB, Chen WB, Zhang XC, Jiao YN, Eichler EE, Li GH, Liu X, Gao LZ. (2020). The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis. Mol Plant Feb 3;13(2):336-350.

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Beighley JS, Hudac CM, Arnett AB, Peterson JL, Gerdts J, Wallace AS, Mefford HC, Hoekzema K, Turner TN, O’Roak BJ, Eichler EE, Bernier RA. (2020). Clinical Phenotypes of Carriers of Mutations in CHD8 or Its Conserved Target Genes. Biol Psychiatry Jan 15;87(2):123-131.
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Turner TN, Wilfert AB, Bakken TE, Bernier RA, Pepper MR, Zhang Z, Torene RI, Retterer K, Eichler EE. (2019). Sex-based analysis of de novo variants in neurodevelopmental disorders. Am J Hum Genet Dec 5;105(6):1274-1285.

Giannuzzi G, Schmidt PJ, Porcu E, Willemin G, Munson KM, Nuttle X, Earl R, Chrast J, Hoekzema K, Risso D, Männik K, De Nittis P, Baratz ED; 16p11.2 Consortium, Herault Y, Gao X, Philpott CC, Bernier RA, Kutalik Z, Fleming MD, Eichler EE, Reymond A. (2019). The Human-Specific BOLA2 Duplication Modifies Iron Homeostasis and Anemia Predisposition in Chromosome 16p11.2 Autism Individuals. Am J Hum Genet Nov 7;105(5):947-958.

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Hsieh P, Vollger MR, Dang V, Porubsky D, Baker C, Cantsilieris S, Hoekzema K, Lewis AP, Munson KM, Sorensen M, Kronenberg ZN, Murali S, Nelson BJ, Chiatante G, Maggiolini FAM, Blanché H, Underwood JG, Antonacci F, Deleuze JF, Eichler EE. (2019). Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes. Science Oct 18;366(6463).

Guo H, Bettella E, Marcogliese PC, Zhao R, Andrews JC, Nowakowski TJ, Gillentine MA, Hoekzema K, Wang T, Wu H, Jangam S, Liu C, Ni H, Willemsen MH, van Bon BW, Rinne T, Stevens SJC, Kleefstra T, Brunner HG, Yntema HG, Long M, Zhao W, Hu Z, Colson C, Richard N, Schwartz CE, Romano C, Castiglia L, Bottitta M, Dhar SU, Erwin DJ, Emrick L, Keren B, Afenjar A, Zhu B, Bai B, Stankiewicz P, Herman K; University of Washington Center for Mendelian Genomics, Mercimek-Andrews S, Juusola J, Wilfert AB, Abou Jamra R, Büttner B, Mefford HC, Muir AM, Scheffer IE, Regan BM, Malone S, Gecz J, Cobben J, Weiss MM, Waisfisz Q, Bijlsma EK, Hoffer MJV, Ruivenkamp CAL, Sartori S, Xia F, Rosenfeld JA, Bernier RA, Wangler MF, Yamamoto S, Xia K, Stegmann APA, Bellen HJ, Murgia A, Eichler EE. (2019). Disruptive mutations in TANC2 define a neurodevelopmental syndrome associated with psychiatric disorders. Nat Commun Oct 15;10(1):4679.

Guo H, Li Y, Shen L, Wang T, Jia X, Liu L, Xu T, Ou M, Hoekzema K, Wu H, Gillentine MA, Liu C, Ni H, Peng P, Zhao R, Zhang Y, Phornphutkul C, Stegmann APA, Prada CE, Hopkin RJ, Shieh JT, McWalter K, Monaghan KG, van Hasselt PM, van Gassen K, Bai T, Long M, Han L, Quan Y, Chen M, Zhang Y, Li K, Zhang Q, Tan J, Zhu T, Liu Y, Pang N, Peng J, Scott DA, Lalani SR, Azamian M, Mancini GMS, Adams DJ, Kvarnung M, Lindstrand A, Nordgren A, Pevsner J, Osei-Owusu IA, Romano C, Calabrese G, Galesi O, Gecz J, Haan E, Ranells J, Racobaldo M, Nordenskjold M, Madan-Khetarpal S, Sebastian J, Ball S, Zou X, Zhao J, Hu Z, Xia F, Liu P, Rosenfeld JA, de Vries BBA, Bernier RA, Xu ZD, Li H, Xie W, Hufnagel RB, Eichler EE, Xia K. (2019). Disruptive variants of CSDE1 associate with autism and interfere with neuronal development and synaptic transmission. Sci Adv Sep 25;5(9):eaax2166. doi: 10.1126/sciadv.aax2166. eCollection 2019 Sep.

He Y, Luo X, Zhou B, Hu T, Meng X, Audano PA, Kronenberg ZN, Eichler EE, Jin J, Guo Y, Yang Y, Qi X, Su B. (2019). Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants. Nat Commun Sep 17;10(1):4233.

Feliciano P, Zhou X, Astrovskaya I, Turner TN, Wang T, Brueggeman L, Barnard R, Hsieh A, Snyder LG, Muzny DM, Sabo A; SPARK Consortium, Gibbs RA, Eichler EE, O’Roak BJ, Michaelson JJ, Volfovsky N, Shen Y, Chung WK. (2019). Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. NPJ Genom Med Aug 23;4:19.

Nellåker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FPJ, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogné B, Dawkins HJS, deVries BBA, Douzgou S, Dudding-Byth T, Eichler EE, Ferlaino M, Fieggen K, Firth HV, FitzPatrick DR, Gration D, Groza T, Haendel M, Hallowell N, Hamosh A, Hehir-Kwa J, Hitz MP, Hughes M, Kini U, Kleefstra T, Kooy RF, Krawitz P, Küry S, Lees M, Lyon GJ, Lyonnet S, Marcadier JL, Meyn S, Moslerová V, Politei JM, Poulton CC, Raymond FL, Reijnders MRF, Robinson PN, Romano C, Rose CM, Sainsbury DCG, Schofield L, Sutton VR, Turnovec M, Van Dijck A, Van Esch H, Wilkie AOM; Minerva Consortium. (2019). Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative. Front Genet Jul 29;10:611.

Gao LZ, Liu YL, Zhang D, Li W, Gao J, Liu Y, Li K, Shi C, Zhao Y, Zhao YJ, Jiao JY, Mao SY, Gao CW, Eichler EE. (2019). Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats. Commun Biol Jul 26;2:278.

Salpietro V, Dixon CL, Guo H, Bello OD, Vandrovcova J, Efthymiou S, Maroofian R, Heimer G, Burglen L, Valence S, Torti E, Hacke M, Rankin J, Tariq H, Colin E, Procaccio V, Striano P, Mankad K, Lieb A, Chen S, Pisani L, Bettencourt C, Männikkö R, Manole A, Brusco A, Grosso E, Ferrero GB, Armstrong-Moron J, Gueden S, Bar-Yosef O, Tzadok M, Monaghan KG, Santiago-Sim T, Person RE, Cho MT, Willaert R, Yoo Y, Chae JH, Quan Y, Wu H, Wang T, Bernier RA, Xia K, Blesson A, Jain M, Motazacker MM, Jaeger B, Schneider AL, Boysen K, Muir AM, Myers CT, Gavrilova RH, Gunderson L, Schultz-Rogers L, Klee EW, Dyment D, Osmond M, Parellada M, Llorente C, Gonzalez-Peñas J, Carracedo A, Van Haeringen A, Ruivenkamp C, Nava C, Heron D, Nardello R, Iacomino M, Minetti C, Skabar A, Fabretto A; SYNAPS Study Group, Raspall-Chaure M, Chez M, Tsai A, Fassi E, Shinawi M, Constantino JN, De Zorzi R, Fortuna S, Kok F, Keren B, Bonneau D, Choi M, Benzeev B, Zara F, Mefford HC, Scheffer IE, Clayton-Smith J, Macaya A, Rothman JE, Eichler EE, Kullmann DM, Houlden H. (2019). AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders. Nat Commun Jul 12;10(1):3094.

Eichler EE. (2019). Genetic Variation, Comparative Genomics, and the Diagnosis of Disease. N Engl J Med Jul 4;381(1):64-74. Review

Fenckova M, Blok LER, Asztalos L, Goodman DP, Cizek P, Singgih EL, Glennon JC, IntHout J, Zweier C, Eichler EE, von Reyn CR, Bernier RA, Asztalos Z, Schenck A. (2019). Habituation Learning Is a Widely Affected Mechanism in Drosophila Models of Intellectual Disability and Autism Spectrum Disorders. Biol Psychiatry Aug 15;86(4):294-305.

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. (2019). Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun Apr 16;10(1):1784.

Tilghman JM, Ling AY, Turner TN, Sosa MX, Krumm N, Chatterjee S, Kapoor A, Coe BP, Nguyen KH, Gupta N, Gabriel S, Eichler EE, Berrios C, Chakravarti A. (2019). Molecular Genetic Anatomy and Risk Profile of Hirschsprung’s Disease. N Engl J Med Apr 11;380(15):1421-1432.

Maggiolini FAM, Cantsilieris S, D’Addabbo P, Manganelli M, Coe BP, Dumont BL, Sanders AD, Pang AWC, Vollger MR, Palumbo O, Palumbo P, Accadia M, Carella M, Eichler EE, Antonacci F. (2019). Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus. PLoS Genet Mar 27;15(3):e1008075.

Rogers J, Raveendran M, Harris RA, Mailund T, Leppala K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, Noll A, Kothe M, Kopp GH, Liu Y, Murali S, Billis K, Martin FJ, Muffato M, Cox L, Else J, Disotell T, Muzny DM, Phillips-Conroy J, Aken B, Eichler EE, Marques-Bonet T, Kosiol C, Batzer MA, Hahn MW, Tung J, Zinner D, Roos C, Jolly CJ, Gibbs RA, Worley KC; Baboon Genome Analysis Consortium. (2019). The comparative genomics and complex population history of Papio baboons. Sci Adv Jan 30;5(1):eaau6947.

Cogne B, Ehresmann S, Beauregard-Lacroix E, Rousseau J, Besnard T, Garcia T, Petrovski S, Avni S, McWalter K, Blackburn PR, Sanders SJ, Uguen K, Harris J, Cohen JS, Blyth M, Lehman A, Berg J, Li MH, Kini U, Joss S, von der Lippe C, Gordon CT, Humberson JB, Robak L, Scott DA, Sutton VR, Skraban CM, Johnston JJ, Poduri A, Nordenskjöld M, Shashi V, Gerkes EH, Bongers EMHF, Gilissen C, Zarate YA, Kvarnung M, Lally KP, Kulch PA, Daniels B, Hernandez-Garcia A, Stong N, McGaughran J, Retterer K, Tveten K, Sullivan J, Geisheker MR, Stray-Pedersen A, Tarpinian JM, Klee EW, Sapp JC, Zyskind J, Holla OL, Bedoukian E, Filippini F, Guimier A, Picard A, Busk OL, Punetha J, Pfundt R, Lindstrand A, Nordgren A, Kalb F, Desai M, Ebanks AH, Jhangiani SN, Dewan T, Coban Akdemir ZH, Telegrafi A, Zackai EH, Begtrup A, Song X, Toutain A, Wentzensen IM, Odent S, Bonneau D, Latypova X, Deb W; CAUSES Study, Redon S, Bilan F, Legendre M, Troyer C, Whitlock K, Caluseriu O, Murphree MI, Pichurin PN, Agre K, Gavrilova R, Rinne T, Park M, Shain C, Heinzen EL, Xiao R, Amiel J, Lyonnet S, Isidor B, Biesecker LG, Lowenstein D, Posey JE, Denomme-Pichon AS; Deciphering Developmental Disorders study, Ferec C, Yang XJ, Rosenfeld JA, Gilbert-Dussardier B, Audebert-Bellanger S, Redon R, Stessman HAF, Nellaker C, Yang Y, Lupski JR, Goldstein DB, Eichler EE, Bolduc F, Bezieau S, Kury S, Campeau PM. (2019). Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability. Am J Hum Genet Mar 7;104(3):530-541.

Pollen AA, Bhaduri A, Andrews MG, Nowakowski TJ, Meyerson OS, Mostajo-Radji MA, Di Lullo E, Alvarado B, Bedolli M, Dougherty ML, Fiddes IT, Kronenberg ZN, Shuga J, Leyrat AA, West JA, Bershteyn M, Lowe CB, Pavlovic BJ, Salama SR, Haussler D, Eichler EE, Kriegstein AR. (2019). Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. Cell Feb 7;176(4):743-756.e17.

Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE. (2019). Characterizing the Major Structural Variant Alleles of the Human Genome. Cell Jan 24;176(3):663–675.

Ang CE, Ma Q, Wapinski OL, Fan S, Flynn RA, Lee QY, Coe B, Onoguchi M, Olmos VH, Do BT, Dukes-Rimsky L, Xu J, Tanabe K, Wang L, Elling U, Penninger JM, Zhao Y, Qu K, Eichler EE, Srivastava A, Wernig M, Chang HY. (2019). The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders. Elife Jan 10;8. pii: e41770.

Turner TN, Eichler EE. (2019). The Role of De Novo Noncoding Regulatory Mutations in Neurodevelopmental Disorders. Trends Neurosci Feb;42(2):115-127. Epub 2018 Dec 15.

Coe BP, Stessman HAF, Sulovari A, Geisheker MR, Bakken TE, Lake AM, Dougherty JD, Lein ES, Hormozdiari F, Bernier RA, Eichler EE. (2019). Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nat Genet Jan;51(1):106-116. doi: 10.1038/s41588-018-0288-4. Epub 2018 Dec 17.

Vollger MR, Dishuck PC, Sorensen M, Welch AE, Dang V, Dougherty ML, Graves-Lindsay TA, Wilson RK, Chaisson MJP, Eichler EE. (2019). Long-read sequence and assembly of segmental duplications. Nat Methods Jan;16(1):88-94. Epub 2018 Dec 17.

Guo H, Duyzend MH, Coe BP, Baker C, Hoekzema K, Gerdts J, Turner TN, Zody MC, Beighley JS, Murali SC, Nelson BJ; University of Washington Center for Mendelian Genomics, Bamshad MJ, Nickerson DA, Bernier RA, Eichler EE. (2019). Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes. Genet Med Jul;21(7):1611-1620. Epub 2018 Dec 3.

Van Dijck A, Vulto-van Silfhout AT, Cappuyns E, van der Werf IM, Mancini GM, Tzschach A, Bernier R, Gozes I, Eichler EE, Romano C, Lindstrand A, Nordgren A; ADNP Consortium, Kvarnung M, Kleefstra T, de Vries BBA, Küry S, Rosenfeld JA, Meuwissen ME, Vandeweyer G, Kooy RF. (2019). Clinical Presentation of a Complex Neurodevelopmental Disorder Caused by Mutations in ADNP. Biol Psychiatry Feb 15;85(4):287-297. Epub 2018 Mar 15.

Guo H, Wang T, Wu H, Long M, Coe BP, Li H, Xun G, Ou J, Chen B, Duan G, Bai T, Zhao N, Shen Y, Li Y, Wang Y, Zhang Y, Baker C, Liu Y, Pang N, Huang L, Han L, Jia X, Liu C, Ni H, Yang X, Xia L, Chen J, Shen L, Li Y, Zhao R, Zhao W, Peng J, Pan Q, Long Z, Su W, Tan J, Du X, Ke X, Yao M, Hu Z, Zou X, Zhao J, Bernier RA, Eichler EE, Xia K. (2018). Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model. Mol Autism Dec 13;9:64. doi: 10.1186/s13229-018-0247-z. eCollection 2018.

Dougherty ML, Underwood JG, Nelson BJ, Tseng E, Munson KM, Penn O, Nowakowski TJ, Pollen AA, Eichler EE. (2018). Transcriptional fates of human-specific segmental duplications in brain. Genome Res Oct;28(10):1566-1576.

Arnett AB, Rhoads CL, Hoekzema K, Turner TN, Gerdts J, Wallace AS, Bedrosian-Sermone S, Eichler EE, Bernier RA. (2018). The autism spectrum phenotype in ADNP syndrome. Autism Res Sep;11(9):1300-1310.

Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. (2018). Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science Aug 3;361(6401):511-516. doi: 10.1126/science.aar8486.

Ghareghani M, Porubsky D, Sanders AD, Meiers S, Eichler EE, Korbel JO, Marschall T. (2018). Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. Bioinformatics Jul 1;34(13):i115-i123.

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. (2018). Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res Jul;28(7):1029-1038.

Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. (2018). High-resolution comparative analysis of great ape genomes. Science Jun 8;360(6393). pii: eaar6343. doi: 10.1126/science.aar6343.

