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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
Plant B Vitamin Pathways and their Compartmentation: a Guide for the Perplexed.
Published in:
Journal of Experimental Botany, 2012, v. 63, n. 15, p. 5379, doi. 10.1093/jxb/ers208
By:
- Gerdes, Svetlana;
- Lerma-Ortiz, Claudia;
- Frelin, Océane;
- Seaver, Samuel M. D.;
- Henry, Christopher S.;
- de Crécy-Lagard, Valérie;
- Hanson, Andrew D.
Publication type:
Article
Genome-wide metabolic network reconstruction of the picoalga Ostreococcus.
Published in:
Journal of Experimental Botany, 2012, v. 63, n. 6, p. 2353, doi. 10.1093/jxb/err407
By:
- Krumholz, Elias W.;
- Yang, Hong;
- Weisenhorn, Pamela;
- Henry, Christopher S.;
- Libourel, Igor G. L.
Publication type:
Article
Frontiers in metabolic reconstruction and modeling of plant genomes.
Published in:
Journal of Experimental Botany, 2012, v. 63, n. 6, p. 2247, doi. 10.1093/jxb/err371
By:
- Seaver, Samuel M. D.;
- Henry, Christopher S.;
- Hanson, Andrew D.
Publication type:
Article
A plastidial pantoate transporter with a potential role in pantothenate synthesis.
Published in:
Biochemical Journal, 2018, v. 475, n. 4, p. 813, doi. 10.1042/BCJ20170883
By:
- Lili Huang;
- Pyc, Michal;
- Alseekh, Saleh;
- McCarty, Donald R.;
- de Crécy-Lagard, Valérie;
- Gregory III, Jesse F.;
- Henry, Christopher S.;
- Fernie, Alisdair R.;
- Mullen, Robert T.;
- Hanson, Andrew D.
Publication type:
Article
Co-occurrence of analogous enzymes determines evolution of a novel (βα)<sub>8</sub>-isomerase sub-family after non-conserved mutations in flexible loop.
Published in:
Biochemical Journal, 2016, v. 473, n. 9, p. 1141, doi. 10.1042/BJ20151271
By:
- Verduzco-Castro, Ernesto A.;
- Michalska, Karolina;
- Endres, Michael;
- Juárez-Vazquez, Ana L.;
- Noda-García, Lianet;
- Changsoo Chang;
- Henry, Christopher S.;
- Babnigg, Gyorgy;
- Joachimiak, Andrzej;
- Barona-Gómez, Francisco
Publication type:
Article
A directed-overflow and damage-control N-glycosidase in riboflavin biosynthesis.
Published in:
Biochemical Journal, 2015, v. 466, n. 1, p. 137, doi. 10.1042/BJ20141237
By:
- Frelin, Océane;
- Huang, Lili;
- Hasnain, Ghulam;
- Jeffryes, James G.;
- Ziemak, Michael J.;
- Rocca, James R.;
- Bing Wang;
- Rice, Jennifer;
- Roje, Sanja;
- Yurgel, Svetlana N.;
- Gregory III, Jesse F.;
- Edison, Arthur S.;
- Henry, Christopher S.;
- de Crecy-Lagard, Valerie;
- Hanson, Andrew D.
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
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Published in:
Nucleic Acids Research, 2017, v. 45, n. D1, p. D535, doi. 10.1093/nar/gkw1017
By:
- Wattam, Alice R.;
- Davis, James J.;
- Assaf, Rida;
- Boisvert, Sébastien;
- Brettin, Thomas;
- Bun, Christopher;
- Conrad, Neal;
- Dietrich, Emily M.;
- Disz, Terry;
- Gabbard, Joseph L.;
- Gerdes, Svetlana;
- Henry, Christopher S.;
- Kenyon, Ronald W.;
- Machi, Dustin;
- Chunhong Mao;
- Nordberg, Eric K.;
- Olsen, Gary J.;
- Murphy-Olson, Daniel E.;
- Olson, Robert;
- Overbeek, Ross
Publication type:
Article
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model.
