Siu Hung Joshua Chan - Dissemin

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All papers authored by Siu Hung Joshua Chan

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2024 Parsa Ghadermazi, Jorge L. Rico, Ethan Rimmelman, Siri Stenmark, Kenneth F. Reardon, Susan De Long, Siu Hung Joshua Chan

ORCID

ADToolbox: Incorporating Metagenomics Data for Improved Prediction of Anaerobic Digestion Dynamics

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Parsa Ghadermazi

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, Siu Hung Joshua Chan

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

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2023 Emily Jean Wilson, Nagabhishek Sirpu Natesh

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, Parsa Ghadermazi

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, Ramesh Pothuraju, Dipakkumar R. Prajapati

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, Sanjit Pandey, Jussuf T. Kaifi

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, John R. Dodam, Jeffrey N. Bryan, Christian L. Lorson

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, Aude A. Watrelot

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, Jason M. Foster, Thomas J. Mansell

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, Siu Hung Joshua Chan

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, Surinder K. Batra

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and 2 other authors

Red Cabbage Juice-Mediated Gut Microbiota Modulation Improves Intestinal Epithelial Homeostasis and Ameliorates Colitis

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Michael Shaffer

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, Kelly C. Wrighton

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, Mikayla A. Borton, Ben Bolduc, José P. Faria

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, Rory M. Flynn, Parsa Ghadermazi, Janaka N. Edirisinghe, Elisha M. Wood-Charlson, Christopher S. Miller

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, Siu Hung Joshua Chan

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, Matthew B. Sullivan

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, Christopher S. Henry, Others

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

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2022 Petronella R. Hove

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, Nora Jean Nealon

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, Siu Hung Joshua Chan

ORCID

, Shea M. Boyer

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, Hannah B. Haberecht

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, Elizabeth P. Ryan

ORCID

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

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2020 Kyle Bittinger

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, Chunyu Zhao, Yun Li, Eileen Ford, Elliot S. Friedman

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, Josephine Ni, Chiraag V. Kulkarni, Jingwei Cai, Yuan Tian, Qing Liu, Andrew D. Patterson, Debolina Sarkar, S.-I.-U. H. J. Chan

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, Costas Maranas, Anumita Saha-Shah and 14 other authors

Bacterial colonization reprograms the neonatal gut metabolome

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Carolina A. Contador

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, Siu-Kit Lo, Siu H. J. Chan

ORCID

ORCID

Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling

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2019 Satyakam Dash, Daniel G. Olson, Siu Hung Joshua Chan

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, Daniel Amador-Noguez, Lee R. Lynd

ORCID

, Costas D. Maranas

Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum

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Siu H. J. Chan

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, Elliot S. Friedman

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, Gary D. Wu, Costas D. Maranas

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

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Siu Hung Joshua Chan

ORCID

Bridging traditional evolutionary game theory and metabolic models for predicting Nash equilibrium of microbial metabolic interactions

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Jianming Liu, Siu Hung Joshua Chan

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, Jun Chen, Christian Solem, Peter Ruhdal Jensen

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

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Hoang V. Dinh

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, Patrick F. Suthers, Siu Hung Joshua Chan

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, Yihui Shen, Tianxia Xiao, Anshu Deewan, Sujit Sadashiv Jagtap

ORCID

, Joshua D. Rabinowitz, Huimin Zhao, Christopher V. Rao, Costas D. Maranas

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

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Laurent Heirendt, Sylvain Arreckx, Thomas Pfau

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, Sebastián N. Mendoza

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, Anne Richelle, Almut Heinken, Hulda S. Haraldsdóttir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdóttir, Chiam Yu Ng, German Preciat, Alise Žagare, Siu H. J. Chan

ORCID

and 40 other authors

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

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2018 Siu H. J. Chan

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, Lin Wang, Satyakam Dash, Costas D. Maranas

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

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2017 Siu H. J. Chan

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, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle

ORCID

, Costas D. Maranas

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

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Siu H. J. Chan

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, Margaret Simons, Costas D. Maranas

Computational Modeling of Microbial Communities

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Godefroid Charbon

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, Christopher Campion, Siu Hung Joshua Chan

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, Louise Bj, Louise Bjørn

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, Allan Weimann, Luis Cláudio Nascimento da Silva

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, Peter Ruhdal Jensen

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, Anders Løbner-Olesen

ORCID

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

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2016 Zhihao Wang, Siu Hung Joshua Chan

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, Suresh Sudarsan, Lars M. Blank, Peter Ruhdal Jensen, Christian Solem

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

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Limin Zhang, Cen Xie, Robert G. Nichols, Nichols Rg, Siu Hung Joshua Chan

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, Chan Sh, Changtao Jiang, Ruixin Hao, Smith Pb, Philip B. Smith, Jingwei Cai, Simons Mn, Margaret N. Simons, Emmanuel Hatzakis, Maranas Cd and 5 other authors

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

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Jianming Liu

ORCID

, Siu Hung Joshua Chan

ORCID

, Theis Brock-Nannestad, Jun Chen, Sang Yup Lee, Christian Solem, Peter Ruhdal Jensen

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

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