diff --git a/content/00.front-matter.md b/content/00.front-matter.md
index f208b9f4..b111f900 100644
--- a/content/00.front-matter.md
+++ b/content/00.front-matter.md
@@ -37,33 +37,136 @@ on {{manubot.date}}.
{% if author.orcid is defined -%}
[{height="11px" width="11px"}](https://orcid.org/{{author.orcid}})
{%- endif %}
- {{author.name}}{{author.affiliation_numbers | join(',')}}♠{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}
+ {{author.name}}{% for number in author.affiliation_numbers %}2.{{number}}{%- if not loop.last -%},{%- endif -%}{% endfor %}♠{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}
{%- if not loop.last -%}, {%- endif -%}
{%- endif -%}
-{% endfor %}
+{% endfor %},
+[The Version 1.0 Deep Review Authors](#version-1.0-authors)
-♠ --- Author order for version 2.0 is currently arbitrary.
+♠ --- Author order for version 2.0 is currently randomized [with each new build](https://github.com/greenelab/deep-review/pull/997).
† --- To whom correspondence should be addressed: greenescientist@gmail.com (C.S.G.)
+
+
+{% for affiliation in manubot.affiliations %}
+2.{{affiliation.affiliation_number}}. {{affiliation.affiliation}}
+{%- endfor %}
+
+
+
### Version 1.0 Authors
-{% for author in manubot.authors %}
- {% if author.v1 -%}
- {% if author.orcid is defined -%}
- [{height="11px" width="11px"}](https://orcid.org/{{author.orcid}})
- {%- endif %}
- {{author.name}}{{author.affiliation_numbers | join(',')}}{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}
- {%- if not loop.last -%}, {%- endif -%}
- {%- endif -%}
-{% endfor %}
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-5577-3516)
+ Travers Ching1.1,☯,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-3012-7446)
+ Daniel S. Himmelstein1.2,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-6700-1468)
+ Brett K. Beaulieu-Jones1.3,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-4563-3226)
+ Alexandr A. Kalinin1.4,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-4992-2623)
+ Brian T. Do1.5,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-0503-9348)
+ Gregory P. Way1.2,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-8362-100X)
+ Enrico Ferrero1.8,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-1126-1479)
+ Paul-Michael Agapow1.9,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-0539-630X)
+ Michael Zietz1.2,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-4517-1562)
+ Michael M. Hoffman1.10,1.11,1.12,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-1871-6846)
+ Wei Xie1.13,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-1763-5750)
+ Gail L. Rosen1.14,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0001-8690-9554)
+ Benjamin J. Lengerich1.15,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-1633-5780)
+ Johnny Israeli1.16,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-0811-0944)
+ Jack Lanchantin1.17,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-0568-298X)
+ Stephen Woloszynek1.14,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-1555-8261)
+ Anne E. Carpenter1.18,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-6443-4671)
+ Avanti Shrikumar1.19,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0001-7111-4839)
+ Jinbo Xu1.20,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-3877-0433)
+ Evan M. Cofer1.21,1.22,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-7762-1089)
+ Christopher A. Lavender1.23,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-3247-6487)
+ Srinivas C. Turaga1.24,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0001-8655-8109)
+ Amr M. Alexandari1.19,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0001-9998-916X)
+ Zhiyong Lu1.25,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-3332-9307)
+ David J. Harris1.26,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0001-8931-9461)
+ Dave DeCaprio1.27,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-5796-7453)
+ Yanjun Qi1.17,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-3084-2287)
+ Anshul Kundaje1.19,1.28,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0001-9309-8331)
+ Yifan Peng1.25,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0001-6681-9754)
+ Laura K. Wiley1.29,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0001-8008-0546)
+ Marwin H.S. Segler1.30,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-1400-3398)
+ Simina M. Boca1.31,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-2191-0778)
+ S. Joshua Swamidass1.32,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0003-1349-4030)
+ Austin Huang1.33,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0002-5324-9833)
+ Anthony Gitter1.34,1.35,†,
+ [{height="11px" width="11px"}](https://orcid.org/0000-0001-8713-9213)
+ Casey S. Greene1.2,†
☯ --- Author order was determined with a randomized algorithm
† --- To whom correspondence should be addressed: gitter@biostat.wisc.edu (A.G.) and greenescientist@gmail.com (C.S.G.)