Catacchio CR, Maggiolini FAM, D’Addabbo P, Bitonto M, Capozzi O, Signorile ML, Miroballo M, Archidiacono N, Eichler EE, Ventura M, Antonacci F. (2018). Inversion variants in human and primate genomes. Genome Res Jun;28(6):910-920.

Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A, Bishara A, Rosenkrantz JL, Lorig-Roach R, Field AR, Haeussler M, Russo L, Bhaduri A, Nowakowski TJ, Pollen AA, Dougherty ML, Nuttle X, Addor MC, Zwolinski S, Katzman S, Kriegstein A, Eichler EE, Salama SR, Jacobs FMJ, Haussler D. (2018). Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell May 31;173(6):1356-1369.e22.

Cantsilieris S, Nelson BJ, Huddleston J, Baker C, Harshman L, Penewit K, Munson KM, Sorensen M, Welch AE, Dang V, Grassmann F, Richardson AJ, Guymer RH, Graves-Lindsay TA, Wilson RK, Weber BHF, Baird PN, Allikmets R, Eichler EE. (2018). Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H (CFH) gene family. Proc Natl Acad Sci U S A May 8;115(19):E4433-E4442.

Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT. (2018). The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nat Genet Feb;50(2):270-277.

Cheng H, Dharmadhikari AV, Varland S, Ma N, Domingo D, Kleyner R, Rope AF, Yoon M, Stray-Pedersen A, Posey JE, Crews SR, Eldomery MK, Akdemir ZC, Lewis AM, Sutton VR, Rosenfeld JA, Conboy E, Agre K, Xia F, Walkiewicz M, Longoni M, High FA, van Slegtenhorst MA, Mancini GMS, Finnila CR, van Haeringen A, den Hollander N, Ruivenkamp C, Naidu S, Mahida S, Palmer EE, Murray L, Lim D, Jayakar P, Parker MJ, Giusto S, Stracuzzi E, Romano C, Beighley JS, Bernier RA, Küry S, Nizon M, Corbett MA, Shaw M, Gardner A, Barnett C, Armstrong R, Kassahn KS, Van Dijck A, Vandeweyer G, Kleefstra T, Schieving J, Jongmans MJ, de Vries BBA, Pfundt R, Kerr B, Rojas SK, Boycott KM, Person R, Willaert R, Eichler EE, Kooy RF, Yang Y, Wu JC, Lupski JR, Arnesen T, Cooper GM, Chung WK, Gecz J, Stessman HAF, Meng L, Lyon GJ. (2018). Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies. Am J Hum Genet May 3;102(5):985-994.

Aneichyk T, Hendriks WT, Yadav R, Shin D, Gao D, Vaine CA, Collins RL, Domingo A, Currall B, Stortchevoi A, Multhaupt-Buell T, Penney EB, Cruz L, Dhakal J, Brand H, Hanscom C, Antolik C, Dy M, Ragavendran A, Underwood J, Cantsilieris S, Munson KM, Eichler EE, Acuna P, Go C, Jamora RDG, Rosales RL, Church DM, Williams SR, Garcia S, Klein C, Muller U, Wilhelmsen KC, Timmers HTM, Sapir Y, Wainger BJ, Henderson D, Ito N, Weisenfeld N, Jaffe D, Sharma N, Breakefield XO, Ozelius LJ, Bragg DC, Talkowski ME. (2018). Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly. Cell Feb 22;172(5):897-909.e21.

Jansen S, Hoischen A, Coe BP, Carvill GL, Van Esch H, Bosch DGM, Andersen UA, Baker C, Bauters M, Bernier RA, van Bon BW, Claahsen-van der Grinten HL, Gecz J, Gilissen C, Grillo L, Hackett A, Kleefstra T, Koolen D, Kvarnung M, Larsen MJ, Marcelis C, McKenzie F, Monin ML, Nava C, Schuurs-Hoeijmakers JH, Pfundt R, Steehouwer M, Stevens SJC, Stumpel CT, Vansenne F, Vinci M, van de Vorst M, Vries P, Witherspoon K, Veltman JA, Brunner HG, Mefford HC, Romano C, Vissers LELM, Eichler EE, de Vries BBA. (2018). A genotype-first approach identifies an intellectual disability-overweight syndrome caused by PHIP haploinsufficiency. Eur J Hum Genet Jan;26(1):54-63.

Wallace AS, Hudac CM, Steinman KJ, Peterson JL, DesChamps TD, Duyzend MH, Nuttle X, Eichler EE, Bernier RA. (2017). Longitudinal report of child with de novo 16p11.2 triplication. Clin Case Rep Dec 6;6(1):147-154. doi: 10.1002/ccr3.1236. eCollection 2018 Jan.

Luhrs K, Ward T, Hudac CM, Gerdts J, Stessman HAF, Eichler EE, Bernier RA. (2017). Associations between Familial Rates of Psychiatric Disorders and De Novo Genetic Mutations in Autism. Autism Res Treat 2017:9371964. doi: 10.1155/2017/9371964. Epub 2017 Nov 8.

Wilfert AB, Sulovari A, Turner TN, Coe BP, Eichler EE. (2017). Recurrent de novo mutations in neurodevelopmental disorders: properties and clinical implications. Genome Med Nov 27;9(1):101.

Kury S, van Woerden GM, Besnard T, Proietti Onori M, Latypova X, Towne MC, Cho MT, Prescott TE, Ploeg MA, Sanders S, Stessman HAF, Pujol A, Distel B, Robak LA, Bernstein JA, Denomme-Pichon AS, Lesca G, Sellars EA, Berg J, Carre W, Busk OL, van Bon BWM, Waugh JL, Deardorff M, Hoganson GE, Bosanko KB, Johnson DS, Dabir T, Holla OL, Sarkar A, Tveten K, de Bellescize J, Braathen GJ, Terhal PA, Grange DK, van Haeringen A, Lam C, Mirzaa G, Burton J, Bhoj EJ, Douglas J, Santani AB, Nesbitt AI, Helbig KL, Andrews MV, Begtrup A, Tang S, van Gassen KLI, Juusola J, Foss K, Enns GM, Moog U, Hinderhofer K, Paramasivam N, Lincoln S, Kusako BH, Lindenbaum P, Charpentier E, Nowak CB, Cherot E, Simonet T, Ruivenkamp CAL, Hahn S, Brownstein CA, Xia F, Schmitt S, Deb W, Bonneau D, Nizon M, Quinquis D, Chelly J, Rudolf G, Sanlaville D, Parent P, Gilbert-Dussardier B, Toutain A, Sutton VR, Thies J, Peart-Vissers LELM, Boisseau P, Vincent M, Grabrucker AM, Dubourg C; Undiagnosed Diseases Network, Tan WH, Verbeek NE, Granzow M, Santen GWE, Shendure J, Isidor B, Pasquier L, Redon R, Yang Y, State MW, Kleefstra T, Cogne B; GEM HUGO; Deciphering Developmental Disorders Study, Petrovski S, Retterer K, Eichler EE, Rosenfeld JA, Agrawal PB, Bezieau S, Odent S, Elgersma Y, Mercier S. (2017). De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability. Am J Hum Genet Nov 2;101(5):768-788. doi: 10.1016/j.ajhg.2017.10.003.

Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes I, Armstrong J, Laayouni H, Gordon D, Huddleston J, Perez RG, Povolotskaya I, Armero AS, Garrido JG, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T. (2017). A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan_tro_3.0). Gigascience Nov 1;6(11):1-6.

Siper PM, De Rubeis S, Trelles MDP, Durkin A, Di Marino D, Muratet F, Frank Y, Lozano R, Eichler EE, Kelly M, Beighley J, Gerdts J, Wallace AS, Mefford HC, Bernier RA, Kolevzon A, Buxbaum JD. (2017). Prospective investigation of FOXP1 syndrome. Mol Autism Oct 24;8:57.

Earl RK, Turner TN, Mefford HC, Hudac CM, Gerdts J, Eichler EE, Bernier RA. (2017). Clinical phenotype of ASD-associated DYRK1A haploinsufficiency. Mol Autism Oct 5;8:54.

Prufer K, de Filippo C, Grote S, Mafessoni F, Korlevic P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyregne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kucan Z, Gusic I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andres A, Kelso J, Meyer M, Paabo S. (2017). A high-coverage Neandertal genome from Vindija Cave in Croatia. Science Nov 3;358(6363):655-658.

Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB, Eichler EE. (2017). Genomic Patterns of De Novo Mutation in Simplex Autism. Cell Oct 19;171(3):710-722.e12.

Arnett AB, Cairney BE, Wallace AS, Gerdts J, Turner TN, Eichler EE, Bernier RA. (2017). Comorbid symptoms of inattention, autism, and executive cognition in youth with putative genetic risk. J Child Psychol Psychiatry Mar;59(3):268-276.

Chaisson MJ, Mukherjee S, Kannan S, Eichler EE. (2017). Resolving multicopy duplications de novo using polyploid phasing. Res Comput Mol Biol May;10229:117-133.

Geisheker MR, Heymann G, Wang T, Coe BP, Turner TN, Stessman HAF, Hoekzema K, Kvarnung M, Shaw M, Friend K, Liebelt J, Barnett C, Thompson EM, Haan E, Guo H, Anderlid BM, Nordgren A, Lindstrand A, Vandeweyer G, Alberti A, Avola E, Vinci M, Giusto S, Pramparo T, Pierce K, Nalabolu S, Michaelson JJ, Sedlacek Z, Santen GWE, Peeters H, Hakonarson H, Courchesne E, Romano C, Kooy RF, Bernier RA, Nordenskjöld M, Gecz J, Xia K, Zweifel LS,Eichler EE. (2017). Hotspots of missense mutation identify neurodevelopmental disorder genes and functional domains. Nat Neurosci Aug;20(8):1043-1051.

Hudac CM, Stessman HAF, DesChamps TD, Kresse A, Faja S, Neuhaus E, Webb SJ, Eichler EE, Bernier RA. (2017). Exploring the heterogeneity of neural social indices for genetically distinct etiologies of autism. J Neurodev Disord May 26;9:24. doi: 10.1186/s11689-017-9199-4. eCollection 2017.

Xia EH, Yang DR, Jiang JJ, Zhang QJ, Liu Y, Liu YL, Zhang Y, Zhang HB, Shi C, Tong Y, Kim C, Chen H, Peng YQ, Yu Y, Zhang W, Eichler EE, Gao LZ. (2017). The caterpillar fungus, Ophiocordyceps sinensis, genome provides insights into highland adaptation of fungal pathogenicity. Sci Rep May 11;7(1):1806. doi: 10.1038/s41598-017-01869-z.

Xia EH, Zhang HB, Sheng J, Li K, Zhang QJ, Kim C, Zhang Y, Liu Y, Zhu T, Li W, Huang H, Tong Y, Nan H, Shi C, Shi C, Jiang JJ, Mao SY, Jiao JY, Zhang D, Zhao Y, Zhao YJ, Zhang LP, Liu YL, Liu BY, Yu Y, Shao SF, Ni DJ, Eichler EE, Gao LZ. (2017). The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis. Mol Plant Jun 5;10(6):866-877.

Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. (2017). Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res May;27(5):849-864.

Chiatante G, Giannuzzi G, Calabrese FM, Eichler EE, Ventura M. (2017). Centromere destiny in dicentric chromosomes: New insights from the evolution of human chromosome 2 ancestral centromeric region. Mol Biol Evol Jul 1;34(7):1669-1681.

Kim DS, Burt AA, Ranchalis JE, Wilmot B, Smith JD, Patterson KE, Coe BP, Li YK, Bamshad MJ, Nikolas M, Eichler EE, Swanson JM, Nigg JT, Nickerson DA, Jarvik GP; University of Washington Center for Mendelian Genomics. (2017). Sequencing of sporadic Attention-Deficit Hyperactivity Disorder (ADHD) identifies novel and potentially pathogenic de novo variants and excludes overlap with genes associated with autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet Jun;174(4):381-389.

Dougherty ML, Nuttle X, Penn O, Nelson BJ, Huddleston J, Baker C, Harshman L, Duyzend MH, Ventura M, Antonacci F, Sandstrom R, Dennis MY, Eichler EE. (2017). The birth of a human-specific neural gene by incomplete duplication and gene fusion. Genome Biol Mar 9;18(1):49.

Dennis MY, Harshman L, Nelson BJ, Penn O, Cantsilieris S, Huddleston J, Antonacci F, Penewit K, Denman L, Raja A, Baker C, Mark K, Malig M, Janke N, Espinoza C, Stessman HAF, Nuttle X, Hoekzema K, Lindsay-Graves TA, Wilson RK, Eichler EE. (2017). The evolution and population diversity of human-specific segmental duplications. Nat Ecol Evol Feb 17;1:69. doi:10.1038/s41559-016-0069.

Stessman HA, Xiong B, Coe BP, Wang T, Hoekzema K, Fenckova M, Kvarnung M, Gerdts J, Trinh S, Cosemans N, Vives L, Lin J, Turner TN, Santen G, Ruivenkamp C, Kriek M, van Haeringen A, Aten E, Friend K, Liebelt J, Barnett C, Haan E, Shaw M, Gecz J, Anderlid BM, Nordgren A, Lindstrand A, Schwartz C, Kooy RF, Vandeweyer G, Helsmoortel C, Romano C, Alberti A, Vinci M, Avola E, Giusto S, Courchesne E, Pramparo T, Pierce K, Nalabolu S, Amaral DG, Scheffer IE, Delatycki MB, Lockhart PJ, Hormozdiari F, Harich B, Castells-Nobau A, Xia K, Peeters H, Nordenskjold M, Schenck A, Bernier RA, Eichler EE. (2017). Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases. Nat Genet Apr;49(4):515-526. (Corrected Tables 1 and 2)

Tolomeo D, Capozzi O, Stanyon RR, Archidiacono N, D’Addabbo P, Catacchio CR, Purgato S, Perini G, Schempp W, Huddleston J, Malig M, Eichler EE, Rocchi M. (2017). Epigenetic origin of evolutionary novel centromeres. Sci Rep Feb 3;7:41980. doi: 10.1038/srep41980.

Kury S, Besnard T, Ebstein F, Khan TN, Gambin T, Douglas J, Bacino CA, Sanders SJ, Lehmann A, Latypova X, Khan K, Pacault M, Sacharow S, Glaser K, Bieth E, Perrin-Sabourin L, Jacquemont ML, Cho MT, Roeder E, Denomme-Pichon AS, Monaghan KG, Yuan B, Xia F, Simon S, Bonneau D, Parent P, Gilbert-Dussardier B, Odent S, Toutain A, Pasquier L, Barbouth D, Shaw CA, Patel A, Smith JL, Bi W, Schmitt S, Deb W, Nizon M, Mercier S, Vincent M, Rooryck C, Malan V, Briceno I, Gomez A, Nugent KM, Gibson JB, Cogne B, Lupski JR, Stessman HA, Eichler EE, Retterer K, Yang Y, Redon R, Katsanis N, Rosenfeld JA, Kloetzel PM, Golzio C, Bezieau S, Stankiewicz P, Isidor B. (2017). De novo disruption of the proteasome regulatory subunit PSMD12 causes a syndromic neurodevelopmental disorder. Am J Hum Genet Feb 2;100(2):352-363.

Eslami Rasekh M, Chiatante G, Miroballo M, Tang J, Ventura M, Amemiya CT, Eichler EE, Antonacci F, Alkan C. (2017). Discovery of large genomic inversions using long range information. BMC Genomics Jan 10;18(1):65.

Cantsilieris S, Stessman HA, Shendure J, Eichler EE. (2017). Targeted capture and high-throughput sequencing using molecular inversion probes (MIPs). Methods Mol Biol 1492:95-106.

Huddleston J, Chaisson MJ, Meltz Steinberg K, Warren W, Hoekzema K, Gordon DS, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, Eichler EE. (2017). Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res May;27(5):677-685. doi: 10.1101/gr.214007.116. Epub 2016 Nov 28.

Bramswig NC, Lüdecke HJ, Pettersson M, Albrecht B, Bernier RA, Cremer K, Eichler EE, Falkenstein D, Gerdts J, Jansen S, Kuechler A, Kvarnung M, Lindstrand A, Nilsson D, Nordgren A, Pfundt R, Spruijt L, Surowy HM, de Vries BB, Wieland T, Engels H, Strom TM, Kleefstra T, Wieczorek D. (2017). Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism. Hum Genet Feb;136(2):179-192. Epub 2016 Nov 15.

Turner TN, Yi Q, Krumm N, Huddleston J, Hoekzema K, Stessman HAF, Doebley A, Bernier RA, Nickerson DA, Eichler EE. (2017). denovo-db: a compendium of human de novo variants. Nucl Acids Res Jan 4;45(D1):D804-D811. Epub 2016 Oct 5.

