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Supratim Mukherjee
Supratim Mukherjee
Staff Data Scientist at Joint Genome Institute, LBNL
Verified email at lbl.gov
Title
Cited by
Cited by
Year
Microbial species delineation using whole genome sequences
NJ Varghese, S Mukherjee, N Ivanova, KT Konstantinidis, K Mavrommatis, ...
Nucleic Acids Research, 2015
7412015
A genomic catalog of Earth’s microbiomes
S Nayfach, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, ...
Nature biotechnology 39 (4), 499-509, 2021
7182021
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
S Mukherjee, R Seshadri, NJ Varghese, EA Eloe-Fadrosh, ...
Nature biotechnology 35 (7), 676-683, 2017
2672017
Genome-Based Taxonomic Classification of Bacteroidetes
RL Hahnke, JP Meier-Kolthoff, M García-López, S Mukherjee, ...
Frontiers in microbiology 7, 2003, 2016
2362016
Genomes OnLine database (GOLD) v. 7: updates and new features
S Mukherjee, D Stamatis, J Bertsch, G Ovchinnikova, HY Katta, A Mojica, ...
Nucleic acids research 47 (D1), D649-D659, 2019
2272019
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
AP Camargo, S Nayfach, IMA Chen, K Palaniappan, A Ratner, K Chu, ...
Nucleic acids research 51 (D1), D733-D743, 2023
2162023
Genomes OnLine Database (GOLD) v. 8: overview and updates
S Mukherjee, D Stamatis, J Bertsch, G Ovchinnikova, JC Sundaramurthi, ...
Nucleic acids research 49 (D1), D723-D733, 2021
2032021
Genomes OnLine Database (GOLD) v. 6: data updates and feature enhancements
S Mukherjee, D Stamatis, J Bertsch, G Ovchinnikova, O Verezemska, ...
Nucleic acids research, gkw992, 2016
1992016
The IMG/M data management and analysis system v. 7: content updates and new features
IMA Chen, K Chu, K Palaniappan, A Ratner, J Huang, M Huntemann, ...
Nucleic acids research 51 (D1), D723-D732, 2023
1902023
Large-scale contamination of microbial isolate genomes by Illumina PhiX control
S Mukherjee, M Huntemann, N Ivanova, NC Kyrpides, A Pati
Standards in genomic sciences 10, 1-4, 2015
1782015
DOE JGI metagenome workflow
A Clum, M Huntemann, B Bushnell, B Foster, B Foster, S Roux, PP Hajek, ...
Msystems 6 (3), 10.1128/msystems. 00804-20, 2021
862021
Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v. 9
S Mukherjee, D Stamatis, CT Li, G Ovchinnikova, J Bertsch, ...
Nucleic acids research 51 (D1), D957-D963, 2023
852023
Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom
B Nowinski, CB Smith, CM Thomas, K Esson, R Marin III, CM Preston, ...
Scientific Data 6 (1), 129, 2019
472019
The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole
K Martin, K Schmidt, A Toseland, CA Boulton, K Barry, B Beszteri, ...
Nature Communications 12 (1), 5483, 2021
442021
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot
AP Camargo, RSC de Souza, J Jose, IR Gerhardt, RA Dante, ...
The ISME journal 17 (3), 354-370, 2023
372023
Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes
R Seshadri, S Roux, KJ Huber, D Wu, S Yu, D Udwary, L Call, S Nayfach, ...
Cell genomics 2 (12), 2022
332022
The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections
Boundy-Mills K, H M, B AR, R M, K S, N D, E JA, I P, S IR, T T, B DR, C J, ...
Applied and Environmental Microbiology, 2015
312015
<? mode longmeta?> IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
AP Camargo, L Call, S Roux, S Nayfach, M Huntemann, K Palaniappan, ...
Nucleic acids research 52 (D1), D164-D173, 2024
262024
The role of zinc in the adaptive evolution of polar phytoplankton
N Ye, W Han, A Toseland, Y Wang, X Fan, D Xu, C van Oosterhout, ...
Nature ecology & evolution 6 (7), 965-978, 2022
252022
Impact of soil salinity on the cowpea nodule-microbiome and the isolation of halotolerant PGPR strains to promote plant growth under salinity stress
S Mukhtar, AM Hirsch, N Khan, KA Malik, EA Humm, M Pellegrini, B Shi, ...
Phytobiomes Journal 4 (4), 364-374, 2020
252020
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