Works by Chen, I-Min

Results: 47
    1
    2

    The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4).

    Published in:
    Standards in Genomic Sciences, 2016, v. 11, n. 1, p. 1, doi. 10.1186/s40793-016-0138-x
    By:
    • Huntemann, Marcel;
    • Ivanova, Natalia;
    • Mavromatis, Konstantinos;
    • Tripp, H.;
    • Paez-Espino, David;
    • Tennessen, Kristin;
    • Palaniappan, Krishnaveni;
    • Szeto, Ernest;
    • Pillay, Manoj;
    • Chen, I-Min;
    • Pati, Amrita;
    • Nielsen, Torben;
    • Markowitz, Victor;
    • Kyrpides, Nikos
    Publication type:
    Article
    3
    4

    Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557.

    Published in:
    Standards in Genomic Sciences, 2014, v. 9, n. 3, p. 540, doi. 10.4056/sigs.4548266
    By:
    • Reeve, Wayne;
    • Ardley, Julie;
    • Tian, Rui;
    • Meyer, Sofie;
    • Terpolilli, Jason;
    • Melino, Vanessa;
    • Tiwari, Ravi;
    • Yates, Ronald;
    • O'Hara, Graham;
    • Howieson, John;
    • Ninawi, Mohamed;
    • Zhang, Xiaojing;
    • Bruce, David;
    • Detter, Chris;
    • Tapia, Roxanne;
    • Han, Cliff;
    • Wei, Chia-Lin;
    • Huntemann, Marcel;
    • Han, James;
    • Chen, I-Min
    Publication type:
    Article
    5

    Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417.

    Published in:
    Standards in Genomic Sciences, 2013, v. 9, n. 2, p. 273, doi. 10.4056/sigs.4518260
    By:
    • Reeve, Wayne;
    • Terpolilli, Jason;
    • Melino, Vanessa;
    • Ardley, Julie;
    • Tian, Rui;
    • Meyer, Sofie;
    • Tiwari, Ravi;
    • Yates, Ronald;
    • O'Hara, Graham;
    • Howieson, John;
    • Ninawi, Mohamed;
    • Teshima, Hazuki;
    • Bruce, David;
    • Detter, Chris;
    • Tapia, Roxanne;
    • Han, Cliff;
    • Wei, Chia-Lin;
    • Huntemann, Marcel;
    • Han, James;
    • Chen, I-Min
    Publication type:
    Article
    6

    Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1.

    Published in:
    Standards in Genomic Sciences, 2013, v. 9, n. 2, p. 243, doi. 10.4056/sigs.4488254
    By:
    • Reeve, Wayne;
    • Tian, Rui;
    • Meyer, Sofie;
    • Melino, Vanessa;
    • Terpolilli, Jason;
    • Ardley, Julie;
    • Tiwari, Ravi;
    • Howieson, John;
    • Yates, Ronald;
    • O'Hara, Graham;
    • Ninawi, Mohamed;
    • Teshima, Hazuki;
    • Bruce, David;
    • Detter, Chris;
    • Tapia, Roxanne;
    • Han, Cliff;
    • Wei, Chia-Lin;
    • Huntemann, Marcel;
    • Han, James;
    • Chen, I-Min
    Publication type:
    Article
    7

    Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471.

    Published in:
    Standards in Genomic Sciences, 2013, v. 9, n. 2, p. 254, doi. 10.4056/sigs.4498256
    By:
    • Reeve, Wayne;
    • Meyer, Sofie;
    • Terpolilli, Jason;
    • Melino, Vanessa;
    • Ardley, Julie;
    • Tian, Rui;
    • Tiwari, Ravi;
    • Howieson, John;
    • Yates, Ronald;
    • O'Hara, Graham;
    • Ninawi, Mohamed;
    • Lu, Megan;
    • Bruce, David;
    • Detter, Chris;
    • Tapia, Roxanne;
    • Han, Cliff;
    • Wei, Chia-Lin;
    • Huntemann, Marcel;
    • Han, James;
    • Chen, I-Min
    Publication type:
    Article
    8

    Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597.

