Found: 29

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  • Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.

    Published in:
    Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03826-8
    By:
    • Oliver, Tiffany;
    • Varghese, Neha;
    • Roux, Simon;
    • Schulz, Frederik;
    • Huntemann, Marcel;
    • Clum, Alicia;
    • Foster, Brian;
    • Foster, Bryce;
    • Riley, Robert;
    • LaButti, Kurt;
    • Egan, Robert;
    • Hajek, Patrick;
    • Mukherjee, Supratim;
    • Ovchinnikova, Galina;
    • Reddy, T. B. K.;
    • Calhoun, Sara;
    • Hayes, Richard D.;
    • Rohwer, Robin R.;
    • Zhou, Zhichao;
    • Daum, Chris
    Publication type:
    Article

  • Draft genome sequence of Actinotignum schaalii DSM 15541<sup>T</sup>: Genetic insights into the lifestyle, cell fitness and virulence.

    Published in:
    PLoS ONE, 2017, v. 12, n. 12, p. 1, doi. 10.1371/journal.pone.0188914
    By:
    • Yassin, Atteyet F.;
    • Langenberg, Stefan;
    • Huntemann, Marcel;
    • Clum, Alicia;
    • Pillay, Manoj;
    • Palaniappan, Krishnaveni;
    • Varghese, Neha;
    • Mikhailova, Natalia;
    • Mukherjee, Supratim;
    • Reddy, T. B. K.;
    • Daum, Chris;
    • Shapiro, Nicole;
    • Ivanova, Natalia;
    • Woyke, Tanja;
    • Kyrpides, Nikos C.
    Publication type:
    Article

  • Draft genome sequence of Marinobacterium rhizophilum CL-YJ9<sup>T</sup> (DSM 18822<sup>T</sup>), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.

    Published in:
    Standards in Genomic Sciences, 2017, v. 12, p. 1, doi. 10.1186/s40793-017-0275-x
    By:
    • Dong Han Choi;
    • Gwang II Jang;
    • Lapidus, Alla;
    • Copeland, Alex;
    • Reddy, T. B. K.;
    • Mukherjee, Supratim;
    • Huntemann, Marcel;
    • Varghese, Neha;
    • Ivanova, Natalia;
    • Pillay, Manoj;
    • Tindall, Brian J.;
    • Göker, Markus;
    • Woyke, Tanja;
    • Klenk, Hans-Peter;
    • Kyrpides, Nikos C.;
    • Byung Cheol Cho
    Publication type:
    Article

  • Large-scale contamination of microbial isolate genomes by Illumina PhiX control.

    Published in:
    Standards in Genomic Sciences, 2015, v. 10, n. 1, p. 1, doi. 10.1186/1944-3277-10-18
    By:
    • Mukherjee, Supratim;
    • Huntemann, Marcel;
    • Ivanova, Natalia;
    • Kyrpides, Nikos C.;
    • Pati, Amrita
    Publication type:
    Article

  • High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1<sup>T</sup> (DSM 17521<sup>T</sup>) isolated from muddy waters of a drainage system in Chandigarh, India.

    Published in:
    Standards in Genomic Sciences, 2015, v. 10, n. 1, p. 1, doi. 10.1186/1944-3277-10-8
    By:
    • Mukherjee, Supratim;
    • Lapidus, Alla;
    • Shapiro, Nicole;
    • Jan-Fang Cheng;
    • Han, James;
    • Reddy, T. B. K.;
    • Huntemann, Marcel;
    • Ivanova, Natalia;
    • Mikhailova, Natalia;
    • Amy Chen;
    • Palaniappan, Krishna;
    • Spring, Stefan;
    • Göker, Markus;
    • Markowitz, Victor;
    • Woyke, Tanja;
    • Tindall, Brian J.;
    • Klenk, Hans-Peter;
    • Kyrpides, Nikos C.;
    • Pati, Amrita
    Publication type:
    Article

  • IMG/M data management and analysis system v.7: content updates and new features.

