Perspectives on ENCODE

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression 1 . The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

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Change history

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Acknowledgements

We thank S. Moore, E. Cahill, M. Kellis and J. Li for their assistance, and B. Wold for helpful comments. This work was supported by grants from the NIH: U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U41HG007234, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442.

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Authors and Affiliations

  1. Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA Nicholas J. Addleman, Jessika Adrian, Ulugbek K. Baymuradov, Anand Bhaskar, Nathan Boley, Lulu Cao, Hassan Chaib, Esther T. Chan, Songjie Chen, J. Michael Cherry, Timothy R. Dreszer, Idan Gabdank, Fabian Grubert, Nastaran Heidari, Jason A. Hilton, Benjamin C. Hitz, Lixia Jiang, Maya Kasowski, Trupti Kawli, Daniel Sunwook Kim, Anshul Kundaje, Jin Wook Lee, Yang I. Li, Yining Li, Shin Lin, Tejaswini Mishra, Anil M. Narasimha, Aditi K. Narayanan, Kathrina C. Onate, Jonathan K. Pritchard, Anil Raj, Lucia Ramirez, Denis N. Salins, Eilon Sharon, Minyi Shi, Teri Slifer, Cricket A. Sloan, Michael P. Snyder, Damek V. Spacek, Rohith Srivas, J. Seth Strattan, Forrest Y. Tanaka, Oana Ursu, Nathaniel K. Watson, Xinqiong Yang, Jie Zhai, Michael P. Snyder, Benjamin C. Hitz & J. Michael Cherry
  2. Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, USA Michael P. Snyder & Michael P. Snyder
  3. Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA Cassidy Danyko, Carrie A. Davis, Alexander Dobin, Thomas R. Gingeras, Alexandra Scavelli, Lei Hoon See, Chris Zaleski & Thomas R. Gingeras
  4. University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA Gregory R. Andrews, Tyler Borrman, Jason A. Brooks, Hao Chen, Shaimae I. Elhajjajy, Kaili Fan, Kevin Fortier, Yu Fu, Mingshi Gao, Jack Huey, Eugenio Mattei, Jill E. Moore, Nishigandha N. Phalke, Henry E. Pratt, Michael J. Purcaro, Thomas M. Reimonn, Shuo Shan, Junko Tsuji, Arjan G. van der Velde, Zhiping Weng, Taylor Young, Xiao-Ou Zhang, Jill E. Moore & Zhiping Weng
  5. Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai, China Lingling Cai, Shaliu Fu, Shuyu Hou, Xiangrui Li, Ying Li, Yan Liu, Aiping Lu, Qin Wang, Zhijie Wei, Zhiping Weng, Tianxiong Yu, Peng Zhang & Zhiping Weng
  6. Bioinformatics Program, Boston University, Boston, MA, USA Hao Chen, Arjan G. van der Velde, Zhiping Weng & Zhiping Weng
  7. Yale University, New Haven, CT, USA Declan Clarke, Timur Galeev, Mark B. Gerstein, Mengting Gu, Gamze Gursoy, Arif Harmanci, Sushant Kumar, Donghoon Lee, Jason Liu, Shaoke Lou, Fabio C. P. Navarro, Baikang Pei, Joel Rozowsky, Anurag Sethi, Cristina Sisu, Jinrui Xu, Koon-Kiu Yan, Jing Zhang & Mark B. Gerstein
  8. Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA Sora Chee, David U. Gorkin, Hui Huang, Samantha Kuan, Ah Young Lee, Bin Li, Sebastian Preissl, Bing Ren, Yin Shen, Yanxiao Zhang, Yuan Zhao & Bing Ren
  9. Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA David U. Gorkin, Bing Ren & Bing Ren
  10. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA Belinda M. Giardine, Ross C. Hardison, Cheryl A. Keller, Maria Long & Ross C. Hardison
  11. Altius Institute for Biomedical Sciences, Seattle, WA, USA Reyes Acosta, Daniel Bates, Michael Buckley, Andres Castillo, Daniel R. Chee, Morgan Diegel, Douglass Dunn, Alister P. W. Funnell, Grigorios Georgolopoulos, Jessica Halow, Eric Haugen, Sean Ibarrientos, Mineo Iwata, Audra Johnson, Rajinder Kaul, Tanya Kutyavin, John Lazar, Kristen Lee, Wouter Meuleman, Vivek Nandakumar, Patrick Navas, Jemma Nelson, Shane Neph, Fidencio Jun Neri, Andrew Nishida, Ericka Otterman, Alex Reynolds, Eric Rynes, Richard Sandstrom, Anthony Shafer, Kyle Siebenthall, John A. Stamatoyannopoulos, Sandra Stehling-Sun, Benjamin Van Biber, Jeff Vierstra, Shinny Vong, Hao Wang, Robert E. Welikson, Yongqi Yan & John A. Stamatoyannopoulos
  12. Department of Genome Sciences, University of Washington, Seattle, WA, USA William S. Noble, John A. Stamatoyannopoulos, Galip Gürkan Yardımcı & John A. Stamatoyannopoulos
