A conclusion is the part where you got tired of thinking.
--- Steven Wright


Eichler Lab

Department of Genome Sciences,
University of Washington

Publications



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. (PDF)

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 Oct 30. doi: 10.1093/gigascience/gix098. [Epub ahead of print] (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary TableS1) (Supplementary TableS2) (Supplementary TableS3) (Supplementary TableS4)

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 Sep 18. doi: 10.1111/jcpp.12815. [Epub ahead of print] (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Table2) (Supplementary Table3) (Supplementary Table4) (Supplementary Table5) (Supplementary Table6) (Supplementary Table7) (Supplementary Table8) (Supplementary Table9) (Supplementary Table10)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary FASTA File) (Supplementary Tables 9-10)

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. (PDF) (Supplementary Material) (Supplementary Tables) (Supplementary Dataset 1) (Supplementary Dataset 2)

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. (PDF) (Supplementary Material, Figures, Tables) (Supplementary Tables) (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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Tables) (Supplementary Code)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Data1) (Supplementary Data2) (Supplementary Data3) (Supplementary Data4) (Supplementary Data5) (Supplementary Data6) (Supplementary Data7) (Supplementary Data8) (Supplementary Data9) (Supplementary Data10) (Supplementary Data11)

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. (PDF) (Supplementary Material) (Supplementary Tables1-14)

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. (PDF) (Supplementary Material)

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. (PDF)

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

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Tables)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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

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. (PDF) (Supplementary Material) (Supplementary Tables) (Supplementary Table S36)

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. (PDF) (Supplementary Material) (Supplementary Tables)

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

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. (PDF)

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. (PDF) (Supplementary Figures) (Supplementary Tables)

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. (PDF) (Supplementary Material & Figures) (Supplementary Tables)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Extended Data Figures) (Supplementary Tables)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Table1) (Supplementary Table2) (Supplementary Table3) (Supplementary Table4) (Supplementary Table5) (Simons Genome Diversity Project Dataset) (Sequence data at the ENA) (Signed Letter Request)

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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. (PDF)

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. (PDF) (Supplementary Figures1-13) (Supplementary Tables1-14) (Supplementary Data Set)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Video)

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. (PDF) (Corrigendum)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Table1)

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. (PDF) (Supplementary Material) (Supplementary Tables) (Additional Data)

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. (PDF)

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. (PDF) (Supplementary Info & Figs) (Supplementary Data1) (Supplementary Data2)

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. (PDF)

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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. (PDF)

Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M. (2014). The contribution of de novo coding mutations to autism spectrum disorder. Nature Nov 13;515(7526):216-21. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Tables)

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. (PDF)

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. (PDF)

Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prufer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GB, Cali F, Churnosov M, Cole DE, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Ku.inskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Nakkalajarvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Paabo S, Kelso J, Reich D, Krause J. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature Sep 18;513(7518):409-13. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Tables) (Supplementary Data Set)

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvak Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA. (2014). Gibbon genome and the fast karyotype evolution of small apes. Nature Sep 11;513(7517):195-201. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Figure1) (Supplementary Figure2) (Supplementary Figure3) (Supplementary Table1) (Supplementary Table2) (Supplementary Table3) (Supplementary Table4) (Supplementary Table5) (Supplementary Table6) (Supplementary Table7)

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. (PDF) (Supplementary Material) (Supplementary TablesS1-4) (Supplementary TablesS5)

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. (PDF) (Supplementary Table1)

Hoischen A, Krumm N, Eichler EE. (2014). Prioritization of neurodevelopmental disease genes by discovery of new mutations. Nat Neurosci Jun;17(6):764-72. (PDF) (Supplementary Table1)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Figures & Tables) (Supplementary Figure Legends) (Supplementary Data)

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. (PDF) (Supplementary Material)

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. (PDF)

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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. (PDF)

Dumont BL, Eichler EE. (2013). Signals of historical interlocus gene conversion in human segmental duplications. PLoS One Oct 4;8(10):e75949. (PDF) (FigureS1) (FigureS2) (TableS1) (TableS2) (TableS3) (TableS4) (TableS5) (TableS6) (TableS7) (TableS8) (Supplementary TextS1)

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. (PDF) (Supplementary Material) (Supplementary Tables)

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. (PDF) (Supplementary Material) (Supplementary Tables S1-12)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Table2) (Supplementary Table3) (Supplementary Table4) (Supplementary Table5) (Supplementary Table6) (Supplementary Table11)

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. (PDF) (Supplementary Material) (Supplementary Table1)

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. (PDF) (Supplementary Material) (Supplementary Tables)

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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. (PDF) (Supplementary Material) (Supplementary Tables)

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. (PDF)

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

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. (PDF)

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. (PDF)

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. (PDF)

