Literature DB >> 23538863

Drilling into big cancer-genome data.

Vivien Marx1.   

Abstract

Entities:  

Year:  2013        PMID: 23538863     DOI: 10.1038/nmeth.2410

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


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  5 in total

Review 1.  Making sense of cancer genomic data.

Authors:  Lynda Chin; William C Hahn; Gad Getz; Matthew Meyerson
Journal:  Genes Dev       Date:  2011-03-15       Impact factor: 11.361

2.  Identifying personal genomes by surname inference.

Authors:  Melissa Gymrek; Amy L McGuire; David Golan; Eran Halperin; Yaniv Erlich
Journal:  Science       Date:  2013-01-18       Impact factor: 47.728

3.  International network of cancer genome projects.

Authors:  Thomas J Hudson; Warwick Anderson; Axel Artez; Anna D Barker; Cindy Bell; Rosa R Bernabé; M K Bhan; Fabien Calvo; Iiro Eerola; Daniela S Gerhard; Alan Guttmacher; Mark Guyer; Fiona M Hemsley; Jennifer L Jennings; David Kerr; Peter Klatt; Patrik Kolar; Jun Kusada; David P Lane; Frank Laplace; Lu Youyong; Gerd Nettekoven; Brad Ozenberger; Jane Peterson; T S Rao; Jacques Remacle; Alan J Schafer; Tatsuhiro Shibata; Michael R Stratton; Joseph G Vockley; Koichi Watanabe; Huanming Yang; Matthew M F Yuen; Bartha M Knoppers; Martin Bobrow; Anne Cambon-Thomsen; Lynn G Dressler; Stephanie O M Dyke; Yann Joly; Kazuto Kato; Karen L Kennedy; Pilar Nicolás; Michael J Parker; Emmanuelle Rial-Sebbag; Carlos M Romeo-Casabona; Kenna M Shaw; Susan Wallace; Georgia L Wiesner; Nikolajs Zeps; Peter Lichter; Andrew V Biankin; Christian Chabannon; Lynda Chin; Bruno Clément; Enrique de Alava; Françoise Degos; Martin L Ferguson; Peter Geary; D Neil Hayes; Thomas J Hudson; Amber L Johns; Arek Kasprzyk; Hidewaki Nakagawa; Robert Penny; Miguel A Piris; Rajiv Sarin; Aldo Scarpa; Tatsuhiro Shibata; Marc van de Vijver; P Andrew Futreal; Hiroyuki Aburatani; Mónica Bayés; David D L Botwell; Peter J Campbell; Xavier Estivill; Daniela S Gerhard; Sean M Grimmond; Ivo Gut; Martin Hirst; Carlos López-Otín; Partha Majumder; Marco Marra; John D McPherson; Hidewaki Nakagawa; Zemin Ning; Xose S Puente; Yijun Ruan; Tatsuhiro Shibata; Michael R Stratton; Hendrik G Stunnenberg; Harold Swerdlow; Victor E Velculescu; Richard K Wilson; Hong H Xue; Liu Yang; Paul T Spellman; Gary D Bader; Paul C Boutros; Peter J Campbell; Paul Flicek; Gad Getz; Roderic Guigó; Guangwu Guo; David Haussler; Simon Heath; Tim J Hubbard; Tao Jiang; Steven M Jones; Qibin Li; Nuria López-Bigas; Ruibang Luo; Lakshmi Muthuswamy; B F Francis Ouellette; John V Pearson; Xose S Puente; Victor Quesada; Benjamin J Raphael; Chris Sander; Tatsuhiro Shibata; Terence P Speed; Lincoln D Stein; Joshua M Stuart; Jon W Teague; Yasushi Totoki; Tatsuhiko Tsunoda; Alfonso Valencia; David A Wheeler; Honglong Wu; Shancen Zhao; Guangyu Zhou; Lincoln D Stein; Roderic Guigó; Tim J Hubbard; Yann Joly; Steven M Jones; Arek Kasprzyk; Mark Lathrop; Nuria López-Bigas; B F Francis Ouellette; Paul T Spellman; Jon W Teague; Gilles Thomas; Alfonso Valencia; Teruhiko Yoshida; Karen L Kennedy; Myles Axton; Stephanie O M Dyke; P Andrew Futreal; Daniela S Gerhard; Chris Gunter; Mark Guyer; Thomas J Hudson; John D McPherson; Linda J Miller; Brad Ozenberger; Kenna M Shaw; Arek Kasprzyk; Lincoln D Stein; Junjun Zhang; Syed A Haider; Jianxin Wang; Christina K Yung; Anthony Cros; Anthony Cross; Yong Liang; Saravanamuttu Gnaneshan; Jonathan Guberman; Jack Hsu; Martin Bobrow; Don R C Chalmers; Karl W Hasel; Yann Joly; Terry S H Kaan; Karen L Kennedy; Bartha M Knoppers; William W Lowrance; Tohru Masui; Pilar Nicolás; Emmanuelle Rial-Sebbag; Laura Lyman Rodriguez; Catherine Vergely; Teruhiko Yoshida; Sean M Grimmond; Andrew V Biankin; David D L Bowtell; Nicole Cloonan; Anna deFazio; James R Eshleman; Dariush