content/00.front-matter.md
{##
This file contains a Jinja2 front-matter template that adds version and authorship information.
Changing the Jinja2 templates in this file may cause incompatibility with Manubot updates.
Pandoc automatically inserts title from metadata.yaml, so it is not included in this template.
##}
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[
[]{.fas .fa-info-circle .fa-lg} **Updated Content**<br>
A published version of this manuscript from 04 April 2018, termed version 1.0, is available at <https://doi.org/10.1098/rsif.2017.0387>.
New content added after that publication date is being collected in a version 2.0.
[GitHub issue #959](https://github.com/greenelab/deep-review/issues/959) lists the new version 2.0 authors and sections.
]{.banner .lightred}
{## Template to insert build date and source ##}
<small><em>
This manuscript
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([permalink]({{manubot.ci_source.artifact_url}}))
{% elif manubot.html_url_versioned is defined -%}
([permalink]({{manubot.html_url_versioned}}))
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was automatically generated
{% if manubot.ci_source is defined -%}
from [{{manubot.ci_source.repo_slug}}@{{manubot.ci_source.commit | truncate(length=7, end='', leeway=0)}}](https://github.com/{{manubot.ci_source.repo_slug}}/tree/{{manubot.ci_source.commit}})
{% endif -%}
on {{manubot.date}}.
</em></small>
## Authors
### Version 2.0 authors
{% for author in manubot.authors %}
{% if author.v2 -%}
{% if author.orcid is defined -%}
[{height="11px" width="11px"}](https://orcid.org/{{author.orcid}})
{%- endif %}
{{author.name}}<sup>{% for number in author.affiliation_numbers %}2.{{number}}{%- if not loop.last -%},{%- endif -%}{% endfor %}⚄{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}</sup>
{%- if not loop.last -%}, {%- endif -%}
{%- endif -%}
{% endfor %},
[The Version 1.0 Deep Review Authors](#version-1.0-authors)
<sup>⚄</sup> --- Author order for version 2.0 is currently randomized [with each new build](https://github.com/greenelab/deep-review/pull/997).<br>
<sup>†</sup> --- To whom correspondence should be addressed: gitter@biostat.wisc.edu (A.G.) and greenescientist@gmail.com (C.S.G.)
<small>
{% for affiliation in manubot.affiliations %}
2.{{affiliation.affiliation_number}}. {{affiliation.affiliation}}<br>
{%- endfor %}
</small>
### Version 1.0 authors
[{height="11px" width="11px"}](https://orcid.org/0000-0002-5577-3516)
Travers Ching<sup>1.1,☯</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-3012-7446)
Daniel S. Himmelstein<sup>1.2</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-6700-1468)
Brett K. Beaulieu-Jones<sup>1.3</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-4563-3226)
Alexandr A. Kalinin<sup>1.4</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-4992-2623)
Brian T. Do<sup>1.5</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-0503-9348)
Gregory P. Way<sup>1.2</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-8362-100X)
Enrico Ferrero<sup>1.8</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-1126-1479)
Paul-Michael Agapow<sup>1.9</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-0539-630X)
Michael Zietz<sup>1.2</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-4517-1562)
Michael M. Hoffman<sup>1.10,1.11,1.12</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-1871-6846)
Wei Xie<sup>1.13</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-1763-5750)
Gail L. Rosen<sup>1.14</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0001-8690-9554)
Benjamin J. Lengerich<sup>1.15</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-1633-5780)
Johnny Israeli<sup>1.16</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-0811-0944)
Jack Lanchantin<sup>1.17</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-0568-298X)
Stephen Woloszynek<sup>1.14</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-1555-8261)
Anne E. Carpenter<sup>1.18</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-6443-4671)
Avanti Shrikumar<sup>1.19</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0001-7111-4839)
Jinbo Xu<sup>1.20</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-3877-0433)
Evan M. Cofer<sup>1.21,1.22</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-7762-1089)
Christopher A. Lavender<sup>1.23</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-3247-6487)
Srinivas C. Turaga<sup>1.24</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0001-8655-8109)
Amr M. Alexandari<sup>1.19</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0001-9998-916X)
Zhiyong Lu<sup>1.25</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-3332-9307)
David J. Harris<sup>1.26</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0001-8931-9461)
Dave DeCaprio<sup>1.27</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-5796-7453)
Yanjun Qi<sup>1.17</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-3084-2287)
Anshul Kundaje<sup>1.19,1.28</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0001-9309-8331)
Yifan Peng<sup>1.25</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0001-6681-9754)
Laura K. Wiley<sup>1.29</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0001-8008-0546)
Marwin H.S. Segler<sup>1.30</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-1400-3398)
Simina M. Boca<sup>1.31</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-2191-0778)
S. Joshua Swamidass<sup>1.32</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0003-1349-4030)
Austin Huang<sup>1.33</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0002-5324-9833)
Anthony Gitter<sup>1.34,1.35,†</sup>,
[{height="11px" width="11px"}](https://orcid.org/0000-0001-8713-9213)
Casey S. Greene<sup>1.2,†</sup>
<sup>☯</sup> --- Author order was determined with a randomized algorithm<br>
<sup>†</sup> --- To whom correspondence should be addressed: gitter@biostat.wisc.edu (A.G.) and greenescientist@gmail.com (C.S.G.)
<small>
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
</small>