Watson CT, Steinberg KM, Huddleston J, Warren RL, Malig M, Schein J, Willsey AJ, Joy JB, Scott JK, Graves TA, Wilson RK, Holt RA, Eichler EE, Breden F. (2013). Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation. Am J Hum Genet Apr 4;92(4):530-46. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF) (Supplementary FigsS1-S5) (Supplementary Tables) (Supplementary Material3) (Supplementary Material4) (Supplementary Material5) (Supplementary Material6)

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. (PDF)

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. (PDF)

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. (PDF) (Response)

Giannuzzi G, Siswara P, Malig M, Marques-Bonet T, NISC Comparative Sequencing Program, Mullikin JC, Ventura M, Eichler EE. (2013). Evolutionary dynamism of the primate LRRC37 gene family. Genome Res Jan;23(1):46-59. doi: 10.1101/gr.138842.112. Epub 2012 Oct 11. (PDF) (Supplementary Material) (Supplementary Tables)

O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O'Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Eichler EE, Shendure J. (2012). Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science Dec 21;338(6114):1619-22. (PDF) (Supplementary Material) (Supplementary TableS4)

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. (PDF) (Supplementary Material) (Supplementary Table5) (Supplementary Table7)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Table1)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

Coe BP, Girirajan S, Eichler EE. (2012). A genetic model for neurodevelopmental disease. Curr Opin Neurobiol Oct;22(5):829-6. (PDF)

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. (PDF) (Supplementary TablesS1-S6)

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. (PDF)

Coe BP, Girirajan S, Eichler EE. (2012). The genetic variability and commonality of neurodevelopmental disease. Am J Med Genet C Semin Med Genet May 15;160C(2):118-29. (PDF)

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. (PDF) (Supplementary Material & Tables) (Supplementary TableS6)

O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE. (2012). Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature Apr 4;485(7397):246-250. (PDF) (Supplementary Material) (Supplementary Tables)

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. (PDF) (Supplementary Material)

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. (PDF) (Supplementary Figures) (Supplementary Table1) (Supplementary Table2) (Supplementary Table3)

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. (PDF)

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. (PDF)

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. (2012). Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res Apr;22(4):778-90. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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

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. (PDF)

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 Dec 18;9(2):176-8. (PDF) (Supplementary Material)

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. (PDF) (DatasetS1) (DatasetS2) (DatasetS3) (DatasetS4) (FigureS1) (FigureS2) (FigureS3) (TableS1) (TableS2) (TableS3) (TableS4) (TableS5) (TableS6) (TableS7) (TableS8) (TableS9) (TableS10)

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 microdeletion syndrome. Epilepsia Dec;52(12):e194-8. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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

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. (PDF)

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. (PDF) (Supplementary Tables 2-11, Supplementary Figures 1-13 & Supplementary Note) (Supplementary Table1) (Supplementary Table12) (Supplementary Table13) (CNV Calls as submitted to dbVar (Cases) (Controls)) (Corrigendum)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Table1) (Supplementary Table2)

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. (PDF) (Supplementary Material) (Supplementary Figures & Tables) (Supplementary Figure Legends)

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. (PDF)

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.(PDF)

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. (PDF) (Supplementary Note, Supplementary Figures 1-5 and Supplementary Tables 2-4 and 6-9) (Supplementary Table1) (Supplementary Table5)

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. (PDF) (Supplementary Figures) (Supplementary Tables)

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. (PDF) (Supplementary Material) (Supplementary Table S2) (Supplementary Table S3) (Supplementary Table S7) (Supplementary Table S8) (Supplementary Table S9)

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

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stutz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project. (2011). Mapping copy number variation by population-scale genome sequencing. Nature Feb 3;470(7332):59-65. (PDF)

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. (PDF)

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darre F, Farre D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Valle GD, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordonez GR, Lopez-Otin C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK. (2011). Comparative and demographic analysis of orang-utan genomes. Nature Jan 27;469(7331):529-533. (PDF)

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. (PDF)

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. (PDF) (Supplementary Figures 1.2, Supplementary Table 2, Supplementary Note) (Supplementary Table1) (Supplementary Table3) (Supplementary Table4) (Supplementary Table5)

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 satellites from multiple mammalian genomes. Genome Res Jan;21(1):137-45. Epub 2010 Nov 16. (PDF) (Supplementary Material) (Supplementary Table S1)

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Paabo S. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature Dec 23;468(7327):1053-60. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Tables S1,S4-S8) (Supplementary Table S2) (Supplementary Table S3)

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project, Eichler EE. (2010). Diversity of human copy number variation and multicopy genes. Science October 29;330(6004):641-646. (PDF) (Supplementary Material) (Supplementary Gene Table)

The 1000 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature Oct 28;467(7319):1061-73. *Contributors Aksay G, Alkan C, Hormozdiari F, Kidd JM, Sudmant PH, Eichler EE to structural variation analyses of the manuscript, pages 1063-1066. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Figures)

