Literature DB >> 27418159

Crowdsourcing biomedical research: leveraging communities as innovation engines.

Julio Saez-Rodriguez1,2, James C Costello3, Stephen H Friend4, Michael R Kellen4, Lara Mangravite4, Pablo Meyer5, Thea Norman4, Gustavo Stolovitzky5,6.   

Abstract

The generation of large-scale biomedical data is creating unprecedented opportunities for basic and translational science. Typically, the data producers perform initial analyses, but it is very likely that the most informative methods may reside with other groups. Crowdsourcing the analysis of complex and massive data has emerged as a framework to find robust methodologies. When the crowdsourcing is done in the form of collaborative scientific competitions, known as Challenges, the validation of the methods is inherently addressed. Challenges also encourage open innovation, create collaborative communities to solve diverse and important biomedical problems, and foster the creation and dissemination of well-curated data repositories.

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Year:  2016        PMID: 27418159      PMCID: PMC5918684          DOI: 10.1038/nrg.2016.69

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  83 in total

1.  Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.

Authors:  Michael F Berger; Anthony A Philippakis; Aaron M Qureshi; Fangxue S He; Preston W Estep; Martha L Bulyk
Journal:  Nat Biotechnol       Date:  2006-09-24       Impact factor: 54.908

2.  Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.

Authors:  Rhiju Das; Bin Qian; Srivatsan Raman; Robert Vernon; James Thompson; Philip Bradley; Sagar Khare; Michael D Tyka; Divya Bhat; Dylan Chivian; David E Kim; William H Sheffler; Lars Malmström; Andrew M Wollacott; Chu Wang; Ingemar Andre; David Baker
Journal:  Proteins       Date:  2007

Review 3.  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

4.  Scientific rigor through videogames.

Authors:  Adrien Treuille; Rhiju Das
Journal:  Trends Biochem Sci       Date:  2014-10-06       Impact factor: 13.807

Review 5.  Mitigating risk in academic preclinical drug discovery.

Authors:  Jayme L Dahlin; James Inglese; Michael A Walters
Journal:  Nat Rev Drug Discov       Date:  2015-04       Impact factor: 84.694

6.  Global optimization of somatic variant identification in cancer genomes with a global community challenge.

Authors:  Paul C Boutros; Adam A Margolin; Joshua M Stuart; Adam D Ewing; Kyle Ellrott; Thea C Norman; Kristen K Dang; Yin Hu; Michael R Kellen; Christine Suver; J Christopher Bare; Lincoln D Stein; Paul T Spellman; Gustavo Stolovitzky; Stephen H Friend
Journal:  Nat Genet       Date:  2014-04       Impact factor: 38.330

7.  The Prostate Cancer DREAM Challenge: A Community-Wide Effort to Use Open Clinical Trial Data for the Quantitative Prediction of Outcomes in Metastatic Prostate Cancer.

Authors:  Kald Abdallah; Charles Hugh-Jones; Thea Norman; Stephen Friend; Gustavo Stolovitzky
Journal:  Oncologist       Date:  2015-03-16

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

9.  A community effort to assess and improve drug sensitivity prediction algorithms.

Authors:  James C Costello; Laura M Heiser; Elisabeth Georgii; Mehmet Gönen; Michael P Menden; Nicholas J Wang; Mukesh Bansal; Muhammad Ammad-ud-din; Petteri Hintsanen; Suleiman A Khan; John-Patrick Mpindi; Olli Kallioniemi; Antti Honkela; Tero Aittokallio; Krister Wennerberg; James J Collins; Dan Gallahan; Dinah Singer; Julio Saez-Rodriguez; Samuel Kaski; Joe W Gray; Gustavo Stolovitzky
Journal:  Nat Biotechnol       Date:  2014-06-01       Impact factor: 54.908

10.  Big Data: Astronomical or Genomical?

Authors:  Zachary D Stephens; Skylar Y Lee; Faraz Faghri; Roy H Campbell; Chengxiang Zhai; Miles J Efron; Ravishankar Iyer; Michael C Schatz; Saurabh Sinha; Gene E Robinson
Journal:  PLoS Biol       Date:  2015-07-07       Impact factor: 8.029

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  50 in total

1.  EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS.

Authors:  Ariella Cohain; Aparna A Divaraniya; Kuixi Zhu; Joseph R Scarpa; Andrew Kasarskis; Jun Zhu; Rui Chang; Joel T Dudley; Eric E Schadt
Journal:  Pac Symp Biocomput       Date:  2017

2.  Scientific Discovery Games for Biomedical Research.

Authors:  Rhiju Das; Benjamin Keep; Peter Washington; Ingmar H Riedel-Kruse
Journal:  Annu Rev Biomed Data Sci       Date:  2019-07

3.  The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies.

Authors:  Jennifer El Diaz; Mehmet Eren Ahsen; Thomas Schaffter; Xintong Chen; Ronald B Realubit; Charles Karan; Andrea Califano; Bojan Losic; Gustavo Stolovitzky
Journal:  Elife       Date:  2020-09-18       Impact factor: 8.140

4.  Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.

Authors:  Daniel K Wells; Marit M van Buuren; Kristen K Dang; Vanessa M Hubbard-Lucey; Kathleen C F Sheehan; Katie M Campbell; Andrew Lamb; Jeffrey P Ward; John Sidney; Ana B Blazquez; Andrew J Rech; Jesse M Zaretsky; Begonya Comin-Anduix; Alphonsus H C Ng; William Chour; Thomas V Yu; Hira Rizvi; Jia M Chen; Patrice Manning; Gabriela M Steiner; Xengie C Doan; Taha Merghoub; Justin Guinney; Adam Kolom; Cheryl Selinsky; Antoni Ribas; Matthew D Hellmann; Nir Hacohen; Alessandro Sette; James R Heath; Nina Bhardwaj; Fred Ramsdell; Robert D Schreiber; Ton N Schumacher; Pia Kvistborg; Nadine A Defranoux
Journal:  Cell       Date:  2020-10-09       Impact factor: 41.582

5.  Blind prediction of deleterious amino acid variations with SNPs&GO.

Authors:  Emidio Capriotti; Pier Luigi Martelli; Piero Fariselli; Rita Casadio
Journal:  Hum Mutat       Date:  2017-05-02       Impact factor: 4.878

6.  Collaborating with Undergraduates To Contribute to Biochemistry Community Resources.

Authors:  Kathryn L Haas; Jennifer M Heemstra; Marnix H Medema; Louise K Charkoudian
Journal:  Biochemistry       Date:  2017-11-02       Impact factor: 3.162

7.  Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.

Authors:  Justin Guinney; Tao Wang; Teemu D Laajala; Kimberly Kanigel Winner; J Christopher Bare; Elias Chaibub Neto; Suleiman A Khan; Gopal Peddinti; Antti Airola; Tapio Pahikkala; Tuomas Mirtti; Thomas Yu; Brian M Bot; Liji Shen; Kald Abdallah; Thea Norman; Stephen Friend; Gustavo Stolovitzky; Howard Soule; Christopher J Sweeney; Charles J Ryan; Howard I Scher; Oliver Sartor; Yang Xie; Tero Aittokallio; Fang Liz Zhou; James C Costello
Journal:  Lancet Oncol       Date:  2016-11-16       Impact factor: 41.316

8.  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

9.  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

Review 10.  How Machine Learning Will Transform Biomedicine.

Authors:  Jeremy Goecks; Vahid Jalili; Laura M Heiser; Joe W Gray
Journal:  Cell       Date:  2020-04-02       Impact factor: 41.582

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