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Research

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  DNA methylation contributes to natural human variation

  • Holger Heyn,
  • Sebastian Moran,
  • Irene Hernando-Herraez,
  • Sergi Sayols,
  • Antonio Gomez,
  • Juan Sandoval,
  • Dave Monk,
  • Kenichiro Hata,
  • Tomas Marques-Bonet,
  • Liewei Wang,
  • and Manel Esteller

  Genome Res. September 2013 23: 1363-1372; Published in Advance August 1, 2013, doi:10.1101/gr.154187.112
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  Evolution and diversity of copy number variation in the great ape lineage

  • Peter H. Sudmant,
  • John Huddleston,
  • Claudia R. Catacchio,
  • Maika Malig,
  • LaDeana W. Hillier,
  • Carl Baker,
  • Kiana Mohajeri,
  • Ivanela Kondova,
  • Ronald E. Bontrop,
  • Stephan Persengiev,
  • Francesca Antonacci,
  • Mario Ventura,
  • Javier Prado-Martinez,
  • Great Ape Genome Project,
  • Tomas Marques-Bonet,
  • and Evan E. Eichler

  Genome Res. September 2013 23: 1373-1382; Published in Advance July 3, 2013, doi:10.1101/gr.158543.113
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  Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles

  • Philip M. Boone,
  • Ian M. Campbell,
  • Brett C. Baggett,
  • Zachry T. Soens,
  • Mitchell M. Rao,
  • Patricia M. Hixson,
  • Ankita Patel,
  • Weimin Bi,
  • Sau Wai Cheung,
  • Seema R. Lalani,
  • Arthur L. Beaudet,
  • Pawel Stankiewicz,
  • Chad A. Shaw,
  • and James R. Lupski

  Genome Res. September 2013 23: 1383-1394; Published in Advance May 16, 2013, doi:10.1101/gr.156075.113
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  NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits

  • Piotr Dittwald,
  • Tomasz Gambin,
  • Przemyslaw Szafranski,
  • Jian Li,
  • Stephen Amato,
  • Michael Y. Divon,
  • Lisa Ximena Rodríguez Rojas,
  • Lindsay E. Elton,
  • Daryl A. Scott,
  • Christian P. Schaaf,
  • Wilfredo Torres-Martinez,
  • Abby K. Stevens,
  • Jill A. Rosenfeld,
  • Satish Agadi,
  • David Francis,
  • Sung-Hae L. Kang,
  • Amy Breman,
  • Seema R. Lalani,
  • Carlos A. Bacino,
  • Weimin Bi,
  • Aleksandar Milosavljevic,
  • Arthur L. Beaudet,
  • Ankita Patel,
  • Chad A. Shaw,
  • James R. Lupski,
  • Anna Gambin,
  • Sau Wai Cheung,
  • and Pawel Stankiewicz

  Genome Res. September 2013 23: 1395-1409; Published in Advance May 8, 2013, doi:10.1101/gr.152454.112
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  The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome

  • M. Reza Sailani,
  • Periklis Makrythanasis,
  • Armand Valsesia,
  • Federico A. Santoni,
  • Samuel Deutsch,
  • Konstantin Popadin,
  • Christelle Borel,
  • Eugenia Migliavacca,
  • Andrew J. Sharp,
  • Genevieve Duriaux Sail,
  • Emilie Falconnet,
  • Kelly Rabionet,
  • Clara Serra-Juhé,
  • Stefano Vicari,
  • Daniela Laux,
  • Yann Grattau,
  • Guy Dembour,
  • Andre Megarbane,
  • Renaud Touraine,
  • Samantha Stora,
  • Sofia Kitsiou,
  • Helena Fryssira,
  • Chariklia Chatzisevastou-Loukidou,
  • Emmanouel Kanavakis,
  • Giuseppe Merla,
  • Damien Bonnet,
  • Luis A. Pérez-Jurado,
  • Xavier Estivill,
  • Jean M. Delabar,
  • and Stylianos E. Antonarakis

  Genome Res. September 2013 23: 1410-1421; Published in Advance June 19, 2013, doi:10.1101/gr.147991.112
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  Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

  • Zhengyan Kan,
  • Hancheng Zheng,
  • Xiao Liu,
  • Shuyu Li,
  • Thomas D. Barber,
  • Zhuolin Gong,
  • Huan Gao,
  • Ke Hao,
  • Melinda D. Willard,
  • Jiangchun Xu,
  • Robert Hauptschein,
  • Paul A. Rejto,
  • Julio Fernandez,
  • Guan Wang,
  • Qinghui Zhang,
  • Bo Wang,
  • Ronghua Chen,
  • Jian Wang,
  • Nikki P. Lee,
  • Wei Zhou,
  • Zhao Lin,
  • Zhiyu Peng,
  • Kang Yi,
  • Shengpei Chen,
  • Lin Li,
  • Xiaomei Fan,
  • Jie Yang,
  • Rui Ye,
  • Jia Ju,
  • Kai Wang,
  • Heather Estrella,
  • Shibing Deng,
  • Ping Wei,
  • Ming Qiu,
  • Isabella H. Wulur,
  • Jiangang Liu,
  • Mariam E. Ehsani,
  • Chunsheng Zhang,
  • Andrey Loboda,
  • Wing Kin Sung,
  • Amit Aggarwal,
  • Ronnie T. Poon,
  • Sheung Tat Fan,
  • Jun Wang,
  • James Hardwick,
  • Christoph Reinhard,
  • Hongyue Dai,
  • Yingrui Li,
  • John M. Luk,
  • and Mao Mao