    Published in:
    Nucleic Acids Research, 2023, v. 51, n. D1, p. D723, doi. 10.1093/nar/gkac976
    By:
    • Chen, I-Min A;
    • Chu, Ken;
    • Palaniappan, Krishnaveni;
    • Ratner, Anna;
    • Huang, Jinghua;
    • Huntemann, Marcel;
    • Hajek, Patrick;
    • Ritter, Stephan J;
    • Webb, Cody;
    • Wu, Dongying;
    • Varghese, Neha J;
    • Reddy, T B K;
    • Mukherjee, Supratim;
    • Ovchinnikova, Galina;
    • Nolan, Matt;
    • Seshadri, Rekha;
    • Roux, Simon;
    • Visel, Axel;
    • Woyke, Tanja;
    • Eloe-Fadrosh, Emiley A
    Publication type:
    Article

  • Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9.

    Published in:
    Nucleic Acids Research, 2023, v. 51, n. D1, p. D957, doi. 10.1093/nar/gkac974
    By:
    • Mukherjee, Supratim;
    • Stamatis, Dimitri;
    • Li, Cindy Tianqing;
    • Ovchinnikova, Galina;
    • Bertsch, Jon;
    • Sundaramurthi, Jagadish Chandrabose;
    • Kandimalla, Mahathi;
    • Nicolopoulos, Paul A;
    • Favognano, Alessandro;
    • Chen, I-Min A;
    • Kyrpides, Nikos C;
    • Reddy, T B K
    Publication type:
    Article

  • IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.

    Published in:
    Nucleic Acids Research, 2023, v. 51, n. D1, p. D733, doi. 10.1093/nar/gkac1037
    By:
    • Camargo, Antonio Pedro;
    • Nayfach, Stephen;
    • Chen, I-Min A;
    • Palaniappan, Krishnaveni;
    • Ratner, Anna;
    • Chu, Ken;
    • Ritter, Stephan J;
    • Reddy, T B K;
    • Mukherjee, Supratim;
    • Schulz, Frederik;
    • Call, Lee;
    • Neches, Russell Y;
    • Woyke, Tanja;
    • Ivanova, Natalia N;
    • Eloe-Fadrosh, Emiley A;
    • Kyrpides, Nikos C;
    • Roux, Simon
    Publication type:
    Article

  • Evaluation of fuzzy membership function by cubic spline: A case study.

    Published in:
    Mathematics in Engineering, Science & Aerospace (MESA), 2023, v. 14, n. 3, p. 991
    By:
    • Narjinary, James Dinakaran;
    • Kar, Rahul;
    • Mukherjee, Supratim
    Publication type:
    Article

  • Evaluation of Covid-19 pandemic effects in Indian tourism.

    Published in:
    Mathematics in Engineering, Science & Aerospace (MESA), 2023, v. 14, n. 2, p. 507
    By:
    • Narjinary, James Dinakaran;
    • Kar, Rahul;
    • Mukherjee, Supratim
    Publication type:
    Article

  • Standardized naming of microbiome samples in Genomes OnLine Database.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2023, v. 2023, p. 1, doi. 10.1093/database/baad001
    By:
    • Mukherjee, Supratim;
    • Ovchinnikova, Galina;
    • Stamatis, Dimitri;
    • Li, Cindy Tianqing;
    • Chen, I-Min A;
    • Kyrpides, Nikos C;
    • Reddy, T B K
    Publication type:
    Article

  • Medicago root nodule microbiomes: insights into a complex ecosystem with potential candidates for plant growth promotion.

    Published in:
    Plant & Soil, 2022, v. 471, n. 1/2, p. 507, doi. 10.1007/s11104-021-05247-7
    By:
    • Martínez-Hidalgo, Pilar;
    • Humm, Ethan A.;
    • Still, David W.;
    • Shi, Baochen;
    • Pellegrini, Matteo;
    • de la Roca, Gabriela;
    • Veliz, Esteban;
    • Maymon, Maskit;
    • Bru, Pierrick;
    • Huntemann, Marcel;
    • Clum, Alicia;
    • Palaniappan, Krishnaveni;
    • Varghese, Neha;
    • Mukherjee, Supratim;
    • Reddy, T. B. K.;
    • Daum, Chris;
    • Ivanova, Natalia N.;
    • Kyrpides, Nikos C.;
    • Shapiro, Nicole;
    • Eloe-Fadrosh, Emiley A.
    Publication type:
    Article

  • Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.

