Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
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
Published in Nature biotechnology (01.09.2023)
Published in Nature biotechnology (01.09.2023)
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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
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, Mao, Chunhong, Nordberg, Eric K, Olsen, Gary J, Murphy-Olson, Daniel E, Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D, Shukla, Maulik, Vonstein, Veronika, Warren, Andrew, Xia, Fangfang, Yoo, Hyunseung, Stevens, Rick L
Published in Nucleic acids research (04.01.2017)
Published in Nucleic acids research (04.01.2017)
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High-throughput generation, optimization and analysis of genome-scale metabolic models
Henry, Christopher S, DeJongh, Matthew, Best, Aaron A, Frybarger, Paul M, Linsay, Ben, Stevens, Rick L
Published in Nature biotechnology (01.09.2010)
Published in Nature biotechnology (01.09.2010)
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Journal Article
Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis
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
Published in Nature communications (28.05.2021)
Published in Nature communications (28.05.2021)
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Journal Article
Competitive and cooperative metabolic interactions in bacterial communities
Freilich, Shiri, Zarecki, Raphy, Eilam, Omer, Segal, Ella Shtifman, Henry, Christopher S., Kupiec, Martin, Gophna, Uri, Sharan, Roded, Ruppin, Eytan
Published in Nature communications (13.12.2011)
Published in Nature communications (13.12.2011)
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Journal Article
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models
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
Published in PloS one (24.10.2012)
Published in PloS one (24.10.2012)
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Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks
Jankowski, Matthew D., Henry, Christopher S., Broadbelt, Linda J., Hatzimanikatis, Vassily
Published in Biophysical journal (01.08.2008)
Published in Biophysical journal (01.08.2008)
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Journal Article
Metabolic Reconstruction and Modeling Microbial Electrosynthesis
Marshall, Christopher W., Ross, Daniel E., Handley, Kim M., Weisenhorn, Pamela B., Edirisinghe, Janaka N., Henry, Christopher S., Gilbert, Jack A., May, Harold D., Norman, R. Sean
Published in Scientific reports (21.08.2017)
Published in Scientific reports (21.08.2017)
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A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
Palsson, Bernhard Ø, Feist, Adam M, Henry, Christopher S, Reed, Jennifer L, Krummenacker, Markus, Joyce, Andrew R, Karp, Peter D, Broadbelt, Linda J, Hatzimanikatis, Vassily
Published in Molecular systems biology (2007)
Published in Molecular systems biology (2007)
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'Nothing of chemistry disappears in biology': the Top 30 damage-prone endogenous metabolites
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
Published in Biochemical Society transactions (15.06.2016)
Published in Biochemical Society transactions (15.06.2016)
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MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics
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
Published in Journal of cheminformatics (28.08.2015)
Published in Journal of cheminformatics (28.08.2015)
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Journal Article
A directed-overflow and damage-control N-glycosidase in riboflavin biosynthesis
Frelin, Océane, Huang, Lili, Hasnain, Ghulam, Jeffryes, James G, Ziemak, Michael J, Rocca, James R, Wang, Bing, Rice, Jennifer, Roje, Sanja, Yurgel, Svetlana N, Gregory, 3rd, Jesse F, Edison, Arthur S, Henry, Christopher S, de Crécy-Lagard, Valérie, Hanson, Andrew D
Published in Biochemical journal (15.02.2015)
Published in Biochemical journal (15.02.2015)
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High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
Seaver, Samuel M. D., Gerdes, Svetlana, Frelin, Océane, Lerma-Ortiz, Claudia, Bradbury, Louis M. T., Zallot, Rémi, Hasnain, Ghulam, Niehaus, Thomas D., Yacoubi, Basma El, Pasternak, Shiran, Olson, Robert, Pusch, Gordon, Overbeek, Ross, Stevens, Rick, de Crécy-Lagard, Valérie, Ware, Doreen, Hanson, Andrew D., Henry, Christopher S.
Published in Proceedings of the National Academy of Sciences - PNAS (01.07.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (01.07.2014)
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Comparative genomics of cultured and uncultured strains suggests genes essential for free-living growth of Liberibacter
Fagen, Jennie R, Leonard, Michael T, McCullough, Connor M, Edirisinghe, Janaka N, Henry, Christopher S, Davis, Michael J, Triplett, Eric W
Published in PloS one (08.01.2014)
Published in PloS one (08.01.2014)
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Journal Article
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model
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
Published in Nucleic acids research (01.01.2013)
Published in Nucleic acids research (01.01.2013)
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Journal Article
Metabolite Damage and Damage Control in a Minimal Genome
Haas, Drago, Thamm, Antje M, Sun, Jiayi, Huang, Lili, Sun, Lijie, Beaudoin, Guillaume A W, Wise, Kim S, Lerma-Ortiz, Claudia, Bruner, Steven D, Breuer, Marian, Luthey-Schulten, Zaida, Lin, Jiusheng, Wilson, Mark A, Brown, Greg, Yakunin, Alexander F, Kurilyak, Inna, Folz, Jacob, Fiehn, Oliver, Glass, John I, Hanson, Andrew D, Henry, Christopher S, de Crécy-Lagard, Valérie
Published in mBio (30.08.2022)
Published in mBio (30.08.2022)
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Journal Article
Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism
Henry, Christopher S., Jankowski, Matthew D., Broadbelt, Linda J., Hatzimanikatis, Vassily
Published in Biophysical journal (15.02.2006)
Published in Biophysical journal (15.02.2006)
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