  Genome Res. September 2013 23: 1422-1433; Published in Advance June 20, 2013, doi:10.1101/gr.154492.113
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  Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance

  • Peilin Jia,
  • Hailing Jin,
  • Catherine B. Meador,
  • Junfeng Xia,
  • Kadoaki Ohashi,
  • Lin Liu,
  • Valentina Pirazzoli,
  • Kimberly B. Dahlman,
  • Katerina Politi,
  • Franziska Michor,
  • Zhongming Zhao,
  • and William Pao

  Genome Res. September 2013 23: 1434-1445; Published in Advance June 3, 2013, doi:10.1101/gr.152322.112
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  CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

  • Hui Ling,
  • Riccardo Spizzo,
  • Yaser Atlasi,
  • Milena Nicoloso,
  • Masayoshi Shimizu,
  • Roxana S. Redis,
  • Naohiro Nishida,
  • Roberta Gafà,
  • Jian Song,
  • Zhiyi Guo,
  • Cristina Ivan,
  • Elisa Barbarotto,
  • Ingrid De Vries,
  • Xinna Zhang,
  • Manuela Ferracin,
  • Mike Churchman,
  • Janneke F. van Galen,
  • Berna H. Beverloo,
  • Maryam Shariati,
  • Franziska Haderk,
  • Marcos R. Estecio,
  • Guillermo Garcia-Manero,
  • Gijs A. Patijn,
  • David C. Gotley,
  • Vikas Bhardwaj,
  • Imad Shureiqi,
  • Subrata Sen,
  • Asha S. Multani,
  • James Welsh,
  • Ken Yamamoto,
  • Itsuki Taniguchi,
  • Min-Ae Song,
  • Steven Gallinger,
  • Graham Casey,
  • Stephen N. Thibodeau,
  • Loïc Le Marchand,
  • Maarit Tiirikainen,
  • Sendurai A. Mani,
  • Wei Zhang,
  • Ramana V. Davuluri,
  • Koshi Mimori,
  • Masaki Mori,
  • Anieta M. Sieuwerts,
  • John W.M. Martens,
  • Ian Tomlinson,
  • Massimo Negrini,
  • Ioana Berindan-Neagoe,
  • John A. Foekens,
  • Stanley R. Hamilton,
  • Giovanni Lanza,
  • Scott Kopetz,
  • Riccardo Fodde,
  • and George A. Calin

  Genome Res. September 2013 23: 1446-1461; Published in Advance June 24, 2013, doi:10.1101/gr.152942.112
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  Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase

  • Ayako Yamanishi,
  • Kosuke Yusa,
  • Kyoji Horie,
  • Masahiro Tokunaga,
  • Kohji Kusano,
  • Chikara Kokubu,
  • and Junji Takeda

  Genome Res. September 2013 23: 1462-1473; Published in Advance August 1, 2013, doi:10.1101/gr.152744.112
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  The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease

  • Laure K. Case,
  • Emma H. Wall,
  • Julie A. Dragon,
  • Naresha Saligrama,
  • Dimitry N. Krementsov,
  • Mohamad Moussawi,
  • James F. Zachary,
  • Sally A. Huber,
  • Elizabeth P. Blankenhorn,
  • and Cory Teuscher

  Genome Res. September 2013 23: 1474-1485; Published in Advance June 25, 2013, doi:10.1101/gr.156703.113
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  Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution

  • Gang Li,
  • Brian W. Davis,
  • Terje Raudsepp,
  • Alison J. Pearks Wilkerson,
  • Victor C. Mason,
  • Malcolm Ferguson-Smith,
  • Patricia C. O'Brien,
  • Paul D. Waters,
  • and William J. Murphy

  Genome Res. September 2013 23: 1486-1495; Published in Advance June 20, 2013, doi:10.1101/gr.154286.112
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  Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

  • Daniel A. Skelly,
  • Gennifer E. Merrihew,
  • Michael Riffle,
  • Caitlin F. Connelly,
  • Emily O. Kerr,
  • Marnie Johansson,
  • Daniel Jaschob,
  • Beth Graczyk,
  • Nicholas J. Shulman,
  • Jon Wakefield,
  • Sara J. Cooper,
  • Stanley Fields,
  • William S. Noble,
  • Eric G.D. Muller,
  • Trisha N. Davis,
  • Maitreya J. Dunham,
  • Michael J. MacCoss,
  • and Joshua M. Akey

  Genome Res. September 2013 23: 1496-1504; Published in Advance May 29, 2013, doi:10.1101/gr.155762.113
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  HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses

  • Rafael Contreras-Galindo,
  • Mark H. Kaplan,
  • Shirley He,
  • Angie C. Contreras-Galindo,
  • Marta J. Gonzalez-Hernandez,
  • Ferdinand Kappes,
  • Derek Dube,
  • Susana M. Chan,
  • Dan Robinson,
  • Fan Meng,
  • Manhong Dai,
  • Scott D. Gitlin,
  • Arul M. Chinnaiyan,
  • Gilbert S. Omenn,
  • and David M. Markovitz

  Genome Res. September 2013 23: 1505-1513; Published in Advance May 8, 2013, doi:10.1101/gr.144303.112
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