Literature DB >> 21904331

Verification of systems biology research in the age of collaborative competition.

Pablo Meyer1, Leonidas G Alexopoulos, Thomas Bonk, Andrea Califano, Carolyn R Cho, Alberto de la Fuente, David de Graaf, Alexander J Hartemink, Julia Hoeng, Nikolai V Ivanov, Heinz Koeppl, Rune Linding, Daniel Marbach, Raquel Norel, Manuel C Peitsch, J Jeremy Rice, Ajay Royyuru, Frank Schacherer, Joerg Sprengel, Katrin Stolle, Dennis Vitkup, Gustavo Stolovitzky.   

Abstract

Mesh：

Year:  2011        PMID： 21904331     DOI： 10.1038/nbt.1968

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  21 in total

1.  Systematic discovery of in vivo phosphorylation networks.

Authors:  Rune Linding; Lars Juhl Jensen; Gerard J Ostheimer; Marcel A T M van Vugt; Claus Jørgensen; Ioana M Miron; Francesca Diella; Karen Colwill; Lorne Taylor; Kelly Elder; Pavel Metalnikov; Vivian Nguyen; Adrian Pasculescu; Jing Jin; Jin Gyoon Park; Leona D Samson; James R Woodgett; Robert B Russell; Peer Bork; Michael B Yaffe; Tony Pawson
Journal:  Cell       Date:  2007-06-14       Impact factor: 41.582

Review 2.  Genome-wide association studies for complex traits: consensus, uncertainty and challenges.

Authors:  Mark I McCarthy; Gonçalo R Abecasis; Lon R Cardon; David B Goldstein; Julian Little; John P A Ioannidis; Joel N Hirschhorn
Journal:  Nat Rev Genet       Date:  2008-05       Impact factor: 53.242

Review 3.  Network-based drugs and biomarkers.

Authors:  Janine T Erler; Rune Linding
Journal:  J Pathol       Date:  2010-01       Impact factor: 7.996

Review 4.  Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference.

Authors:  Gustavo Stolovitzky; Don Monroe; Andrea Califano
Journal:  Ann N Y Acad Sci       Date:  2007-10-09       Impact factor: 5.691

5.  Peer review: Trial by Twitter.

Authors:  Apoorva Mandavilli
Journal:  Nature       Date:  2011-01-20       Impact factor: 49.962

6.  Retraction.

Authors:  Paola Sebastiani; Nadia Solovieff; Annibale Puca; Stephen W Hartley; Efthymia Melista; Stacy Andersen; Daniel A Dworkis; Jemma B Wilk; Richard H Myers; Martin H Steinberg; Monty Montano; Clinton T Baldwin; Thomas T Perls
Journal:  Science       Date:  2011-07-22       Impact factor: 47.728

7.  Predicting relapse in patients with medulloblastoma by integrating evidence from clinical and genomic features.

Authors:  Pablo Tamayo; Yoon-Jae Cho; Aviad Tsherniak; Heidi Greulich; Lauren Ambrogio; Netteke Schouten-van Meeteren; Tianni Zhou; Allen Buxton; Marcel Kool; Matthew Meyerson; Scott L Pomeroy; Jill P Mesirov
Journal:  J Clin Oncol       Date:  2011-02-28       Impact factor: 44.544

8.  Towards a rigorous assessment of systems biology models: the DREAM3 challenges.

Authors:  Robert J Prill; Daniel Marbach; Julio Saez-Rodriguez; Peter K Sorger; Leonidas G Alexopoulos; Xiaowei Xue; Neil D Clarke; Gregoire Altan-Bonnet; Gustavo Stolovitzky
Journal:  PLoS One       Date:  2010-02-23       Impact factor: 3.240

Review 9.  What the papers say: text mining for genomics and systems biology.

Authors:  Nathan Harmston; Wendy Filsell; Michael P H Stumpf
Journal:  Hum Genomics       Date:  2010-10       Impact factor: 4.639

10.  Automatic policing of biochemical annotations using genomic correlations.

Authors:  Tzu-Lin Hsiao; Olga Revelles; Lifeng Chen; Uwe Sauer; Dennis Vitkup
Journal:  Nat Chem Biol       Date:  2009-11-22       Impact factor: 15.040
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  33 in total

1.  Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.

