Christopher Henry

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Janaka N EdirisingheAssistant Scientist, Argonne National Labs / University of Chicago, IL, USAVerified email at anl.gov
Rick StevensProfessor of Computer Science, University of ChicagoVerified email at ci.uchicago.edu
Andrew D. HansonHorticultural Sciences Department, University of FloridaVerified email at ufl.edu
José P. FariaAssistant Computational BiologistVerified email at anl.gov
Vassily HatzimanikatisAssociate Professor, EPFLVerified email at epfl.ch
Sam SeaverComputational Scientist, Argonne National LaboratoryVerified email at mcs.anl.gov
Jack A GilbertUniversity of California, San DiegoVerified email at ucsd.edu
James JeffryesPostdoctoral Researcher, Argonne National LaboratoryVerified email at mcs.anl.gov
Valérie de Crécy-LagardDistinguished Professor, Microbiology and Cell Science Dpt, University of FloridaVerified email at ufl.edu
Fangfang XiaScientist, Argonne National LaboratoryVerified email at anl.gov
Veronika VonsteinFellowship for Interpretation of GenomesVerified email at theFIG.info
Eytan RuppinChief, Cancer Data Science Lab (CDSL), NCI/NIHVerified email at nih.gov
Thomas D NiehausAssistant Professor, University of MinnesotaVerified email at umn.edu
Keith TyoAssociate Professor of Chemical and Biological Engineering, Northwestern UniversityVerified email at northwestern.edu
Robert OlsonArgonne National LaboratoryVerified email at mcs.anl.gov
Scott DevoidExperimental Computer Systems, Argonne National LaboratoryVerified email at anl.gov
Uri GophnaThe Shmunis School of Biomedicine and Cancer Research, Tel Aviv UniversityVerified email at tauex.tau.ac.il
Rob EdwardsMatthew Flinders Fellow of Bioinformatics, Flinders University, Adelaide, SA, AustraliaVerified email at flinders.edu.au
Hyun-Seob SongUniversity of Nebraska-Lincoln (UNL)Verified email at unl.edu
Miguel RochaAssociate Professor, Dept. Informatics and Centre Biological Engineering, Universidade do MinhoVerified email at di.uminho.pt

Christopher Henry

Computational Biologist, Argonne National Laboratory

Verified email at mcs.anl.gov

Metabolic Modeling and Computational Biology


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A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information AM Feist, CS Henry, JL Reed, M Krummenacker, AR Joyce, PD Karp, ... Molecular systems biology 3 (1), 121, 2007	1776	2007
Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center AR Wattam, JJ Davis, R Assaf, S Boisvert, T Brettin, C Bun, N Conrad, ... Nucleic acids research 45 (D1), D535-D542, 2017	1653	2017
KBase: the United States department of energy systems biology knowledgebase AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, ... Nature biotechnology 36 (7), 566-569, 2018	1401	2018
High-throughput generation, optimization and analysis of genome-scale metabolic models CS Henry, M DeJongh, AA Best, PM Frybarger, B Linsay, RL Stevens Nature biotechnology 28 (9), 977-982, 2010	1259	2010
Thermodynamics-based metabolic flux analysis CS Henry, LJ Broadbelt, V Hatzimanikatis Biophysical journal 92 (5), 1792-1805, 2007	762	2007
A genomic catalog of Earth’s microbiomes S Nayfach, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, ... Nature biotechnology 39 (4), 499-509, 2021	736	2021
Competitive and cooperative metabolic interactions in bacterial communities S Freilich, R Zarecki, O Eilam, ES Segal, CS Henry, M Kupiec, U Gophna, ... Nature communications 2 (1), 589, 2011	566	2011
Group contribution method for thermodynamic analysis of complex metabolic networks MD Jankowski, CS Henry, LJ Broadbelt, V Hatzimanikatis Biophysical journal 95 (3), 1487-1499, 2008	508	2008
Exploring the diversity of complex metabolic networks V Hatzimanikatis, C Li, JA Ionita, CS Henry, MD Jankowski, LJ Broadbelt Bioinformatics 21 (8), 1603-1609, 2005	442	2005
MEMOTE for standardized genome-scale metabolic model testing C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ... Nature biotechnology 38 (3), 272-276, 2020	426	2020
Genome-scale thermodynamic analysis of Escherichia coli metabolism CS Henry, MD Jankowski, LJ Broadbelt, V Hatzimanikatis Biophysical journal 90 (4), 1453-1461, 2006	282	2006
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics JG Jeffryes, RL Colastani, M Elbadawi-Sidhu, T Kind, TD Niehaus, ... Journal of cheminformatics 7, 1-8, 2015	242	2015
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models RK Aziz, S Devoid, T Disz, RA Edwards, CS Henry, GJ Olsen, R Olson, ... PloS one 7 (10), e48053, 2012	230	2012
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations CS Henry, JF Zinner, MP Cohoon, RL Stevens Genome Biol 10 (6), R69, 2009	214	2009
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes SMD Seaver, F Liu, Q Zhang, J Jeffryes, JP Faria, JN Edirisinghe, ... Nucleic acids research 49 (D1), D575-D588, 2021	213	2021
Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3‐hydroxypropanoate CS Henry, LJ Broadbelt, V Hatzimanikatis Biotechnology and bioengineering 106 (3), 462-473, 2010	197	2010
Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED S Devoid, R Overbeek, M DeJongh, V Vonstein, AA Best, C Henry Systems metabolic engineering: methods and protocols, 17-45, 2013	172	2013
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine A Heinken, J Hertel, G Acharya, DA Ravcheev, M Nyga, OE Okpala, ... Nature Biotechnology 41 (9), 1320-1331, 2023	171	2023
Metabolic reconstruction and modeling microbial electrosynthesis CW Marshall, DE Ross, KM Handley, PB Weisenhorn, JN Edirisinghe, ... Scientific Reports 7 (1), 8391, 2017	136	2017
Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis D van der Lelie, A Oka, S Taghavi, J Umeno, TJ Fan, KE Merrell, ... Nature communications 12 (1), 3105, 2021	133	2021

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