Dr Ophelia Venturelli, Ph.D.

Research Interests

Systems biology, synthetic biology, computational modeling, microbiomes, host-microbiome interactions, microbial metabolism

Education

• Ph.D. California Institute of Technology, 2013

Positions

• Associate Professor in the Department of Biomedical Engineering

Courses Taught

• BME 791: Graduate Independent Study
• BME 260L: Modeling Cellular and Molecular Systems

Publications

• Sulaiman JE, Thompson J, Cheung PLK, Qian Y, Mill J, James I, et al. Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile. Cell host & microbe. 2025 Jan;33(1):42-58.e10.
• Lan F, Saba J, Ross TD, Zhou Z, Krauska K, Anantharaman K, et al. Publisher Correction: Massively parallel single-cell sequencing of diverse microbial populations. Nature methods. 2024 Nov;
• Weiss A, Gralka M, Faust K, Gutierrez DB, Pienta K, Zhou X, et al. How can concepts from ecology enable insights about cellular communities? Cell systems. 2024 Nov;15(11):1103.
• Weiss A, Gralka M, Faust K, Basanta Gutierrez D, Pienta K, Zhou X, et al. How can concepts from ecology enable insights about cellular communities? Cell systems. 2024 Oct;15(10):885–90.
• Juang DS, Wightman WE, Lozano GL, Juang TD, Barkal LJ, Yu J, et al. Microbial community interactions on a chip. Proceedings of the National Academy of Sciences of the United States of America. 2024 Sep 24;121(39).
• Sulaiman JE, Thompson J, Qian Y, Vivas EI, Diener C, Gibbons SM, et al. Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. Nature communications. 2024 Aug;15(1):7416.
• Quinn-Bohmann N, Wilmanski T, Sarmiento KR, Levy L, Lampe JW, Gurry T, et al. Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. Nature microbiology. 2024 Jul;9(7):1700–12.
• Harmer ZP, Thompson JC, Cole DL, Venturelli OS, Zavala VM, McClean MN. Dynamic Multiplexed Control and Modeling of Optogenetic Systems Using the High-Throughput Optogenetic Platform, Lustro. ACS synthetic biology. 2024 May;13(5):1424–33.
• Lan F, Saba J, Ross TD, Zhou Z, Krauska K, Anantharaman K, et al. Massively parallel single-cell sequencing of diverse microbial populations. Nature methods. 2024 Feb;21(2):228–35.
• Thompson J, MacKinnon L, Venturelli OS, Zavala VM. A Parametric Bayesian Optimization Framework for Batch Dynamical Systems. In: Proceedings of the American Control Conference. 2024. p. 4333–8.
• Connors BM, Thompson J, Ertmer S, Clark RL, Pfleger BF, Venturelli OS. Control points for design of taxonomic composition in synthetic human gut communities. Cell systems. 2023 Dec;14(12):1044-1058.e13.
• Thompson JC, Zavala VM, Venturelli OS. Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions. PLoS computational biology. 2023 Sep;19(9):e1011436.
• Lan F, Saba J, Qian Y, Ross T, Landick R, Venturelli OS. Single-cell analysis of multiple invertible promoters reveals differential inversion rates as a strong determinant of bacterial population heterogeneity. Science advances. 2023 Aug;9(31):eadg5476.
• Shaska J, Gursoy MC, Ross TD, Cheng YY, Krieger A, Thairu M, et al. Microbes as Communication & Decision-Making Networked Communities. IEEE Nanotechnology Magazine. 2023 Jun 1;17(3):32–41.
• Hromada S, Venturelli OS. Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics. PLoS biology. 2023 May;21(5):e3002100.
• Cheng Y-Y, Chen Z, Cao X, Ross TD, Falbel TG, Burton BM, et al. Programming bacteria for multiplexed DNA detection. Nature communications. 2023 Apr;14(1):2001.
• Cheng Y-Y, Zhou Z, Papadopoulos JM, Zuke JD, Falbel TG, Anantharaman K, et al. Efficient plasmid transfer via natural competence in a microbial co-culture. Molecular systems biology. 2023 Mar;19(3):e11406.
• Venturelli OS, Wang HH, Estrela S, Huang KC, Ledesma-Amaro R, Fedorec AJH, et al. What is the key challenge in engineering microbiomes? Cell systems. 2023 Feb;14(2):85–90.
• Ostrem Loss E, Thompson J, Cheung PLK, Qian Y, Venturelli OS. Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations. Nature ecology & evolution. 2023 Jan;7(1):127–42.
• Baranwal M, Clark RL, Thompson J, Sun Z, Hero AO, Venturelli OS. Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics. eLife. 2022 Jun;11:e73870.