Wang T, Guo H, Xiong B, Stessman HA, Wu H, Coe BP, Turner TN, Liu Y, Zhao W, Hoekzema K, Vives L, Xia L, Tang M, Ou J, Chen B, Shen Y, Xun G, Long M, Lin J, Kronenberg ZN, Peng Y, Bai T, Li H, Ke X, Hu Z, Zhao J, Zou X, Xia K, Eichler EE. (2016). De novo genic mutations among a Chinese autism spectrum disorder cohort. Nat Commun Nov 8;7:13316.

Mohajeri K, Cantsilieris S, Huddleston J, Nelson BJ, Coe BP, Campbell CD, Baker C, Harshman L, Munson KM, Kronenberg ZN, Kremitzki M, Raja A, Catacchio CR, Graves TA, Wilson RK, Ventura M, Eichler EE. (2016). Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region. Genome Res Nov;26(11):1453-1467.

Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer EW, van Dijk F, Hormozdiari F; Genome of the Netherlands Consortium., Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PI, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V. (2016). A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nat Commun Oct 6;7:12989. doi: 10.1038/ncomms12989.

Dennis MY, Eichler EE. (2016). Human adaptation and evolution by segmental duplication. Curr Opin Genet Dev Aug 29;41:44-52.

Epi4K Consortium. (2016). De novo mutations in SLC1A2 and CACNA1A are important causes of epileptic encephalopathies. Am J Hum Genet Aug 4;99(2):287-98.

Fox K, Johnsen JM, Coe BP, Frazar CD, Reiner AP; NHLBI Exome Sequencing Project, Minority Health-GRID Network, Eichler EE, Nickerson DA. (2016). Analysis of exome sequencing data sets reveals structural variation in the coding region of ABO in individuals of African ancestry. Transfusion 56;2744–2749.

Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MC, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE. (2016). Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. Nature Aug 11;536(7615):205-9.

Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, Lintner KE, Ding Q, Wang Z, Hu J, Wang D, Wang F, Wang L, Lyon GJ, Guan Y, Shen Y, Evgrafov OV, Knowles JA, Thibaud-Nissen F, Schneider V, Yu CY, Zhou L, Eichler EE, So KF, Wang K. (2016). Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun Jun 30;7:12065.

Mamiya PC, Richards TL, Coe BP, Eichler EE, Kuhl PK. (2016). Brain white matter structure and COMT gene are linked to second-language learning in adults. Proc Natl Acad Sci U S A Jun 28;113(26):7249-54.

Rafati N, Andersson LS, Mikko S, Feng C, Raudsepp T, Pettersson J, Janecka J, Wattle O, Ameur A, Thyreen G, Eberth J, Huddleston J, Malig M, Bailey E, Eichler EE, Dalin G, Chowdary B, Anderssson L, Lindgren G, Rubin CJ. (2016). Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies. G3 (Bethesda) Jul 7;6(7):2213-23.

Priest JR, Osoegawa K, Mohammed N, Nanda V, Kundu R, Schultz K, Lammer EJ, Girirajan S, Scheetz T, Waggott D, Haddad F, Reddy S, Bernstein D, Burns T, Steimle JD, Yang XH, Moskowitz IP, Hurles M, Lifton RP, Nickerson D, Bamshad M, Eichler EE, Mital S, Sheffield V, Quertermous T, Gelb BD, Portman M, Ashley EA. (2016). De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects. PLoS Genet Apr 8;12(4):e1005963.

Huddleston J, Eichler EE. (2016). An Incomplete Understanding of Human Genetic Variation. Genetics Apr;202(4):1251-4.

Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin CS, Eichler EE. (2016). Long-read sequence assembly of the gorilla genome. Science Apr 1;352(6281):aae0344.

Stessman HA, Willemsen MH, Fenckova M, Penn O, Hoischen A, Xiong B, Wang T, Hoekzema K, Vives L, Vogel I, Brunner HG, van der Burgt I, Ockeloen CW, Schuurs-Hoeijmakers JH, Klein Wassink-Ruiter JS, Stumpel C, Stevens SJ, Vles HS, Marcelis CM, van Bokhoven H, Cantagrel V, Colleaux L, Nicouleau M, Lyonnet S, Bernier RA, Gerdts J, Coe BP, Romano C, Alberti A, Grillo L, Scuderi C, Nordenskjöld M, Kvarnung M, Guo H, Xia K, Piton A, Gerard B, Genevieve D, Delobel B, Lehalle D, Perrin L, Prieur F, Thevenon J, Gecz J, Shaw M, Pfundt R, Keren B, Jacquette A, Schenck A, Eichler EE, Kleefstra T. (2016). Disruption of POGZ Is Associated with Intellectual Disability and Autism Spectrum Disorders. Am J Hum Genet Mar 3;98(3):541-552.

Stessman HA, Turner TN, Eichler EE. (2016). Molecular subtyping and improved treatment of neurodevelopmental disease. Genome Med Feb 25;8(1):22.

Lugtenberg D, Reijnders MR, Fenckova M, Bijlsma EK, Bernier R, van Bon BW, Smeets E, Vulto-van Silfhout AT, Bosch D, Eichler EE, Mefford HC, Carvill GL, Bongers EM, Schuurs-Hoeijmakers JH, Ruivenkamp CA, Santen GW, van den Maagdenberg AM, Peeters-Scholte CM, Kuenen S, Verstreken P, Pfundt R, Yntema HG, de Vries PF, Veltman JA, Hoischen A, Gilissen C, de Vries BB, Schenck A, Kleefstra T, Vissers LE. (2016). De novo loss-of-function mutations in WAC cause a recognizable intellectual disability syndrome and learning deficits in Drosophila. Eur J Hum Genet Aug;24(8):1145-53.

Turner TN, Hormozdiari F, Duyzend MH, McClymont SA, Hook PW, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman HA, Zody MC, Nelson BJ, Huddleston J, Sandstrom R, Smith JD, Hanna D, Swanson JM, Faustman EM, Bamshad MJ, Stamatoyannopoulos J, Nickerson DA, McCallion AS, Darnell R, Eichler EE. (2016). Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. Am J Hum Genet Jan 7;98(1):58-74. Epub 2015 Dec 31.

Duyzend MH, Nuttle X, Coe BP, Baker C, Nickerson DA, Bernier R, Eichler EE. (2016). Maternal Modifiers and Parent-of-Origin Bias of the Autism-Associated 16p11.2 CNV. Am J Hum Genet Jan 7;98(1):45-57. Epub 2015 Dec 31.

Ba W, Yan Y, Reijnders MR, Schuurs-Hoeijmakers JH, Feenstra I, Bongers EM, Bosch DG, de Leeuw N, Pfundt R, Gilissen C, de Vries PF, Veltman JA, Hoischen A, Mefford HC, Eichler EE, Eipper BA, Mains RE, Vissers LE, Nadif Kasri N, de Vries BB. (2016). TRIO loss of function is associated with mild intellectual disability and affects dendritic branching and synapse function. Hum Mol Genet Mar 1;25(5):892-902. Epub 2015 Dec 31.

Koolen DA, Pfundt R, Linda K, Beunders G, Veenstra-Knol HE, Conta JH, Fortuna AM, Gillessen-Kaesbach G, Dugan S, Halbach S, Abdul-Rahman OA, Winesett HM, Chung WK, Dalton M, Dimova PS, Mattina T, Prescott K, Zhang HZ, Saal HM, Hehir-Kwa JY, Willemsen MH, Ockeloen CW, Jongmans MC, Van der Aa N, Failla P, Barone C, Avola E, Brooks AS, Kant SG, Gerkes EH, Firth HV, Ounap K, Bird LM, Masser-Frye D, Friedman JR, Sokunbi MA, Dixit A, Splitt M; DDD Study, Kukolich MK, McGaughran J, Coe BP, Florez J, Nadif Kasri N, Brunner HG, Thompson EM, Gecz J, Romano C, Eichler EE, de Vries BB. (2016). The Koolen-de Vries syndrome: a phenotypic comparison of patients with a 17q21.31 microdeletion versus a KANSL1 sequence variant. Eur J Hum Genet May;24(5):652-9. Epub 2015 Aug 26.

van Bon BW, Coe BP, Bernier R, Green C, Gerdts J, Witherspoon K, Kleefstra T, Willemsen MH, Kumar R, Bosco P, Fichera M, Li D, Amaral D, Cristofoli F, Peeters H, Haan E, Romano C, Mefford HC, Scheffer I, Gecz J, de Vries BB, Eichler EE. (2016). Disruptive de novo mutations of DYRK1A lead to a syndromic form of autism and ID. Mol Psychiatry Jan;21(1):126.132. doi: 10.1038/mp.2015.5. Epub 2015 Feb 24.

Chen J, Huddleston J, Buckley RM, Malig M, Lawhon SD, Skow LC, Lee MO, Eichler EE, Andersson L, Womack JE. (2015). Bovine NK-lysin: Copy number variation and functional diversification. Proc Natl Acad Sci U S A Dec 29;112(52):E7223-9.

Chen DH, Meneret A, Friedman JR, Korvatska O, Gad A, Bonkowski ES, Stessman HA, Doummar D, Mignot C, Anheim M, Bernes S, Davis MY, Damon-Perriere N, Degos B, Grabli D, Gras D, Hisama FM, Mackenzie KM, Swanson PD, Tranchant C, Vidailhet M, Winesett S, Trouillard O, Amendola LM, Dorschner MO, Weiss M, Eichler EE, Torkamani A, Roze E, Bird TD, Raskind WH. (2015). ADCY5-related dyskinesia: Broader spectrum and genotype-phenotype correlations. Neurology Dec 8;85(23):2026-35.

Chaisson MJ, Wilson RK, Eichler EE. (2015). Genetic variation and the de novo assembly of human genomes. Nat Rev Genet Nov;16(11):627-40.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stutz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. (2015). An integrated map of structural variation in 2,504 human genomes. Nature Oct 1;526(7571):75-81.

Mitchell E, Douglas A, Kjaegaard S, Callewaert B, Vanlander A, Janssens S, Lawson Yuen A, Skinner C, Failla P, Alberti A, Avola E, Fichera M, Kibaek M, Digilio MC, Hannibal MC, den Hollander NS, Bizzarri V, Renieri A, Mencarelli MA, Fitzgerald T, Piazzolla S, van Oudenhove E, Romano C, Schwartz C, Eichler EE, Slavotinek A, Escobar L, Rajan D, Crolla J, Carter N, Hodge JC, Mefford HC. (2015). Recurrent duplications of 17q12 associated with variable phenotypes. Am J Med Genet A Dec;167(12):3038-45.

Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JT, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer M, Khusainova R, Khusnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE. (2015). Global diversity, population stratification, and selection of human copy number variation. Science Sep 11;349(6253):aab3761.(Simons Genome Diversity Project Dataset)
(Sequence data at the ENA)
(Signed Letter Request)

Snijders Blok L, Madsen E, Juusola J, Gilissen C, Baralle D, Reijnders MR, Venselaar H, Helsmoortel C, Cho MT, Hoischen A, Vissers LE, Koemans TS, Wissink-Lindhout W, Eichler EE, Romano C, Van Esch H, Stumpel C, Vreeburg M, Smeets E, Oberndorff K, van Bon BW, Shaw M, Gecz J, Haan E, Bienek M, Jensen C, Loeys BL, Van Dijck A, Innes AM, Racher H, Vermeer S, Di Donato N, Rump A, Tatton-Brown K, Parker MJ, Henderson A, Lynch SA, Fryer A, Ross A, Vasudevan P, Kini U, Newbury-Ecob R, Chandler K, Male A; DDD Study, Dijkstra S, Schieving J, Giltay J, van Gassen KL, Schuurs-Hoeijmakers J, Tan PL, Pediaditakis I, Haas SA, Retterer K, Reed P, Monaghan KG, Haverfield E, Natowicz M, Myers A, Kruer MC, Stein Q, Strauss KA, Brigatti KW, Keating K, Burton BK, Kim KH, Charrow J, Norman J, Foster-Barber A, Kline AD, Kimball A, Zackai E, Harr M, Fox J, McLaughlin J, Lindstrom K, Haude KM, van Roozendaal K, Brunner H, Chung WK, Kooy RF, Pfundt R, Kalscheuer V, Mehta SG, Katsanis N, Kleefstra T. (2015). Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling. Am J Hum Genet Aug 6;97(2):343-52.

Houge G, Haesen D, Vissers LE, Mehta S, Parker MJ, Wright M, Vogt J, McKee S, Tolmie JL, Cordeiro N, Kleefstra T, Willemsen MH, Reijnders MR, Berland S, Hayman E, Lahat E, Brilstra EH, van Gassen KL, Zonneveld-Huijssoon E, de Bie CI, Hoischen A, Eichler EE, Holdhus R, Steen VM, Doskeland SO, Hurles ME, FitzPatrick DR, Janssens V. (2015). B56.-related protein phosphatase 2A dysfunction identified in patients with intellectual disability. J Clin Invest Aug 3;125(8):3051-62.

Krumm N, Turner TN, Baker C, Vives L, Mohajeri K, Witherspoon K, Raja A, Coe BP, Stessman HA, He ZX, Leal SM, Bernier R, Eichler EE. (2015). Excess of rare, inherited truncating mutations in autism. Nat Genet Jun;47(6):582-8.

Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer EW, Moed MH, Koval V, Renkens I, van Roosmalen MJ, Arp P, Karssen LC, Coe BP, Handsaker RE, Suchiman ED, Cuppen E, Thung DT, McVey M, Wendl MC, Uitterlinden A, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Schonhuth A, Eichler EE, de Bakker PI, Ye K, Guryev V. (2015). Characteristics of de novo structural changes in the human genome. Genome Res Jun;25(6):792-801.

Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN, de Manuel M, Hernandez-Rodriguez J, Lobon I, Siegismund HR, Pagani L, Quail MA, Hvilsom C, Mudakikwa A, Eichler EE, Cranfield MR, Marques-Bonet T, Tyler-Smith C, Scally A. (2015). Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. Science Apr 10;348(6231):242-5.

Duyzend MH, Eichler EE. (2015). Genotype-first analysis of the 16p11.2 deletion defines a new type of “autism”. Biol Psychiatry May 1;77(9):769-71.

Snyder MW, Simmons LE, Kitzman JO, Coe BP, Henson JM, Daza RM, Eichler EE, Shendure J, Gammill HS. (2015). Copy-number variation and false positive prenatal aneuploidy screening results. N Engl J Med Apr 23;372(17):1639-45.

Carlson KD, Sudmant PH, Press MO, Eichler EE, Shendure J, Queitsch C. (2015). MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. Genome Res May;25(5):750-61.

Mazina V, Gerdts J, Trinh S, Ankenman K, Ward T, Dennis MY, Girirajan S, Eichler EE, Bernier R. (2015). Epigenetics of autism-related impairment: Copy number variation and maternal infection. J Dev Behav Pediatr Feb-Mar;36(2):61-7.

Pino-Yanes M, Gignoux CR, Galanter JM, Levin AM, Campbell CD, Eng C, Huntsman S, Nishimura KK, Gourraud PA, Mohajeri K, O’Roak BJ, Hu D, Mathias RA, Nguyen EA, Roth LA, Padhukasahasram B, Moreno-Estrada A, Sandoval K, Winkler CA, Lurmann F, Davis A, Farber HJ, Meade K, Avila PC, Serebrisky D, Chapela R, Ford JG, Lenoir MA, Thyne SM, Brigino-Buenaventura E, Borrell LN, Rodriguez-Cintron W, Sen S, Kumar R, Rodriguez-Santana JR, Bustamante CD, Martinez FD, Raby BA, Weiss ST, Nicolae DL, Ober C, Meyers DA, Bleecker ER, Mack SJ, Hernandez RD, Eichler EE, Barnes KC, Williams LK, Torgerson DG, Burchard EG. (2015). Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. J Allergy Clin Immunol Jun;135(6):1502-10. Epub 2014 Dec 6.

Hormozdiari F, Penn O, Borenstein E, Eichler EE. (2015). The discovery of integrated gene networks for autism and related disorders. Genome Res Jan;25(1):142-54. Epub 2014 Nov 5.

Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE. (2015). Resolving the complexity of the human genome using single-molecule sequencing. Nature Jan 29;517(7536):608-11. doi: 10.1038/nature13907. Epub 2014 Nov 10.

Watson CT, Steinberg KM, Graves TA, Warren RL, Malig M, Schein J, Wilson RK, Holt RA, Eichler EE, Breden F. (2015). Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity. Genes Immun Jan-Feb;16(1):24-34. Epub 2014 Oct 23.