    Published in:
    Standards in Genomic Sciences, 2013, v. 9, n. 2, p. 264, doi. 10.4056/sigs.4508258
    By:
    • Reeve, Wayne;
    • Terpolilli, Jason;
    • Melino, Vanessa;
    • Ardley, Julie;
    • Tian, Rui;
    • Meyer, Sofie;
    • Tiwari, Ravi;
    • Yates, Ronald;
    • O'Hara, Graham;
    • Howieson, John;
    • Ninawi, Mohamed;
    • Held, Brittany;
    • Bruce, David;
    • Detter, Chris;
    • Tapia, Roxanne;
    • Han, Cliff;
    • Wei, Chia-Lin;
    • Huntemann, Marcel;
    • Han, James;
    • Chen, I-Min
    Publication type:
    Article
    9

    Genome sequence of the Trifolium rueppellianum - nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012.

    Published in:
    Standards in Genomic Sciences, 2013, v. 9, n. 2, p. 283, doi. 10.4056/sigs.4528262
    By:
    • Reeve, Wayne;
    • Melino, Vanessa;
    • Ardley, Julie;
    • Tian, Rui;
    • Meyer, Sofie;
    • Terpolilli, Jason;
    • Tiwari, Ravi;
    • Yates, Ronald;
    • O'Hara, Graham;
    • Howieson, John;
    • Ninawi, Mohamed;
    • Held, Brittany;
    • Bruce, David;
    • Detter, Chris;
    • Tapia, Roxanne;
    • Han, Cliff;
    • Wei, Chia-Lin;
    • Huntemann, Marcel;
    • Han, James;
    • Chen, I-Min
    Publication type:
    Article
    10

    Genome sequence of the Lebeckia ambigua-nodulating ' Burkholderia sprentiae' strain WSM5005.

    Published in:
    Standards in Genomic Sciences, 2013, v. 9, n. 2, p. 385, doi. 10.4056/sigs.4558268
    By:
    • Reeve, Wayne;
    • Meyer, Sofie;
    • Terpolilli, Jason;
    • Melino, Vanessa;
    • Ardley, Julie;
    • Rui, Tian;
    • Tiwari, Ravi;
    • Howieson, John;
    • Yates, Ron;
    • O'Hara, Graham;
    • Lu, Megan;
    • Bruce, David;
    • Detter, Chris;
    • Tapia, Roxanne;
    • Han, Cliff;
    • Wei, Chia-Lin;
    • Huntemann, Marcel;
    • Han, James;
    • Chen, I-Min;
    • Mavromatis, Konstantinos
    Publication type:
    Article
    11
    12
    13

    IMG/M: a data management and analysis system for metagenomes.

    Published in:
    Nucleic Acids Research, 2008, v. 36, p. D534
    By:
    • Markowitz, Victor M.;
    • Ivanova, Natalia N.;
    • Szeto, Ernest;
    • Palaniappan, Krishna;
    • Chu, Ken;
    • Dalevi, Daniel;
    • Chen, I-Min A.;
    • Grechkin, Yuri;
    • Dubchak, Inna;
    • Anderson, Iain;
    • Lykidis, Athanasios;
    • Mavromatis, Konstantinos;
    • Hugenholtz, Philip;
    • Kyrpides, Nikos C.
    Publication type:
    Article
    14
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    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
    18

    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
    19
    20

    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
    21

    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
    22

    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
    23

    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
    24
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    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
    26

    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
    27
    28

    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
    29

    IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.

    Published in:
    Nucleic Acids Research, 2019, v. 47, n. D1, p. D666, doi. 10.1093/nar/gky901
    By:
    • Chen, I-Min A;
    • Chu, Ken;
    • Palaniappan, Krishna;
    • Pillay, Manoj;
    • Ratner, Anna;
    • Huang, Jinghua;
    • Huntemann, Marcel;
    • Varghese, Neha;
    • White, James R;
    • Seshadri, Rekha;
    • Smirnova, Tatyana;
    • Kirton, Edward;
    • Jungbluth, Sean P;
    • Woyke, Tanja;
    • Eloe-Fadrosh, Emiley A;
    • Ivanova, Natalia N;
    • Kyrpides, Nikos C
    Publication type:
    Article
    30
    31

    IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

    Published in:
    Nucleic Acids Research, 2017, v. 45, n. D1, p. D457, doi. 10.1093/nar/gkw1030
    By:
    • Paez-Espino, David;
    • Chen, I.-Min A.;
    • Palaniappan, Krishna;
    • Ratner, Anna;
    • Ken Chu;
    • Szeto, Ernest;
    • Pillay, Manoj;
    • Jinghua Huang;
    • Markowitz, Victor M.;
    • Nielsen, Torben;
    • Huntemann, Marcel;
    • Reddy, T. B. K.;
    • Pavlopoulos, Georgios A.;
    • Sullivan, Matthew B.;
    • Campbell, Barbara J.;
    • Feng Chen;
    • McMahon, Katherine;
    • Hallam, Steve J.;
    • Denef, Vincent;
    • Cavicchioli, Ricardo
    Publication type:
    Article
    32

    IMG/M: integrated genome and metagenome comparative data analysis system.

    Published in:
    Nucleic Acids Research, 2017, v. 45, n. D1, p. D507, doi. 10.1093/nar/gkw929
    By:
    • Chen, I.-Min A.;
    • Markowitz, Victor M.;
    • Ken Chu;
    • Palaniappan, Krishna;
    • Szeto, Ernest;
    • Pillay, Manoj;
    • Ratner, Anna;
    • Jinghua Huang;
    • Andersen, Evan;
    • Huntemann, Marcel;
    • Varghese, Neha;
    • Hadjithomas, Michalis;
    • Tennessen, Kristin;
    • Nielsen, Torben;
    • Ivanova, Natalia N.;
    • Kyrpides, Nikos C.
    Publication type:
    Article
    33

    IMG 4 version of the integrated microbial genomes comparative analysis system.

    Published in:
    Nucleic Acids Research, 2014, v. 42, n. D1, p. D560, doi. 10.1093/nar/gkt963
    By:
    • Markowitz, Victor M.;
    • Chen, I-Min A.;
    • Palaniappan, Krishna;
    • Chu, Ken;
    • Szeto, Ernest;
    • Pillay, Manoj;
    • Ratner, Anna;
    • Huang, Jinghua;
    • Woyke, Tanja;
    • Huntemann, Marcel;
    • Anderson, Iain;
    • Billis, Konstantinos;
    • Varghese, Neha;
    • Mavromatis, Konstantinos;
    • Pati, Amrita;
    • Ivanova, Natalia N.;
    • Kyrpides, Nikos C.
    Publication type:
    Article
    34

    IMG/M 4 version of the integrated metagenome comparative analysis system.

    Published in:
    Nucleic Acids Research, 2014, v. 42, n. D1, p. D568, doi. 10.1093/nar/gkt919
    By:
    • Markowitz, Victor M.;
    • Chen, I-Min A.;
    • Chu, Ken;
    • Szeto, Ernest;
    • Palaniappan, Krishna;
    • Pillay, Manoj;
    • Ratner, Anna;
    • Huang, Jinghua;
    • Pagani, Ioanna;
    • Tringe, Susannah;
    • Huntemann, Marcel;
    • Billis, Konstantinos;
    • Varghese, Neha;
    • Tennessen, Kristin;
    • Mavromatis, Konstantinos;
    • Pati, Amrita;
    • Ivanova, Natalia N.;
    • Kyrpides, Nikos C.
    Publication type:
    Article
    35

    IMG: the integrated microbial genomes database and comparative analysis system.

    Published in:
    Nucleic Acids Research, 2012, p. D115, doi. 10.1093/nar/gkr1044
    By:
    • Markowitz, Victor M.;
    • Chen, I-Min A.;
    • Palaniappan, Krishna;
    • Chu, Ken;
    • Szeto, Ernest;
    • Grechkin, Yuri;
    • Ratner, Anna;
    • Jacob, Biju;
    • Huang, Jinghua;
    • Williams, Peter;
    • Huntemann, Marcel;
    • Anderson, Iain;
    • Mavromatis, Konstantinos;
    • Ivanova, Natalia N.;
    • Kyrpides, Nikos C.
    Publication type:
    Article
    36
    37

    IMG/M: the integrated metagenome data management and comparative analysis system.