• Li C, Humayun M, Walker GM, Park KY, Connors B, Feng J, et al. Under-Oil Autonomously Regulated Oxygen Microenvironments: A Goldilocks Principle-Based Approach for Microscale Cell Culture. Advanced science (Weinheim, Baden-Wurttemberg, Germany). 2022 Apr;9(10):e2104510.
• Feng J, Qian Y, Zhou Z, Ertmer S, Vivas EI, Lan F, et al. Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell host & microbe. 2022 Feb;30(2):200-215.e12.
• Gursoy MC, Gupta S, Venturelli OS, Mitra U. Optimizing the Spatial Topology of Bacterial Relay Systems: Delay Minimization. In: IEEE International Conference on Communications. 2022. p. 1722–7.
• Hromada S, Qian Y, Jacobson TB, Clark RL, Watson L, Safdar N, et al. Negative interactions determine Clostridioides difficile growth in synthetic human gut communities. Molecular systems biology. 2021 Oct;17(10):e10355.
• Qian Y, Lan F, Venturelli OS. Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models. Current opinion in microbiology. 2021 Aug;62:84–92.
• Leggieri PA, Liu Y, Hayes M, Connors B, Seppälä S, O’Malley MA, et al. Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annual review of biomedical engineering. 2021 Jul;23:169–201.
• Clark RL, Connors BM, Stevenson DM, Hromada SE, Hamilton JJ, Amador-Noguez D, et al. Design of synthetic human gut microbiome assembly and butyrate production. Nature communications. 2021 May;12(1):3254.
• Lee ED, Aurand ER, Friedman DC, Engineering Biology Research Consortium Microbiomes Roadmapping Working Group. Engineering Microbiomes-Looking Ahead. ACS synthetic biology. 2020 Dec;9(12):3181–3.
• Gupta S, Ross TD, Gomez MM, Grant JL, Romero PA, Venturelli OS. Investigating the dynamics of microbial consortia in spatially structured environments. Nature communications. 2020 May;11(1):2418.
• Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Löffler FE, O’Malley MA, et al. Common principles and best practices for engineering microbiomes. Nature reviews Microbiology. 2019 Dec;17(12):725–41.
• Hsu RH, Clark RL, Tan JW, Ahn JC, Gupta S, Romero PA, et al. Microbial Interaction Network Inference in Microfluidic Droplets. Cell systems. 2019 Sep;9(3):229-242.e4.
• Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, et al. EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nature methods. 2019 Jul;16(7):567–71.
• Shin S, Venturelli OS, Zavala VM. Scalable nonlinear programming framework for parameter estimation in dynamic biological system models. PLoS computational biology. 2019 Mar;15(3):e1006828.
• Cao X, Hamilton JJ, Venturelli OS. Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities. Biochemistry. 2019 Jan;58(2):94–107.
• Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, et al. Deciphering microbial interactions in synthetic human gut microbiome communities. Molecular systems biology. 2018 Jun;14(6):e8157.
• Venturelli OS, Tei M, Bauer S, Chan LJG, Petzold CJ, Arkin AP. Programming mRNA decay to modulate synthetic circuit resource allocation. Nature communications. 2017 Apr;8:15128.
• Venturelli OS, Egbert RG, Arkin AP. Towards Engineering Biological Systems in a Broader Context. Journal of molecular biology. 2016 Feb;428(5 Pt B):928–44.
• Chevalier M, Venturelli O, El-Samad H. The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks. PLoS computational biology. 2015 Oct;11(10):e1004462.
• Venturelli OS, Zuleta I, Murray RM, El-Samad H. Population diversification in a yeast metabolic program promotes anticipation of environmental shifts. PLoS biology. 2015 Jan;13(1):e1002042.
• Venturelli OS, El-Samad H, Murray RM. Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response. Proceedings of the National Academy of Sciences of the United States of America. 2012 Nov;109(48):E3324–33.
• Renault VM, Thekkat PU, Hoang KL, White JL, Brady CA, Kenzelmann Broz D, et al. The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor. Oncogene. 2011 Jul;30(29):3207–21.
• Bloom JD, Lu Z, Chen D, Raval A, Venturelli OS, Arnold FH. Evolution favors protein mutational robustness in sufficiently large populations. BMC biology. 2007 Jul;5:29.

In The News

• Four Newly Promoted or Hired Faculty Named Langford Lecturers (Sep 25, 2024 | Office of the Provost)
• Ophelia Venturelli Wants to Engineer Our Guts (Sep 23, 2024 | Pratt School of Engineering)