3
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Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D. Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res 2019; 46:D1181-D1189. [PMID: 29165610 PMCID: PMC5753211 DOI: 10.1093/nar/gkx1111] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/25/2017] [Indexed: 12/24/2022] Open
Abstract
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.
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Affiliation(s)
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Joshua C Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Michael Campbell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Matthew J Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Young Koung Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Division of Biological Sciences and Institute for Basic Science, Wonkwang University, Iksan 54538, Korea
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joseph Mulvaney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - James Thomason
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Daniel M Bolser
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Guy Naamati
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Electra Tapanari
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Nuno Fonseca
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Laura Huerta
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Haider Iqbal
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Maria Keays
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | | | - Amy Tang
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Antonio Fabregat
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Peter D'Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Joel Weiser
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
| | - Lincoln D Stein
- Adaptive Oncology Program, Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada
| | - Robert Petryszak
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Irene Papatheodorou
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Paul J Kersey
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Patti Lockhart
- American Society of Plant Biologists, 15501 Monona Drive, Rockville, MD 20855-2768, USA
| | - Crispin Taylor
- American Society of Plant Biologists, 15501 Monona Drive, Rockville, MD 20855-2768, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
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4
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Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 2018; 36:566-569. [PMID: 29979655 PMCID: PMC6870991 DOI: 10.1038/nbt.4163] [Citation(s) in RCA: 676] [Impact Index Per Article: 112.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rick L Stevens
- Computer Science Department and Computation Institute, University of Chicago, Chicago, Illinois, USA.,Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Sergei Maslov
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Paramvir Dehal
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Fernando Perez
- Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Berkeley Institute for Data Science, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Shane Canon
- National Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael W Sneddon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew L Henderson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William J Riehl
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dan Murphy-Olson
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Stephen Y Chan
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Roy T Kamimura
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Meghan M Drake
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Thomas S Brettin
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Elizabeth M Glass
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dylan Chivian
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dan Gunter
- Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Benjamin H Allen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jason Baumohl
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aaron A Best
- Department of Biology, Hope College, Holland, Michigan, USA
| | - Ben Bowen
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Christopher C Bun
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jer-Ming Chia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Ric Colasanti
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Neal Conrad
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - James J Davis
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, Michigan, USA
| | - Scott Devoid
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Emily Dietrich
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Inna Dubchak
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Janaka N Edirisinghe
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.,Computation Institute, University of Chicago, Chicago, Illinois, USA
| | - Gang Fang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - José P Faria
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Paul M Frybarger
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Wolfgang Gerlach
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Annette Greiner
- National Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - James Gurtowski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Holly L Haun
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Fei He
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Rashmi Jain
- Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcin P Joachimiak
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kevin P Keegan
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Shinnosuke Kondo
- Department of Computer Science, Hope College, Holland, Michigan, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Miriam L Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Folker Meyer
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Marissa Mills
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Taeyun Oh
- Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Gary J Olsen
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert Olson
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Bruce Parrello
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sarah S Poon
- Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Gavin A Price
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Srividya Ramakrishnan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Pamela C Ronald
- Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Samuel M D Seaver
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Maulik Shukla
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Roman A Sutormin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mustafa H Syed
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - James Thomason
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Nathan L Tintle
- Department of Mathematics, Hope College, Holland, Michigan, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Daifeng Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Fangfang Xia
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Hyunseung Yoo
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Shinjae Yoo
- Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA
| | - Dantong Yu
- Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
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