Publications
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Year âŒ
ORT: A workflow linking genome-scale metabolic models with reactive transport codes Bioinformatics 38 (3) 778-784 | 2022 |
Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome Microbial Systems Biology 291-320 | 2022 |
Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions Metabolic Engineering 69 302-312 | 2022 |
kb_DRAM: Annotating and functional profiling of genomes with DRAM in KBase bioRxiv | 2022 |
Dynamic genetic adaptation of Bacteroides thetaiotaomicron murine gut colonization bioRxiv | 2022 |
A genomic catalog of Earthâs microbiomes Nature biotechnology 39 (4) 499-509 | 2021 |
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes Nucleic acids research 49 (D1) D575-D588 | 2021 |
The number of catalytic cycles in an enzymeâs lifetime and why it matters to metabolic engineering Proceedings of the National Academy of Sciences 118 (13) | 2021 |
Quantum mechanical methods predict accurate thermodynamics of biochemical reactions ACS omega 6 (14) 9948-9959 | 2021 |
TranSyT, the Transport Systems Tracker bioRxiv | 2021 |
Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis Nature communications 12 (1) 1-17 | 2021 |
Elruna: elimination rule-based network alignment Journal of Experimental Algorithmics (JEA) 26 1-32 | 2021 |
Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis Nature Communications 12 (1) 1-17 | 2021 |
The Moderately (D) efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair Biochemistry 60 (47) 3555-3565 | 2021 |
A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum. Current Plant Biology 28 100229 | 2021 |
Genome Extraction from Shotgun Metagenome Sequence Data | 2021 |
Metabolite Damage and Damage-Control in a Minimal Genome bioRxiv | 2021 |
Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community Science advances 6 (33) eaba0353 | 2020 |
MEMOTE for standardized genome-scale metabolic model testing Nature biotechnology 38 (3) 272-276 | 2020 |
Enzymes as parts in need of replacementâand how to extend their working life Trends in Plant Science 25 (7) 661-669 | 2020 |
The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes bioRxiv | 2020 |
Draft Genome Sequence of 2-Methylpyridine-, 2-Ethylpyridine-, and 2-Hydroxypyridine-Degrading Arthrobacter sp. Strain ATCC 49987 Microbiology resource announcements 9 (34) e00748-20 | 2020 |
Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials Scientific reports 10 (1) 1-16 | 2020 |
Draft Genome Sequence of Pseudarthrobacter sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium Microbiology resource announcements 9 (38) e00299-20 | 2020 |
AGORA2: large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities BioRxiv | 2020 |
Microbial and metabolic succession on common building materials under high humidity conditions Nature communications 10 (1) 1-12 | 2019 |
Metabolic in silico network expansions to predict and exploit enzyme promiscuity Microbial Metabolic Engineering 11-21 | 2019 |
Draft genome sequence of Enterobacter sp. strain A8, a Carbazole-Degrading bacterium Microbiology Resource Announcements 8 (18) e00301-19 | 2019 |
Draft genome sequence of Rhodococcus sp. strain ATCC 49988, a quinoline-degrading bacterium Microbiology resource announcements 8 (25) e00403-19 | 2019 |
Network Alignment by Propagating Reliable Similarities CoRR | 2019 |
Reconstruction and analysis of central metabolism in microbes Metabolic Network Reconstruction and Modeling 111-129 | 2018 |
Metabolic network modeling for computer-aided design of microbial interactions Emerg. Areas Bioeng 2 793-801 | 2018 |
A plastidial pantoate transporter with a potential role in pantothenate synthesis Biochemical Journal 475 (4) 813-825 | 2018 |
A pathway for every product? Tools to discover and design plant metabolism Plant Science 273 61-70 | 2018 |
PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency The Plant Journal 95 (6) 1102-1113 | 2018 |
Memote: A community driven effort towards a standardized genome-scale metabolic model test suite BioRxiv 350991 | 2018 |
KBase: the United States department of energy systems biology knowledgebase Nature biotechnology 36 (7) 566-569 | 2018 |
Methods for automated genome-scale metabolic model reconstruction Biochemical Society Transactions 46 (4) 931-936 | 2018 |
