metadata.yaml

---
title: Opportunities and obstacles for deep learning in biology and medicine
keywords:
  - deep learning
  - review
  - precision medicine
  - genomics
  - machine learning
  - neural networks
  - collaborative
  - manubot
lang: en-US
author_info:
  - github: traversc
    name: Travers Ching
    orcid: 0000-0002-5577-3516
    email: traversc@gmail.com
    affiliations:
      - Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI
    symbol_str: "☯"
  - github: dhimmel
    name: Daniel S. Himmelstein
    orcid: 0000-0002-3012-7446
    email: daniel.himmelstein@gmail.com
    affiliations:
      - Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
    funders: GBMF GBMF4552
  - github: brettbj
    name: Brett K. Beaulieu-Jones
    orcid: 0000-0002-6700-1468
    email: brettbe@upenn.edu
    affiliations:
      - Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
    funders: NIH R01AI116794
  - github: alxndrkalinin
    name: Alexandr A. Kalinin
    orcid: 0000-0003-4563-3226
    email: akalinin@umich.edu
    affiliations:
      - Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI
  - github: bdo311
    name: Brian T. Do
    orcid: 0000-0003-4992-2623
    email: brian_do@hms.harvard.edu
    affiliations:
      - Harvard Medical School, Boston, MA
    funders: NIH T32GM007753
  - github: gwaygenomics
    name: Gregory P. Way
    orcid: 0000-0002-0503-9348
    email: gregory.way@gmail.com
    affiliations:
      - Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
    funders: NIH T32HG000046
  - github: enricoferrero
    name: Enrico Ferrero
    orcid: 0000-0002-8362-100X
    email: enrico.x.ferrero@gsk.com
    affiliations:
      - Computational Biology and Stats, Target Sciences, GlaxoSmithKline, Stevenage, United Kingdom
  - github: agapow
    name: Paul-Michael Agapow
    orcid: 0000-0003-1126-1479
    email: p.agapow@imperial.ac.uk
    affiliations:
      - Data Science Institute, Imperial College London, London, United Kingdom
  - github: zietzm
    name: Michael Zietz
    initials: MZ
    orcid: 0000-0003-0539-630X
    email: zietz@sas.upenn.edu
    affiliations:
      - Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
    funders: Roy and Diana Vagelos Scholars Program in the Molecular Life Sciences
  - github: michaelmhoffman
    name: Michael M. Hoffman
    initials: MMH
    orcid: 0000-0002-4517-1562
    email: michael.hoffman@utoronto.ca
    affiliations:
      - Princess Margaret Cancer Centre, Toronto, ON, Canada
      - Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
      - Department of Computer Science, University of Toronto, Toronto, ON, Canada
    funders: NSERC RGPIN-2015-3948
  - github: xieconnect
    name: Wei Xie
    orcid: 0000-0002-1871-6846
    email: wei.xie@vanderbilt.edu
    affiliations:
      - Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN
  - github: gailrosen
    name: Gail L. Rosen
    orcid: 0000-0003-1763-5750
    email: gailr@ece.drexel.edu
    affiliations:
      - Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA
    funders: NSF 1245632
  - github: blengerich
    name: Benjamin J. Lengerich
    orcid: 0000-0001-8690-9554
    email: blengeri@cs.cmu.edu
    affiliations:
      - Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
  - github: jisraeli
    name: Johnny Israeli
    orcid: 0000-0003-1633-5780
    email: jisraeli@stanford.edu
    affiliations:
      - Biophysics Program, Stanford University, Stanford, CA
  - github: jacklanchantin
    name: Jack Lanchantin
    orcid: 0000-0003-0811-0944
    email: jjl5sw@virginia.edu
    affiliations:
      - Department of Computer Science, University of Virginia, Charlottesville, VA
  - github: sw1
    name: Stephen Woloszynek
    orcid: 0000-0003-0568-298X
    email: sw424@drexel.edu
    affiliations:
      - Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA
  - github: annecarpenter
    name: Anne E. Carpenter
    orcid: 0000-0003-1555-8261
    email: anne@broadinstitute.org
    affiliations:
      - Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA
    funders: NIH R01GM089652
  - github: AvantiShri
    name: Avanti Shrikumar
    orcid: 0000-0002-6443-4671
    email: avanti@stanford.edu
    affiliations:
      - Department of Computer Science, Stanford University, Stanford, CA
  - github: j3xugit
    name: Jinbo Xu