Published in:
Nucleic Acids Research, 2013, v. 41, n. 1, p. 687, doi. 10.1093/nar/gks963
By:
- Tanaka, Kosei;
- Henry, Christopher S.;
- Zinner, Jenifer F.;
- Jolivet, Edmond;
- Cohoon, Matthew P.;
- Xia, Fangfang;
- Bidnenko, Vladimir;
- Ehrlich, S. Dusko;
- Stevens, Rick L.;
- Noirot, Philippe
Publication type:
Article
Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23460-x
By:
- van der Lelie, Daniel;
- Oka, Akihiko;
- Taghavi, Safiyh;
- Umeno, Junji;
- Fan, Ting-Jia;
- Merrell, Katherine E.;
- Watson, Sarah D.;
- Ouellette, Lisa;
- Liu, Bo;
- Awoniyi, Muyiwa;
- Lai, Yunjia;
- Chi, Liang;
- Lu, Kun;
- Henry, Christopher S.;
- Sartor, R. Balfour
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
KBase: The United States Department of Energy Systems Biology Knowledgebase.
Published in:
Nature Biotechnology, 2018, v. 36, n. 7, p. 566, doi. 10.1038/nbt.4163
By:
- Arkin, Adam P;
- Cottingham, Robert W;
- Henry, Christopher S;
- Harris, Nomi L;
- Stevens, Rick L;
- Maslov, Sergei;
- Dehal, Paramvir;
- Ware, Doreen;
- Perez, Fernando;
- Canon, Shane;
- Sneddon, Michael W;
- Henderson, Matthew L;
- Riehl, William J;
- Murphy-Olson, Dan;
- Chan, Stephen Y;
- Kamimura, Roy T;
- Kumari, Sunita;
- Drake, Meghan M;
- Brettin, Thomas S;
- Glass, Elizabeth M
Publication type:
Article
High-throughput generation, optimization and analysis of genome-scale metabolic models.
Published in:
Nature Biotechnology, 2010, v. 28, n. 9, p. 977, doi. 10.1038/nbt.1672
By:
- Henry, Christopher S.;
- DeJongh, Matthew;
- Best, Aaron A.;
- Frybarger, Paul M.;
- Linsay, Ben;
- Stevens, Rick L.
Publication type:
Article
TranSyT, an innovative framework for identifying transport systems.
Published in:
Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad466
By:
- Cunha, Emanuel;
- Lagoa, Davide;
- Faria, José P;
- Liu, Filipe;
- Henry, Christopher S;
- Dias, Oscar
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
ORT: a workflow linking genome-scale metabolic models with reactive transport codes.
Published in:
Bioinformatics, 2022, v. 38, n. 3, p. 778, doi. 10.1093/bioinformatics/btab753
By:
- Rubinstein, Rebecca L;
- Borton, Mikayla A;
- Zhou, Haiyan;
- Shaffer, Michael;
- Hoyt, David W;
- Stegen, James;
- Henry, Christopher S;
- Wrighton, Kelly C;
- Versteeg, Roelof
Publication type:
Article
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.
Published in:
Briefings in Bioinformatics, 2014, v. 15, n. 4, p. 592, doi. 10.1093/bib/bbs071
By:
- Faria, José P.;
- Overbeek, Ross;
- Xia, Fangfang;
- Rocha, Miguel;
- Rocha, Isabel;
- Henry, Christopher S.
Publication type:
Article
PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency.
Published in:
Plant Journal, 2018, v. 95, n. 6, p. 1102, doi. 10.1111/tpj.14003
By:
- Seaver, Samuel M. D.;
- Lerma‐Ortiz, Claudia;
- Conrad, Neal;
- Mikaili, Arman;
- Sreedasyam, Avinash;
- Hanson, Andrew D.;
- Henry, Christopher S.
Publication type:
Article
Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms.
Published in:
PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0098372
By:
- Zarecki, Raphy;
- Oberhardt, Matthew A.;
- Yizhak, Keren;
- Wagner, Allon;
- Shtifman Segal, Ella;
- Freilich, Shiri;
- Henry, Christopher S.;
- Gophna, Uri;
- Ruppin, Eytan
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
SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models.
