Publications by authors named "Joshua J Hamilton"

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Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions.
Jun Feng, Yili Qian, Zhichao Zhou, Sarah Ertmer, Eugenio I Vivas, Joshua J Hamilton

Cell Host Microbe· February 2022

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Design of synthetic human gut microbiome assembly and butyrate production.
Ryan L Clark, Bryce M Connors, David M Stevenson, Susan E Hromada, Joshua J Hamilton

Nat Commun· May 2021

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Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models.
Matthew J Scarborough, Joshua J Hamilton, Elizabeth A Erb, Timothy J Donohue, Daniel R Noguera

mSystems· September 2020

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Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities.
Xinyun Cao, Joshua J Hamilton, Ophelia S Venturelli

Biochemistry· January 2019

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acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively Synthesized Retinal.
Jeffrey R Dwulit-Smith, Joshua J Hamilton, David M Stevenson, Shaomei He, Ben O Oyserman

Appl Environ Microbiol· December 2018

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Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome.
Matthew J Scarborough, Christopher E Lawson, Joshua J Hamilton, Timothy J Donohue, Daniel R Noguera

mSystems· November 2018

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TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.
Robin R Rohwer, Joshua J Hamilton, Ryan J Newton, Katherine D McMahon

mSphere· September 2018

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Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.
Sarahi L Garcia, Moritz Buck, Joshua J Hamilton, Christian Wurzbacher, Hans-Peter Grossart

mSphere· June 2018

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Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.
Joshua J Hamilton, Sarahi L Garcia, Brittany S Brown, Ben O Oyserman, Francisco Moya-Flores

mSystems· August 2017

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Metabolic network analysis reveals microbial community interactions in anammox granules.
Christopher E Lawson, Sha Wu, Ananda S Bhattacharjee, Joshua J Hamilton, Katherine D McMahon

Nat Commun· May 2017

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Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A.
Elena Vinay-Lara, Joshua J Hamilton, Buffy Stahl, Jeff R Broadbent, Jennifer L Reed

PLoS One· August 2015

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Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community.
Joshua J Hamilton, Montserrat Calixto Contreras, Jennifer L Reed

PLoS Comput Biol· July 2015

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Software platforms to facilitate reconstructing genome-scale metabolic networks.
Joshua J Hamilton, Jennifer L Reed

Environ Microbiol· January 2014

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Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.
Joshua J Hamilton, Vivek Dwivedi, Jennifer L Reed

Biophys J· July 2013

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Identification of functional differences in metabolic networks using comparative genomics and constraint-based models.
Joshua J Hamilton, Jennifer L Reed

PLoS One· August 2012

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