2021

Baranwal M, Clark RL, Thompson J, Sun Z, Hero AO and Venturelli OS. Deep learning enables design of multifunctional synthetic human gut microbiome dynamics. Submitted. BioRxiv preprint: doi:10.1101/2021.09.27.461983.

Feng J, Qian Y, Zhou Z, Ertmer S, Vivas E, Lan F, Rey FE, Anantharaman K and Venturelli OS. Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Submitted. BioRxiv preprint: doi:10.1101/2021.06.12.448201.

Hromada S, Qian Y, Jacobson TB, Clark RL, Watson L, Safdar N, Amador-Noguez D and Venturelli OS (2021). Negative interactions determine the growth of C. difficile in synthetic human gut communities. Mol. Syst. Biol. 17:e10355

Clark RL, Connors B, Stevenson DM, Hromada SE, Hamilton JJ, Amador-Noguez D and Venturelli OS (2021). Design of synthetic human gut microbiome assembly and butyrate production. Nat Commun 12:3254 https://doi.org/10.1038/s41467-021-22938-y.

See Research Highlights in Nat Chem Biol 2021

Leggieri PA, Liu Y, Hayes H, Connors B, Seppala S, O'Malley MA and Venturelli OS (2021). Integrating systems and synthetic biology to understand and engineer microbiomes. Annual Review of Biomedical Engineering. 23:1 doi: 10.1146/annurev-bioeng-082120-022836.

Qian Y, Lan F and Venturelli OS (2021). Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models. Curr. Opin. Microbiol. 12, 84-92.

2020

Li C, Humayun M, Park KY, Connors B, Feng J, Li J, Feng J, Clark RL Hefti H, Schrope J, Venturelli OS and Beebe DJ. Under-oil autonomously regulated oxygen microenvironments for cell culture. Submitted. BioRxiv preprint: doi:10.1101/2020.21.16.423117

Cheng YY, Papadopoulos JM, Falbel T, Burton BM and Venturelli OS. Donor-recipient interactions drive dynamics of horizontal gene transfer via natural competence. Submitted. BioRxiv preprint: doi:10.1101/2020.10.19.342733

Gupta S, Ross TD, Gomez MM, Grant JL, Romero PA and Venturelli OS (2020). Investigating the dynamics of microbial consortia in spatially structured environments. Nature Commun. 11, DOI: 10.1038/s41467-020-16200-0.

2019

Lawson, C. E., Harcombe, W. R., Hatzenpichler, R., Lindemann, S. R., Löffler, F. E., O’Malley, M. A., ... & Weissbrodt, D. G. (2019). Common principles and best practices for engineering microbiomes. Nature Reviews Microbiology, 1-17 Common principles and best practices for engineering microbiomes. Nature Reviews Microbiology, 1-17.

Zengler Karsten et al. EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nature methods 16.7 (2019): 567-571.

Hsu RH, Clark RL, Tan JW, Ahn JC, Gupta G, Romero PA and Venturelli OS. Microbial interaction network inference in microfluidic droplets. Cell Systems 9, 1-14.

Shin S, Venturelli OS and Zavala V. Scalable Nonlinear Programming Framework for Parameter Estimation in Dynamic Biological System Models. PLoS Comp Biol, 15(3), e1006828.

Cao X, Hamilton JJ and Venturelli OS. Understanding and controlling distributed biochemical pathways in microbial communities. Biochemistry 58(2), 94-107.

2018

Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T and Arkin AP. Deciphering microbial interactions in synthetic human gut microbiome communities. Mol Syst Biol 14, e8425.

See C Abreu et al. News & Views (MSB) and featured on the cover of MSB

2017

Venturelli OS. What Is the Role of Circuit Design in the Advancement of Synthetic Biology? Cell Systems. 4(5) 476-77.

Venturelli OS. Tei M, Bauer S, Chan JGL, Petzold, C and Arkin AP (2017). Programming mRNA decay to modulate synthetic circuit resource allocation. Nat Commun. DOI: 10.1038/ncomms15128

Venturelli OS, Egbert RG and Arkin AP (2016). Towards engineering biological systems in a broader context. J. Mol. Biol. 428(5):928-944

2015

Chevalier M, Venturelli OS and El-Samad H (2015). The impact of different sources of fluctuations on mutual information in biochemical networks. PLoS Comput Biol. 11(10):e1004462.

Venturelli OS, Zuleta I, Murray RM, El-Samad H (2015). Population diversification in a yeast metabolic program promotes anticipation of environmental shifts. PLoS Biol. 13(1):e1002042.

Prior to 2015

Venturelli OS, El-Samad H, Murray RM (2012). Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response. Proc Natl Acad Sci USA. 109(48):E3324-33.

Renault VM, Thekkat PU, Hoang KL, White JL, Brady CA, Kenzelmann Broz D, Venturelli OS, Johnson TM, Oskoui PR, Xuan Z, Santo EE, Zhang MQ, Vogel H, Attardi LD, Brunet A (2011). The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor. Oncogene. 30(29):3207-21

Bloom JD, Lu Z, Chen D, Raval A, Venturelli OS, Arnold FH (2007). Evolution favors protein mutational robustness in sufficiently large populations. BMC Biol. 30(29):3207-21