S. H. Chan

发表

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0.

Francisco J. Planes, Ronan M. T. Fleming, Sarah M. Keating, 2017, 1710.04038.

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

Hoang V. Dinh, C. V. Rao, C. Maranas, 2019, bioRxiv.

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

Hoang V. Dinh, C. V. Rao, C. Maranas, 2019, bioRxiv.

Computational Modeling of Microbial Communities

Margaret N. Simons, C. Maranas, S. H. Chan, 2017 .

Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production

Hoang V. Dinh, C. Maranas, J. Rabinowitz, 2020, Metabolic engineering communications.

Creation and analysis of biochemical constraint-based models : the COBRA Toolbox v 3 . 0 26 th February 2018

Francisco J. Planes, Ronan M. T. Fleming, Maike K. Aurich, 2018 .

Integrated Profiling of Gram-Positive and Gram-Negative Probiotic Genomes, Proteomes and Metabolomes Revealed Small Molecules with Differential Growth Inhibition of Antimicrobial-Resistant Pathogens

E. Ryan, S. H. Chan, N. J. Nealon, 2022, Journal of dietary supplements.

Acetate Kinase Isozymes Confer Robustness in Acetate Metabolism

P. R. Jensen, S. H. Chan, C. Solem, 2014, PloS one.

Elucidating Flux Regulation of the Fermentation Modes of Lactococcus lactis: A Mutlilevel Study

P. R. Jensen, S. H. Chan, C. Solem, 2014 .

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Anne Richelle, Iñigo Apaolaza, Lin Wang, 2019, Nature Protocols.

Systems Biology – A Guide for Understanding and Developing Improved Strains of Lactic Acid Bacteria

Peter Ruhdal Jensen, Jun Chen, Jianming Liu, 2019, Front. Microbiol..

Re-wiring of energy metabolism promotes viability during hyperreplication stress in E. coli

P. R. Jensen, S. H. Chan, Godefroid Charbon, 2017, PLoS genetics.

Combining metabolic engineering and biocompatible chemistry for high-yield production of homo-diacetyl and homo-(S,S)-2,3-butanediol.

Peter Ruhdal Jensen, Christian Solem, Jun Chen, 2016, Metabolic engineering.

Predicting the Longitudinally and Radially Varying Gut Microbiota Composition Using Multi-Scale Microbial Metabolic Modeling

C. Maranas, S. H. Chan, E. Friedman, 2019, Processes.

SteadyCom: Predicting microbial abundances while ensuring community stability

Costas D. Maranas, Siu Hung Joshua Chan, Margaret N. Simons, 2017, PLoS Comput. Biol..

Predicting Nash equilibria for microbial metabolic interactions

Jingyi Cai, Siu Hung Joshua Chan, Tianwei Tan, 2020, Bioinform..

Bridging evolutionary game theory and metabolic models for predicting microbial metabolic interactions

Jingyi Cai, Tianwei Tan, Siu Hung Joshua Chan, 2019, bioRxiv.

Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

P. R. Jensen, S. H. Chan, Mike Vestergaard, 2016, Scientific Reports.

Bacterial colonization reprograms the neonatal gut metabolome

F. Bushman, B. Garcia, C. Maranas, 2020, Nature Microbiology.

Nissle probiotic 1 supernatants identify distinct pathways that mediate growth suppression of antimicrobial-2 resistant pathogens 3 4 *

E. Ryan, S. H. Chan, N. J. Nealon, 2020 .

Accelerating flux balance calculations in genome‐scale metabolic models by localizing the application of loopless constraints

Lin Wang, Costas D. Maranas, Satyakam Dash, 2017, Bioinform..

Standardizing biomass reactions and ensuring complete mass balance in genome‐scale metabolic models

Lin Wang, Jingyi Cai, Siu H. J. Chan, 2017, Bioinform..

Elucidation of the regulatory role of the fructose operon reveals a novel target for enhancing the NADPH supply in Corynebacterium glutamicum.

L. Blank, P. R. Jensen, S. H. Chan, 2016, Metabolic engineering.

Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism

Limin Zhang, Costas D. Maranas, Frank J. Gonzalez, 2016, mSystems.

A decomposition approach for computing elementary flux modes in genome-scale metabolic networks

Siu-hung Joshua Chan, S. H. Chan, 2011 .

Metabolic Engineering Interventions for Sustainable 2,3-Butanediol Production in Gas-Fermenting Clostridium autoethanogenum

S. H. Chan, Angela Re, Parsa Ghadermazi, 2022, mSystems.

Estimating biological elementary flux modes that decompose a flux distribution by the minimal branching property

Peter Ruhdal Jensen, Ping Ji, Christian Solem, 2014, Bioinform..

Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks

Ping Ji, Siu Hung Joshua Chan, P. Ji, 2011, Bioinform..

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

José P. Faria, C. Henry, S. H. Chan, 2022, bioRxiv.

Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution

S. H. Chan, Parsa Ghadermazi, 2024, bioRxiv.

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

Hoang V. Dinh, C. V. Rao, C. Maranas, 2019, bioRxiv.

Metabolomics and proteomics of L. rhamnosus GG and E. coli Nissle probiotic supernatants identify distinct pathways that mediate growth suppression of antimicrobial-resistant pathogens

E. Ryan, S. H. Chan, N. J. Nealon, 2020, bioRxiv.

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

José P. Faria, Janaka N. Edirisinghe, C. Henry, 2023, Bioinformatics.

Elucidation of the regulatory role of the fructose operon reveals a novel target for enhancing the NADPH supply in Corynebacterium glutamicum.

L. Blank, P. R. Jensen, S. H. Chan, 2016, Metabolic engineering.

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Sarah M. Keating, Maike K. Aurich, H. S. Hinton, 2019, Nature Protocols.