Implementing and evaluating a Gaussian mixture framework for identifying gene function from TnSeq data BIOCOMPUTING 2019: Proceedings of the Pacific Symposium 172-183 | 2018 |
Environmental sources of bacteria differentially influence host-associated microbial dynamics MSystems 3 (3) e00052-18 | 2018 |
Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite. BioRxiv, 350991 | 2018 |
Metabolic reconstruction and modeling microbial electrosynthesis Scientific reports 7 (1) 1-12 | 2017 |
Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center Nucleic acids research 45 (D1) D535-D542 | 2017 |
The microbiome as a source of new enterprises and job creation: considering clinical faecal and synthetic microbiome transplants and therapeutic regulation Microbial Biotechnology 10 (1) 4 | 2017 |
A novel signal transduction protein: Combination of solute binding and tandem PASâlike sensor domains in one polypeptide chain Protein Science 26 (4) 857-869 | 2017 |
Generation and validation of the iKp1289 metabolic model for Klebsiella pneumoniae KPPR1 The Journal of infectious diseases 215 (suppl_1) S37-S43 | 2017 |
Evolution of substrate specificity in a retained enzyme driven by gene loss Elife 6 e22679 | 2017 |
Metabolite damage and repair in metabolic engineering design Metabolic engineering 44 150-159 | 2017 |
Comparative'Omics and Modeling Microbial Community Interactions Using the DOE Systems Biology Knowledgebase (KBase) 2017 ESA Annual Meeting (August 6--11) | 2017 |
Metabolite damage and metabolite damage control in plants Annual review of plant biology 67 131-152 | 2016 |
Systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5â-phosphate production in E. coli PLoS computational biology 12 (1) e1004705 | 2016 |
Co-occurrence of analogous enzymes determines evolution of a novel (ÎČα) 8-isomerase sub-family after non-conserved mutations in flexible loop Biochemical Journal 473 (9) 1141-1152 | 2016 |
Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data Frontiers in Microbiology 7 275 | 2016 |
Experimental and metabolic modeling evidence for a folate-cleaving side-activity of ketopantoate hydroxymethyltransferase (PanB) Frontiers in microbiology 7 431 | 2016 |
Microbial community metabolic modeling: a community dataâdriven network reconstruction Journal of cellular physiology 231 (11) 2339-2345 | 2016 |
Draft genome sequence of a multidrug-resistant Klebsiella quasipneumoniae subsp. similipneumoniae isolate from a clinical source Genome Announcements 4 (3) e00422-16 | 2016 |
âNothing of chemistry disappears in biologyâ: the Top 30 damage-prone endogenous metabolites Biochemical Society Transactions 44 (3) 961-971 | 2016 |
Constructing and analyzing metabolic flux models of microbial communities Hydrocarbon and Lipid Microbiology Protocols 247-273 | 2016 |
Systematic identification and analysis of frequent gene fusion events in metabolic pathways BMC genomics 17 (1) 1-17 | 2016 |
Modeling central metabolism and energy biosynthesis across microbial life Bmc Genomics 17 (1) 1-11 | 2016 |
Computing and applying atomic regulons to understand gene expression and regulation Frontiers in microbiology 7 1819 | 2016 |
Commentary Article BIOCHEMICAL JOURNAL 473 (part 9) | 2016 |
Co-occurrence of analogous enzymes determines evolution of a novel () 8-isomerase sub-family after non-conserved mutations in flexible loop Biochemical Journal 473 (9) | 2016 |
From DNA to FBA: how to build your own genome-scale metabolic model Frontiers in microbiology 7 907 | 2016 |
Network-based metabolic analysis and microbial community modeling Current Opinion in Microbiology 31 124-131 | 2016 |
Elucidating genomic gaps using phenotypic profiles F1000Research 3 210 | 2016 |
Enabling comparative modeling of closely related genomes: example genus Brucella 3 Biotech 5 (1) 101-105 | 2015 |
Long-term phenotypic evolution of bacteria Nature 517 (7534) 369-372 | 2015 |
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm Frontiers in plant science 6 142 | 2015 |
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics Journal of cheminformatics 7 (1) 1-8 | 2015 |
A directed-overflow and damage-control N-glycosidase in riboflavin biosynthesis Biochemical journal 466 (1) 137-145 | 2015 |
Predicting ecosystem emergent properties at multiple scales Environmental microbiology reports 7 (1) 20-22 | 2015 |
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models Briefings in bioinformatics 15 (4) 592-611 | 2014 |