-{% for affiliation in manubot.affiliations %}
-{{affiliation.affiliation_number}}. {{affiliation.affiliation}}
-{%- endfor %}
-
+1.1. Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI
+1.2. Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
+1.3. Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
+1.4. Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI
+1.5. Harvard Medical School, Boston, MA
+1.6. Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH
+1.7. Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH
+1.8. Computational Biology and Stats, Target Sciences, GlaxoSmithKline, Stevenage, United Kingdom
+1.9. Data Science Institute, Imperial College London, London, United Kingdom
+1.10. Princess Margaret Cancer Centre, Toronto, ON, Canada
+1.11. Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
+1.12. Department of Computer Science, University of Toronto, Toronto, ON, Canada
+1.13. Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN
+1.14. Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA
+1.15. Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
+1.16. Biophysics Program, Stanford University, Stanford, CA
+1.17. Department of Computer Science, University of Virginia, Charlottesville, VA
+1.18. Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA
+1.19. Department of Computer Science, Stanford University, Stanford, CA
+1.20. Toyota Technological Institute at Chicago, Chicago, IL
+1.21. Department of Computer Science, Trinity University, San Antonio, TX
+1.22. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
+1.23. Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
+1.24. Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA
+1.25. National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD
+1.26. Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
+1.27. ClosedLoop.ai, Austin, TX
+1.28. Department of Genetics, Stanford University, Stanford, CA
+1.29. Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO
+1.30. Institute of Organic Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
+1.31. Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
+1.32. Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO
+1.33. Department of Medicine, Brown University, Providence, RI
+1.34. Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
+1.35. Morgridge Institute for Research, Madison, WI
diff --git a/content/08.methods.md b/content/08.methods.md
index c8a2ff30..96160f5d 100644
--- a/content/08.methods.md
+++ b/content/08.methods.md
@@ -31,12 +31,20 @@ The ability to irrefutably prove manuscript existence at a past time could be im
#### Version 2.0
-We continued using the open repository on the GitHub version control platform ([`greenelab/deep-review`](https://github.com/greenelab/deep-review)) [@url:https://github.com/greenelab/deep-review], which was established to write the Version 1.0 manuscript.
-{% for v2, authors in manubot.authors|groupby('v2') %}
- {% if v2|length %}
-{{ v2 }}: {% for author in authors %}{{author.name }}{%- if not loop.last -%}, {%- endif -%}{% endfor %}.
- {% endif %}
-{% endfor %}
+We continued using the open repository on the GitHub version control platform ([`greenelab/deep-review`](https://github.com/greenelab/deep-review)) [@url:https://github.com/greenelab/deep-review], which was established to write the Version 1.0 manuscript. {% for v2, authors in manubot.authors|groupby('v2') %}{% if v2|length %}{{ v2 }}: {% for author in authors %}{{author.name }}{%- if not loop.last -%}, {%- endif -%}{% endfor %}. {% endif %}{% endfor %}
+
+##### Version 2.0 Competing Interests
+
+|Author|Competing Interests|Last Reviewed|
+|---|---|---|{% for author in manubot.authors %}
+|{{author.name}}|{{author.coi.string}}|{{author.coi.lastapproved}}|{% endfor %}
+
+##### Version 2.0 Funding Statement
+
+We acknowledge funding from the Gordon and Betty Moore Foundation award GBMF4552 (C.S.G. and D.S.H.);
+the National Institutes of Health awards R01HG010067 (C.S.G. and D.S.H.), R01CA237170 (C.S.G), T32LM012204 (A.J.T.), R01CA216265 (B.C.C.);
+the Burroughs Wellcome Fund Big Data in the Life Sciences training grant at Dartmouth (J.L.L,);
+and the Dartmouth College Neukom Institute for Computational Science CompX award (B.C.C.).
#### Version 1.0
@@ -48,27 +56,54 @@ drafted the manuscript or provided substantial critical revisions;
approved the final manuscript draft; and agreed to be accountable in all aspects of the work.
Individuals who did not contribute in all of these ways, but who did participate, are acknowledged below.
We grouped authors into the following four classes of approximately equal contributions and randomly ordered authors within each contribution class.
