Found: 12

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  • Modeling central metabolism and energy biosynthesis across microbial life.

    Published in:
    BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2887-8
    By:
    • Edirisinghe, Janaka N.;
    • Weisenhorn, Pamela;
    • Conrad, Neal;
    • Fangfang Xia;
    • Overbeek, Ross;
    • Stevens, Rick L.;
    • Henry, Christopher S.
    Publication type:
    Article

  • Evolution of substrate specificity in a retained enzyme driven by gene loss.

    Published in:
    eLife, 2017, p. 1, doi. 10.7554/eLife.22679
    By:
    • Juá Rez-Vázquez, Ana Lilia;
    • Edirisinghe, Janaka N.;
    • Verduzco-Castro, Ernesto A.;
    • Michalska, Karolina;
    • Chenggang Wu;
    • Noda-Garcıa, Lianet;
    • Babnigg, Gyorgy;
    • Endres, Michael;
    • Medina-Ruız, Sofıa;
    • Santoyo-Flores, Julián;
    • Carrillo-Tripp, Mauricio;
    • Hung Ton-That;
    • Joachimiak, Andrzej;
    • Henry, Christopher S.;
    • Barona-Gómez, Francisco
    Publication type:
    Article

  • Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.

    Published in:
    Frontiers in Microbiology, 2016, v. 7, p. 1, doi. 10.3389/fmicb.2016.01819
    By:
    • Faria, José P.;
    • Davis, James J.;
    • Edirisinghe, Janaka N.;
    • Taylor, Ronald C.;
    • Weisenhorn, Pamela;
    • Olson, Robert D.;
    • Stevens, Rick L.;
    • Rocha, Miguel;
    • Rocha, Isabel;
    • Best, Aaron A.;
    • DeJongh, Matthew;
    • Tintle, Nathan L.;
    • Parrello, Bruce;
    • Overbeek, Ross;
    • Henry, Christopher S.
    Publication type:
    Article

  • kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase.

    Published in:
    Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad110
    By:
    • Shaffer, Michael;
    • Borton, Mikayla A;
    • Bolduc, Ben;
    • Faria, José P;
    • Flynn, Rory M;
    • Ghadermazi, Parsa;
    • Edirisinghe, Janaka N;
    • Wood-Charlson, Elisha M;
    • Miller, Christopher S;
    • Chan, Siu Hung Joshua;
    • Sullivan, Matthew B;
    • Henry, Christopher S;
    • Wrighton, Kelly C
    Publication type:
    Article

  • Comparative Genomics of Cultured and Uncultured Strains Suggests Genes Essential for Free-Living Growth of <i>Liberibacter</i>.

    Published in:
    PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0084469
    By:
    • Fagen, Jennie R.;
    • Leonard, Michael T.;
    • McCullough, Connor M.;
    • Edirisinghe, Janaka N.;
    • Henry, Christopher S.;
    • Davis, Michael J.;
    • Triplett, Eric W.
    Publication type:
    Article

  • The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.

    Published in:
    Nucleic Acids Research, 2021, v. 49, n. D1, p. D575, doi. 10.1093/nar/gkaa746
    By:
    • Seaver, Samuel M D;
    • Liu, Filipe;
    • Zhang, Qizhi;
    • Jeffryes, James;
    • Faria, José P;
    • Edirisinghe, Janaka N;
    • Mundy, Michael;
    • Chia, Nicholas;
    • Noor, Elad;
    • Beber, Moritz E;
    • Best, Aaron A;
    • DeJongh, Matthew;
    • Kimbrel, Jeffrey A;
    • D'haeseleer, Patrik;
    • McCorkle, Sean R;
    • Bolton, Jay R;
    • Pearson, Erik;
    • Canon, Shane;
    • Wood-Charlson, Elisha M;
    • Cottingham, Robert W
    Publication type:
    Article

  • Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.

    Published in:
    Nature Biotechnology, 2023, v. 41, n. 9, p. 1320, doi. 10.1038/s41587-022-01628-0
    By:
    • Heinken, Almut;
    • Hertel, Johannes;
    • Acharya, Geeta;
    • Ravcheev, Dmitry A.;
    • Nyga, Malgorzata;
    • Okpala, Onyedika Emmanuel;
    • Hogan, Marcus;
    • Magnúsdóttir, Stefanía;
    • Martinelli, Filippo;
    • Nap, Bram;
    • Preciat, German;
    • Edirisinghe, Janaka N.;
    • Henry, Christopher S.;
    • Fleming, Ronan M. T.;
    • Thiele, Ines
    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

  • Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.

    Published in:
    2020
    By:
    • Lieven, Christian;
    • Beber, Moritz E.;
    • Olivier, Brett G.;
    • Bergmann, Frank T.;
    • Ataman, Meric;
    • Babaei, Parizad;
    • Bartell, Jennifer A.;
    • Blank, Lars M.;
    • Chauhan, Siddharth;
    • Correia, Kevin;
    • Diener, Christian;
    • Dräger, Andreas;
    • Ebert, Birgitta E.;
    • Edirisinghe, Janaka N.;
    • Faria, José P.;
    • Feist, Adam M.;
    • Fengos, Georgios;
    • Fleming, Ronan M. T.;
    • García-Jiménez, Beatriz;
    • Hatzimanikatis, Vassily
    Publication type:
    Correction Notice

  • MEMOTE for standardized genome-scale metabolic model testing.

    Published in:
    2020
    By:
    • Lieven, Christian;
    • Beber, Moritz E.;
    • Olivier, Brett G.;
    • Bergmann, Frank T.;
    • Ataman, Meric;
    • Babaei, Parizad;
    • Bartell, Jennifer A.;
    • Blank, Lars M.;
    • Chauhan, Siddharth;
    • Correia, Kevin;
    • Diener, Christian;
    • Dräger, Andreas;
    • Ebert, Birgitta E.;
    • Edirisinghe, Janaka N.;
    • Faria, José P.;
    • Feist, Adam M.;
    • Fengos, Georgios;
    • Fleming, Ronan M. T.;
    • García-Jiménez, Beatriz;
    • Hatzimanikatis, Vassily
    Publication type:
    Letter