Literature DB >> 23117078

Breakthroughs in genomics data integration for predicting clinical outcome.

Yves A Lussier, Haiquan Li.   

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Year:  2012        PMID: 23117078      PMCID: PMC3632294          DOI: 10.1016/j.jbi.2012.10.003

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


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  22 in total

Review 1.  Next-generation genomics: an integrative approach.

Authors:  R David Hawkins; Gary C Hon; Bing Ren
Journal:  Nat Rev Genet       Date:  2010-07       Impact factor: 53.242

2.  Gene prioritization through genomic data fusion.

Authors:  Stein Aerts; Diether Lambrechts; Sunit Maity; Peter Van Loo; Bert Coessens; Frederik De Smet; Leon-Charles Tranchevent; Bart De Moor; Peter Marynen; Bassem Hassan; Peter Carmeliet; Yves Moreau
Journal:  Nat Biotechnol       Date:  2006-05       Impact factor: 54.908

3.  Genetic architecture of transcript-level variation in humans.

Authors:  Shiwei Duan; R Stephanie Huang; Wei Zhang; Wasim K Bleibel; Cheryl A Roe; Tyson A Clark; Tina X Chen; Anthony C Schweitzer; John E Blume; Nancy J Cox; M Eileen Dolan
Journal:  Am J Hum Genet       Date:  2008-04-24       Impact factor: 11.025

4.  Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.

Authors:  Vessela N Kristensen; Charles J Vaske; Josie Ursini-Siegel; Peter Van Loo; Silje H Nordgard; Ravi Sachidanandam; Therese Sørlie; Fredrik Wärnberg; Vilde D Haakensen; Åslaug Helland; Bjørn Naume; Charles M Perou; David Haussler; Olga G Troyanskaya; Anne-Lise Børresen-Dale
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-09       Impact factor: 11.205

5.  MicroRNA expression profiles classify human cancers.

Authors:  Jun Lu; Gad Getz; Eric A Miska; Ezequiel Alvarez-Saavedra; Justin Lamb; David Peck; Alejandro Sweet-Cordero; Benjamin L Ebert; Raymond H Mak; Adolfo A Ferrando; James R Downing; Tyler Jacks; H Robert Horvitz; Todd R Golub
Journal:  Nature       Date:  2005-06-09       Impact factor: 49.962

6.  Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.

Authors:  Charles J Vaske; Stephen C Benz; J Zachary Sanborn; Dent Earl; Christopher Szeto; Jingchun Zhu; David Haussler; Joshua M Stuart
Journal:  Bioinformatics       Date:  2010-06-15       Impact factor: 6.937

7.  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

8.  Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.

Authors:  Shihua Zhang; Chun-Chi Liu; Wenyuan Li; Hui Shen; Peter W Laird; Xianghong Jasmine Zhou
Journal:  Nucleic Acids Res       Date:  2012-08-08       Impact factor: 16.971

9.  Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles.

Authors:  Parminder K Mankoo; Ronglai Shen; Nikolaus Schultz; Douglas A Levine; Chris Sander
Journal:  PLoS One       Date:  2011-11-03       Impact factor: 3.240

10.  Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer.

Authors:  Meng Li; Curt Balch; John S Montgomery; Mikyoung Jeong; Jae Hoon Chung; Pearlly Yan; Tim H M Huang; Sun Kim; Kenneth P Nephew
Journal:  BMC Med Genomics       Date:  2009-06-08       Impact factor: 3.063

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  10 in total

1.  Predicting censored survival data based on the interactions between meta-dimensional omics data in breast cancer.

Authors:  Dokyoon Kim; Ruowang Li; Scott M Dudek; Marylyn D Ritchie
Journal:  J Biomed Inform       Date:  2015-06-03       Impact factor: 6.317

2.  Incorporating inter-relationships between different levels of genomic data into cancer clinical outcome prediction.

Authors:  Dokyoon Kim; Hyunjung Shin; Kyung-Ah Sohn; Anurag Verma; Marylyn D Ritchie; Ju Han Kim
Journal:  Methods       Date:  2014-02-18       Impact factor: 3.608

3.  A Novel Attention-Mechanism Based Cox Survival Model by Exploiting Pan-Cancer Empirical Genomic Information.

Authors:  Xiangyu Meng; Xun Wang; Xudong Zhang; Chaogang Zhang; Zhiyuan Zhang; Kuijie Zhang; Shudong Wang
Journal:  Cells       Date:  2022-04-22       Impact factor: 7.666

4.  Identification of epigenetic interactions between miRNA and DNA methylation associated with gene expression as potential prognostic markers in bladder cancer.

Authors:  Manu Shivakumar; Younghee Lee; Lisa Bang; Tullika Garg; Kyung-Ah Sohn; Dokyoon Kim
Journal:  BMC Med Genomics       Date:  2017-05-24       Impact factor: 3.063

5.  Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction.

Authors:  Dokyoon Kim; Je-Gun Joung; Kyung-Ah Sohn; Hyunjung Shin; Yu Rang Park; Marylyn D Ritchie; Ju Han Kim
Journal:  J Am Med Inform Assoc       Date:  2014-07-07       Impact factor: 4.497

6.  Intra-relation reconstruction from inter-relation: miRNA to gene expression.

Authors:  Dokyoon Kim; Hyunjung Shin; Je-Gun Joung; Su-Yeon Lee; Ju Han Kim
Journal:  BMC Syst Biol       Date:  2013-10-16

7.  Relative impact of multi-layered genomic data on gene expression phenotypes in serous ovarian tumors.

Authors:  Kyung-Ah Sohn; Dokyoon Kim; Jaehyun Lim; Ju Han Kim
Journal:  BMC Syst Biol       Date:  2013-12-13

8.  Improved survival analysis by learning shared genomic information from pan-cancer data.

Authors:  Sunkyu Kim; Keonwoo Kim; Junseok Choe; Inggeol Lee; Jaewoo Kang
Journal:  Bioinformatics       Date:  2020-07-01       Impact factor: 6.937

9.  Min-redundancy and max-relevance multi-view feature selection for predicting ovarian cancer survival using multi-omics data.

Authors:  Yasser El-Manzalawy; Tsung-Yu Hsieh; Manu Shivakumar; Dokyoon Kim; Vasant Honavar
Journal:  BMC Med Genomics       Date:  2018-09-14       Impact factor: 3.063

Review 10.  On fusion methods for knowledge discovery from multi-omics datasets.

Authors:  Edwin Baldwin; Jiali Han; Wenting Luo; Jin Zhou; Lingling An; Jian Liu; Hao Helen Zhang; Haiquan Li
Journal:  Comput Struct Biotechnol J       Date:  2020-03-05       Impact factor: 7.271

  10 in total

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