  13. Department of Medicine, University of Washington, Seattle, WA, USA Rajinder Kaul, John A. Stamatoyannopoulos & John A. Stamatoyannopoulos
  14. Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA Michael O. Duff, Brenton R. Graveley, Sara Olson, Xintao Wei, Lijun Zhan & Brenton R. Graveley
  15. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA Omar Al Jammal, Eileen Cahill, Julie Coursen, Elise A. Feingold, Daniel A. Gilchrist, Samuel H. Moore, Preetha Nandi, Hannah Naughton, Briana Nuñez, Michael Pagan, Michael J. Pazin, Jeffery A. Schloss, Yekaterina Vaydylevich, Simona Volpi, Xiao-Qiao Zhou, Elise A. Feingold, Michael J. Pazin, Michael Pagan & Daniel A. Gilchrist
  16. Broad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA Bradley E. Bernstein & Bradley E. Bernstein
  17. Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA Surya B. Chhetri, Candice J. Coppola, Eric M. Mendenhall & Eric M. Mendenhall
  18. HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA Laurel A. Brandsmeier, Surya B. Chhetri, Candice J. Coppola, Rachel C. Evans, Shawn Levy, Mark Mackiewicz, Megan McEown, Sarah K. Meadows, Eric M. Mendenhall, Christopher L. Messer, Dianna E. Moore, Richard M. Myers, Amy R. Nesmith, J. Scott Newberry, Kimberly M. Newberry, Rosy Nguyen, E. Christopher Partridge, Florencia Pauli-Behn, Brian Roberts, Collin White, Eric M. Mendenhall & Richard M. Myers
  19. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK Bronwen Aken, If H. A. Barnes, Daniel Barrell, Ruth Bennett, Andrew Berry, Alexandra Bignell, Claire Davidson, Sarah Donaldson, Paul Flicek, Adam Frankish, Carlos Garcia Giron, Jose M. Gonzalez, Matthew Hardy, Toby Hunt, Osagie Izuogu, Michael Kay, Jane Loveland, Fergal J. Martin, Jonathan M. Mudge, Emily H. Perry, Marie-Marthe Suner, Daniel R. Zerbino, Daniel R. Zerbino, Adam Frankish & Paul Flicek
  20. The Broad Institute of Harvard and MIT, Cambridge, MA, USA Kristin G. Ardlie, Samantha Beik, Charles B. Epstein, Nina Farrell, Alon Goren, Meital Hatan, David Hendrickson, Shanna Hsu, Robbyn Issner, Irwin Jungreis, Manolis Kellis, Oren Ram, Joseph Raymond, Noam Shoresh, Danielle Tenen, Mia C. Uziel, Christopher M. Vockley & David Wine
  21. MGH, Boston, MA, USA Yotam Drier, Shawn Gillespie, Michael Mannstadt, Dylan Rausch, Miguel Rivera & Russell Ryan
  22. Dana-Farber Cancer Institute, Boston, MA, USA Mariateresa Fulciniti, Birgit Knoechel & Nikhil Munshi
  23. Harvard Medical School, Boston, MA, USA Qian Qin & Jonathan Scheiman
  24. Boston Children’s Hospital, Boston, MA, USA Birgit Knoechel
  25. Harvard University, Cambridge, MA, USA David Kelley
  26. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA Carles Boix, Jose Davila-Velderrain, Matthew D. Edwards, David K. Gifford, Yuchun Guo, Tatsunori B. Hashimoto, Lei Hou, Tommi Jaakkola, Irwin Jungreis, Manolis Kellis, Pouya Kheradpour, Yue Li, Dianbo Liu, Yaping Liu, Eva Maria Novoa, Charles W. O’Donnell, Yongjin Park, Tahin Syed, Maxim Wolf, Haoyang Zeng & Zhizhuo Zhang
  27. Max Planck Institute for Molecular Genetics, Department of Genome Regulation, Berlin, Germany Alex Meissner
  28. University of Colorado Boulder, Boulder, CO, USA John Rinn
  29. Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain Beatrice Borsari, Alessandra Breschi, Sarah Djebali, Roderic Guigó, Rory Johnson, Julien Lagarde, Dmitri D. Pervouchine, Barbara Uszczynska-Ratajczak & Anna Vlasova
  30. IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, U1220, CHU Purpan, CS60039, Toulouse, France Sarah Djebali
  31. Skolkovo Institute for Science and Technology, Moscow, Russia Dmitri D. Pervouchine
  32. Functional Genomics, Cold Spring Harbor Laboratory, Woodbury, NY, USA Jorg Drenkow
  33. Department of Clinical Research, University of Bern, Bern, Switzerland Rory Johnson
  34. International Institute of Molecular and Cell Biology, Warsaw, Poland Barbara Uszczynska-Ratajczak
  35. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA Cassandra Bazile, Christopher B. Burge, Daniel Dominguez, Abigail Hochman, Nicole J. Lambert, Tsultrim Palden & Amanda Su
  36. Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA Steven M. Blue, Keri Elkins, Chelsea Anne Gelboin-Burkhart, Thai B. Nguyen, Gabriel A. Pratt, Ines Rabano, Shashank Sathe, Rebecca Stanton, Balaji Sundararaman, Eric L. Van Nostrand, Ruth Wang, Brian A. Yee & Gene W. Yeo