    Published in:
    Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0222-3
    By:
    • Högfors-Rönnholm, Eva;
    • Lopez-Fernandez, Margarita;
    • Christel, Stephan;
    • Brambilla, Diego;
    • Huntemann, Marcel;
    • Clum, Alicia;
    • Foster, Brian;
    • Foster, Bryce;
    • Roux, Simon;
    • Palaniappan, Krishnaveni;
    • Varghese, Neha;
    • Mukherjee, Supratim;
    • Reddy, T. B. K.;
    • Daum, Chris;
    • Copeland, Alex;
    • Chen, I-Min A.;
    • Ivanova, Natalia N.;
    • Kyrpides, Nikos C.;
    • Harmon-Smith, Miranda;
    • Eloe-Fadrosh, Emiley A.
    Publication type:
    Article

  • Genome-Based Taxonomic Classification of Bacteroidetes.

    Published in:
    Frontiers in Microbiology, 2016, v. 7, p. 1, doi. 10.3389/fmicb.2016.02003
    By:
    • Hahnke, Richard L.;
    • Meier-Kolthoff, Jan P.;
    • García-López, Marina;
    • Mukherjee, Supratim;
    • Huntemann, Marcel;
    • Ivanova, Natalia N.;
    • Woyke, Tanja;
    • Kyrpides, Nikos C.;
    • Klenk, Hans-Peter;
    • Göker, Markus
    Publication type:
    Article

  • 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

    Published in:
    Nature Biotechnology, 2017, v. 35, n. 7, p. 676, doi. 10.1038/nbt.3886
    By:
    • Mukherjee, Supratim;
    • Seshadri, Rekha;
    • Varghese, Neha J;
    • Eloe-Fadrosh, Emiley A;
    • Meier-Kolthoff, Jan P;
    • Göker, Markus;
    • Coates, R Cameron;
    • Hadjithomas, Michalis;
    • Pavlopoulos, Georgios A;
    • Paez-Espino, David;
    • Yoshikuni, Yasuo;
    • Visel, Axel;
    • Whitman, William B;
    • Garrity, George M;
    • Eisen, Jonathan A;
    • Hugenholtz, Philip;
    • Pati, Amrita;
    • Ivanova, Natalia N;
    • Woyke, Tanja;
    • Klenk, Hans-Peter
    Publication type:
    Article

  • The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole.

    Published in:
    Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25646-9
    By:
    • Martin, Kara;
    • Schmidt, Katrin;
    • Toseland, Andrew;
    • Boulton, Chris A.;
    • Barry, Kerrie;
    • Beszteri, Bánk;
    • Brussaard, Corina P. D.;
    • Clum, Alicia;
    • Daum, Chris G.;
    • Eloe-Fadrosh, Emiley;
    • Fong, Allison;
    • Foster, Brian;
    • Foster, Bryce;
    • Ginzburg, Michael;
    • Huntemann, Marcel;
    • Ivanova, Natalia N.;
    • Kyrpides, Nikos C.;
    • Lindquist, Erika;
    • Mukherjee, Supratim;
    • Palaniappan, Krishnaveni
    Publication type:
    Article

  • Population Level Analysis of Evolved Mutations Underlying Improvements in Plant Hemicellulose and Cellulose Fermentation by <i>Clostridium phytofermentans</i>.

    Published in:
    PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0086731
    By:
    • Mukherjee, Supratim;
    • Thompson, Lynmarie K.;
    • Godin, Stephen;
    • Schackwitz, Wendy;
    • Lipzen, Anna;
    • Martin, Joel;
    • Blanchard, Jeffrey L.
    Publication type:
    Article

  • Bone-muscle interaction of the fractured femur.

    Published in:
    Journal of Orthopaedic Research, 2008, v. 26, n. 8, p. 1159, doi. 10.1002/jor.20611
    By:
    • Graham, Andrew E.;
    • Xie, Sheng Q.;
    • Aw, Kean C.;
    • Mukherjee, Supratim;
    • Xu, Wei L.
    Publication type:
    Article

  • Genomes OnLine Database (GOLD) v.8: overview and updates.

