Publications
Jiang Z, Hubley R, Smit A, Eichler EE. (2008). DupMasker: A tool for annotating primate segmental duplications. Genome Res May 23 [Epub ahead of print]. (PDF)
She X, Cheng Z, Zollner S, Church DM, Eichler EE. (2008). Mouse segmental duplication and copy number variation. Nat Genet May 22 [Epub ahead of print]. (PDF) (Supplementary Material)
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):175-183. [Epub ahead of print]. (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. [Epub ahead of print]. (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 Apr 29 [Epub ahead of print]. (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. Epub 2008 Mar 27. (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 Feb 17 [Epub ahead of print]. (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 [Epub ahead of print]. (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)
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 (20 April 2007). (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 Seqeuncing 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;437(7055):50-51. *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)
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):860-920. *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. Nature Genetics 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)