  37. Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada Louis Philip Benoit Bouvrette, Neal A. L. Cody, Eric Lécuyer & Xiaofeng Wang
  38. Division of Experimental Medicine, McGill University, Quebec, Canada Louis Philip Benoit Bouvrette, Neal A. L. Cody, Eric Lécuyer & Xiaofeng Wang
  39. Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Quebec, Canada Louis Philip Benoit Bouvrette, Neal A. L. Cody, Eric Lécuyer & Xiaofeng Wang
  40. Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA Peter Freese
  41. Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, San Diego, CA, USA Jia-Yu Chen, Xiang-Dong Fu, Hairi Li & Rui Xiao
  42. Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA Daniel Savic
  43. Division of Biology, California Institute of Technology, Pasadena, CA, USA Henry Amrhein, Igor Antoshechkin, Gilberto DeSalvo, Katherine Fisher-Aylor, Peng He, Anthony Kirilusha, Georgi K. Marinov, Kenneth McCue, Diane E. Trout, Sean A. Upchurch, Jost Vielmetter, Brian A. Williams & Barbara Wold
  44. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA Stacie M. Anderson, David M. Bodine & Elisabeth F. Heuston
  45. Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA Timothy E. Reddy
  46. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA Anthony M. D’Ippolito & Timothy E. Reddy
  47. Biological Sciences, University of California, Irvine, Irvine, CA, USA Nicole El-Ali, Camden Jansen, Ali Mortazavi, Rabi Murad, Ricardo N. Ramirez & Weihua Zeng
  48. Salk Institute for Biological Studies, La Jolla, CA, USA Rosa G. Castanon, Huaming Chen, Joseph R. Ecker, Manoj Hariharan, Yupeng He, Graham McVicker & Joseph R. Nery
  49. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA Veena Afzal, Jennifer A. Akiyama, Iros Barozzi, Diane E. Dickel, Yoko Fukuda-Yuzawa, Tyler H. Garvin, Anne Harrington, Momoe Kato, Elizabeth Lee, Brandon J. Mannion, Catherine S. Novak, Len A. Pennacchio, Quan Pham, Ingrid Plajzer-Frick, Valentina Snetkova & Axel Visel
  50. Department of Chemistry and Biochemistry, Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA Bo Ding, Nan Li, Vu Ngo, Tung Nguyen, Mengchi Wang, Tao Wang, Wei Wang, John W. Whitaker, Andre Wildberg, Kai Zhang & Yun Zhu
  51. Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA Yin Shen
  52. Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA Feng Yue
  53. Penn State Health Milton S. Hershey Medical Center, Hershey, PA, USA Tingting Liu, Yanli Wang, Jie Xu, Hongbo Yang, Feng Yue, Bo Zhang & Lijun Zhang
  54. US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA Len A. Pennacchio & Axel Visel
  55. School of Natural Sciences, University of California, Merced, Merced, CA, USA Axel Visel
  56. Comparative Biochemistry Program, University of California, Berkeley, CA, USA Len A. Pennacchio
  57. Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA Joseph R. Ecker
  58. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA Alan P. Boyle
  59. Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA Alan P. Boyle
  60. Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Palo Alto, CA, USA Catharine Eastman
  61. Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada Andrew Emili, Jack F. Greenblatt, Hongbo Guo, Timothy R. Hughes, Ernest Radovani & Guoqing Zhong
  62. Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA Peng Gong, Jin Lian, Xinghua Pan, Quan Shen, Sherman M. Weissman & Jialing Zhang
  63. Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA Peggy J. Farnham, Yu Guo, Suhn K. Rhie & Heather N. Witt
  64. Department of Radiation Oncology, School of Medicine, Stanford University, Palo Alto, CA, USA Nastaran Heidari
  65. Department of Human Genetics, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA Cory Holgren, Nader Jameel, Madhura Kadaba, Mary Kasparian, Lijia Ma, Matthew G. Milton, Jennifer Moran, Dave Steffan, Matt Szynkarek, Dave Toffey & Alec Victorsen
  66. Division of General Surgery, Section of Transplant Surgery, School of Medicine, Washington University, St. Louis, MO, USA Yiing Lin
  67. Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China Xinghua Pan
  68. Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China Xinghua Pan
  69. Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Doug H. Phanstiel