Etemadmoghadam; Brooke B Gardiner; Brooke A Gardiner; James G Kench; Aldo Scarpa; Robert L Sutherland; Margaret A Tempero; Nicola J Waddell; Peter J Wilson; John D McPherson; Steve Gallinger; Ming-Sound Tsao; Patricia A Shaw; Gloria M Petersen; Debabrata Mukhopadhyay; Lynda Chin; Ronald A DePinho; Sarah Thayer; Lakshmi Muthuswamy; Kamran Shazand; Timothy Beck; Michelle Sam; Lee Timms; Vanessa Ballin; Youyong Lu; Jiafu Ji; Xiuqing Zhang; Feng Chen; Xueda Hu; Guangyu Zhou; Qi Yang; Geng Tian; Lianhai Zhang; Xiaofang Xing; Xianghong Li; Zhenggang Zhu; Yingyan Yu; Jun Yu; Huanming Yang; Mark Lathrop; Jörg Tost; Paul Brennan; Ivana Holcatova; David Zaridze; Alvis Brazma; Lars Egevard; Egor Prokhortchouk; Rosamonde Elizabeth Banks; Mathias Uhlén; Anne Cambon-Thomsen; Juris Viksna; Fredrik Ponten; Konstantin Skryabin; Michael R Stratton; P Andrew Futreal; Ewan Birney; Ake Borg; Anne-Lise Børresen-Dale; Carlos Caldas; John A Foekens; Sancha Martin; Jorge S Reis-Filho; Andrea L Richardson; Christos Sotiriou; Hendrik G Stunnenberg; Giles Thoms; Marc van de Vijver; Laura van't Veer; Fabien Calvo; Daniel Birnbaum; Hélène Blanche; Pascal Boucher; Sandrine Boyault; Christian Chabannon; Ivo Gut; Jocelyne D Masson-Jacquemier; Mark Lathrop; Iris Pauporté; Xavier Pivot; Anne Vincent-Salomon; Eric Tabone; Charles Theillet; Gilles Thomas; Jörg Tost; Isabelle Treilleux; Fabien Calvo; Paulette Bioulac-Sage; Bruno Clément; Thomas Decaens; Françoise Degos; Dominique Franco; Ivo Gut; Marta Gut; Simon Heath; Mark Lathrop; Didier Samuel; Gilles Thomas; Jessica Zucman-Rossi; Peter Lichter; Roland Eils; Benedikt Brors; Jan O Korbel; Andrey Korshunov; Pablo Landgraf; Hans Lehrach; Stefan Pfister; Bernhard Radlwimmer; Guido Reifenberger; Michael D Taylor; Christof von Kalle; Partha P Majumder; Rajiv Sarin; T S Rao; M K Bhan; Aldo Scarpa; Paolo Pederzoli; Rita A Lawlor; Massimo Delledonne; Alberto Bardelli; Andrew V Biankin; Sean M Grimmond; Thomas Gress; David Klimstra; Giuseppe Zamboni; Tatsuhiro Shibata; Yusuke Nakamura; Hidewaki Nakagawa; Jun Kusada; Tatsuhiko Tsunoda; Satoru Miyano; Hiroyuki Aburatani; Kazuto Kato; Akihiro Fujimoto; Teruhiko Yoshida; Elias Campo; Carlos López-Otín; Xavier Estivill; Roderic Guigó; Silvia de Sanjosé; Miguel A Piris; Emili Montserrat; Marcos González-Díaz; Xose S Puente; Pedro Jares; Alfonso Valencia; Heinz Himmelbauer; Heinz Himmelbaue; Victor Quesada; Silvia Bea; Michael R Stratton; P Andrew Futreal; Peter J Campbell; Anne Vincent-Salomon; Andrea L Richardson; Jorge S Reis-Filho; Marc van de Vijver; Gilles Thomas; Jocelyne D Masson-Jacquemier; Samuel Aparicio; Ake Borg; Anne-Lise Børresen-Dale; Carlos Caldas; John A Foekens; Hendrik G Stunnenberg; Laura van't Veer; Douglas F Easton; Paul T Spellman; Sancha Martin; Anna D Barker; Lynda Chin; Francis S Collins; Carolyn C Compton; Martin L Ferguson; Daniela S Gerhard; Gad Getz; Chris Gunter; Alan Guttmacher; Mark Guyer; D Neil Hayes; Eric S Lander; Brad Ozenberger; Robert Penny; Jane Peterson; Chris Sander; Kenna M Shaw; Terence P Speed; Paul T Spellman; Joseph G Vockley; David A Wheeler; Richard K Wilson; Thomas J Hudson; Lynda Chin; Bartha M Knoppers; Eric S Lander; Peter Lichter; Lincoln D Stein; Michael R Stratton; Warwick Anderson; Anna D Barker; Cindy Bell; Martin Bobrow; Wylie Burke; Francis S Collins; Carolyn C Compton; Ronald A DePinho; Douglas F Easton; P Andrew Futreal; Daniela S Gerhard; Anthony R Green; Mark Guyer; Stanley R Hamilton; Tim J Hubbard; Olli P Kallioniemi; Karen L Kennedy; Timothy J Ley; Edison T Liu; Youyong Lu; Partha Majumder; Marco Marra; Brad Ozenberger; Jane Peterson; Alan J Schafer; Paul T Spellman; Hendrik G Stunnenberg; Brandon J Wainwright; Richard K Wilson; Huanming Yang
Journal:  Nature       Date:  2010-04-15       Impact factor: 49.962