De Rocker N, Vergult S, Koolen D, Jacobs E, Hoischen A, Zeesman S, Bang B, Bena F, Bockaert N, Bongers EM, de Ravel T, Devriendt K, Giglio S, Faivre L, Joss S, Maas S, Marle N, Novara F, Nowaczyk MJ, Peeters H, Polstra A, Roelens F, Rosenberg C, Thevenon J, Tumer Z, Vanhauwaert S, Varvagiannis K, Willaert A, Willemsen M, Willems M, Zuffardi O, Coucke P, Speleman F, Eichler EE, Kleefstra T, Menten B. (2015). Refinement of the critical 2p25.3 deletion region: the role of MYT1L in intellectual disability and obesity. Genet Med Jun;17(6):460.466. Epub 2014 Sep 18.

O’Roak BJ, Stessman HA, Boyle EA, Witherspoon KT, Martin B, Lee C, Vives L, Baker C, Hiatt JB, Nickerson DA, Bernier R, Shendure J, Eichler EE. (2014). Recurrent de novo mutations implicate novel genes underlying simplex autism risk. Nat Commun Nov 24;5:5595.

Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R, Thurman RE, Johnson AK, Vong S, Lee K, Bates D, Neri F, Diegel M, Giste E, Haugen E, Dunn D, Wilken MS, Josefowicz S, Samstein R, Chang KH, Eichler EE, De Bruijn M, Reh TA, Skoultchi A, Rudensky A, Orkin SH, Papayannopoulou T, Treuting PM, Selleri L, Kaul R, Groudine M, Bender MA, Stamatoyannopoulos JA. (2014). Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science Nov 21;346(6212):1007-12.

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Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R, Huddleston J, Shiryev SA, Morgulis A, Surti U, Warren WC, Church DM, Eichler EE, Wilson RK. (2014). Single haplotype assembly of the human genome from a hydatidiform mole. Genome Res Dec;24(12):2066-76.

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Antonacci F, Dennis MY, Huddleston J, Sudmant PH, Steinberg KM, Rosenfeld JA, Miroballo M, Graves TA, Vives L, Malig M, Denman L, Raja A, Stuart A, Tang J, Munson B, Shaffer LG, Amemiya CT, Wilson RK, Eichler EE. (2014). Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Nat Genet Dec;46(12):1293-302.

Deriziotis P, O’Roak BJ, Graham SA, Estruch SB, Dimitropoulou D, Bernier RA, Gerdts J, Shendure J, Eichler EE, Fisher SE. (2014). De novo TBR1 mutations in sporadic autism disrupt protein functions. Nat Commun Sep 18;5:4954.

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Coe BP, Witherspoon K, Rosenfeld JA, van Bon BW, Vulto-van Silfhout AT, Bosco P, Friend KL, Baker C, Buono S, Vissers LE, Schuurs-Hoeijmakers JH, Hoischen A, Pfundt R, Krumm N, Carvill GL, Li D, Amaral D, Brown N, Lockhart PJ, Scheffer IE, Alberti A, Shaw M, Pettinato R, Tervo R, de Leeuw N, Reijnders MR, Torchia BS, Peeters H, Thompson E, O’Roak BJ, Fichera M, Hehir-Kwa JY, Shendure J, Mefford HC, Haan E, Gecz J, de Vries BB, Romano C, Eichler EE. (2014). Refining analyses of copy number variation identifies specific genes associated with developmental delay. Nat Genet Oct;46(10):1063-71.

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Lozano R, Hagerman RJ, Duyzend M, Budimirovic DB, Eichler EE, Tassone F. (2014). Genomic studies in fragile X premutation carriers. J Neurodev Disord 2014;6(1):27.

Vandeweyer G, Helsmoortel C, Van Dijck A, Vulto-van Silfhout AT, Coe BP, Bernier R, Gerdts J, Rooms L, van den Ende J, Bakshi M, Wilson M, Nordgren A, Hendon LG, Abdulrahman OA, Romano C, de Vries BB, Kleefstra T, Eichler EE, Van der Aa N, Kooy RF. (2014). The transcriptional regulator ADNP links the BAF (SWI/SNF) complexes with autism. Am J Med Genet C Semin Med Genet Sep;166(3):315-26.

Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O’Roak BJ, Krumm N, Vives L, Lee C, Roth LA, Rodriguez-Cintron W, Rodriguez-Santana J, Brigino-Buenaventura E, Davis A, Meade K, LeNoir MA, Thyne S, Jackson DJ, Gern JE, Lemanske RF Jr, Shendure J, Abney M, Burchard EG, Ober C, Eichler EE. (2014). Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. PLOS One Aug 12;9(8):e104396.

Bernier R, Golzio C, Xiong B, Stessman HA, Coe BP, Penn O, Witherspoon K, Gerdts J, Baker C, Vulto-van Silfhout AT, Schuurs-Hoeijmakers JH, Fichera M, Bosco P, Buono S, Alberti A, Failla P, Peeters H, Steyaert J, Vissers LE, Francescatto L, Mefford HC, Rosenfeld JA, Bakken T, O’Roak BJ, Pawlus M, Moon R, Shendure J, Amaral DG, Lein E, Rankin J, Romano C, de Vries BB, Katsanis N, Eichler EE. (2014). Disruptive CHD8 mutations define a subtype of autism early in development. Cell Jul 17;158(2):263-76.

Nuttle X, Itsara A, Shendure J, Eichler EE. (2014). Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing. Nat Protoc Jun;9(6):1496-513.

Hoischen A, Krumm N, Eichler EE. (2014). Prioritization of neurodevelopmental disease genes by discovery of new mutations. Nat Neurosci Jun;17(6):764-72.

Hach F, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. (2014). mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Res Jul;42(W1):W494-500.

Vulto-van Silfhout AT, Rajamanickam S, Jensik PJ, Vergult S, de Rocker N, Newhall KJ, Raghavan R, Reardon SN, Jarrett K, McIntyre T, Bulinski J, Ownby SL, Huggenvik JI, McKnight GS, Rose GM, Cai X, Willaert A, Zweier C, Endele S, de Ligt J, van Bon BW, Lugtenberg D, de Vries PF, Veltman JA, van Bokhoven H, Brunner HG, Rauch A, de Brouwer AP, Carvill GL, Hoischen A, Mefford HC, Eichler EE, Vissers LE, Menten B, Collard MW, de Vries BB. (2014). Mutations affecting the SAND domain of DEAF1 cause intellectual Disability with severe speech impairment and behavioral problems. Am J Hum Genet May 1;94(5):649-61.

Falchi M, El-Sayed Moustafa JS, Takousis P, Pesce F, Bonnefond A, Andersson-Assarsson JC, Sudmant PH, Dorajoo R, Al-Shafai MN, Bottolo L, Ozdemir E, So HC, Davies RW, Patrice A, Dent R, Mangino M, Hysi PG, Dechaume A, Huyvaert M, Skinner J, Pigeyre M, Caiazzo R, Raverdy V, Vaillant E, Field S, Balkau B, Marre M, Visvikis-Siest S, Weill J, Poulain-Godefroy O, Jacobson P, Sjostrom L, Hammond CJ, Deloukas P, Sham PC, McPherson R, Lee J, Tai ES, Sladek R, Carlsson LM, Walley A, Eichler EE, Pattou F, Spector TD, Froguel P. (2014). Low copy number of the salivary amylase gene predisposes to obesity. Nat Genet May;46(5):492-7.

Stong N, Deng Z, Gupta R, Hu S, Paul S, Weiner AK, Eichler EE, Graves T, Fronick CC, Courtney L, Wilson RK, Lieberman P, Davuluri RV, Riethman H. (2014). Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. Genome Res Jun;24(6):1039-50.

Jacquemont S, Coe BP, Hersch M, Duyzend MH, Krumm N, Bergmann S, Beckmann JS, Rosenfeld JA, Eichler EE. (2014). A Higher Mutational Burden in Females Supports a “Female Protective Model” in Neurodevelopmental Disorders. Am J Hum Genet Mar 6;94(3):415-25.

Stessman HA, Bernier R, Eichler EE. (2014). A genotype-first approach to defining the subtypes of a complex disease. Cell Feb 27;156(5):872-7.

Helsmoortel C, Vulto-van Silfhout AT, Coe BP, Vandeweyer G, Rooms L, van den Ende J, Schuurs-Hoeijmakers JH, Marcelis CL, Willemsen MH, Vissers LE, Yntema HG, Bakshi M, Wilson M, Witherspoon KT, Malmgren H, Nordgren A, Anneren G, Fichera M, Bosco P, Romano C, de Vries BB, Kleefstra T, Kooy RF, Eichler EE, Van der Aa N. (2014). A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP. Nat Genet Apr;46(4):380-4.

Morris DW, Pearson RD, Cormican P, Kenny EM, O’Dushlaine CT, Lemieux Perreault LP, Giannoulatou E, Tropea D, Maher BS, Wormley B, Kelleher E, Fahey C, Molinos I, Bellini S, Pirinen M, Strange A, Freeman C, Thiselton DL, Elves RL, Regan R, Ennis S, Dinan TG, McDonald C, Murphy KC, O’Callaghan E, Waddington JL, Walsh D, O’Donovan M, Grozeva D, Craddock N, Stone J, Scolnick E, Purcell S, Sklar P, Coe B, Eichler EE, Ophoff R, Buizer J, Szatkiewicz J, Hultman C, Sullivan P, Gurling H, McQuillin A, St Clair D, Rees E, Kirov G, Walters J, Blackwood D, Johnstone M, Donohoe G; International Schizophrenia Consortium; SGENE+ Consortium, O’Neill FA; Wellcome Trust Case Control Consortium 2, Kendler KS, Gill M, Riley BP, Spencer CC, Corvin A. (2014). An inherited duplication at the gene p21 Protein-Activated Kinase 7 (PAK7) is a risk factor for psychosis. Hum Mol Genet Jun 15;23(12):3316-26.

Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE. (2014). Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res Apr;24(4):688-96.

Krumm N, O’Roak BJ, Shendure J, Eichler EE. (2014). A de novo convergence of autism genetics and molecular neuroscience. Trends Neurosci Feb;37(2):95-105. Epub 2013 Dec 30.

He Z, O’Roak BJ, Smith JD, Wang G, Hooker S, Santos-Cortez RL, Li B, Kan M, Krumm N, Nickerson DA, Shendure J, Eichler EE, Leal SM. (2014). Rare-Variant Extensions of the Transmission Disequilibrium Test: Application to Autism Exome Sequence Data. Am J Hum Genet Jan 2;94(1):33-46. Epub 2013 Dec 19.

Prufer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EELein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Paabo S. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature Jan 2;505(7481):43-9. Epub 2013 Dec 18.

Dao P, Numanagic I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC. (2014). ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Bioinformatics Mar 1;30(5):644-51. Epub 2013 Oct 15.

McMichael G, Girirajan S, Moreno-De-Luca A, Gecz J, Shard C, Nguyen LS, Nicholl J, Gibson C, Haan E, Eichler EE, Martin CL, MacLennan A. (2014). Rare copy number variation in cerebral palsy. Eur J Hum Genet Jan;22(1):40-5.

Dumont BL, Eichler EE. (2013). Signals of historical interlocus gene conversion in human segmental duplications. PLoS One Oct 4;8(10):e75949.

Giannuzzi G, Pazienza M, Huddleston J, Antonacci F, Malig M, Vives L, Eichler EE, Ventura M. (2013). Hominoid fission of chromosome 14/15 and the role of segmental duplications. Genome Res Nov;23(11):1763-73.

Krumm N, O’Roak BJ, Karakoc E, Mohajeri K, Nelson B, Vives L, Jacquemont S, Munson J, Bernier R, Eichler EE. (2013). Transmission disequilibrium of small CNVs in simplex autism. Am J Hum Genet Oct 3;93(4):595-606.

Epi4K Consortium, Allen AS, Berkovic SF, Cossette P, Delanty N, Dlugos D, Eichler EE, Epstein MP, Glauser T, Goldstein DB, Han Y, Heinzen EL, Hitomi Y, Howell KB, Johnson MR, Kuzniecky R,Lowenstein DH, Lu YF, Madou MR, Marson AG, Mefford HC, Esmaeeli Nieh S, O’Brien TJ, Ottman R, Petrovski S, Poduri A, Ruzzo EK, Scheffer IE, Sherr EH, Yuskaitis CJ; Epilepsy Phenome/Genome Project, Abou-Khalil B, Alldredge BK, Bautista JF, Berkovic SF, Boro A, Cascino GD, Consalvo D, Crumrine P, Devinsky O, Dlugos D, Epstein MP, Fiol M, Fountain NB, French J, Friedman D, Geller EB, Glauser T, Glynn S, Haut SR, Hayward J, Helmers SL, Joshi S, Kanner A, Kirsch HE, Knowlton RC, Kossoff EH, Kuperman R, Kuzniecky R, Lowenstein DH, McGuire SM, Motika PV, Novotny EJ, Ottman R, Paolicchi JM, Parent JM, Park K, Poduri A, Scheffer IE, Shellhaas RA, Sherr EH, Shih JJ, Singh R, Sirven J, Smith MC, Sullivan J, Lin Thio L, Venkat A, Vining EP, Von Allmen GK, Weisenberg JL, Widdess-Walsh P, Winawer MR. (2013). De novo mutations in epileptic encephalopathies. Nature Sep 12;501(7466):217-21.

Nuttle X, Huddleston J, O’Roak BJ, Antonacci F, Fichera M, Romano C, Shendure J, Eichler EE. (2013). Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions. Nat Methods Aug;10(9):903-9.

Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C; Great Ape Genome Project, Marques-Bonet T, Ventura M, Batzer MA, Eichler EE. (2013). Rates and patterns of great ape retrotransposition. Proc Natl Acad Sci U S A Aug 13;110(33):13457-62.

Sudmant PH, Huddleston J, Catacchio CR, Malig M, Hillier LW, Baker C, Mohajeri K, Kondova I, Bontrop RE, Persengiev S, Antonacci F, Ventura M, Prado Martinez J, Marques-Bonet T, Eichler EE. (2013). Evolution and diversity of copy number variation in the great ape lineage. Genome Res Sep;23(9):1373-82.

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O’Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prufer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubi C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andres AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. (2013). Great ape genetic diversity and population history. Nature Jul 25;499(7459):471-5.Great Ape Genome Project (mirror)

Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Rainieri E, Estelle J, Fernandez-Callejo M, Valles M, Ritscher L, Schoneberg T, de la Calle-Mustienes E, Casillas S, Rubio-Acero R, Mele M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Bertranpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, Lalueza-Fox C, Navarro A, Marques-Bonet T. (2013). The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. BMC Genomics May 31;14(1):363.

Campbell CD, Eichler EE. (2013). Properties and rates of germline mutations in humans. Trends Genet Oct;29(10):575-84.

Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. (2013). Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods Jun;10(6):563-9.

Korvatska O, Strand NS, Berndt JD, Strovas T, Chen DH, Leverenz JB, Kiianitsa K, Mata IF, Karakoc E, Greenup JL, Bonkowski E, Chuang J, Moon RT, Eichler EE, Nickerson DA, Zabetian CP, Kraemer BC, Bird TD, Raskind WH. (2013). Altered splicing of ATP6AP2 causes X-linked parkinsonism with spasticity (XPDS). Hum Mol Genet Aug 15;22(16):3259-68.

Timms AE, Dorschner MO, Wechsler J, Choi KY, Kirkwood R, Girirajan S, Baker C, Eichler EE, Korvatska O, Roche KW, Horwitz MS, Tsuang DW. (2013). Support for the N -Methyl-D-Aspartate receptor hypofunction hypothesis of schizophrenia from exome sequencing in multiplex families. JAMA Psychiatry Jun 1;70(6):582-90.

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Girirajan S, Johnson RL, Tassone F, Balciuniene J, Katiyar N, Fox K, Baker C, Srikanth A, Yeoh KH, Khoo SJ, Nauth TB, Hansen R, Ritchie M, Hertz-Picciotto I, Eichler EE, Pessah IN, Selleck SB. (2013). Global increases in both common and rare copy number load associated with autism. Hum Mol Genet Jul 15;22(14):2870-80.

Girirajan S, Dennis MY, Baker C, Malig M, Coe BP, Campbell CD, Mark K, Vu TH, Alkan C, Cheng Z, Biesecker LG, Bernier R, Eichler EE. (2013). Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder. Am J Hum Genet Feb 7;92(2):221-37.