    Published in:
    Nucleic Acids Research, 2021, v. 49, n. D1, p. D723, doi. 10.1093/nar/gkaa983
    By:
    • Mukherjee, Supratim;
    • Stamatis, Dimitri;
    • Bertsch, Jon;
    • Ovchinnikova, Galina;
    • Sundaramurthi, Jagadish Chandrabose;
    • Lee, Janey;
    • Kandimalla, Mahathi;
    • Chen, I-Min A;
    • Kyrpides, Nikos C;
    • Reddy, T B K
    Publication type:
    Article

  • Genomes OnLine database (GOLD) v.7: updates and new features.

    Published in:
    Nucleic Acids Research, 2019, v. 47, n. D1, p. D649, doi. 10.1093/nar/gky977
    By:
    • Mukherjee, Supratim;
    • Stamatis, Dimitri;
    • Bertsch, Jon;
    • Ovchinnikova, Galina;
    • Katta, Hema Y;
    • Mojica, Alejandro;
    • Chen, I-Min A;
    • Kyrpides, Nikos C;
    • Reddy, TBK
    Publication type:
    Article

  • Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements.

    Published in:
    Nucleic Acids Research, 2017, v. 45, n. D1, p. D446, doi. 10.1093/nar/gkw992
    By:
    • Mukherjee, Supratim;
    • Stamatis, Dimitri;
    • Bertsch, Jon;
    • Ovchinnikova, Galina;
    • Verezemska, Olena;
    • Isbandi, Michelle;
    • Thomas, Alex D.;
    • Ali, Rida;
    • Sharma, Kaushal;
    • Kyrpides, Nikos C.;
    • Reddy, T. B. K.
    Publication type:
    Article

  • Microbial species delineation using whole genome sequences.

    Published in:
    Nucleic Acids Research, 2015, v. 43, n. 14, p. 6761, doi. 10.1093/nar/gkv657
    By:
    • Varghese, Neha J.;
    • Mukherjee, Supratim;
    • Ivanova, Natalia;
    • Konstantinidis, Konstantinos T.;
    • Mavrommatis, Kostas;
    • Kyrpides, Nikos C.;
    • Pati, Amrita
    Publication type:
    Article

  • Author Correction: A genomic catalog of Earth's microbiomes.

    Published in:
    2021
    By:
    • Nayfach, Stephen;
    • Roux, Simon;
    • Seshadri, Rekha;
    • Udwary, Daniel;
    • Varghese, Neha;
    • Schulz, Frederik;
    • Wu, Dongying;
    • Paez-Espino, David;
    • Chen, I-Min;
    • Huntemann, Marcel;
    • Palaniappan, Krishna;
    • Ladau, Joshua;
    • Mukherjee, Supratim;
    • Reddy, T. B. K.;
    • Nielsen, Torben;
    • Kirton, Edward;
    • Faria, José P.;
    • Edirisinghe, Janaka N.;
    • Henry, Christopher S.;
    • Jungbluth, Sean P.
    Publication type:
    Correction Notice

  • Publisher Correction: A genomic catalog of Earth's microbiomes.

    Published in:
    2021
    By:
    • Nayfach, Stephen;
    • Roux, Simon;
    • Seshadri, Rekha;
    • Udwary, Daniel;
    • Varghese, Neha;
    • Schulz, Frederik;
    • Wu, Dongying;
    • Paez-Espino, David;
    • Chen, I-Min;
    • Huntemann, Marcel;
    • Palaniappan, Krishna;
    • Ladau, Joshua;
    • Mukherjee, Supratim;
    • Reddy, T. B. K.;
    • Nielsen, Torben;
    • Kirton, Edward;
    • Faria, José P.;
    • Edirisinghe, Janaka N.;
    • Henry, Christopher S.;
    • Jungbluth, Sean P.
    Publication type:
    Correction Notice

  • A genomic catalog of Earth's microbiomes.

