| A Bayesian Experimental Design Framework for Optimizing Microbial Communities J Thompson, O Venturelli, V Zavala 2022 AIChE Annual Meeting, 2022 | | 2022 |
| 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 | 15 | 2023 |
| Cell-based dna sensors and methods of using same O Venturelli, YY Cheng, C Zhengyi US Patent App. 18/067,194, 2024 | | 2024 |
| Common principles and best practices for engineering microbiomes CE Lawson, WR Harcombe, R Hatzenpichler, SR Lindemann, FE Löffler, ... Nature Reviews Microbiology 17 (12), 725-741, 2019 | 424 | 2019 |
| 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 | 12* | 2023 |
| D Microbes as Communication & Decision-Making Networked Communities OS VENTURELLI, J BOEDICKER, JO HANDELSMAN, U MITRA | | |
| Deciphering microbial interactions in synthetic human gut microbiome communities OS Venturelli, AV Carr, G Fisher, RH Hsu, R Lau, BP Bowen, S Hromada, ... Molecular systems biology 14 (6), e8157, 2018 | 434 | 2018 |
| Deciphering multi-scale interaction networks driving microbial community dynamics and functions O Venturelli Bulletin of the American Physical Society, 2024 | | 2024 |
| Design of synthetic human gut microbiome assembly and butyrate production RL Clark, BM Connors, DM Stevenson, SE Hromada, JJ Hamilton, ... Nature communications 12 (1), 3254, 2021 | 127 | 2021 |
| Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro ZP Harmer, JC Thompson, DL Cole, OS Venturelli, VM Zavala, ... ACS Synthetic Biology 13 (5), 1424-1433, 2024 | | 2024 |
| EcoFABs: advancing microbiome science through standardized fabricated ecosystems K Zengler, K Hofmockel, NS Baliga, SW Behie, HC Bernstein, JB Brown, ... Nature methods 16 (7), 567-571, 2019 | 106 | 2019 |
| Efficient plasmid transfer via natural competence in a microbial co-culture YY Cheng, Z Zhou, JM Papadopoulos, JD Zuke, TG Falbel, ... Molecular Systems Biology 19 (e11406), 2023 | 11 | 2023 |
| Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes JE Sulaiman, J Thompson, Y Qian, EI Vivas, C Diener, SM Gibbons, ... bioRxiv, 2024 | | 2024 |
| Emerging Mathematical Challenges in Synthetic Biological Network Design E Yeung, A Gyorgy, M Khammash, O Venturelli | | 2023 |
| Engineered lysins to modulate human gut microbiome communities JRD Rodriguez, W Lu, J Papadopoulos, OS Venturelli, PA Romero bioRxiv, 2024.05. 14.594189, 2024 | | 2024 |
| Evolution favors protein mutational robustness in sufficiently large populations JD Bloom, Z Lu, D Chen, A Raval, OS Venturelli, FH Arnold BMC biology 5, 1-21, 2007 | 129 | 2007 |
| Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics S Hromada, OS Venturelli Plos Biology 21 (5), e3002100, 2023 | 9 | 2023 |
| High-Throughput Single-Cell Sequencing of B. Fragilis Populations in the Mouse Gut C Stark, O Venturelli, F Lan 2023 AIChE Annual Meeting, 2023 | | 2023 |
| Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile JE Sulaiman, J Thompson, PLK Cheung, Y Qian, J Mill, I James, E Vivas, ... bioRxiv, 2024.07. 15.603560, 2024 | | 2024 |
| 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 |
Ryan Hon HsuSalk Institute for Biological Science / University of California, San DiegoVerified email at health.ucsd.edu