Tucci A, Kara E, Schossig A, Wolf NI, Plagnol V, Fawcett K, Paisan-Ruiz C, Moore M, Hernandez D, Musumeci S, Tennison M, Hennekam R, Palmeri S, Malandrini A, Raskin S, Donnai D, Hennig C, Tzschach A, Hordijk R, Bast T, Wimmer K, Lo CN, Shorvon S, Mefford H, Eichler EE, Hall R, Hayes I, Hardy J, Singleton A, Zschocke J, Houlden H. (2013). Kohlschutter-Tonz syndrome: Mutations in ROGDI and evidence of genetic heterogeneity. Hum Mutat Feb;34(2):296-300. Epub 2012 Nov 27.

Lorente-Galdos B, Bleyhl J, Santpere G, Vives L, Ramirez O, Hernandez J, Anglada R, Cooper GM, Navarro A, Eichler EE, Marques-Bonet T. (2013). Accelerated exon evolution within primate segmental duplications. Genome Biol Jan 29;14(1):R9.

Beunders G, Voorhoeve E, Golzio C, Pardo LM, Rosenfeld JA, Talkowski ME, Simonic I, Lionel AC, Vergult S, Pyatt RE, van de Kamp J, Nieuwint A, Weiss MM, Rizzu P, Verwer LE, van Spaendonk RM, Shen Y, Wu BL, Yu T, Yu Y, Chiang C, Gusella JF, Lindgren AM, Morton CC, van Binsbergen E, Bulk S, van Rossem E, Vanakker O, Armstrong R, Park SM, Greenhalgh L, Maye U, Neill NJ, Abbott KM, Sell S, Ladda R, Farber DM, Bader PI, Cushing T, Drautz JM, Konczal L, Nash P, Reyes ED, Carter MT, Hopkins E, Marshall CR, Osborne LR, Gripp KW, Thrush DL, Hashimoto S, Gastier-Foster JM, Astbury C, Ylstra B, Meijers-Heijboer H, Posthuma D, Menten B, Mortier G, Scherer SW, Eichler EE, Girirajan S, Katsanis N, Groffen AJ, Sistermans EA. (2013). Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus. Am J Hum Genet Feb 7;92(2):210-20.

Mueller M, Barros P, Witherden AS, Roberts AL, Zhang Z, Schaschl H, Yu CY, Hurles ME, Schaffner C, Floto RA, Game L, Steinberg KM, Wilson RK, Graves TA, Eichler EE, Cook HT, Vyse TJ, Aitman TJ. (2013). Genomic pathology of SLE-associated copy-number variation at the FCGR2C/FCGR3B/FCGR2B locus. Am J Hum Genet Jan 10;92(1):28-40. Epub 2012 Dec 20.

Rosenfeld JA, Coe BP, Eichler EE, Cuckle H, Shaffer LG. (2013). Estimates of penetrance for recurrent pathogenic copy-number variations. Genet Med Jun;15(6):478-81. Epub 2012 Dec 20.

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Campbell CD, Chong JX, Malig M, Ko A, Dumont BL, Han L, Vives L, O’Roak BJ, Sudmant PH, Shendure J, Abney M, Ober C, Eichler EE. (2012). Estimating the human mutation rate using autozygosity in a founder population. Nat Genet Nov;44(11):1277-81.

Girirajan S, Rosenfeld JA, Coe BP, Parikh S, Friedman N, Goldstein A, Filipink RA, McConnell JS, Angle B, Meschino WS, Nezarati MM, Asamoah A, Jackson KE, Gowans GC, Martin JA, Carmany EP, Stockton DW, Schnur RE, Penney LS, Martin DM, Raskin S, Leppig K, Thiese H, Smith R, Aberg E, Niyazov DM, Escobar LF, El-Khechen D, Johnson KD, Lebel RR, Siefkas K, Ball S, Shur N, McGuire M, Brasington CK, Spence JE, Martin LS, Clericuzio C, Ballif BC, Shaffer LG, Eichler EE. (2012). Phenotypic heterogeneity of genomic disorders and rare copy-number variants. N Engl J Med Oct 4;367(14):1321-31.

Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andres AM, Eichler EE, Slatkin M, Reich D, Kelso J, Paabo S. (2012). A high-coverage genome sequence from an archaic denisovan individual. Science Oct 12;338(6104):222-6.

Tabor HK, Murray JC, Gammill HS, Kitzman JO, Snyder MW, Ventura M, Lewis AP, Qiu R, Simmons LE, Rubens CE, Santillan MK, Eichler EE, Cheng EY, Bamshad MJ, Shendure J. (2012). Non-invasive fetal genome sequencing: Opportunities and challenges. Am J Med Genet A Oct;158A(10):2382-4.

Smith JJ, Baker C, Eichler EE, Amemiya CT. (2012). Genetic consequences of programmed genome rearrangement. Curr Biol Aug 21;22(16):1524-9.

Chen YZ, Matsushita MM, Robertson P, Rieder M, Girirajan S, Antonacci F, Lipe H, Eichler EE, Nickerson DA, Bird TD, Raskind WH. (2012). Autosomal dominant familial dyskinesia and facial myokymia: single exome sequencing identifies a mutation in adenylyl cyclase 5. Arch Neurol May 1;69(5):630-5.

Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE. (2012). Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nat Genet Jul 1;44(8):872-80.

Prufer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoc E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, Andre C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andres AM, Kelso J, Paabo S. (2012). The bonobo genome compared with the chimpanzee and human genomes. Nature Jun 28;486(7404):527-31.

Kitzman JO, Snyder MW, Ventura M, Lewis AP, Qiu R, Simmons LE, Gammill HS, Rubens CE, Santillan DA, Murray JC, Tabor HK, Bamshad MJ, Eichler EE, Shendure J. (2012). Noninvasive whole-genome sequencing of a human fetus. Sci Transl Med Jun 6;4(137):137ra76.

Krumm N, Sudmant PH, Ko A, O’Roak BJ, Malig M, Coe BP, Nhlbi Exome Sequencing Project N, Quinlan AR, Nickerson DA, Eichler EE. (2012). Copy number variation detection and genotyping from exome sequence data. Genome Res Aug;22(8):1525-32.

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Dennis MY, Nuttle X, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S, Malig M, Kotkiewicz H, Curry CJ, Shafer S, Shaffer LF, de Jong PJ, Wilson RK, Eichler EE. (2012). Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell May 11;149(4):912-22.

Priest JR, Girirajan S, Vu TH, Olson A, Eichler EE, Portman MA. (2012). Rare copy number variants in isolated sporadic and syndromic atrioventricular septal defects. Am J Med Genet A Jun;158A(6):1279-84.

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Itsara A, Vissers LELM, Steinberg KM, Meyer KJ, Zody MC, Koolen DA, de Ligt J, Cuppen E, Baker C, Lee C, Graves TA, Wilson RK, Jenkins RB, Veltman JA, Eichler EE. (2012). Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing. Am J Hum Genet Apr 6;90(4):599-613.

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Ventura M, Catacchio C, Sajjadian S, Vives L, Sudmant P, Marques-Bonet T, Graves TA, Wilson RK, Eichler EE. (2012). The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2. Genome Res Jun;22(6):1036-49.

Bekpen C, Tastekin I, Siswara P, Akdis CA, Eichler EE. (2012). Primate segmental duplication creates novel promoters for the LRRC37 gene family within the 17q21.31 inversion polymorphism region. Genome Res Jun;22(6):1050-8.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O’Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. (2012). Insights into hominid evolution from the gorilla genome sequence. Nature Mar 7;483(7388):169-75.

Veeramah KR, O’Brien JE, Meisler MH, Cheng X, Dib-Hajj SD, Waxman SG, Talwar D, Girirajan S, Eichler EE, Restifo LL, Erickson RP, Hammer MF. (2012). De novo pathogenic SCN8A mutation identified by whole-genome sequencing of a family quartet affected by infantile epileptic encephalopathy and SUDEP. Am J Hum Genet Mar 9;90(3):502-510.

Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF, Garcia JF, Van Tassell CP, Sonstegard TS, Eichler EE, Liu GE.
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Lamb AN, Rosenfeld JA, Neill NJ, Talkowski ME, Blumenthal I, Girirajan S, Keelean-Fuller D, Fan Z, Pouncey J, Stevens C, Mackay-Loder L, Terespolsky D, Bader P, Rosenbaum K, Vallee S, Moeschler JB, Ladda R, Sell S, Martin J, Ryan S, Jones MC, Moran R, Shealy A, Madan-Khetarpal S, McConnell J, Surti U, Delahaye A, Heron-Longe B, Pipiras E, Benzacken B, Passemard S, Verloes A, Isidor B, Caignec CL, Glew GM, Opheim KE, Eichler EE, Morton CC, Gusella JF, Schultz RA, Ballif BC, Shaffer LG. (2012). Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features. Hum Mutat Apr;33(4):728-40.

Mefford HC, Rosenfeld JA, Shur N, Slavotinek AM, Cox VA, Hennekam RC, Firth HV, Willatt L, Wheeler P, Morrow EM, Cook J, Sullivan R, Oh A, McDonald MT, Zonana J, Keller K, Hannibal MC, Ball S, Kussmann J, Gorski J, Zelewski S, Banks V, Smith W, Smith R, Paull L, Rosenbaum KN, Amor DJ, Silva J, Lamb A, Eichler EE. (2012). Further clinical and molecular delineation of the 15q24 microdeletion syndrome. J Med Genet Feb;49(2):110-8. Epub 2011 Dec 17.

Chen YZ, Matsushita M, Girirajan S, Lisowski M, Sun E, Sul Y, Bernier R, Estes A, Dawson G, Minshew N, Shellenberg GD, Eichler EE, Rieder MJ, Nickerson DA, Tsuang DW, Tsuang MT, Wijsman EM,Raskind WH, Brkanac Z. (2012). Evidence for involvement of GNB1L in autism. Am J Med Genet B Neuropsychiatr Genet Jan;159B(1):61-71. Epub 2011 Nov 16.

Girirajan S, Eichler EE. (2011). De novo CNVs in bipolar disorder: recurrent themes or new directions? Neuron Dec 22;72(6):885-7.

Mefford HC, Yendle SC, Hsu C, Cook J, Geraghty E, McMahon JM, Eeg-Olofsson O, Sadleir LG, Gill D, Ben-Zeev B, Lerman-Sagie T, Mackay M, Freeman JL, Andermann E, Pelakanos JT, Andrews I, Wallace G, Eichler EE, Berkovic SF, Scheffer IE. (2011). Rare copy number variants are an important cause of epileptic encephalopathies. Ann Neurol Dec;70(6):974-85.

Karakoc E, Alkan C, O’Roak BJ, Dennis MY, Vives L, Mark K, Rieder MJ, Nickerson DA, Eichler EE. (2011). Detection of structural variants and indels within exome data. Nat Methods
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Girirajan S, Brkanac Z, Coe BP, Baker C, Vives L, Vu TH, Shafer N, Bernier R, Ferrero GB, Silengo M, Warren ST, Moreno CS, Fichera M, Romano C, Raskind WH, Eichler EE. (2011). Relative Burden of Large CNVs on a Range of Neurodevelopmental Phenotypes. PLoS Genet Nov;7(11):e1002334.

Muhle H, Mefford HC, Obermeier T, von Spiczak S, Eichler EE, Stephani U, Sander T, Helbig I. (2011). Absence seizures with intellectual disability as a phenotype of the 15q13.3
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Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC. (2011). Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Genome Res Dec;21(12):2203-12.

Sivakumaran TA, Igo RP Jr, Kidd JM, Itsara A, Kopplin LJ, Chen W, Hagstrom SA, Peachey NS, Francis PJ, Klein ML, Chew EY, Ramprasad VL, Tay WT, Mitchell P, Seielstad M, Stambolian DE, Edwards AO, Lee KE, Leontiev DV, Jun G, Wang Y, Tian L, Qiu F, Henning AK, LaFramboise T, Sen P, Aarthi M, George R, Raman R, Das MK, Vijaya L, Kumaramanickavel G, Wong TY, Swaroop A, Abecasis GR, Klein R, Klein BE, Nickerson DA, Eichler EE, Iyengar SK. (2011). A 32 kb critical region excluding Y402H in CFH mediates risk for age-related macular degeneration. PLoS One 6(10):e25598.

Renton AE, Majounie E, Waite A, Simon-Sahez J, Rollinson S, Gibbs JR, Schymick JC, Laaksovirta H, van Swieten JC, Myllykangas L, Kalimo H, Paetau A, Abramzon Y, Remes AM, Kaganovich A, Scholz SW, Duckworth J, Ding J, Harmer DW, Hernandez DG, Johnson JO, Mok K, Ryten M, Trabzuni D, Guerreiro RJ, Orrell RW, Neal J, Murray A, Pearson J, Jansen IE, Sondervan D, Seelaar H, Blake D, Young K, Halliwell N, Callister JB, Toulson G, Richardson A, Gerhard A, Snowden J, Mann D, Neary D, Nalls MA, Peuralinna T, Jansson L, Isoviita VM, Kaivorinne AL, Holtta-Vuori M, Ikonen E, Sulkava R, Benatar M, Wuu J, Chio A, Restagno G, Borghero G, Sabatelli M; ITALSGEN Consortium, Heckerman D, Rogaeva E, Zinman L, Rothstein JD, Sendtner M, Drepper C, Eichler EE, Alkan C, Abdullaev Z, Pack SD, Dutra A, Pak E, Hardy J, Singleton A, Williams NM, Heutink P, Pickering-Brown S, Morris HR, Tienari PJ, Traynor BJ. (2011). A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron Oct 20;72(2):257-68.

Girirajan S, Campbell CD, Eichler EE. (2011). Human copy number variation and complex genetic disease. Annu Rev Genet 45:203-26.

Nicholas TJ, Baker C, Eichler EE, Akey JM. (2011). A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog. BMC Genomics Aug 16;12(1):414.

Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig V, Abdel-Hamid H, Bader P, McCracken E, Niyazov D, Leppig K, Thiese H, Hummel M, Alexander N, Gorski J, Kussmann J, Shashi V, Johnson K, Rehder C, Ballif BC, Shaffer LG, Eichler EE. (2011). A copy number variation morbidity map of developmental delay. Nat Genet Aug 14;43(9):838-46.(CNV Calls as submitted to dbVar (Controls))

Gazave E, Darre F, Morcillo-Suarez C, Petit-Marty N, Carreno A, Marigorta UM, Ryder OA, Blancher A, Rocchi M, Bosch E, Baker C, Marques-Bonet T, Eichler EE, Navarro A. (2011). Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome Res Oct;21(10):1626-39.

Vu TH, Coccaro EF, Eichler EE, Girirajan S. (2011). Genomic architecture of aggression: Rare copy number variants in intermittent explosive disorder. Am J Med Genet B Neuropsychiatr Genet Dec;156B(7):808-16.

Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, Graves TA, Hormozdiari F, Navarro A, Malig M, Baker C, Lee C, Turner EH, Chen L, Kidd JM, Archidiacono N, Shendure J, Wilson RK, Eichler EE. (2011). Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Res Oct;21(10):1640-9.

Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GR, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, Wollam A, Trani L, Fulton L, Fulton R, Matthews L, Whitehead S, Chow W, Torrance J, Dunn M, Harden G, Threadgold G, Wood J, Collins J, Heath P, Griffiths G, Pelan S, Grafham D, Eichler EE, Weinstock G, Mardis ER, Wilson RK, Howe K, Flicek P, Hubbard T. (2011). Modernizing reference genome assemblies. PLoS Biol Jul;9(7):e1001091.

Hormozdiari F, Hach F, Sahinalp SC, Eichler EE, Alkan C. (2011). Sensitive and fast mapping of di-base encoded reads. Bioinformatics Jul 15;27(14):1915-21.

O’Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, Karakoc E, Mackenzie AP, Ng SB, Baker C, Rieder MJ, Nickerson DA, Bernier R, Fisher SE, Shendure J, Eichler EE. (2011). Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet Jun;43(6):585-9.

Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, Eichler EE. (2011). Alu repeat discovery and characterization within human genomes. Genome Res Jun;21(6):840-9. Epub 2010 Dec 3.

Campbell CD, Sampas N, Tsalenko A, Sudmant PH, Kidd JM, Malig M, Vu TH, Vives L, Tsang P, Bruhn L, Eichler EE. (2011). Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet Mar 11;88(3):317-32.

Alkan C, Coe BP, Eichler EE. (2011). Genome structural variation discovery and genotyping. Nat Rev Genet May;12(5):363-76.

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Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J. (2011). Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol Jan;29(1):59-63. Epub 2010 Dec 19.

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Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF, Comparative Sequencing Program N, Eichler EE, Ornitz DM, Green ED. (2011). Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses. BMC Evol Biol Jan 24;11(1):23.