Published in:
PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0048053
By:
- Aziz, Ramy K.;
- Devoid, Scott;
- Disz, Terrence;
- Edwards, Robert A.;
- Henry, Christopher S.;
- Olsen, Gary J.;
- Olson, Robert;
- Overbeek, Ross;
- Parrello, Bruce;
- Pusch, Gordon D.;
- Stevens, Rick L.;
- Vonstein, Veronika;
- Xia, Fangfang
Publication type:
Article
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
Systematic identification and analysis of frequent gene fusion events in metabolic pathways.
Published in:
BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2782-3
By:
- Henry, Christopher S.;
- Lerma-Ortiz, Claudia;
- Gerdes, Svetlana Y.;
- Mullen, Jeffrey D.;
- Colasanti, Ric;
- Zhukov, Aleksey;
- Frelin, Océane;
- Thiaville, Jennifer J.;
- Zallot, Rémi;
- Niehaus, Thomas D.;
- Hasnain, Ghulam;
- Conrad, Neal;
- Hanson, Andrew D.;
- de Crécy-Lagard, Valérie
Publication type:
Article
Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate.
Published in:
Biotechnology & Bioengineering, 2010, v. 106, n. 3, p. 462, doi. 10.1002/bit.22673
By:
- Henry, Christopher S.;
- Broadbelt, Linda J.;
- Hatzimanikatis, Vassily
Publication type:
Article
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics.
Published in:
Journal of Cheminformatics, 2015, v. 7, n. 1, p. 1, doi. 10.1186/s13321-015-0087-1
By:
- Jeffryes, James G.;
- Colastani, Ricardo L.;
- Elbadawi-Sidhu, Mona;
- Kind, Tobias;
- Niehaus, Thomas D.;
- Broadbelt, Linda J.;
- Hanson, Andrew D.;
- Fiehn, Oliver;
- Tyo, Keith E. J.;
- Henry, Christopher S.
Publication type:
Article
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
Published in:
Molecular Systems Biology, 2007, v. 3, n. 1, p. 121, doi. 10.1038/msb4100155
By:
- Feist, Adam M;
- Henry, Christopher S;
- Reed, Jennifer L;
- Krummenacker, Markus;
- Joyce, Andrew R;
- Karp, Peter D;
- Broadbelt, Linda J;
- Hatzimanikatis, Vassily;
- Palsson, Bernhard Ø
Publication type:
Article
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli.
Published in:
PLoS Computational Biology, 2016, v. 12, n. 1, p. 1, doi. 10.1371/journal.pcbi.1004705
By:
- Oberhardt, Matthew A.;
- Zarecki, Raphy;
- Reshef, Leah;
- Xia, Fangfang;
- Duran-Frigola, Miquel;
- Schreiber, Rachel;
- Henry, Christopher S.;
- Ben-Tal, Nir;
- Dwyer, Daniel J.;
- Gophna, Uri;
- Ruppin, Eytan
Publication type:
Article
Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models.
Published in:
PLoS Computational Biology, 2014, v. 10, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003882
By:
- Benedict, Matthew N.;
- Mundy, Michael B.;
- Henry, Christopher S.;
- Chia, Nicholas;
- Price, Nathan D.
Publication type:
Article
Cash in the Pocket, Cash in the Cloud: Cash Holdings of Bitcoin Owners.
Published in:
International Journal of Central Banking (IJCB), 2024, v. 20, n. 3, p. 115
By:
- Balutel, Daniela;
- Henry, Christopher S.;
- Huynh, Kim P.;
- Voia, Marcel C.
Publication type:
Article
Methods for automated genome-scale metabolic model reconstruction.
Published in:
Biochemical Society Transactions, 2018, v. 46, n. 4, p. 931, doi. 10.1042/BST20170246
By:
- Faria, José P.;
- Rocha, Miguel;
- Rocha, Isabel;
- Henry, Christopher S.