Authors:  Adi L Tarca; Mario Lauria; Michael Unger; Erhan Bilal; Stephanie Boue; Kushal Kumar Dey; Julia Hoeng; Heinz Koeppl; Florian Martin; Pablo Meyer; Preetam Nandy; Raquel Norel; Manuel Peitsch; Jeremy J Rice; Roberto Romero; Gustavo Stolovitzky; Marja Talikka; Yang Xiang; Christoph Zechner
Journal:  Bioinformatics       Date:  2013-08-20       Impact factor: 6.937

Review 2.  Crowdsourcing biomedical research: leveraging communities as innovation engines.

Authors:  Julio Saez-Rodriguez; James C Costello; Stephen H Friend; Michael R Kellen; Lara Mangravite; Pablo Meyer; Thea Norman; Gustavo Stolovitzky
Journal:  Nat Rev Genet       Date:  2016-07-15       Impact factor: 53.242

3.  How to preserve the original mission of research in the omics era?

Authors:  Srđan Kesić
Journal:  EMBO Rep       Date:  2019-12-10       Impact factor: 8.807

Review 4.  Future Challenges in Plant Systems Biology.

Authors:  Mikaël Lucas
Journal:  Methods Mol Biol       Date:  2022

5.  Human blood gene signature as a marker for smoking exposure: computational approaches of the top ranked teams in the sbv IMPROVER Systems Toxicology challenge.

Authors:  Adi L Tarca; Xiaofeng Gong; Roberto Romero; Wenxin Yang; Zhongqu Duan; Hao Yang; Chengfang Zhang; Peixuan Wang
Journal:  Comput Toxicol       Date:  2017-07-18

6.  Species translatable blood gene signature as a marker of exposure to smoking: computational approaches of the top ranked teams in the sbv IMPROVER Systems Toxicology challenge.

Authors:  Ömer Sinan Saraç; Rahul Kumar; Sandeep Kumar Dhanda; Ali Tuğrul Balcı; İsmail Bilgen; Roberto Romero; Adi L Tarca
Journal:  Comput Toxicol       Date:  2017-04-28

7.  Enhancement of COPD biological networks using a web-based collaboration interface.

Authors:  Stephanie Boue; Brett Fields; Julia Hoeng; Jennifer Park; Manuel C Peitsch; Walter K Schlage; Marja Talikka; Ilona Binenbaum; Vladimir Bondarenko; Oleg V Bulgakov; Vera Cherkasova; Norberto Diaz-Diaz; Larisa Fedorova; Svetlana Guryanova; Julia Guzova; Galina Igorevna Koroleva; Elena Kozhemyakina; Rahul Kumar; Noa Lavid; Qingxian Lu; Swapna Menon; Yael Ouliel; Samantha C Peterson; Alexander Prokhorov; Edward Sanders; Sarah Schrier; Golan Schwaitzer Neta; Irina Shvydchenko; Aravind Tallam; Gema Villa-Fombuena; John Wu; Ilya Yudkevich; Mariya Zelikman
Journal:  F1000Res       Date:  2015-01-29

8.  Navigating cancer network attractors for tumor-specific therapy.

Authors:  Pau Creixell; Erwin M Schoof; Janine T Erler; Rune Linding
Journal:  Nat Biotechnol       Date:  2012-09       Impact factor: 54.908

Review 9.  Industrial methodology for process verification in research (IMPROVER): toward systems biology verification.

Authors:  Pablo Meyer; Julia Hoeng; J Jeremy Rice; Raquel Norel; Jörg Sprengel; Katrin Stolle; Thomas Bonk; Stephanie Corthesy; Ajay Royyuru; Manuel C Peitsch; Gustavo Stolovitzky
Journal:  Bioinformatics       Date:  2012-03-14       Impact factor: 6.937

10.  Improving breast cancer survival analysis through competition-based multidimensional modeling.

Authors:  Erhan Bilal; Janusz Dutkowski; Justin Guinney; In Sock Jang; Benjamin A Logsdon; Gaurav Pandey; Benjamin A Sauerwine; Yishai Shimoni; Hans Kristian Moen Vollan; Brigham H Mecham; Oscar M Rueda; Jorg Tost; Christina Curtis; Mariano J Alvarez; Vessela N Kristensen; Samuel Aparicio; Anne-Lise Børresen-Dale; Carlos Caldas; Andrea Califano; Stephen H Friend; Trey Ideker; Eric E Schadt; Gustavo A Stolovitzky; Adam A Margolin
Journal:  PLoS Comput Biol       Date:  2013-05-09       Impact factor: 4.475
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