Alkan C, Sajjadian S, Eichler EE. (2011). Limitations of next-generation genome sequence assembly. Nat Methods Jan;8(1):61-5. Epub 2010 Nov 21.

Alkan C, Cardone MF, Catacchio CR, Antonacci F, O’Brien SJ, Ryder OA, Purgato S, Zoli M, Della Valle G, Eichler EE, Ventura M. (2011). Genome-wide characterization of centromeric
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Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, Kallicki J, Kaul R, Wilson RK, Eichler EE. (2010). A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell Nov 24;143(5):837-47.

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Itsara A, Wu H, Smith JD, Nickerson DA, Romieu I, London SJ, Eichler EE. (2010). De novo rates and selection of large copy number variation. Genome Res Nov;20(11):1469-81.

Bachmann-Gagescu R, Mefford HC, Cowan C, Glew GM, Hing AV, Wallace S, Bader PI, Hamati A, Reitnauer PJ, Smith R, Stockton DW, Muhle H, Helbig I, Eichler EE, Ballif BC, Rosenfeld J, Tsuchiya KD. (2010). Recurrent 200-kb deletions of 16p11.2 that include the SH2B1 gene are associated with developmental delay and obesity. Genet Med Oct;12(10):641-7.

Girirajan S, Eichler EE. (2010). Phenotypic variability and genetic susceptibility to genomic disorders. Hum Mol Genet Oct 15;19(R2):R176-87.

Bekpen C, Xavier RJ, Eichler EE. (2010). Human IRGM gene “to be or not to be”. Semin Immunopathol Dec;32(4):437-44.

Antonacci F, Kidd JM, Marques-Bonet T, Teague B, Ventura M, Girirajan S, Alkan C, Campbell CD, Vives L, Malig M, Rosenfeld JA, Ballif BC, Shaffer LG, Graves TA, Wilson RK, Schwartz DC, Eichler EE. (2010). A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nat Genet Sep;42(9):745-50. Epub 2010 Aug 22.

Mefford HC, Shafer N, Antonacci F, Tsai JM, Park SS, Hing AV, Rieder MJ, Smyth MD, Speltz ML, Eichler EE, Cunningham ML. (2010). Copy number variation analysis in single-suture
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Collie AM, Landsverk ML, Ruzzo E, Mefford HC, Buysse K, Adkins JR, Knutzen DM, Barnett K, Brown RH Jr, Parry GJ, Yum SW, Simpson DA, Olney RK, Chinnery PF, Eichler EE, Chance PF, Hannibal MC. (2010). Non-recurrent SEPT9 duplications cause hereditary neuralgic amyotrophy. J Med Genet Sep;47(9):601-7. Epub 2009 Nov 25.

Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. (2010). mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat Methods Aug;7(8):576-7.

Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, Moran JV. (2010). LINE-1 retrotransposition activity in human genomes. Cell Jun 25;141(7):1159-70.

Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM, Kohn S, Runnheim R, Lamers C, Forrest D, Newton MA, Eichler EE, Kent-First M, Surti U, Livny M, Schwartz DC. (2010). High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A Jun 15;107(24):10848-53.

Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC. (2010). Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics Jun 15;26(12):i350-7.

Mefford HC, Muhle H, Ostertag P, von Spiczak S, Buysse K, Baker C, Franke A, Malafosse A, Genton P, Thomas P, Gurnett CA, Schreiber S, Bassuk AG, Guipponi M, Stephani U, Helbig I, Eichler EE. (2010). Genome-wide copy number variation in epilepsy: novel susceptibility loci in idiopathic generalized and focal epilepsies. PLoS Genet May 20;6(5):e1000962.

Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH. (2010). Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev
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Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. (2010). Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet May 14;86(5):749-64.

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prufer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Hober B, Hoffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Paabo S. (2010). A draft sequence of the Neandertal genome. Science May 7;328(5979):710-22.

Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G, Kallicki J, Anderson P, Tsalenko A, Yamada NA, Tsang P, Kaul R, Wilson RK, Bruhn L, Eichler EE. (2010). Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods May;7(5):365-71.

Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC. (2010). Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics May 15;26(10):1277-83.

Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK. (2010). The genome of a songbird. Nature Apr 1;464(7289):757-62.

Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell’aquila ME, Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, Regitano LC, Smith TP, Song J, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW. (2010). Analysis of copy number variations among diverse cattle breeds. Genome Res May;20(5):693-703.

Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. (2010). Complete Khoisan and Bantu genomes from southern Africa. Nature Feb 18;463(7283):943-7.

Rosenfeld JA, Coppinger J, Bejjani BA, Girirajan S, Eichler EE, Shaffer LG, Ballif BC. (2010). Speech delays and behavioral problems are the predominant features in individuals with
developmental delays and 16p11.2 microdeletions and microduplications. Journal of Neurodevelopmental Disorders Mar;2(1):26-38.

Girirajan S, Rosenfeld JA, Cooper GM, Antonacci F, Siswara P, Itsara A, Vives L, Walsh T, McCarthy SE, Baker C, Mefford HC, Kidd JM, Browning SR, Browning BL, Dickel DE, Levy DL, Ballif BC, Platky K, Farber DM, Gowans GC, Wetherbee JJ, Asamoah A, Weaver DD, Mark PR, Dickerson J, Garg BP, Ellingwood SA, Smith R, Banks VC, Smith W, McDonald MT, Hoo JJ, French BN, Hudson C, Johnson JP, Ozmore JR, Moeschler JB, Surti U, Escobar LF, El-Khechen D, Gorski JL, Kussmann J, Salbert B, Lacassie Y, Biser A, McDonald-McGinn DM, Zackai EH, Deardorff MA, Shaikh TH, Haan E, Friend KL, Fichera M, Romano C, Gecz J, Delisi LE, Sebat J, King MC, Shaffer LG, Eichler EE. (2010). A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet Mar;42(3):203-9.

Silengo M, Belligni E, Molinatto C, Baldassare G, Biamino E, Chiesa N, Zuffardi O, Girirajan S, Eichler EE, Ferrero GB. (2010). Eyebrow anomalies as a diagnostic sign of genomic disorders. Clin Genet Jan;77(1):28-31.

Hansen S, Eichler EE, Fullerton SM, Carrell D. (2010). SPANX Gene Variation in Fertile and Infertile Males. Syst Biol Reprod Med Feb;55:18-26.

Zerr T, Cooper GM, Eichler EE, Nickerson DA. (2010). Targeted interrogation of copy number variation using SCIMMkit. Bioinformatics Jan 1;26(1):120-2.

de Kovel CG, Trucks H, Helbig I, Mefford HC, Baker C, Leu C, Kluck C, Muhle H, von Spiczak S, Ostertag P, Obermeier T, KleefuB-Lie AA, Hallmann K, Steffens M, Gaus V, Klein KM, Hamer HM, Rosenow F, Brilstra EH, Kasteleijn-Nolst Trenite D, Swinkels ME, Weber YG, Unterberger I, Zimprich F, Urak L, Feucht M, Fuchs K, Moller RS, Hjalgrim H, De Jonghe P, Suls A, Ruckert IM, Wichmann HE, Franke A, Schreiber S, Nurnberg P, Elger CE, Lerche H, Stephani U, Koeleman BP, Lindhout D, Eichler EE, Sander T. (2010). Recurrent microdeletions at 15q11.2 and 16p13.11 predispose to idiopathic generalized epilepsies. Brain Jan;133(Pt 1):23-32. Epub 2009 Oct 20.

Liu GE, Ventura M, Cellamare A, Chen L, Cheng Z, Zhu B, Li C, Song J, Eichler EE. (2009). Analysis of recent segmental duplications in the bovine genome. BMC Genomics Dec
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Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM. (2009). Finding the missing heritability of complex diseases. Nature Oct 8;461(7265):747-53.

Marques-Bonet T, Girirajan S, Eichler EE. (2009). The origins and impact of primate segmental duplications. Trends Genet Oct;25(10):443-54.

Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE. (2009). Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet Oct;41(10):1061-7.

Marques-Bonet T, Eichler EE. (2009). The Evolution of Human Segmental Duplications and the Core Duplicon Hypothesis. Cold Spring Harb Symp Quant Biol 74:355-62.

Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J. (2009). Targeted capture and massively parallel sequencing of 12 human exomes. Nature Sep 10;461(7261):272-6.

Marques-Bonet T, Ryder OA, Eichler EE. (2009). Sequencing Primate Genomes: What Have We Learned? Annu Rev Genomics Hum Genet 10:355-86.

Dibbens LM, Mullen S, Helbig I, Mefford HC, Bayly MA, Bellows S, Leu C, Trucks H, Obermeier T, Wittig M, Franke A, Caglayan H, Yapici Z; EPICURE Consortium, Sander T, Eichler EE, Scheffer IE, Mulley JC, Berkovic SF. (2009). Familial and sporadic 15q13.3 microdeletions in idiopathic generalized epilepsy: Precedent for disorders with complex inheritance. Hum Mol Genet Oct 1;18(19):3626-31.

Smith JJ, Antonacci F, Eichler EE, Amemiya CT. (2009). Programmed loss of millions of base pairs from a vertebrate genome. Proc Natl Acad Sci U S A Jul 7;106(27):11212-7.

McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. (2009). Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding. Genome Res Sep;19(9):1527-41.

Mefford HC, Cooper GM, Zerr T, Smith JD, Baker C, Shafer N, Thorland EC, Skinner C, Schwartz CE, Nickerson DA, Eichler EE. (2009). A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease. Genome Res Sep;19(9):1579-85.

De Bustos C, Ramos E, Young JM, Tran RK, Menzel U, Langford CF, Eichler EE, Hsu L, Henikoff S, Dumanski JP, Trask BJ. (2009). Tissue-specific variation in DNA methylation levels along human chromosome 1. Epigenetics Chromatin Jun 8;2(1):7.

Mefford HC, Eichler EE. (2009). Duplication hotspots, rare genomic disorders, and common disease. Curr Opin Genet Dev Jun;19(3):196-204.

Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, Hlavina W, Kapustin Y, Meric P, Maglott D, Birtle Z, Marques AC, Graves T, Zhou S, Teague B, Potamousis K, Churas C, Place M, Herschleb J, Runnheim R, Forrest D, Amos-Landgraf J, Schwartz DC, Cheng Z, Lindblad-Toh K, Eichler EE, Ponting CP; Mouse Genome Sequencing Consortium. (2009). Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol May 5;7(5):e1000112.

Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. (2009). Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res
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Cellamare A, Catacchio CR, Alkan C, Giannuzzi G, Antonacci F, Cardone MF, Della Valle G, Malig M, Rocchi M, Eichler EE, Ventura M. (2009). New insights into centromere organization and evolution from the white-cheeked gibbon and marmoset. Mol Biol Evol Aug;26(8):1889-900.

Zhao Y, Marotta M, Eichler EE, Eng C, Tanaka H. (2009). Linkage disequilibrium between two high-frequency deletion polymorphisms: implications for association studies involving the glutathione-S transferase (GST) genes. PLoS Genet May;5(5):e1000472.

Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE. (2009). Comparative analysis of Alu repeats in primate genomes. Genome Res May;19(5):876-85.

Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, (298 authors), Zhao FQ. (2009). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science Apr 24;324(5926):522-8.

Antonacci F, Kidd JM, Marques-Bonet T, Ventura M, Siswara P, Jiang Z, Eichler EE. (2009). Characterization of six human disease-associated inversion polymorphisms. Hum Mol Genet Jul 15;18(14):2555-66.

van Bon BW, Mefford HC, Menten B, Koolen DA, Sharp AJ, Nillesen WM, Innis JW, de Ravel TJ, Mercer CL, Fichera M, Stewart H, Connell LE, Ounap K, Lachlan K, Castle B, Van der Aa N, van Ravenswaaij C, Nobrega MA, Serra-Juhe C, Simonic I, de Leeuw N, Pfundt R, Bongers EM, Baker C, Finnemore P, Huang S, Maloney VK, Crolla JA, van Kalmthout M, Elia M, Vandeweyer G, Fryns JP, Janssens S, Foulds N, Reitano S, Smith K, Parkel S, Loeys B, Woods CG, Oostra A, Speleman F, Pereira AC, Kurg A, Willatt L, Knight SJ, Vermeesch JR, Romano C, Barber JC, Mortier G, Perez-Jurado LA, Kooy F, Brunner HG, Eichler EE, Kleefstra T, de Vries BB. (2009). Further delineation of the 15q13 microdeletion and duplication syndromes: A clinical spectrum varying from non-pathogenic to a severe outcome. J Med Genet Aug;46(8):511-23.

Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, Ventura M, Kidd JM, Siswara P, Howard JC, Eichler EE. (2009). Death and resurrection of the human IRGM gene. PLoS Genet Mar;5(3):e1000403.

Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA, Alkan C, Aksay G, Girirajan S, Siswara P, Chen L, Cardone MF, Navarro A, Mardis ER, Wilson RK, Eichler EE. (2009). A burst of segmental duplications in the genome of the African great ape ancestor. Nature Feb 12;457(7231):877-81.

de Cid R, Riveira-Munoz E, Zeeuwen PL, Robarge J, Liao W, Dannhauser EN, Giardina E, Stuart PE, Nair R, Helms C, Escaramis G, Ballana E, Martin-Ezquerra G, den Heijer M, Kamsteeg M, Joosten I, Eichler EE, Lazaro C, Pujol RM, Armengol L, Abecasis G, Elder JT, Novelli G, Armour JA, Kwok PY, Bowcock A, Schalkwijk J, Estivill X. (2009). Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat Genet Feb;41(2):211-5.

Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D, Krauss RM, Myers RM, Ridker PM, Chasman DI, Mefford H, Ying P, Nickerson DA, Eichler EE. (2009). Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet Feb;84(2):148-61.

Degenhardt JD, de Candia P, Chabot A, Schwartz S, Henderson L, Ling B, Hunter M, Jiang Z, Palermo RE, Katze M, Eichler EE, Ventura M, Rogers J, Marx P, Gilad Y, Bustamante CD. (2009). Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). PLoS Genet Jan;5(1):e1000346.

Hannes FD, Sharp AJ, Mefford HC, de Ravel T, Ruivenkamp CA, Breuning MH, Fryns JP, Devriendt K, Van Buggenhout G, Vogels A, Stewart HH, Hennekam RC, Cooper GM, Regan R, Knight SJ, Eichler EE, Vermeesch JR. (2009). Recurrent reciprocal deletions and duplications of 16p13.11: The deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant. J Med Genet Apr;46(4):223-32. Epub 2008 Jun 11.

Landsverk ML, Ruzzo EK, Mefford HC, Buysse K, Buchan JG, Eichler EE, Petty EM, Peterson EA, Knutzen DM, Barnett K, Farlow MR, Caress J, Parry GJ, Quan D, Gardner KL, Hong M, Simmons Z, Bird TD, Chance PF, Hannibal MC. (2009). Duplication within the SEPT9 gene associated with a founder effect in North American families with Hereditary Neuralgic Amyotrophy. Hum Mol Genet Apr 1;18(7):1200-8.

Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM. (2009). The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res Mar;19(3):491-9.

Helbig I, Mefford HC, Sharp AJ, Guipponi M, Fichera M, Franke A, Muhle H, de Kovel C, Baker C, von Spiczak S, Kron KL, Steinich I, Kleefuss-Lie AA, Leu C, Gaus V, Schmitz B, Klein KM, Reif PS, Rosenow F, Weber Y, Lerche H, Zimprich F, Urak L, Fuchs K, Feucht M, Genton P, Thomas P, Visscher F, de Haan GJ, Moller RS, Hjalgrim H, Luciano D, Wittig M, Nothnagel M, Elger CE, Nurnberg P, Romano C, Malafosse A, Koeleman BP, Lindhout D, Stephani U, Schreiber S, Eichler EE, Sander T. (2009). 15q13.3 microdeletions increase risk of idiopathic generalized epilepsy. Nat Genet Feb;41(2):160-2.

Girirajan S, Chen L, Graves T, Marques T, Ventura M, Fronick C, Fulton L, Rocchi M, Fulton RS, Wilson RK, Mardis ER, Eichler EE. (2009). Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites. Genome Res Feb;19(2):178-90. Epub 2008 Nov 24.

Lomiento M, Jiang Z, D’Addabbo P, Eichler EE, Rocchi M. (2008). Evolutionary-new centromeres preferentially emerge within gene deserts. Genome Biol Dec 16;9(12):R173.

Kidd JM, Cheng Z, Graves T, Wilson R, Eichler EE. (2008). Haplotype sorting using human fosmid clone end-sequence pairs. Genome Res Dec;18(12):2016-23.

Varki A, Geschwind DH, Eichler EE. (2008). Explaining human uniqueness: genome interactions with environment, behaviour and culture. Nat Rev Genet Oct;9(10):749-63.

Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, Buysse K, Huang S, Maloney VK, Crolla JA, Baralle D, Collins A, Mercer C, Norga K, de Ravel T, Devriendt K, Bongers EM, de Leeuw N, Reardon W, Gimelli S, Bena F, Hennekam RC, Male A, Gaunt L, Clayton-Smith J, Simonic I, Park SM, Mehta SG, Nik-Zainal S, Woods CG, Firth HV, Parkin G, Fichera M, Reitano S, Giudice ML, Li KE, Casuga I, Broomer A, Conrad B, Schwerzmann M, Raber L, Gallati S, Striano P, Coppola A, Tolmie JL, Tobias ES, Lilley C, Armengol L, Spysschaert Y, Verloo P, De Coene A, Goossens L, Mortier G, Speleman F, van Binsbergen E, Nelen MR, Hochstenbach R, Poot M, Gallagher L, Gill M, McClellan J, King MC, Regan R, Skinner C, Stevenson RE, Antonarakis SE, Chen C, Estivill X, Menten B, Gimelli G, Gribble S, Schwartz S, Sutcliffe JS, Walsh T, Knight SJ, Sebat J, Romano C, Schwartz CE, Veltman JA, de Vries BB, Vermeesch JR, Barber JC, Willatt L, Tassabehji M, Eichler EE. (2008). Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med Oct 16;359(16):1685-99.

Cooper GM, Zerr T, Kidd JM, Eichler EE, Nickerson DA. (2008). Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat Genet Oct;40(10):1199-203.

Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, Redon R. (2008). Copy number variation and evolution in humans and chimpanzees. Genome Res Nov;18(11):1698-710.

Marques-Bonet T, Cheng Z, She X, Eichler EE, Navarro A. (2008). The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements. BMC Genomics Aug 12;9(1):384.

Zody MC, Jiang Z, Fung HC, Antonacci F, Hillier LW, Cardone MF, Graves TA, Kidd JM, Cheng Z, Abouelleil A, Chen L, Wallis J, Glasscock J, Wilson RK, Reily AD, Duckworth J, Ventura M, Hardy J, Warren WC, Eichler EE. (2008). Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat Genet Sep;40(9): 1076-1083.

Koolen DA, Sharp AJ, Hurst JA, Firth HV, Knight SJ, Goldenberg A, Saugier-Veber P, Pfundt R, Vissers LE, Destree A, Grisart B, Rooms L, Van der Aa N, Field M, Hackett A, Bell K, Nowaczyk MJ, Mancini GM, Poddighe PJ, Schwartz CE, Rossi E, De Gregori M, Antonacci-Fulton LL, McLellan MD 2nd, Garrett JM, Wiechert MA, Miner TL, Crosby S, Ciccone R, Willatt L, Rauch A, Zenker M, Aradhya S, Manning MA, Strom TM, Wagenstaller J, Krepischi-Santos AC, Vianna-Morgante AM, Rosenberg C, Price SM, Stewart H, Shaw-Smith C, Brunner HG, Wilkie AO, Veltman JA, Zuffardi O, Eichler EE, de Vries BB. (2008). Clinical and molecular delineation of the 17q21.31 microdeletion syndrome. J Med Genet Nov;45(11):710-20.

Martin J, Knight SJ, Sharp AJ, Eichler EE, Hurst J, Kini U. (2008). Potocki-Lupski syndrome mimicking a connective tissue disorder. Clinical Dysmorphology July;17(3):211-213.

Jiang Z, Hubley R, Smit A, Eichler EE. (2008). DupMasker: A tool for annotating primate segmental duplications. Genome Res Aug;18(8):1362-1368.

She X, Cheng Z, Zollner S, Church DM, Eichler EE. (2008). Mouse segmental duplication and copy number variation. Nat Genet Jul;40(7):909-14.

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, Lopez-Otin C, Ordonez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Ole Kriegs J, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefevre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Renfree MB, Mardis ER, Wilson RK. (2008). Genome analysis of the platypus reveals unique signatures of evolution. Nature May 8;453(7192):175-83. Erratum in: Sep 11;455(7210):256.

Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tuzun E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE. (2008). Mapping and sequencing of structural variation from eight human genomes. Nature May 1;453(7191):56-64.

Kirsch S, Munch C, Jiang Z, Cheng Z, Chen L, Batz C, Eichler EE, Schempp W. (2008). Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions. Genome Res June;18(6):1030.1042.

Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N, Butler P, Eckstrand K, Noory L, Gochman P, Long R, Chen Z, Davis S, Baker C, Eichler EE, Meltzer PS, Nelson SF, Singleton AB, Lee MK, Rapoport JL, King MC, Sebat J. (2008). Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science Apr 25;320(5875):539-43.

Sharp AJ, Mefford HC, Li K, Baker C, Skinner C, Stevenson RE, Schroer RJ, Novara F, De Gregori M, Ciccone R, Broomer A, Casuga I, Wang Y, Xiao C, Barbacioru C, Gimelli G, Bernardina BD, Torniero C, Giorda R, Regan R, Murday V, Mansour S, Fichera M, Castiglia L, Failla P, Ventura M, Jiang Z, Cooper GM, Knight SJ, Romano C, Zuffardi O, Chen C, Schwartz CE, Eichler EE. (2008). A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nat Genet Mar;40(3):322-328.

Cardone MF, Jiang Z, D’Addabbo P, Archidiacono N, Rocchi M, Eichler EE, Ventura M. (2008). Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication. Genome Biol Feb 7;9(2):R28.

Eichler EE, Zimmerman AW. (2008). A hot spot of genetic instability in autism. N Engl J Med Feb 14;358(7):737-739 (Jan 9 2008).

Bailey JA, Kidd JM, Eichler EE. (2008). Human copy number polymorphic genes. Cytogenet Genome Res 123(1-4):234-43.

Bovee D, Zhou Y, Haugen E, Wu Z, Hayden HS, Gillett W, Tüzün E, Cooper GM, Sampas N, Phelps K, Levy R, Morrison VA, Sprague J, Jewett D, Buckley D, Subramaniam S, Chang J, Smith DR, Olson MV, Eichler EE, Kaul R. (2008). Closing gaps in the human genome with fosmid resources generated from multiple individuals. Nat Genet Jan;40(1):96-101.

Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner P, Eichler EE. (2007). Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet Nov;39(11):1361-1368 (7 Oct 2007).

Mefford HC, Clauin S, Sharp AJ, Moller RS, Ullmann R, Kapur R, Pinkel D, Cooper GM, Ventura M, Ropers HH, Tommerup N, Eichler EE, Bellanne-Chantelot C. (2007). Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes and epilepsy. Am J Hum Genet Nov;81(5):1057-1069 (26 Sept 2007).

Sharp AJ, Itsara A, Cheng Z, Alkan C, Schwartz S, Eichler EE. (2007). Optimal design of oligonucleotide microarrays for measurement of DNA copy-number. Hum Mol Genet
Nov;16(22):2770-2779 (28 Aug 2007).

Lyle R, Prandini P, Osoegawa K, ten Hallers B, Humphray S, Zhu B, Eyras E, Castelo R, Bird CP, Gagos S, Scott C, Cox A, Deutsch S, Ucla C, Cruts M, Dahoun S, She X, Bena F, Wang SY, Van Broeckhoven C, Eichler EE, Guigo R, Rogers J, de Jong PJ, Reymond A, Antonarakis SE. (2007). Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21. Genome Res Nov;17(11):1690-1696

Alkan C, Ventura M, Archidiacono N, Rocchi M, Sahinalp CS, Eichler EE. (2007). Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. PLOS Comput Biol Sep;3(9):e181 (28 Sept 2007).

Cooper GM, Nickerson DA, Eichler EE. (2007). Mutational and selective effects on copy-number variants in the human genome. Nat Genet Jul;39(7 Suppl):S22-S29 (27 June 2007).

Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L. (2007). Challenges and standards in integrating surveys of structural variation. Nat Genet
Jul;39(7 Suppl):S7-S15 (27 June 2007).

Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, Carter NP, Church DM, Felsenfeld A, Guyer M, Lee C, Lupski JR, Mullikin JC, Pritchard JK, Sebat J, Sherry ST, Smith D, Valle D, Waterston RH. (2007). Completing the map of human genetic variation. Nature May;447(7141):161-165 (10 May 2007).

Kidd JM, Newman TL, Tüzün E, Kaul R, Eichler EE. (2007). Population stratification of a common APOBEC gene deletion polymorphism. PLoS Genet Apr;3(4):e63.

Ventura M, Antonacci F, Cardone MF, Stanyon R, D’Addabbo P, Cellamare A, Sprague LJ, Eichler EE, Archidiacono N, Rocchi M. (2007). Evolutionary formation of new centromeres in macaque. Science Apr;316(5822):243-246.

Rhesus Macaque Genome Sequencing and Analysis Consortium, (12 authors), Eichler EE, (162 authors), Zwieq AS. (2007). Evolutionary and biomedical insights from the rhesus macaque genome. Science Apr;316(5822):222-234.

Sharp AJ, Selzer RR, Veltman JA, Gimelli S, Gimelli G, Striano P, Coppola A, Regan R, Price SM, Knoers NV, Eis PS, Brunner HG, Hennekam RC, Knight SJ, de Vries BB, Zuffardi O, Eichler EE. (2007). Characterization of a recurrent 15q24 microdeletion syndrome. Hum Mol Genet Mar;16(5):567-572 (14 Mar 2007).

Roberto R, Capozzi O, Wilson RK, Mardis ER, Lomiento M, Tüzün E, Cheng Z, Mootnick AR, Archidiacono N, Rocchi M, Eichler EE. (2007). Molecular refinement of gibbon genome
rearrangement. Genome Res Feb;17(2):249-257 (21 Dec 2006).

Wong KK, deLeeuw RJ, Dosanjh NS, Kimm LR, Cheng Z, Horsman DE, MacAulay C, Ng RT, Brown CJ, Eichler EE, Lam WL. (2007). A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet Jan;80(1):91-104 (5 Dec 2006).

Cardone MF, Alonso A, Pazienza M, Ventura M, Montemurro G, Carbone L, de Jong PJ, Stanyon R, D’Addabbo P, Archidiacono N, She X, Eichler EE, Warburton PE, Rocchi M. (2006). Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs. Genome Biol 7(10):R91.

Johnson ME, NISC Comparative Sequencing Program, Cheng Z, Morrison AV, Scherer S, Ventura M, Gibbs RA, Green ED, Eichler EE. (2006). Recurrent duplication-driven transposition of DNA during hominoid evolution. Proc Natl Acad Sci U S A Nov;103(47):17626-17631.

Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA, Stewart H, Price SM, Blair E, Hennekam RC, Fitzpatrick CA, Segraves R, Richmond TA, Guiver C, Albertson DG, Pinkel D, Eis PS, Schwartz S, Knight SJ, Eichler EE. (2006). Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat Genet Sep;38(9):1038-1042.

Locke DP, Sharp AJ, McCarroll SA, McGrath SD, Newman TL, Cheng Z, Schwartz S, Albertson DG, Pinkel D, Altshuler DM, Eichler EE. (2006). Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am J Hum Genet Aug;79(2):275-290.

Bailey JA, Eichler EE. (2006). Primate segmental duplications: Crucibles of evolution, diversity and disease. Nat Rev Genet Jul;7(7):552-564.

She X, Liu G, Ventura M, Zhao S, Misceo D, Roberto R, Cardone MF, Rocchi M, NISC Comparative Sequencing Program, Green ED, Archidiacano N, Eichler EE. (2006). A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Genome Res May;16(5):576-583.

Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Cáceres AM, Iafrate AJ, Tyler-Smith C, Scherer SW, Eichler EE, Stone AC, Lee C. (2006). Hotspots for copy number variation in
chimpanzees and humans. Proc Natl Acad Sci U S A May;103(21):8006-8011.

Newman TL, Rieder MJ, Morrison VA, Sharp AJ, Smith JD, Sprague LJ, Kaul R, Carlson CS, Olson MV, Nickerson DA, Eichler EE. (2006). High-throughput genotyping of intermediate-size structural variation. Hum Mol Genet Apr;15(7):1159-1167.

Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T, Kim DW, She X, Barlow KF, Bloom T, Bruford E, Chang JL, Cuomo CA, Eichler EE, FitzGerald MG, Jaffe DB, LaButti K, Nicol R, Park HS, Seaman C, Sougnez C, Yang X, Zimmer AR, Zody MC, Birren BW, Nusbaum C, Fujiyama A, Hattori M, Rogers J, Lander ES, Sakaki Y. (2006). Human chromosome 11 DNA sequence and analysis including novel gene identification. Nature Mar;440(7083):497-500.

Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O’Neill K, Whittaker CA, Kamal M, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Kodira CD, Madan A, Qin S, Yang X, Abbasi N, Abouelleil A, Arachchi HM, Baradarani L, Birditt B, Bloom S, Bloom T, Borowsky ML, Burke J, Butler J, Cook A, DeArellano K, DeCaprio D, Dorris L 3rd, Dors M, Eichler EE, Engels R, Fahey J, Fleetwood P, Friedman C, Gearin G, Hall JL, Hensley G, Johnson E, Jones C, Kamat A, Kaur A, Locke DP, Madan A, Munson G, Jaffe DB, Lui A, Macdonald P, Mauceli E, Naylor JW, Nesbitt R, Nicol R, O’Leary SB, Ratcliffe A, Rounsley S, She X, Sneddon KM, Stewart S, Sougnez C, Stone SM, Topham K, Vincent D, Wang S, Zimmer AR, Birren BW, Hood L, Lander ES, Nusbaum C. (2006). Analysis of the DNA sequence and duplication history of human chromosome 15. Nature Mar;440(7084):671-675.

Eichler EE. (2006). Widening the spectrum of human genetic variation. Nat Genet Jan;38(1):9-11.

Sharp AJ, Cheng Z, Eichler EE. (2006). Structural variation of the human genome. Annu Rev Genomics Hum Genet 7:407-442.

Yohn CT, Jiang Z, McGrath SD, Hayden KE, Khaitovich P, Johnson ME, Eichler MY, McPherson JD, Zhao S, Pääbo S, Eichler EE. (2005). Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol Apr;3(4):e110.

Locke DP, Jiang Z, Pertz LM, Misceo D, Archidiacono N, Eichler EE. (2005). Molecular evolution of the human chromosome 15 pericentromeric region. Cytogenet Genome Res
108(1-3):73-82.

Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L. (2005). Chromosome evolution in eukaryotes: A multi-kingdom perspective. Trends Genet Dec;21(12):673-682.

Newman TL, Tüzün E, Morrison VA, Hayden KE, Ventura M, McGrath SD, Rocchi M, Eichler EE. (2005). A genome-wide survey of structural variation between human and chimpanzee. Genome Res Oct;15(10):1344-1356.

Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, DeJong P, Wilson RK, Pääbo S, Rocchi M, Eichler EE. (2005). A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature Sep;437(7055):88-93.

Chimpanzee Sequencing and Analysis Consortium. (2005). Initial sequencing of the chimpanzee genome and comparison with the human genome. Nature Sep 1;437(7055):69-87. *Contributors Tüzün E, Cheng Z, Eichler EE to segmental duplication and structural variation analyses of the manuscript, pages 73-75.

Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Samonte RU, Pertz LM, Clark R, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE. (2005). Segmental duplications and copy-number variation in the human genome. Am J Hum Genet Jul;77(1):78-88.

Horvath JE, Gulden CL, Samonte RU, Eichler MY, Ventura M, McPherson JD, Graves TA, Wilson RK, Scwartz S, Rocchi M, Eichler EE. (2005). Punctuated duplication seeding events during the evolution of human chromosome 2p11.Genome Res Jul;15(7):914-927.

Alkan C, Tüzün E, Buard J, Lethiec F, Eichler EE, Bailey JA, Sahinalp SC. (2005). Manipulating multiple sequence alignments via MaM and WebMaM. Nucleic Acids Res Jul
1;33(Web Server issue):W295-298.

Tüzün E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE. (2005). Fine-scale structural variation of the human genome. Nat Genet Jul;37(7):727-732.

Hillier LW, Graves TA, Fulton RS, Fulton LA, (110 Authors), Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK. (2005). Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature Apr 7;434(7034):724-731.

Kirsch S, Weiss B, Miner TL, Waterston RH, Clark RA, Eichler EE, Münch C, Schempp W, Rappold G. (2005). Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome. Genome Res Feb;15(2):195-204.

Alkan C, Eichler EE, Bailey JA, Sahinalp SC, Tüzün E. (2004). The role of unequal crossover in alpha-satellite DNA evolution: A computational analysis. J Comput Biol
11(5):933-944.