4.  DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Authors:  Timothy J Ley; Elaine R Mardis; Li Ding; Bob Fulton; Michael D McLellan; Ken Chen; David Dooling; Brian H Dunford-Shore; Sean McGrath; Matthew Hickenbotham; Lisa Cook; Rachel Abbott; David E Larson; Dan C Koboldt; Craig Pohl; Scott Smith; Amy Hawkins; Scott Abbott; Devin Locke; Ladeana W Hillier; Tracie Miner; Lucinda Fulton; Vincent Magrini; Todd Wylie; Jarret Glasscock; Joshua Conyers; Nathan Sander; Xiaoqi Shi; John R Osborne; Patrick Minx; David Gordon; Asif Chinwalla; Yu Zhao; Rhonda E Ries; Jacqueline E Payton; Peter Westervelt; Michael H Tomasson; Mark Watson; Jack Baty; Jennifer Ivanovich; Sharon Heath; William D Shannon; Rakesh Nagarajan; Matthew J Walter; Daniel C Link; Timothy A Graubert; John F DiPersio; Richard K Wilson
Journal:  Nature       Date:  2008-11-06       Impact factor: 49.962

5.  Comprehensive genomic characterization of squamous cell lung cancers.

Authors: 
Journal:  Nature       Date:  2012-09-09       Impact factor: 49.962

  5 in total
  11 in total

1.  Teaching 'big data' analysis to young immunologists.

Authors:  Joachim L Schultze
Journal:  Nat Immunol       Date:  2015-09       Impact factor: 25.606

2.  Association Analysis of Driver Gene-Related Genetic Variants Identified Novel Lung Cancer Susceptibility Loci with 20,871 Lung Cancer Cases and 15,971 Controls.