-{% for v1, authors in manubot.authors|groupby('v1') %}
- {% if v1|length %}
-{{ v1 }}:{% for author in authors %} {{author.name }}{%- if not loop.last -%}, {%- endif -%}{% endfor %}.
- {% endif %}
-{% endfor %}
+Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion: Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M. Hoffman.
+Drafted one or more sub-sections: Wei Xie, Gail L. Rosen, Benjamin J. Lengerich, Johnny Israeli, Jack Lanchantin, Stephen Woloszynek, Anne E. Carpenter, Avanti Shrikumar, Jinbo Xu, Evan M. Cofer, Christopher A. Lavender, Srinivas C. Turaga, Amr M. Alexandari, Zhiyong Lu.
+Drafted sub-sections, edited the manuscript, reviewed pull requests, and coordinated co-authors: Anthony Gitter, Casey S. Greene.
+Revised specific sub-sections or supervised drafting one or more sub-sections: David J. Harris, Dave DeCaprio, Yanjun Qi, Anshul Kundaje, Yifan Peng, Laura K. Wiley, Marwin H.S. Segler, Simina M. Boca, S. Joshua Swamidass, Austin Huang.
-### Competing interests
+##### Version 1.0 Competing interests
-|Author|Competing Interests|Last Reviewed|
-|---|---|---|{% for author in manubot.authors %}
-|{{author.name}}|{{author.coi.string}}|{{author.coi.lastapproved}}|{% endfor %}
-### Acknowledgements
-
-We gratefully acknowledge Christof Angermueller, Kumardeep Chaudhary, Gökcen Eraslan, Mikael Huss, Bharath Ramsundar and Xun Zhu for their discussion of the manuscript and reviewed papers on GitHub.
-We would like to thank Aaron Sheldon, who contributed text but did not formally approve the manuscript.
-We would like to thank Anna Greene for a careful proofreading of the manuscript in advance of the first submission.
-We would like to thank Sebastian Raschka for clarifying edits to the abstract and introduction.
-We would like to thank Robert Gieseke, Ruibang Luo, Stephen Ra, Sourav Singh, and GitHub user snikumbh for correcting typos, formatting, and references.
-
-### Funding statement
+|Author|Competing Interests|Last Reviewed|
+|---|---|---|
+|Travers Ching|None|2017-05-26|
+|Daniel S. Himmelstein|None|2017-05-26|
+|Brett K. Beaulieu-Jones|None|2017-05-26|
+|Alexandr A. Kalinin|None|2017-05-26|
+|Brian T. Do|None|2017-05-26|
+|Gregory P. Way|None|2017-05-26|
+|Enrico Ferrero|Full-time employee of GlaxoSmithKline.|2017-05-26|
+|Paul-Michael Agapow|None|2017-05-26|
+|Michael Zietz|None|2017-05-26|
+|Michael M. Hoffman|None|2017-05-26|
+|Wei Xie|None|2017-05-26|
+|Gail L. Rosen|None|2017-05-26|
+|Benjamin J. Lengerich|None|2017-05-26|
+|Johnny Israeli|None|2017-05-26|
+|Jack Lanchantin|None|2017-05-26|
+|Stephen Woloszynek|None|2017-05-26|
+|Anne E. Carpenter|None|2017-05-26|
+|Avanti Shrikumar|None|2017-05-26|
+|Jinbo Xu|None|2017-05-26|
+|Evan M. Cofer|None|2017-05-26|
+|Christopher A. Lavender|None|2017-05-26|
+|Srinivas C. Turaga|None|2017-05-26|
+|Amr M. Alexandari|None|2017-05-26|
+|Zhiyong Lu|None|2017-05-26|
+|David J. Harris|None|2017-05-26|
+|Dave DeCaprio|None|2017-05-26|
+|Yanjun Qi|None|2017-05-26|
+|Anshul Kundaje|Advisory Board of Deep Genomics Inc.|2017-05-26|
+|Yifan Peng|None|2017-05-26|
+|Laura K. Wiley|None|2017-05-26|
+|Marwin H.S. Segler|None|2017-05-26|
+|Simina M. Boca|None|2017-05-26|
+|S. Joshua Swamidass|None|2017-05-26|
+|Austin Huang|None|2017-05-26|
+|Anthony Gitter|None|2017-05-26|
+|Casey S. Greene|None|2017-05-26|
+
+##### Version 1.0 Funding Statement
We acknowledge funding from the Gordon and Betty Moore Foundation awards GBMF4552 (C.S.G. and D.S.H.) and GBMF4563 (D.J.H.);
the Howard Hughes Medical Institute (S.C.T.);
@@ -77,3 +112,11 @@ the National Institutes of Health Intramural Research Program and National Libra
the National Science Foundation awards 1245632 (G.L.R.), 1531594 (E.M.C.), and 1564955 (J.X.);
the Natural Sciences and Engineering Research Council of Canada award RGPIN-2015-3948 (M.M.H.);
and the Roy and Diana Vagelos Scholars Program in the Molecular Life Sciences (M.Z.).
