Metabolic network analysis reveals microbial community interactions in anammox granules CE Lawson, S Wu, AS Bhattacharjee, JJ Hamilton, KD McMahon, R Goel, ... Nature communications 8, 15416, 2017 | 567 | 2017 |
Design of synthetic human gut microbiome assembly and butyrate production RL Clark, BM Connors, DM Stevenson, SE Hromada, JJ Hamilton, ... Nature Communications 12 (1), 1-16, 2021 | 130 | 2021 |
Software platforms to facilitate reconstructing genome‐scale metabolic networks JJ Hamilton, JL Reed Environmental microbiology 16 (1), 49-59, 2014 | 104 | 2014 |
Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome MJ Scarborough, CE Lawson, JJ Hamilton, TJ Donohue, DR Noguera mSystems 3 (6), e00221-18, 2018 | 82 | 2018 |
Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models JJ Hamilton, V Dwivedi, JL Reed Biophysical journal 105 (2), 512-522, 2013 | 74 | 2013 |
TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution RR Rohwer, JJ Hamilton, RJ Newton, KD McMahon mSphere 3 (5), e00327-18, 2018 | 71* | 2018 |
Identification of functional differences in metabolic networks using comparative genomics and constraint-based models JJ Hamilton, JL Reed PloS one 7 (4), e34670, 2012 | 68 | 2012 |
Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions J Feng, Y Qian, Z Zhou, S Ertmer, EI Vivas, F Lan, JJ Hamilton, FE Rey, ... Cell Host & Microbe 30 (2), 200-215. e12, 2022 | 54 | 2022 |
Genome–Scale Reconstruction of Metabolic Networks of Lactobacillus casei ATCC 334 and 12A E Vinay-Lara, JJ Hamilton, B Stahl, JR Broadbent, JL Reed, JL Steele PLOS ONE 9 (11), e110785, 2014 | 46 | 2014 |
Thermodynamics and H 2 Transfer in a Methanogenic, Syntrophic Community JJ Hamilton, M Calixto Contreras, JL Reed PLOS Comput Biol 11 (7), e1004364, 2015 | 32 | 2015 |
Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities X Cao, JJ Hamilton, OS Venturelli Biochemistry 58 (2), 94-107, 2018 | 30 | 2018 |
Diagnosing and predicting mixed-culture fermentations with unicellular and guild-based metabolic models MJ Scarborough, JJ Hamilton, EA Erb, TJ Donohue, DR Noguera Msystems 5 (5), e00755-20, 2020 | 28 | 2020 |
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI JJ Hamilton, SL Garcia, BS Brown, BO Oyserman, F Moya-Flores, ... mSystems 2 (4), e00091-17, 2017 | 27* | 2017 |
Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria SL Garcia, M Buck, JJ Hamilton, C Wurzbacher, HP Grossart, ... mSphere 3 (3), e00202-18, 2018 | 25 | 2018 |
acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively Synthesized Retinal JR Dwulit-Smith, JJ Hamilton, DM Stevenson, S He, BO Oyserman, ... Appl. Environ. Microbiol. 84 (24), e01678-18, 2018 | 17 | 2018 |
High-complexity synthetic gut bacterial communities MA Fischbach, AR Brumbaugh, AG Cheng, D Dodd, AJ Aranda-Diaz, ... US Patent App. 17/999,516, 2023 | | 2023 |
Microbial consortia LR Swem, P Kumar, A Bhalla, SA Tripathi, A Parmar, JJ Hamilton, ... US Patent App. 18/060,831, 2023 | | 2023 |
MICROBIAL CONSORTIA FOR THE TREATMENT OF DISEASE L Swem, D Ricci, AR Brumbaugh, J Cremin, JJ Hamilton, S Tripathi, ... US Patent App. 17/906,060, 2023 | | 2023 |
POS-461 CREATION OF RATIONALLY DESIGNED AND METABOLICALLY ACTIVE MICROBIOME CONSORTIA FOR TREATMENT OF ENTERIC HYPEROXALURIA D Ricci, J Hamilton, S Tripathi, A Brumbaugh, J Cremin, N Ou, H LAYMAN, ... Kidney International Reports 7 (2), S204-S205, 2022 | | 2022 |