    Published in:
    Nucleic Acids Research, 2012, p. D123, doi. 10.1093/nar/gkr975
    By:
    • Markowitz, Victor M.;
    • Chen, I-Min A.;
    • Chu, Ken;
    • Szeto, Ernest;
    • Palaniappan, Krishna;
    • Grechkin, Yuri;
    • Ratner, Anna;
    • Jacob, Biju;
    • Pati, Amrita;
    • Huntemann, Marcel;
    • Liolios, Konstantinos;
    • Pagani, Ioanna;
    • Anderson, Iain;
    • Mavromatis, Konstantinos;
    • Ivanova, Natalia N.;
    • Kyrpides, Nikos C.
    Publication type:
    Article
    38
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    Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community.

    Published in:
    Microbiome, 2020, v. 8, n. 1, p. 1, doi. 10.1186/s40168-020-00889-8
    By:
    • Panwar, Pratibha;
    • Allen, Michelle A.;
    • Williams, Timothy J.;
    • Hancock, Alyce M.;
    • Brazendale, Sarah;
    • Bevington, James;
    • Roux, Simon;
    • Páez-Espino, David;
    • Nayfach, Stephen;
    • Berg, Maureen;
    • Schulz, Frederik;
    • Chen, I-Min A.;
    • Huntemann, Marcel;
    • Shapiro, Nicole;
    • Kyrpides, Nikos C.;
    • Woyke, Tanja;
    • Eloe-Fadrosh, Emiley A.;
    • Cavicchioli, Ricardo
    Publication type:
    Article
    42
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    Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan.

    Published in:
    Frontiers in Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fmicb.2021.632731
    By:
    • Thomas, Scott C.;
    • Payne, Devon;
    • Tamadonfar, Kevin O.;
    • Seymour, Cale O.;
    • Jiao, Jian-Yu;
    • Murugapiran, Senthil K.;
    • Lai, Dengxun;
    • Lau, Rebecca;
    • Bowen, Benjamin P.;
    • Silva, Leslie P.;
    • Louie, Katherine B.;
    • Huntemann, Marcel;
    • Clum, Alicia;
    • Spunde, Alex;
    • Pillay, Manoj;
    • Palaniappan, Krishnaveni;
    • Varghese, Neha;
    • Mikhailova, Natalia;
    • Chen, I-Min;
    • Stamatis, Dimitrios
    Publication type:
    Article
    45

    Genomes OnLine Database (GOLD) v.10: new features and updates.

    Published in:
    Nucleic Acids Research, 2025, v. 53, n. D1, p. D989, doi. 10.1093/nar/gkae1000
    By:
    • Mukherjee, Supratim;
    • Stamatis, Dimitri;
    • Li, Cindy Tianqing;
    • Ovchinnikova, Galina;
    • Kandimalla, Mahathi;
    • Handke, Van;
    • Reddy, Anuha;
    • Ivanova, Natalia;
    • Woyke, Tanja;
    • Eloe-Fardosh, Emiley A;
    • Chen, I-Min A;
    • Kyrpides, Nikos C;
    • Reddy, T B K
    Publication type:
    Article
    46

    IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.

    Published in:
    Nucleic Acids Research, 2024, v. 52, n. D1, p. D164, doi. 10.1093/nar/gkad964
    By:
    • Camargo, Antonio Pedro;
    • Call, Lee;
    • Roux, Simon;
    • Nayfach, Stephen;
    • Huntemann, Marcel;
    • Palaniappan, Krishnaveni;
    • Ratner, Anna;
    • Chu, Ken;
    • Mukherjeep, Supratim;
    • Reddy, T B K;
    • Chen, I-Min A;
    • Ivanova, Natalia N;
    • Eloe-Fadrosh, Emiley A;
    • Woyke, Tanja;
    • Baltrus, David A;
    • Castañeda-Barba, Salvador;
    • de la Cruz, Fernando;
    • Funnell, Barbara E;
    • Hall, James P J;
    • Mukhopadhyay, Aindrila
    Publication type:
    Article
    47