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. (PDF)

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

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

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. (PDF) (Supplementary Note and Supplementary Figs 1.4)

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 craniosynostosis: Multiple rare variants including RUNX2 duplication in two cousins with metopic craniosynostosis. Am J Med Genet A Sep;152A(9):2203-10. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Material2)

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. (PDF)

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 Genet Jun;11(6):446-50. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Note, Supplementary Figures 1.7 & Supplementary Tables 2,3,5,9,11,12) (Supplementary Table1) (Supplementary Table4) (Supplementary Table6) (Supplementary Table7) (Supplementary Table8) (Supplementary Table10) (Supplementary Table13) (Supplementary Table14)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Note, Supplementary Figures 1.4 and Supplementary Tables 1.9)

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. (PDF)

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. (PDF)

Zerr T, Cooper GM, Eichler EE, Nickerson DA. (2010). Targeted interrogation of copy number variation using SCIMMkit. Bioinformatics Jan 1;26(1):120-2. (PDF) (Supplementary Material) (Supplementary Data1) (Supplementary Data2) SCIMMkit Homepage

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. (PDF)

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 1;10(1):571. (PDF)

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. (PDF)

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

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. (PDF) (Supplementary Material) (Supplementary Table4) (Supplementary Table5)

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. (PDF)

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. (PDF)

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

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Table1)

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. (PDF)

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

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. (PDF)

Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. (2009). Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res Jul;19(7):1270-8. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Tables S1-S9)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF) (Supplementary Material) (Supplementary Figures) (Supplementary Tables)

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. (PDF)

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. (PDF) (Supplementary Material) (Table S1) (Table S1 - ParcCoded)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF) (Supplementary Figure Legends) (Supplementary File 1) (Supplementary File 2) (Supplementary File 3) (Supplementary File 4) (Supplementary Figures) (Supplementary Data) (Supplementary Tables 1-11)

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. (PDF)

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. (PDF) (Supplementary Table1) (Supplementary Table2)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF) (Supplementary Material, Supplementary Tables 1, 3-6, 9, 10 and Supplementary Figures) (Supplementary Table2) (Supplementary Table7) (Supplementary Table8)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Figure1a) (Supplementary Figure1b-d) (Supplementary Figure2) (Supplementary Table1) (Supplementary Table2) (Supplementary Table3) (Supplementary Table4) (Supplementary Table5)

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. (PDF)

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. (PDF)

Jiang Z, Hubley R, Smit A, Eichler EE. (2008). DupMasker: A tool for annotating primate segmental duplications. Genome Res Aug;18(8):1362-1368. (PDF) (Supplementary Table 1) (Supplementary Table 2)

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. (PDF) (Supplementary Material) (Supplementary Figure) (Supplementary Table1) (Supplementary Table2) (Supplementary Table3) (Supplementary Table4) (Supplementary Table5) (Supplementary Table6) (Supplementary Table7) (Supplementary Table8)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF) (Supplementary Material)

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. (PDF)

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). (PDF)

Bailey JA, Kidd JM, Eichler EE. (2008). Human copy number polymorphic genes. Cytogenet Genome Res 123(1-4):234-43. (PDF) (Supplementary Figures1-2) (Supplementary Table1-9)

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. (PDF) (Supplementary Material)

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). (PDF) (Supplementary Material)

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). (PDF)

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). (PDF) (Supplementary Material)

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 (PDF) (Supplementary Material)

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). (PDF) (Supplementary Figures) (Supplementary Table1) (Supplementary Table2) (Supplementary Table3) (Supplementary Table4) (Supplementary Table5)

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). (PDF) (Supplementary Material) (Supplementary Table1) (Supplementary Table2)

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). (PDF)

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). (PDF)

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. (PDF) (Supplementary Figures) (Supplementary Table 1) (Supplementary Table 4) (Supplementary Tables 2,3,5,6,7)

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. (PDF)

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. (PDF)

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). (PDF) (Supplementary Material)

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). (PDF) (Supplementary Material)

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). (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF) (Supplementary Material)

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. (PDF)

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

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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

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

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material) (Supplementary Figure1a) (Supplementary Figure1b) (Supplementary Table1) (Supplementary Table2) (Supplementary Table3) (Supplementary Table4)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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

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. (PDF)

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. (PDF) (Supplementary Material)

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

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. (PDF)

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. (PDF)

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 (2003). Am J Hum Genet Oct;73(4):898-925. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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

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

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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

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. (PDF) (Supplementary Material)

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

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF) (Supplementary Material)

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

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. (PDF)

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. (PDF)

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. (PDF) (Supplementary Material)

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. (PDF)

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. (PDF)

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. (PDF)

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

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. (PDF)

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

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. (PDF)

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. (PDF)

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. (PDF)

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

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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. (PDF)

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

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. (PDF)

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. (PDF)