Supratim Mukherjee
Joint Genome Institute
52 Papers
50 Citations
Supratim Mukherjee is an academic researcher from Joint Genome Institute. The author has contributed to research in topics: Biology & Medicine. The author has an hindex of 11, co-authored 39 publications. Previous affiliations of Supratim Mukherjee include United States Department of Energy & University of Massachusetts Amherst.
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Papers
A genomic catalog of Earth’s microbiomes
Stephen Nayfach,Simon Roux,Rekha Seshadri,Daniel W. Udwary,Neha Varghese,Frederik Schulz,Dongying Wu,David Paez-Espino,I-Min Chen,Marcel Huntemann,Krishna Palaniappan,Joshua Ladau,Supratim Mukherjee,T. B. K. Reddy,Torben Nielsen,Edward Kirton,José P. Faria,Janaka N. Edirisinghe,Christopher S. Henry,Sean P. Jungbluth,Dylan Chivian,Paramvir S. Dehal,Elisha M. Wood-Charlson,Adam P. Arkin,Susannah G. Tringe,Axel Visel,Tanja Woyke,Nigel J Mouncey,Natalia Ivanova,Nikos C. Kyrpides,Emiley A. Eloe-Fadrosh +30 more
TL;DR: The utility of this collection of >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans is demonstrated for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses.
Microbial species delineation using whole genome sequences
Neha Varghese,Supratim Mukherjee,Natalia Ivanova,Konstantinos T. Konstantinidis,Kostas Mavrommatis,Nikos C. Kyrpides,Amrita Pati +6 more
TL;DR: This work demonstrates that the combination of gANI and the alignment fraction between two genomes accurately reflects their genomic relatedness, and proposes this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, to be used to address previous inconsistencies in species classification.
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Supratim Mukherjee,Rekha Seshadri,Neha Varghese,Emiley A. Eloe-Fadrosh,Jan P. Meier-Kolthoff,Markus Göker,R. Cameron Coates,R. Cameron Coates,Michalis Hadjithomas,Georgios A. Pavlopoulos,David Paez-Espino,Yasuo Yoshikuni,Axel Visel,William B. Whitman,George M. Garrity,Jonathan A. Eisen,Philip Hugenholtz,Amrita Pati,Amrita Pati,Natalia Ivanova,Tanja Woyke,Hans-Peter Klenk,Nikos C. Kyrpides +22 more
TL;DR: 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative are presented, selected to maximize sequence coverage of phylogenetic space.
Genome-Based Taxonomic Classification of Bacteroidetes.
Richard L. Hahnke,Jan P. Meier-Kolthoff,Marina García-López,Supratim Mukherjee,Marcel Huntemann,Natalia Ivanova,Tanja Woyke,Nikos C. Kyrpides,Hans-Peter Klenk,Markus Göker +9 more
TL;DR: A large collection of type-strain genomes from Bacteroidetes and closely related phyla are assessed based on the principles of phylogenetic classification and trees inferred from genome-scale data and corrected G+C content values have a significantly better fit to the phylogeny.
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.
Antonio P. Camargo,Stephen Nayfach,I-Min A. Chen,Krishna Palaniappan,Anna Ratner,Ken Chu,Stephan Ritter,T. B. K. Reddy,Supratim Mukherjee,Frederik Schulz,Lee Call,Russell Y. Neches,Tanja Woyke,Natalia Ivanova,Emiley A. Eloe-Fadrosh,Nikos C. Kyrpides,Simon Roux +16 more
TL;DR: IMG/VR as discussed by the authors provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata, enabling users to efficiently browse and search viruses based on genome features and/or sequence similarity.
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