| Machine learning to predict microbial community functions: an analysis of dissolved organic carbon from litter decomposition J Thompson, R Johansen, J Dunbar, B Munsky PLoS One 14 (7), e0215502, 2019 | 96 | 2019 |
| Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics M Baranwal, RL Clark, J Thompson, Z Sun, AO Hero, OS Venturelli Elife 11, e73870, 2022 | 33* | 2022 |
| Microbial communities influence soil dissolved organic carbon concentration by altering metabolite composition TP Campbell, DEM Ulrich, J Toyoda, J Thompson, B Munsky, ... Frontiers in Microbiology 12, 799014, 2022 | 22 | 2022 |
| Soil bacterial and fungal richness forecast patterns of early pine litter decomposition MBN Albright, R Johansen, J Thompson, D Lopez, LV Gallegos-Graves, ... Frontiers in Microbiology 11, 542220, 2020 | 17 | 2020 |
| Differences in substrate use linked to divergent carbon flow during litter decomposition MBN Albright, J Thompson, ME Kroeger, R Johansen, DEM Ulrich, ... FEMS Microbiology Ecology 96 (8), fiaa135, 2020 | 16 | 2020 |
| Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations E Ostrem Loss, J Thompson, PLK Cheung, Y Qian, OS Venturelli Nature ecology & evolution 7 (1), 127-142, 2023 | 11 | 2023 |
| Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions JC Thompson, VM Zavala, OS Venturelli PLOS Computational Biology 19 (9), e1011436, 2023 | 10 | 2023 |
| Control points for design of taxonomic composition in synthetic human gut communities BM Connors, J Thompson, S Ertmer, RL Clark, BF Pfleger, OS Venturelli Cell Systems 14 (12), 1044-1058. e13, 2023 | 9* | 2023 |
| Microbial community composition controls carbon flux across litter types in early phase of litter decomposition ME Kroeger, M Rae DeVan, J Thompson, R Johansen, ... Environmental Microbiology 23 (11), 6676-6693, 2021 | 5 | 2021 |
| Kinetic modeling and parameter estimation of a prebiotic peptide reaction network H Boigenzahn, LD González, JC Thompson, VM Zavala, J Yin Journal of Molecular Evolution 91 (5), 730-744, 2023 | 1 | 2023 |
| Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes J Sulaiman, J Thompson, Y Qian, E Vivas, C Diener, SM Gibbons, ... bioRxiv, 2024.04. 13.589383, 2024 | | 2024 |
| Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway Y Liu, YY Cheng, J Thompson, Z Zhou, EI Vivas, MF Warren, FE Rey, ... bioRxiv, 2023.01. 10.523442, 2023 | | 2023 |
| Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro ZP Harmer, JC Thompson, DL Cole, VM Zavala, MN McClean bioRxiv, 2023.12. 19.572411, 2023 | | 2023 |
| A Bayesian Experimental Design Framework for Optimizing Microbial Communities J Thompson, O Venturelli, V Zavala 2022 AIChE Annual Meeting, 2022 | | 2022 |
| Probabilistic Ranking Of Microbiomes Plus Taxa Selection to discover and validate microbiome function models for multiple litter decomposition studies J Thompson, N Lubbers, M Kroeger, R DeVan, R Johansen, J Dunbar, ... Available at SSRN 3659991, 2020 | | 2020 |
| Machine Learning Methods to Discover Patterns in Microbially Driven Soil Carbon Sequestration J Thompson Colorado State University, 2020 | | 2020 |
Ophelia VenturelliUniversity of Wisconsin-MadisonVerified email at wisc.edu