Authors:  Yuzhuo Wang; Olga Y Gorlova; Ivan P Gorlov; Meng Zhu; Juncheng Dai; Demetrius Albanes; Stephen Lam; Adonina Tardon; Chu Chen; Gary E Goodman; Stig E Bojesen; Maria Teresa Landi; Mattias Johansson; Angela Risch; Heunz-Erich Wichmann; Heike Bickeboller; David C Christiani; Gad Rennert; Susanne M Arnold; Paul Brennan; John K Field; Sanjay Shete; Loïc Le Marchand; Olle Melander; Hans Brunnstrom; Geoffrey Liu; Rayjean J Hung; Angeline S Andrew; Lambertus A Kiemeney; Shanbeh Zienolddiny; Kjell Grankvist; Mikael Johansson; Neil E Caporaso; Penella J Woll; Philip Lazarus; Matthew B Schabath; Melinda C Aldrich; Victoria L Stevens; Hongxia Ma; Guangfu Jin; Zhibin Hu; Christopher I Amos; Hongbing Shen
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2020-04-10       Impact factor: 4.254

3.  Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors.

Authors:  Candace D Middlebrooks; A Rouf Banday; Konichi Matsuda; Krizia-Ivana Udquim; Olusegun O Onabajo; Ashley Paquin; Jonine D Figueroa; Bin Zhu; Stella Koutros; Michiaki Kubo; Taro Shuin; Neal D Freedman; Manolis Kogevinas; Nuria Malats; Stephen J Chanock; Montserrat Garcia-Closas; Debra T Silverman; Nathaniel Rothman; Ludmila Prokunina-Olsson
Journal:  Nat Genet       Date:  2016-09-19       Impact factor: 38.330

4.  Metabolic Stress-Induced Phosphorylation of KAP1 Ser473 Blocks Mitochondrial Fusion in Breast Cancer Cells.

Authors:  Chun-Ting Cheng; Ching-Ying Kuo; Ching Ouyang; Chien-Feng Li; Yiyin Chung; David C Chan; Hsing-Jien Kung; David K Ann
Journal:  Cancer Res       Date:  2016-06-30       Impact factor: 12.701

5.  The UCSC Cancer Genomics Browser: update 2015.

Authors:  Mary Goldman; Brian Craft; Teresa Swatloski; Melissa Cline; Olena Morozova; Mark Diekhans; David Haussler; Jingchun Zhu
Journal:  Nucleic Acids Res       Date:  2014-11-11       Impact factor: 19.160

6.  APOBEC-mediated mutagenesis in urothelial carcinoma is associated with improved survival, mutations in DNA damage response genes, and immune response.

Authors:  Alexander P Glaser; Damiano Fantini; Yiduo Wang; Yanni Yu; Kalen J Rimar; Joseph R Podojil; Stephen D Miller; Joshua J Meeks
Journal:  Oncotarget       Date:  2017-12-16

7.  Methylome analysis of extreme chemoresponsive patients identifies novel markers of platinum sensitivity in high-grade serous ovarian cancer.

Authors:  Tushar Tomar; Nicolette G Alkema; Leroy Schreuder; Gert Jan Meersma; Tim de Meyer; Wim van Criekinge; Harry G Klip; Heidi Fiegl; Els van Nieuwenhuysen; Ignace Vergote; Martin Widschwendter; Ed Schuuring; Ate G J van der Zee; Steven de Jong; G Bea A Wisman
Journal:  BMC Med       Date:  2017-06-23       Impact factor: 8.775

8.  Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples.

Authors:  Thomas A Peterson; Iris Ivy M Gauran; Junyong Park; DoHwan Park; Maricel G Kann
Journal:  PLoS Comput Biol       Date:  2017-04-20       Impact factor: 4.475

9.  Antibody targeting of B7-H4 enhances the immune response in urothelial carcinoma.

Authors:  Joseph R Podojil; Alexander P Glaser; Dylan Baker; Elise T Courtois; Damiano Fantini; Yanni Yu; Valerie Eaton; Santhosh Sivajothi; Mingyi Chiang; Arighno Das; Kimberly A McLaughlin; Paul Robson; Stephen D Miller; Joshua J Meeks
Journal:  Oncoimmunology       Date:  2020-04-16       Impact factor: 8.110

Review 10.  Databases and tools for constructing signal transduction networks in cancer.

Authors:  Seungyoon Nam
Journal:  BMB Rep       Date:  2017-01       Impact factor: 4.778

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