GENOME RESEARCH >> Table of Contents — February 2012, 22 (2)

current issue, open here please:
Table of Contents — February 2012, 22 (2)

Research

• Select this article

  Whole genome sequencing of matched primary and metastatic acral melanomas

  • Samra Turajlic,
  • Simon J. Furney,
  • Maryou B. Lambros,
  • Costas Mitsopoulos,
  • Iwanka Kozarewa,
  • Felipe C. Geyer,
  • Alan MacKay,
  • Jarle Hakas,
  • Marketa Zvelebil,
  • Christopher J. Lord,
  • Alan Ashworth,
  • Meirion Thomas,
  • Gordon Stamp,
  • James Larkin,
  • Jorge S. Reis-Filho,
  • and Richard Marais

  Genome Res. February 2012 22: 196-207; Published in Advance December 19, 2011, doi:10.1101/gr.125591.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency

  • Linghua Wang,
  • Shuichi Tsutsumi,
  • Tokuichi Kawaguchi,
  • Koichi Nagasaki,
  • Kenji Tatsuno,
  • Shogo Yamamoto,
  • Fei Sang,
  • Kohtaro Sonoda,
  • Minoru Sugawara,
  • Akio Saiura,
  • Seiko Hirono,
  • Hiroki Yamaue,
  • Yoshio Miki,
  • Minoru Isomura,
  • Yasushi Totoki,
  • Genta Nagae,
  • Takayuki Isagawa,
  • Hiroki Ueda,
  • Satsuki Murayama-Hosokawa,
  • Tatsuhiro Shibata,
  • Hiromi Sakamoto,
  • Yae Kanai,
  • Atsushi Kaneda,
  • Tetsuo Noda,
  • and Hiroyuki Aburatani

  Genome Res. February 2012 22: 208-219; Published in Advance December 7, 2011, doi:10.1101/gr.123109.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Genomic analysis of circulating cell-free DNA infers breast cancer dormancy

  • Jacqueline A. Shaw,
  • Karen Page,
  • Kevin Blighe,
  • Natasha Hava,
  • David Guttery,
  • Becky Ward,
  • James Brown,
  • Chetana Ruangpratheep,
  • Justin Stebbing,
  • Rachel Payne,
  • Carlo Palmieri,
  • Suzy Cleator,
  • Rosemary A. Walker,
  • and R. Charles Coombes

  Genome Res. February 2012 22: 220-231; Published in Advance October 11, 2011, doi:10.1101/gr.123497.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplememental Material

  OPEN ACCESS ARTICLE
• Select this article

  Assessment of palindromes as platforms for DNA amplification in breast cancer

  • Jamie Guenthoer,
  • Scott J. Diede,
  • Hisashi Tanaka,
  • Xiaoyu Chai,
  • Li Hsu,
  • Stephen J. Tapscott,
  • and Peggy L. Porter

  Genome Res. February 2012 22: 232-245; Published in Advance July 13, 2011, doi:10.1101/gr.117226.110
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

  • Gary C. Hon,
  • R. David Hawkins,
  • Otavia L. Caballero,
  • Christine Lo,
  • Ryan Lister,
  • Mattia Pelizzola,
  • Armand Valsesia,
  • Zhen Ye,
  • Samantha Kuan,
  • Lee E. Edsall,
  • Anamaria Aranha Camargo,
  • Brian J. Stevenson,
  • Joseph R. Ecker,
  • Vineet Bafna,
  • Robert L. Strausberg,
  • Andrew J. Simpson,
  • and Bing Ren

  Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription

  • Mukund Patel,
  • Jeremy M. Simon,
  • Michael D. Iglesia,
  • Sam B. Wu,
  • Andrew W. McFadden,
  • Jason D. Lieb,
  • and Ian J. Davis

  Genome Res. February 2012 22: 259-270; Published in Advance November 15, 2011, doi:10.1101/gr.125666.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Genome-scale analysis of aberrant DNA methylation in colorectal cancer

  • Toshinori Hinoue,
  • Daniel J. Weisenberger,
  • Christopher P.E. Lange,
  • Hui Shen,
  • Hyang-Min Byun,
  • David Van Den Berg,
  • Simeen Malik,
  • Fei Pan,
  • Houtan Noushmehr,
  • Cornelis M. van Dijk,
  • Rob A.E.M. Tollenaar,
  • and Peter W. Laird

  Genome Res. February 2012 22: 271-282; Published in Advance June 9, 2011, doi:10.1101/gr.117523.110
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Unique DNA methylome profiles in CpG island methylator phenotype colon cancers

  • Yaomin Xu,
  • Bo Hu,
  • Ae-Jin Choi,
  • Banu Gopalan,
  • Byron H. Lee,
  • Matthew F. Kalady,
  • James M. Church,
  • and Angela H. Ting

  Genome Res. February 2012 22: 283-291; Published in Advance October 11, 2011, doi:10.1101/gr.122788.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