    Published in:
    Nature Biotechnology, 2021, v. 39, n. 4, p. 499, doi. 10.1038/s41587-020-0718-6
    By:
    • Nayfach, Stephen;
    • Roux, Simon;
    • Seshadri, Rekha;
    • Udwary, Daniel;
    • Varghese, Neha;
    • Schulz, Frederik;
    • Wu, Dongying;
    • Paez-Espino, David;
    • Chen, I-Min;
    • Huntemann, Marcel;
    • Palaniappan, Krishna;
    • Ladau, Joshua;
    • Mukherjee, Supratim;
    • Reddy, T. B. K.;
    • Nielsen, Torben;
    • Kirton, Edward;
    • Faria, José P.;
    • Edirisinghe, Janaka N.;
    • Henry, Christopher S.;
    • Jungbluth, Sean P.
    Publication type:
    Article

  • Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

    Published in:
    Nature Biotechnology, 2018, v. 36, n. 4, p. 368, doi. 10.1038/nbt0418-368c
    By:
    • Mukherjee, Supratim;
    • Seshadri, Rekha;
    • Varghese, Neha J;
    • Eloe-Fadrosh, Emiley A;
    • Meier-Kolthoff, Jan P;
    • Göker, Markus;
    • Coates, R Cameron;
    • Hadjithomas, Michalis;
    • Pavlopoulos, Georgios A;
    • Paez-Espino, David;
    • Yoshikuni, Yasuo;
    • Visel, Axel;
    • Whitman, William B;
    • Garrity, George M;
    • Eisen, Jonathan A;
    • Hugenholtz, Philip;
    • Pati, Amrita;
    • Ivanova, Natalia N;
    • Woyke, Tanja;
    • Klenk, Hans-Peter
    Publication type:
    Article

  • Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot.

    Published in:
    Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0141-3
    By:
    • Camargo, Antonio Pedro;
    • de Souza, Rafael Soares Correa;
    • de Britto Costa, Patrícia;
    • Gerhardt, Isabel Rodrigues;
    • Dante, Ricardo Augusto;
    • Teodoro, Grazielle Sales;
    • Abrahão, Anna;
    • Lambers, Hans;
    • Carazzolle, Marcelo Falsarella;
    • Huntemann, Marcel;
    • Clum, Alicia;
    • Foster, Brian;
    • Foster, Bryce;
    • Roux, Simon;
    • Palaniappan, Krishnaveni;
    • Varghese, Neha;
    • Mukherjee, Supratim;
    • Reddy, T. B. K.;
    • Daum, Chris;
    • Copeland, Alex
    Publication type:
    Article

  • Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom.

    Published in:
    Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0132-4
    By:
    • Nowinski, Brent;
    • Smith, Christa B.;
    • Thomas, Courtney M.;
    • Esson, Kaitlin;
    • Marin, Roman;
    • Preston, Christina M.;
    • Birch, James M.;
    • Scholin, Christopher A.;
    • Huntemann, Marcel;
    • Clum, Alicia;
    • Foster, Brian;
    • Foster, Bryce;
    • Roux, Simon;
    • Palaniappan, Krishnaveni;
    • Varghese, Neha;
    • Mukherjee, Supratim;
    • Reddy, T. B. K.;
    • Daum, Chris;
    • Copeland, Alex;
    • Chen, I.-Min A.
    Publication type:
    Article

  • Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels.

    Published in:
    PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0118285
    By:
    • Petit, Elsa;
    • Coppi, Maddalena V.;
    • Hayes, James C.;
    • Tolonen, Andrew C.;
    • Warnick, Thomas;
    • Latouf, William G.;
    • Amisano, Danielle;
    • Biddle, Amy;
    • Mukherjee, Supratim;
    • Ivanova, Natalia;
    • Lykidis, Athanassios;
    • Land, Miriam;
    • Hauser, Loren;
    • Kyrpides, Nikos;
    • Henrissat, Bernard;
    • Lau, Joanne;
    • Schnell, Danny J.;
    • Church, George M.;
    • Leschine, Susan B.;
    • Blanchard, Jeffrey L.
    Publication type:
    Article