Comparative genomics of cultured and uncultured strains suggests genes essential for free-living growth of Liberibacter PLoS One 9 (1) e84469 | 2014 |
Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms PloS one 9 (5) e98372 | 2014 |
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource Proceedings of the National Academy of Sciences 111 (26) 9645-9650 | 2014 |
Tapping the wealth of microbial data in high-throughput metabolic model reconstruction Metabolic Flux Analysis 19-45 | 2014 |
Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models PLoS computational biology 10 (10) e1003882 | 2014 |
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model Nucleic acids research 41 (1) 687-699 | 2013 |
Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED Systems Metabolic Engineering 17-45 | 2013 |
Genome-wide metabolic network reconstruction of the picoalga Ostreococcus Journal of experimental botany 63 (6) 2353-2362 | 2012 |
Frontiers in metabolic reconstruction and modeling of plant genomes Journal of experimental botany 63 (6) 2247-2258 | 2012 |
Plant B vitamin pathways and their compartmentation: a guide for the perplexed Journal of experimental botany 63 (15) 5379-5395 | 2012 |
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models PloS one 7 (10) e48053 | 2012 |
Connecting genotype to phenotype in the era of high-throughput sequencing Biochimica et Biophysica Acta (BBA)-General Subjects 1810 (10) 967-977 | 2011 |
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset Microbial informatics and experimentation 1 (1) 1-11 | 2011 |
Competitive and cooperative metabolic interactions in bacterial communities Nature communications 2 (1) 1-7 | 2011 |
Relative metabolomic flux: Predicting changes in the environmental metabolome from the metagenome Microbial Informatics and Experimentation 1 (4) 1-11 | 2011 |
High-throughput generation, optimization and analysis of genome-scale metabolic models Nature biotechnology 28 (9) 977-982 | 2010 |
Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3âhydroxypropanoate Biotechnology and bioengineering 106 (3) 462-473 | 2010 |
Building the blueprint of life Biotechnology journal 5 (7) 695-704 | 2010 |
Analysis of the effect of reversibility constraints on the predictions of genome-scale metabolic models Advances in Bioinformatics 209-215 | 2010 |
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations Genome Biol 10 (6) R69 | 2009 |
Application of high-performance computing to the reconstruction, analysis, and optimization of genome-scale metabolic models Journal of Physics: Conference Series 180 (1) 012025 | 2009 |
Discovery of novel routes for the production of fuels and chemicals Design for Energy and Environment 10 141-147 | 2009 |
Group contribution method for thermodynamic analysis of complex metabolic networks Biophysical journal 95 (3) 1487-1499 | 2008 |
A genomeâscale metabolic reconstruction for Escherichia coli Kâ12 MG1655 that accounts for 1260 ORFs and thermodynamic information Molecular systems biology 3 (1) 121 | 2007 |
Thermodynamics-based metabolic flux analysis Biophysical journal 92 (5) 1792-1805 | 2007 |
Computational thermodynamic and biosynthetic analysis of genome-scale metabolic models | 2007 |
Genome-scale thermodynamic analysis of Escherichia coli metabolism Biophysical journal 90 (4) 1453-1461 | 2006 |
Exploring the diversity of complex metabolic networks Bioinformatics 21 (8) 1603-1609 | 2005 |
Computational discovery of biochemical routes to specialty chemicals Chemical engineering science 59 (22-23) 5051-5060 | 2004 |
How to scale-up mixing processes in non-Newtonian fluids Chem Eng Prog 99 (5) 44-52 | 2003 |
Automatic generation of genome-scale metabolism and expression models for bacteria | |
Genome to Structure: From Multiple Sequence Alignment to Virtual Ligand Screening Using Co-Evolutionary Protein-Residue Contact-Prediction in KBase | |
High-throughput phenotype profiling for bacterial flux-balance model optimization Proteins 811 19 | |
New pipeline for multi-omics data integration and discovery in KBase to identify the mechanism driving metabolic/OTU dynamics in a microbiome | |
Elucidating genomic gaps using phenotypic profiles [version 1; peer review: 2 approved with reservations] | |
Dynamic Genetic Adaptation of Bacteroides thetaiotaomicron During Murine Gut Colonization Bacteroides thetaiotaomicron |