  • Aleksandar D. Kostic,
  • Dirk Gevers,
  • Chandra Sekhar Pedamallu,
  • Monia Michaud,
  • Fujiko Duke,
  • Ashlee M. Earl,
  • Akinyemi I. Ojesina,
  • Joonil Jung,
  • Adam J. Bass,
  • Josep Tabernero,
  • José Baselga,
  • Chen Liu,
  • Ramesh A. Shivdasani,
  • Shuji Ogino,
  • Bruce W. Birren,
  • Curtis Huttenhower,
  • Wendy S. Garrett,
  • and Matthew Meyerson

  Genome Res. February 2012 22: 292-298; Published in Advance October 18, 2011, doi:10.1101/gr.126573.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

  • Mauro Castellarin,
  • René L. Warren,
  • J. Douglas Freeman,
  • Lisa Dreolini,
  • Martin Krzywinski,
  • Jaclyn Strauss,
  • Rebecca Barnes,
  • Peter Watson,
  • Emma Allen-Vercoe,
  • Richard A. Moore,
  • and Robert A. Holt

  Genome Res. February 2012 22: 299-306; Published in Advance October 18, 2011, doi:10.1101/gr.126516.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer

  • Fátima Valdés-Mora,
  • Jenny Z. Song,
  • Aaron L. Statham,
  • Dario Strbenac,
  • Mark D. Robinson,
  • Shalima S. Nair,
  • Kate I. Patterson,
  • David J. Tremethick,
  • Clare Stirzaker,
  • and Susan J. Clark

  Genome Res. February 2012 22: 307-321; Published in Advance July 25, 2011, doi:10.1101/gr.118919.110
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Cooperation between Polycomb and androgen receptor during oncogenic transformation

  • Jonathan C. Zhao,
  • Jianjun Yu,
  • Christine Runkle,
  • Longtao Wu,
  • Ming Hu,
  • Dayong Wu,
  • Jun S. Liu,
  • Qianben Wang,
  • Zhaohui S. Qin,
  • and Jindan Yu

  Genome Res. February 2012 22: 322-331; Published in Advance December 16, 2011, doi:10.1101/gr.131508.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Genetic variation in radiation-induced cell death

  • Denis A. Smirnov,
  • Lauren Brady,
  • Krzysztof Halasa,
  • Michael Morley,
  • Sonia Solomon,
  • and Vivian G. Cheung

  Genome Res. February 2012 22: 332-339; Published in Advance August 15, 2011, doi:10.1101/gr.122044.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

Methods

• Select this article

  Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations

  • John F. Thompson,
  • Jeffrey G. Reifenberger,
  • Eldar Giladi,
  • Kristen Kerouac,
  • Jaime Gill,
  • Erik Hansen,
  • Avak Kahvejian,
  • Philipp Kapranov,
  • Travis Knope,
  • Doron Lipson,
  • Kathleen E. Steinmann,
  • and Patrice M. Milos

  Genome Res. February 2012 22: 340-345; Published in Advance July 15, 2011, doi:10.1101/gr.122192.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Estimation of rearrangement phylogeny for cancer genomes

  • Chris D. Greenman,
  • Erin D. Pleasance,
  • Scott Newman,
  • Fengtang Yang,
  • Beiyuan Fu,
  • Serena Nik-Zainal,
  • David Jones,
  • King Wai Lau,
  • Nigel Carter,
  • Paul A.W. Edwards,
  • P. Andrew Futreal,
  • Michael R. Stratton,
  • and Peter J. Campbell

  Genome Res. February 2012 22: 346-361; Published in Advance October 12, 2011, doi:10.1101/gr.118414.110
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Calling amplified haplotypes in next generation tumor sequence data

  • Ninad Dewal,
  • Yang Hu,
  • Matthew L. Freedman,
  • Thomas LaFramboise,
  • and Itsik Pe'er

  Genome Res. February 2012 22: 362-374; Published in Advance November 16, 2011, doi:10.1101/gr.122564.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  De novo discovery of mutated driver pathways in cancer

  • Fabio Vandin,
  • Eli Upfal,
  • and Benjamin J. Raphael

  Genome Res. February 2012 22: 375-385; Published in Advance June 7, 2011, doi:10.1101/gr.120477.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material
• Select this article

  Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets

  • Qing Xiong,
  • Nicola Ancona,
  • Elizabeth R. Hauser,
  • Sayan Mukherjee,
  • and Terrence S. Furey

  Genome Res. February 2012 22: 386-397; Published in Advance September 22, 2011, doi:10.1101/gr.124370.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE
• Select this article

  Mutual exclusivity analysis identifies oncogenic network modules

  • Giovanni Ciriello,
  • Ethan Cerami,
  • Chris Sander,
  • and Nikolaus Schultz

  Genome Res. February 2012 22: 398-406; Published in Advance September 9, 2011, doi:10.1101/gr.125567.111
  • Abstract
  • Full Text
  • Full Text (PDF)
  • Supplemental Material

  OPEN ACCESS ARTICLE