  70. Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Doug H. Phanstiel
  71. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Jack F. Greenblatt, Rozita Razavi & Frank W. Schmitges
  72. School of Medicine, Jiangsu University, Zhenjiang, China Quan Shen
  73. Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada Timothy R. Hughes
  74. Tempus Labs, Chicago, IL, USA Kevin P. White
  75. Department of Medicine, University of Washington, Seattle, WA, USA George Stamatoyannopoulos
  76. Fred Hutchinson Cancer Research Center, Seattle, WA, USA M. A. Bender, Rachel Byron & Mark T. Groudine
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  78. University of Massachusetts Amherst, Amherst, MA, USA Yu Fu
  79. Institute for Infocomm Research, Singapore, Singapore Chuan Sheng Foo
  80. Simon Fraser University, Burnaby, British Columbia, Canada Maxwell W. Libbrecht
  81. Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA Peng Jiang, X. Shirley Liu, Clifford Meyer & Chongzhi Zang
  82. Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA Peng Jiang, X. Shirley Liu, Clifford Meyer & Chongzhi Zang
  83. Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA Chongzhi Zang
  84. Molecular Pathology Unit & Cancer Center, Boston, MA, USA Qian Qin
  85. Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA Mingxiang Teng
  86. Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA Amira A. Barkal
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  92. Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA Dongjun Chung
  93. Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA Emery H. Bresnick
  94. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA James E. Hayes & Robert J. Klein
  95. Wellcome Sanger Institute, Cambridge, UK Federico Abascal, Matthew Astley, Gemma Barson, Gloria Despacio-Reyes, Stephen Fitzgerald, Michael Gray, Ed Griffiths, Deepa Manthravadi, Steve Miller, Christoph Schlaffner, Gosia Trynka, Hendrik Weisser & James Wright
  96. Program in Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA Mark Carty, Alvaro Gonzalez, Christina S. Leslie, Yuheng Lu, Alexander R. Perez, Yuri Pritykin & Manu Setty
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  98. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA Michael A. Beer
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  100. University of California, Santa Cruz, Santa Cruz, CA, USA Joel Armstrong, Alden Deran, Mark Diekhans & Benedict Paten
  101. Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland Jacqueline Chrast, Anne-Maud Ferreira & Alexandre Reymond
  102. Centro Nacional de Investigaciones Cardiovasculares (CNIC) and CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain Iakes Ezkurdia & Jesus Vazquez
  103. Spanish National Cancer Research Centre (CNIO), Madrid, Spain Jose Manuel Rodriguez, Michael L. Tress & Alfonso Valencia
  104. Brunel University London, London, UK Cristina Sisu
  105. King’s College London, Guy’s Hospital, London, UK Tim J. Hubbard
  106. ELIXIR Hub, Wellcome Genome Campus, Cambridge, UK Jennifer L. Harrow
  107. Institute of Cancer Research, London, UK Jyoti S. Choudhary
  108. Department of Biological Science, Florida State University, Tallahassee, FL, USA Vishnu Dileep, David M. Gilbert, Juan Carlos Rivera-Mulia, Takayo Sasaki & Jared Zimmerman
  109. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA Juan Carlos Rivera-Mulia
  110. Center for Vaccines and Immunology University of Georgia, Athens, GA, USA Michael J. Kulik
  111. Center for Molecular Medicine and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA Stephen Dalton
  112. Gift of Life Donor Program, Philadelphia, PA, USA Richard D. Hasz
  113. American Society for Radiation Oncology, Arlington, VA, USA Judith C. Keen
  114. National Cancer Institute, National Institutes of Health, Bethesda, MD, USA Helen M. Moore
  115. Leidos Biomedical, Inc, Frederick, MD, USA Anna Smith
  116. National Disease Research Interchange (NDRI), Philadelphia, PA, USA Jeffrey A. Thomas
  117. 4407 Puller Drive, Kensington, MD, USA Peter Good
  118. Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA Rizi Ai
  119. Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA Shantao Li
  1. Michael P. Snyder