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Vivek Kumar
Researcher at Cold Spring Harbor Laboratory
Publications - 7
Citations - 1156
Vivek Kumar is an academic researcher from Cold Spring Harbor Laboratory. The author has contributed to research in topics: Comparative genomics & Ensembl. The author has an hindex of 5, co-authored 7 publications receiving 632 citations.
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Journal ArticleDOI
KBase: The United States Department of Energy Systems Biology Knowledgebase.
Adam P. Arkin,Adam P. Arkin,Robert W. Cottingham,Christopher S. Henry,Nomi L. Harris,Rick Stevens,Sergei Maslov,Paramvir S. Dehal,Doreen Ware,Fernando Perez,Shane Canon,Michael W. Sneddon,Matthew L. Henderson,William J. Riehl,Dan Murphy-Olson,Stephen Y. Chan,Roy T. Kamimura,Sunita Kumari,Meghan M Drake,Thomas Brettin,Elizabeth M. Glass,Dylan Chivian,Dan Gunter,David J. Weston,Benjamin H. Allen,Jason K. Baumohl,Aaron A. Best,Benjamin P. Bowen,Steven E. Brenner,Christopher Bun,John-Marc Chandonia,Jer Ming Chia,R. L. Colasanti,Neal Conrad,James J. Davis,Brian H. Davison,Matthew DeJongh,Scott Devoid,Emily M. Dietrich,Inna Dubchak,Janaka N. Edirisinghe,Janaka N. Edirisinghe,Gang Fang,José P. Faria,Paul M. Frybarger,Wolfgang Gerlach,Mark Gerstein,Annette Greiner,James Gurtowski,Holly L. Haun,Fei He,Rashmi Jain,Rashmi Jain,Marcin P. Joachimiak,Kevin P. Keegan,Shinnosuke Kondo,Vivek Kumar,Miriam Land,Folker Meyer,Mark Mills,Pavel S. Novichkov,Taeyun Oh,Taeyun Oh,Gary J. Olsen,Robert Olson,Bruce Parrello,Shiran Pasternak,Erik Pearson,Sarah S. Poon,Gavin Price,Srividya Ramakrishnan,Priya Ranjan,Priya Ranjan,Pamela C. Ronald,Pamela C. Ronald,Michael C. Schatz,Samuel M. D. Seaver,Maulik Shukla,Roman A. Sutormin,Mustafa H Syed,James Thomason,Nathan L. Tintle,Daifeng Wang,Fangfang Xia,Hyunseung Yoo,Shinjae Yoo,Dantong Yu +86 more
TL;DR: Author(s): Arkin, Adam P; Cottingham, Robert W; Henry, Christopher S; Harris, Nomi L; Stevens, Rick L; Maslov, Sergei; Dehal, Paramvir; Ware, Doreen; Perez, Fernando; Canon, Shane; Sneddon, Michael W; Henderson, Matthew L; Riehl, William J; Murphy-Olson, Dan; Chan, Stephen Y; Kamimura, Roy T.
Journal ArticleDOI
Gramene 2018: unifying comparative genomics and pathway resources for plant research.
Marcela K. Tello-Ruiz,Sushma Naithani,Joshua C. Stein,Parul Gupta,Michael S. Campbell,Andrew Olson,Sharon Wei,Justin Preece,Matthew Geniza,Yinping Jiao,Young Koung Lee,Young Koung Lee,Bo Wang,Joseph Mulvaney,Kapeel Chougule,Justin Elser,Noor Al-Bader,Sunita Kumari,James Thomason,Vivek Kumar,Dan Bolser,Guy Naamati,Electra Tapanari,Nuno A. Fonseca,Laura Huerta,Haider Iqbal,Maria Keays,Alfonso Muñoz-Pomer Fuentes,Y. Amy Tang,Antonio Fabregat,Peter D'Eustachio,Joel Weiser,Lincoln D. Stein,Robert Petryszak,Irene Papatheodorou,Paul J. Kersey,Patti Lockhart,Crispin B. Taylor,Pankaj Jaiswal,Doreen Ware,Doreen Ware +40 more
TL;DR: Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks and 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.
Journal ArticleDOI
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.
Andrew D. Yates,James E. Allen,Ridwan M Amode,Andrey G Azov,Matthieu Barba,Andrés Becerra,Jyothish Bhai,Lahcen I. Campbell,Manuel Carbajo Martinez,Marc Chakiachvili,Kapeel Chougule,Mikkel B. Christensen,Bruno Contreras-Moreira,Alayne Cuzick,Luca Da Rin Fioretto,Paul Davis,Nishadi De Silva,Stavros Diamantakis,Sarah Dyer,Justin Elser,Carla Valeria Filippi,Carla Valeria Filippi,Carla Valeria Filippi,Astrid Gall,Dionysios Grigoriadis,Cristina Guijarro-Clarke,Parul Gupta,Kim E. Hammond-Kosack,Kevin L. Howe,Pankaj Jaiswal,Vinay Kaikala,Vivek Kumar,Sunita Kumari,Nick Langridge,Tuan Le,Manuel Luypaert,Gareth Maslen,Thomas Maurel,Benjamin Moore,Matthieu Muffato,Aleena Mushtaq,Guy Naamati,Sushma Naithani,Andrew Olson,Anne Parker,Michael Paulini,Helder Pedro,Emily Perry,Justin Preece,Mark Quinton-Tulloch,Faye H. Rodgers,Marc Rosello,Magali Ruffier,James Seager,Vasily Sitnik,Michal Szpak,John Tate,Marcela K. Tello-Ruiz,Stephen J. Trevanion,Martin Urban,Doreen Ware,Doreen Ware,Sharon Wei,Gary Williams,Andrea Winterbottom,Magdalena Zarowiecki,Robert D. Finn,Paul Flicek +67 more
TL;DR: Ensembl Genomes as discussed by the authors provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensemblgenomes.org).
Journal ArticleDOI
Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing.
TL;DR: SMS has emerged as advantageous for comprehensive genome annotation including identification of novel genes/isoforms, long non-coding RNAs and fusion transcripts, and its diverse applications in various biological studies are provided.
Journal ArticleDOI
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
Marcela K. Tello-Ruiz,Sushma Naithani,Parul Gupta,Andrew Olson,Sharon Wei,Justin Preece,Yinping Jiao,Bo Wang,Kapeel Chougule,Priyanka Garg,Justin Elser,Sunita Kumari,Vivek Kumar,Bruno Contreras-Moreira,Guy Naamati,Nancy George,Justin Cook,Dan Bolser,Peter D'Eustachio,Lincoln Stein,Lincoln Stein,Amit Gupta,Weijia Xu,Jennifer Regala,Jennifer Regala,Irene Papatheodorou,Paul J. Kersey,Paul J. Kersey,Paul Flicek,Crispin B. Taylor,Pankaj Jaiswal,Doreen Ware,Doreen Ware +32 more
TL;DR: Gramene trains plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and paths in the Plant Reactome.