Publication type:
Article
'Nothing of chemistry disappears in biology': the Top 30 damage-prone endogenous metabolites.
Published in:
Biochemical Society Transactions, 2016, v. 44, n. 3, p. 961, doi. 10.1042/BST20160073
By:
- Lerma-Ortiz, Claudia;
- Jeffryes, James G.;
- Cooper, Arthur J. L.;
- Niehaus, Thomas D.;
- Thamm, Antje M. K.;
- Frelin, Océane;
- Aunins, Thomas;
- Fiehn, Oliver;
- de Crécy-Lagard, Valérie;
- Henry, Christopher S.;
- Hanson, Andrew D.
Publication type:
Article
Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction.
Published in:
Journal of Cellular Physiology, 2016, v. 231, n. 11, p. 2339, doi. 10.1002/jcp.25428
By:
- Henry, Christopher S.;
- Bernstein, Hans C.;
- Weisenhorn, Pamela;
- Taylor, Ronald C.;
- Lee, Joon ‐ Yong;
- Zucker, Jeremy;
- Song, Hyun ‐ Seob
Publication type:
Article
Cover Image, Volume 231, Number 11, November 2016.
Published in:
2016
By:
- Henry, Christopher S.;
- Bernstein, Hans C.;
- Weisenhorn, Pamela;
- Taylor, Ronald C.;
- Lee, Joon ‐ Yong;
- Zucker, Jeremy;
- Song, Hyun ‐ Seob
Publication type:
Other
Long-term phenotypic evolution of bacteria.
Published in:
Nature, 2015, v. 517, n. 7534, p. 369, doi. 10.1038/nature13827
By:
- Plata, Germán;
- Henry, Christopher S.;
- Vitkup, Dennis
Publication type:
Article
Respiratory energy demands and scope for demand expansion and destruction.
Published in:
Plant Physiology, 2023, v. 191, n. 4, p. 2093, doi. 10.1093/plphys/kiac493
By:
- Bathe, Ulschan;
- Leong, Bryan J.;
- Van Gelder, Kristen;
- Barbier, Guillaume G.;
- Henry, Christopher S.;
- Amthor, Jeffrey S.;
- Hanson, Andrew D.
Publication type:
Article
Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB).
Published in:
Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2016.00431
By:
- Thiaville, Jennifer J.;
- Frelin, Océane;
- García-Salinas, Carolina;
- Harrison, Katherine;
- Hasnain, Ghulam;
- Horenstein, Nicole A.;
- De La Garza, Rocio I. Díaz;
- Henry, Christopher S.;
- Hanson, Andrew D.;
- De Crécy-Lagard, Valérie
Publication type:
Article
Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data.
Published in:
Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2016.00275
By:
- Faria, José P.;
- Overbeek, Ross;
- Taylor, Ronald C.;
- Conrad, Neal;
- Vonstein, Veronika;
- Goelzer, Anne;
- Fromion, Vincent;
- Rocha, Miguel;
- Rocha, Isabel;
- Henry, Christopher S.
Publication type:
Article
Explaining bitcoin ownership in Canada: Trends from 2016 to 2021.
Published in:
Canadian Journal of Economics, 2024, v. 57, n. 3, p. 777, doi. 10.1111/caje.12724
By:
- Balutel, Daniela;
- Engert, Walter;
- Henry, Christopher S.;
- Huynh, Kim P.;
- Voia, Marcel
Publication type:
Article
Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1.
Published in:
2017
By:
- Henry, Christopher S.;
- Rotman, Ella;
- Lathem, Wyndham W.;
- Mandel, Mark J.;
- Hauser, Alan R.;
- Tyo, Keith E. J.
Publication type:
journal article
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.
Published in:
Frontiers in Plant Science, 2015, v. 6, p. 1, doi. 10.3389/fpls.2015.00142
By:
- Seaver, Samuel M. D.;
- Bradbury, Louis M. T.;
- Frelin, Océane;
- Zarecki, Raphy;
- Ruppin, Eytan;
- Hanson, Andrew D.;
- Henry, Christopher S.
Publication type:
Article

Found: 44