    orcid: 0000-0001-7111-4839
    email: jinboxu@gmail.com
    affiliations:
      - Toyota Technological Institute at Chicago, Chicago, IL
    funders: NIH R01GM089753, NSF 1564955
  - github: evancofer
    name: Evan M. Cofer
    orcid: 0000-0003-3877-0433
    email: ecofer@princeton.edu
    affiliations:
      - Department of Computer Science, Trinity University, San Antonio, TX
      - Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
    funders: NSF 1531594
  - github: lavenderca
    name: Christopher A. Lavender
    initials: CAL
    orcid: 0000-0002-7762-1089
    email: christopher.lavender@nih.gov
    affiliations:
      - Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
  - github: SriniTuraga
    name: Srinivas C. Turaga
    initials: SCT
    orcid: 0000-0003-3247-6487
    email: turagas@janelia.hhmi.org
    affiliations:
      - Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA
    funders: Howard Hughes Medical Institute
  - github: alexandari
    name: Amr M. Alexandari
    initials: AMA
    orcid: 0000-0001-8655-8109
    email: amr.alexandari@gmail.com
    affiliations:
      - Department of Computer Science, Stanford University, Stanford, CA
  - github: luzh2
    name: Zhiyong Lu
    initials: ZL
    orcid: 0000-0001-9998-916X
    email: zhiyong.lu@nih.gov
    affiliations:
      - National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD
    funders: National Institutes of Health Intramural Research Program and National Library of Medicine
  - github: davharris
    name: David J. Harris
    orcid: 0000-0003-3332-9307
    email: dave@harris-research.me
    affiliations:
      - Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
    funders: GBMF GBMF4563
  - github: DaveDeCaprio
    name: Dave DeCaprio
    orcid: 0000-0001-8931-9461
    email: daved@alum.mit.edu
    affiliations:
      - ClosedLoop.ai, Austin, TX
  - github: qiyanjun
    name: Yanjun Qi
    orcid: 0000-0002-5796-7453
    email: yq2h@virginia.edu
    affiliations:
      - Department of Computer Science, University of Virginia, Charlottesville, VA
  - github: akundaje
    name: Anshul Kundaje
    orcid: 0000-0003-3084-2287
    email: akundaje@stanford.edu
    affiliations:
      - Department of Genetics, Stanford University, Stanford, CA
      - Department of Computer Science, Stanford University, Stanford, CA
    funders: NIH DP2GM123485
  - github: yfpeng
    name: Yifan Peng
    orcid: 0000-0001-9309-8331
    email: yifan.peng@nih.gov
    affiliations:
      - National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD
    funders: National Institutes of Health Intramural Research Program and National Library of Medicine
  - github: laurakwiley
    name: Laura K. Wiley
    orcid: 0000-0001-6681-9754
    email: laura.wiley@ucdenver.edu
    affiliations:
      - Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO
  - github: mrwns
    name: Marwin H.S. Segler
    orcid: 0000-0001-8008-0546
    email: marwin.segler@uni-muenster.de
    affiliations:
      - Institute of Organic Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
  - github: SiminaB
    name: Simina M. Boca
    initials: SMB
    orcid: 0000-0002-1400-3398
    email: smb310@georgetown.edu
    affiliations:
      - Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
    funders: NIH R21CA220398, NIH P30CA051008
  - github: swamidass
    name: S. Joshua Swamidass
    initials: SJS
    orcid: 0000-0003-2191-0778
    email: swamidass@wustl.edu
    affiliations:
      - Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO
    funders: NIH R01LM012222, NIH R01LM012482
  - github: austinvhuang
    name: Austin Huang
    initials: AH
    orcid: 0000-0003-1349-4030
    email: austinh@alum.mit.edu
    affiliations:
      - Department of Medicine, Brown University, Providence, RI
  - github: agitter
    name: Anthony Gitter
    orcid: 0000-0002-5324-9833
    email: gitter@biostat.wisc.edu
    affiliations:
      - Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
      - Morgridge Institute for Research, Madison, WI
    funders: NIH U54AI117924
    symbol_str: "†"
  - github: cgreene
    name: Casey S. Greene
    orcid: 0000-0001-8713-9213
    email: greenescientist@gmail.com
    affiliations:
      - Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
    funders: GBMF GBMF4552
    symbol_str: "†"