+
+### Acknowledgements
+
+We gratefully acknowledge Christof Angermueller, Kumardeep Chaudhary, Gökcen Eraslan, Mikael Huss, Bharath Ramsundar and Xun Zhu for their discussion of the manuscript and reviewed papers on GitHub.
+We would like to thank Aaron Sheldon, who contributed text but did not formally approve the manuscript.
+We would like to thank Anna Greene for a careful proofreading of the manuscript in advance of the first submission.
+We would like to thank Sebastian Raschka for clarifying edits to the abstract and introduction.
+We would like to thank Robert Gieseke, Ruibang Luo, Stephen Ra, Sourav Singh, and GitHub user snikumbh for correcting typos, formatting, and references.
diff --git a/content/metadata.yaml b/content/metadata.yaml
index 07063935..ed7a3040 100644
--- a/content/metadata.yaml
+++ b/content/metadata.yaml
@@ -11,65 +11,6 @@ keywords:
- manubot
lang: en-US
authors:
- - 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: "☯"
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- github: jlevy44
name: Joshua J. Levy
orcid: 0000-0001-8050-1291
@@ -106,376 +47,17 @@ authors:
coi:
string: "None"
lastapproved: !!str 2020-03-07
- - 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
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "Full-time employee of GlaxoSmithKline."
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - github: jisraeli
- name: Johnny Israeli
- orcid: 0000-0003-1633-5780
- email: jisraeli@stanford.edu
- affiliations:
- - Biophysics Program, Stanford University, Stanford, CA
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - github: jacklanchantin
- name: Jack Lanchantin
- orcid: 0000-0003-0811-0944
- email: jjl5sw@virginia.edu
- affiliations:
- - Department of Computer Science, University of Virginia, Charlottesville, VA
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - github: AvantiShri
- name: Avanti Shrikumar
- orcid: 0000-0002-6443-4671
- email: avanti@stanford.edu
- affiliations:
- - Department of Computer Science, Stanford University, Stanford, CA
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Drafted one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - github: DaveDeCaprio
- name: Dave DeCaprio
- orcid: 0000-0001-8931-9461
- email: daved@alum.mit.edu
- affiliations:
- - ClosedLoop.ai, Austin, TX
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - github: qiyanjun
- name: Yanjun Qi
- orcid: 0000-0002-5796-7453
- email: yq2h@virginia.edu
- affiliations:
- - Department of Computer Science, University of Virginia, Charlottesville, VA
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "Advisory Board of Deep Genomics Inc."
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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
- v1: "Revised specific sub-sections or supervised drafting one or more sub-sections"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- - 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: "†"
- v1: "Drafted sub-sections, edited the manuscript, reviewed pull requests, and coordinated co-authors"
- v2: ""
- coi:
- string: "None"
- lastapproved: !!str 2017-05-26
- 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
+ - Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA
+ funders: GBMF GBMF4552, NIH R01HG010067 & R01CA237170, ALSF CCDL
symbol_str: "†"
v1: "Drafted sub-sections, edited the manuscript, reviewed pull requests, and coordinated co-authors"
v2: "Drafted sub-sections, edited the manuscript, reviewed pull requests, and coordinated co-authors"
coi:
string: "None"
- lastapproved: !!str 2020-03-09
+ lastapproved: !!str 2020-03-10