Sahinalp SC, Eichler EE, Goldberg P, Berenbrink P, Friedetzky T, Ergun F. (2004). Identifying uniformly mutated segments within repeats. J Bioinform Comput Biol Dec;2(4):657-668.

International Chicken Genome Sequencing Consortium. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature Dec;432(7018):695-716. *Contributors Tüzün E, Eichler EE to segmental duplication section of the manuscript, pages 708-709.

Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, (109 authors), Rokhsar DS, Eichler EE, Gilna P, Lucas SM, Myers RM, Rubin EM, Pennacchio LA. (2004). The sequence and analysis of duplication-rich human chromosome 16. Nature Dec;432(7020):988-994.

International Human Genome Sequencing Consortium. (2004). Finishing the euchromatic sequence of the human genome. Nature Oct;431(7011):931-45. *Contributors Tüzün E, Eichler EE to segmental duplication, heterochromatin and gap analyses sections of the manuscript, pages 938-941.

She X, Jiang Z, Clark RA, Liu G, Cheng Z, Tüzün E, Church DM, Sutton G, Halpern AL, Eichler EE. (2004). Shotgun sequence assembly and recent segmental duplications within the human genome. Nature Oct;431(7011):927-930.

Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, (60 authors), Cheng JF, Eichler EE, Olsen A, Pennacchio LA, Rokhsar DS, Richardson P, Lucas SM, Myers RM, Rubin EM. (2004). The DNA sequence and comparative analysis of human chromosome 5. Nature Sep;431(7006):268-274.

Ventura M, Weigl S, Carbone L, Cardone MF, Misceo D, Teti M, D.adabbo P, Wandall A, Bjoerck E, de Jong P, She X, Eichler EE, Archidiacono N, Rocchi M. (2004). Recurrent sites for new centromere seeding. Genome Res Sep;14(9):1696-1703.

She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE. (2004). The structure and evolution of centromeric transition regions within the human genome. Nature Aug;430(7002):857-864.

Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, Dietzsch J, Steigele S, Do HH, Weiss G, Enard W, Heissig F, Arendt T, Nieselt-Struwe K, Eichler EE, Pääbo S. (2004).
Regional patterns of gene expression in human and chimpanzee brains. Genome Res Aug;14(8):1462-1473.

Fredman D, White SJ, Potter S, Eichler EE, Den Dunnen JT, Brookes AJ. (2004). Complex SNP-related sequence variation in segmental genome duplications. Nat Genet Aug;36(8):861-866.

Chen DC, Saarela J, Clark RA, Miettinen T, Chi A, Eichler EE, Peltonen L, Palotie A. (2004). Segmental duplications flank the multiple sclerosis locus on chromosome 17q. Genome Res Aug;14(8):1483-1492.

Eichler EE, Clark RA, She X. (2004). An assessment of the sequence gaps: Unfinished business in a finished human genome. Nat Rev Genet May;5(5):345-354.

Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE. (2004). Analysis of segmental duplications and genome assembly in the mouse. Genome Res May;14(5):789-801.

Tüzün E, Bailey JA, Eichler EE. (2004). Recent segmental duplications in the working draft assembly of the Brown Norway Rat. Genome Res Apr;14(4):493-506.

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, (94 authors), Eichler EE, (130 authors), Rat Genome Sequencing Project Consortium. (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature Apr;428(6982):493-521.

Grimwood J, Gordon LA, Olsen A, (87 authors), Eichler EE, Pennacchio LA, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM. (2004). The DNA sequence and biology of human chromosome 19. Nature Apr;428(6982):529-535.

Astbury C, Christ LA, Aughton DJ, Cassidy SB, Kumar A, Eichler EE, Schwartz S. (2004). Detection of deletions in de novo “balanced” chromosome rearrangements: Further evidence for their role in phenotypic abnormalities. Genet Med Mar-Apr;6(2):81-89.

Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. (2004). Hotspots of mammalian chromosomal evolution. Genome Biol Mar;5(4):R23.

Locke DP, Segraves R, Nicholls RD, Schwartz S, Pinkel D, Albertson DG, Eichler EE. (2004). BAC microarray analysis of 15q11-q13 rearrangements and the impact of segmental duplications. J Med Genet Mar;41(3):175-182.

Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, (23 authors), Clark AG, Waterman MS, Eichler EE, Adams MD, Hunkapiller MW, Myers EW, Venter JC. (2004). Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A Feb;101(7):1916-1921.

Eichler EE, Frazer, KA. (2004). The nature, pattern and function of human sequence variation. Genome Biol 5(4):318.

Guy J, Hearn T, Crosier M, Mudge J, Viggiano L, Koczan D, Thiesen HJ, Bailey JA, Horvath JE, Eichler EE, Earthrowl ME, Deloukas P, French L, Rogers J, Bentley D, Jackson MS. (2003). Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p. Genome Res Feb;13(2):159-172.

Bailey JA, Liu G, Eichler EE. (2003). An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet Oct;73(4):823-834.

Chai JH, Locke DP, Greally JM, Knoll JH, Ohta T, Dunai J, Yavor A, Eichler EE, Nicholls RD. (2003). Identification of four highly conserved genes between breakpoint hotspots BP1 and BP2 of the Prader-Willi/Angelman syndromes deletion region that have undergone evolutionary transposition mediated by flanking duplicons. Am J Hum Genet Oct;73(4):898-925.

Horvath JE, Gulden CL, Bailey JA, Yohn C, McPherson JD, Prescott A, Roe BA, De Jong PJ, Ventura M, Misceo D, Archidiacono N, Zhao S, Schwartz S, Rocchi M, Eichler EE. (2003). Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications. Mol Biol Evol Sep;20(9):1463-1479.

Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, (95 authors), McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK. (2003). The DNA sequence of human chromosome 7. Nature Jul;424(6945):157-164.

Locke DP, Archidiacono N, Misceo D, Cardone MF, Deschamps S, Roe B, Rocchi M, Eichler EE. (2003). Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. Genome Biol Jul;4(8):R50.

Locke DP, Segraves R, Carbone L, Archidiacono N, Albertson DG, Pinkel D, Eichler EE. (2003). Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res Mar;13(3):347-357.

Liu G, NISC Comparative Sequencing Program, Zhao S, Bailey JA, Sahinalp SC, Alkan C, Tüzün E, Green ED, Eichler EE. (2003). Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res Mar;13(3):358-368.

Eichler EE, Sankoff D. (2003). Structural dynamics of eukaryotic chromosome evolution. Science Aug;301(5634):793-797.

Eichler EE, Patel NH. (2003). Genomes and evolution: From sequence to organism. Curr Opin Genes Dev Dec;13(6):559-561.

Bailey JA, Eichler EE. (2003). Genome-wide detection and analysis of segmental duplications within mammalian organisms. Cold Spring Harb Symp Quant Biol 68:115-124.

Alkan C, Bailey JA, Eichler EE, Sahinalp CS, Tüzün E. (2002). An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution. Genome Inform
13:93-102.

Eichler EE, Johnson ME, Alkan C, Tüzün E, Sahinalp C, Misceo D, Archidiacono N, Rocchi M. (2002). Divergent origins and concerted expansion of two segmental duplications on
chromosome 16. J Hered Nov-Dec;92(6):468-472.

Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. (2002). Recent segmental duplications in the human genome. Science Aug;297(5583):1003-1007.

Eichler EE, DeJong PJ. (2002). Biomedical applications and studies of molecular evolution: A proposal for a primate genomic library resource. Genome Res May;12(5):673-678.

Kashuk C, SenGupta S, Eichler EE, Chakravarti A. (2002). ViewGene: A graphical tool for polymorphism visualization and characterization. Genome Res Feb;12(2):333-338.

van Geel M, Eichler EE, Beck AF, Shan Z, Haaf T, van der Maarell SM, Frants RR, de Jong PJ. (2002). A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomes. Am J Hum Genet Jan;70(1):269-278.

Bailey JA, Yavor AM, Viggiano L, Misceo D, Horvath JE, Archidiacono N, Schwartz S, Rocchi M, Eichler EE. (2002). Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am J Hum Genet Jan;70(1):83-100.

Samonte RV, Eichler EE. (2002). Segmental duplications and the evolution of the primate genome. Nat Rev Genet Jan;3(1):65-72.

Cutler DJ, Zwick ME, Carrasquillo MM, Yohn CT, Tobin KP, Kashuk C, Mathews DJ, Shah NA, Eichler EE, Warrington JA, Chakravarti A. (2001). High-throughput variation detection and genotyping using microarrays. Genome Res Nov;11(11):1913-1925.

Eichler EE. (2001). Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet Nov;17(11):661-669.

Johnson ME, Viggiano L, Bailey JA, Abdul-Rauf M, Goodwin G, Rocchi M, Eichler EE. (2001). Positive selection of a gene family during the emergence of humans and African apes. Nature Oct;413(6855):514-519.

Horvath JE, Bailey JA, Locke DP, Eichler EE. (2001). Lessons from the human genome: Transitions between euchromatin and heterochromatin. Hum Mol Genet Oct;10(20):2215-2223.

Mathews DJ, Kashuk C, Brightwell G, Eichler EE, Chakravarti A. (2001). Sequence variation within the fragile X locus. Genome Res Aug;11(8):1382-1391.

Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. (2001). Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res Jun;11(6):1005-1017.

Eichler EE. (2001). Segmental duplications: What’s missing, misassigned, and misassembled–and should we care? Genome Res May;11(5):653-656.

Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ. (2001). Integration of cytogenetic landmarks in the draft sequence of the human genome. Nature Feb 15;409(6822):953-958.

International Sequencing Consortium. (2001). Initial sequencing and analysis of the human genome. Nature Feb;409(6822):860-921. *Contributors Bailey JA, Eichler EE to Segmental Duplication section of the manuscript, pages 889-892.

Bailey JA, Carrel L, Chakravarti A, Eichler EE. (2000). Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: The Lyon repeat hypothesis. Proc Natl Acad Sci U S A Jun;97(12):6634-6639.

Horvath JE, Schwartz S, Eichler EE. (2000). The mosaic structure of human pericentromeric DNA: A strategy for characterizing complex regions of the human genome. Genome Res Jun;10(6):839-852.

Ji Y, Eichler EE, Schwartz S, Nicholls RD. (2000). Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res May;10(5):597-610.

Horvath JE, Viggiano L, Loftus BJ, Adams MD, Archidiacono N, Rocchi M, Eichler EE. (2000). Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11. Hum Mol Genet Jan;9(1):113-123.

Eichler EE, Archidiacono N, Rocchi M. (1999). CAGGG repeats and the pericentromeric duplication of the hominoid genome. Genome Res Nov;9(11):1048-1058.

Loftus BJ, Kim UJ, Sneddon VP, Kalush F, Brandon R, Fuhrmann J, Mason T, Crosby ML, Barnstead M, Cronin L, Deslattes Mays A, Cao Y, Xu RX, Kang HL, Mitchell S, Eichler EE, Harris PC, Venter JC, Adams MD. (1999). Genome duplications and other features in 12 Mbp of DNA sequence from human chromosome 16p and 16q. Genomics Sep;60(3):295-308.

Eichler EE. (1999). Repetitive conundrums of centromere structure and function. Hum Mol Genet Feb;8(2):151-155.

Trask BJ, Massa H, Brand-Arpon V, Chan K, Friedman C, Nguyen OT, Eichler EE, van den Engh G, Rouquier S, Shizuya H, Giorgi D. (1998). Large multi-chromosomal duplications encompass many members of the olfactory receptor gene family in the human genome. Hum Mol Genet Dec;7(13):2007-2020.

Her C, Wood TC, Eichler EE, Mohrenweiser HW, Ramagli LS, Siciliano MJ, Weinshilboum RM. (1998). Human hydroxysteroid sulfotransferase SULT2B1: Two enzymes encoded by a single chromosome 19 gene. Genomics Nov;53(3):284-295.

Eichler EE, Hoffman SM, Adamson AA, Gordon LA, McCready P, Lamerdin JE, Mohrenweiser HW. (1998). Complex beta-satellite repeat structures and the expansion of the zinc-finger gene cluster in 19p12. Genome Res Aug;8(8):791-808.

Eichler EE. (1998). Masquerading repeats: Paralogous pitfalls of the human genome. Genome Res Aug;8(8):758-762.

Pearson CE, Eichler EE, Lorenzetti D, Kramer SF, Zoghbi HY, Neslon DL, Sinden RR. (1998). Interruptions in the triplet repeats of SCA1 and FRAXA reduce the propensity and complexity of slipped strand DNA (S-DNA) formation. Biochem Feb;37(8):2701-2708.

Fan W, Christensen M, Eichler EE, Zhang X, Lennon G. (1997). Cloning, sequencing, gene organization, and localization of the human ribosomal protein RPL23A. Genomics
Dec;46(2):234-239.

Wagtmann N, Rojo S, Eichler EE, Mohrenweiser H, Long EO. (1997). A new human gene complex the killer cell inhibitory receptors and related monocyte/macrophage receptors. Curr Biol Aug;7(8):615-618.

Eichler EE, Budarf ML, Rocchi M, Deaven LL, Doggett NA, Baldini A, Nelson DL, Mohrenweiser HW. (1997). Interchromosomal duplications of the adrenoleukodystrophy locus: A phenomenon of pericentromeric plasticity. Hum Mol Genet Jul;6(7):991-1002.

Falik-Zaccai TC, Shachak E, Yalon M, Lis Z, Borochowitz Z, Macpherson JN, Nelson DL, Eichler EE. (1997). Predisposition to the fragile X syndrome in Jews of Tunisian descent is due to the absence of AGG interruptions on a rare Mediterranean haplotype. Am J Hum Genet Jan;60(1):103-112.

Eichler EE, Nelson DL. (1996). Genetic variation and evolutionary stability of the FMR1 CGG repeat in six closed human populations. Am J Med Genet Jul 12;64(1):220-225.

Eichler EE, Lu F, Shen Y, Antonacci R, Jurecic V, Doggett NA, Moyzis RK, Baldini A, Gibbs RA, Nelson DL. (1996). Duplication of a gene-rich cluster between 16p11.1 and Xq28: a novel pericentromeric-directed mechanism for paralogous genome evolution. Hum Mol Genet Jul;5(7):899-912.

Eichler EE, Macpherson JN, Murray A, Jacobs PA, Chakravarti A, Nelson DL. (1996). Haplotype and interspersion analysis of the FMR1 CGG repeat identifies two different mutational pathways for the origin of the fragile X syndrome. Hum Mol Genet Mar;5(3):319-330.

Kunst CB, Zerylnick C, Karickhoff L, Eichler EE, Bullard J, Chalifoux M, Holden JJ, Nelson DL, Warren ST. (1996). FMR1 in global populations. Am J Hum Genet Mar;58(3):513-522.

Chastain PD, Eichler EE, Kang S, Nelson DL, Levene SD, Sinden RR. (1995). Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes. Biochem Dec 12;34(49):16125-16131.

Eichler EE, Hammond HA, Macpherson JN, Ward PA, Nelson DL. (1995). Population survey of the human FMR1 CGG repeat substructure suggests biased polarity for the loss of AGG interruptions. Hum Mol Genet Dec;4(12):2199-2208.

Eichler EE, Kunst CB, Lugenbeel KA, Ryder OA, Davison D, Warren ST, Nelson DL. (1995). Evolution of the cryptic FMR1 CGG repeat. Nat Genet Nov;11(3):301-308.

Eichler EE, Holden JJA, Popovich BW, Reiss AL, Snow K, Thibodeau SN, Richards CS, Ward PA, Nelson DL. (1994). Length of uninterrupted CGG repeats determines instability in the FMR1 gene. Nat Genet Sep;8(1):88-94.

Chong SS, Eichler EE, Nelson DL, Hughes MR. (1994). Robust amplification and ethidium-visible detection of the fragile X syndrome CGG repeat using Pfu polymerase. Am J Med Genet Jul 15;51(4):522-526.

Eichler EE, Richards S, Gibbs RA, Nelson DL. (1993). Fine structure of the human FMR1 gene. Hum Mol Genet Aug;2(8):1147-1153.

Ashley CT, Sutcliffe JS, Kunst CB, Leiner HA, Eichler EE, Nelson DL, Warren ST. (1993). Human and murine FMR-1: Alternative splicing and translational initiation downstream of the
CGG-repeat. Nat Genet Jul;4(3):244-251.

Verkerk AJ, de Graaff E, De Boulle K, Eichler EE, Konecki DS, Reyniers E, Manca A, Poustka A, Willems PJ, Nelson DL, Oostra BA. (1993). Alternative splicing in the fragile X gene FMR1. Hum Mol Genet Apr;2(4):399-404.