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2023
 
Qian Y and Venturelli OS. Predicting microbiome phenotypes from genotypes using a tailored deep learning model structure. Submitted

Sulaiman JE, Thompson JC, Qian Y, Hromada SE, Vivas EI, Diener C, Gibbons SM, Safdar N and Venturelli OS. Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes
. Submitted. 

Quinn-Bohmann N et al. Microbial community-scale metabolic modeling predicts personalized short chain fatty acids production profiles in the human gut. In revision. 


Liu Y, Cheng YY, Zhou Z, Vivas EI, Warren MF, Rey FR, Anantharaman K and Venturelli OS. Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway. bioRxiv preprint: doi:10.1101/2023.01.10.523442.

Lan F, Saba S, Ross TD, Zhou Z, Krauska K, Anantharaman K, Landick R and Venturelli OS. Massively parallel single-cell sequencing of genetic loci in diverse microbial populations. Accepted in principle in Nature Methods bioRxiv preprint: doi:10.1101/2022.11.21.517444.

Connors BM, Thompson J, Ertmer S, Clark RL, Pfleger BF and Venturelli OS. Control points for design of taxonomic composition in synthetic human gut communities. In press in Cell Systems. bioRxiv preprint: doi:10.1101/2022.03.14.484355. 

Thompson J, Zavala V and Venturelli OS. Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functionsPLoS Comp Biol 19(9): e1011436 doi: 10.1371/journal.pcbi.1011436.

Lan F*, Saba J*, Qian Y, Ross TD, Landick R and Venturelli OS. Single-cell analysis of multiple invertible promoters reveals differential inversion rates as a strong determinant of bacterial population heterogeneity. Science Advances 9(31) doi: 10.1126/sciadv.adg5476


Hromada S and Venturelli OS. Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics. PLoS Biology 21(5): e3002100 doi: 10.1371/journal.pbio.3002100

Venturelli OS et al. What is the key challenge in engineering microbiomes? Cell Systems 14, 2 P85-90. 

Shaska J, Gursoy MC, Ross TD, Cheng YY, Krieger A, Thairu M, Venturelli OS, Boedicker J, Handelsman J, Mitra U. Microbes as communication & decision-making networked communities. IEEE Nanotechnology Magazine doi: 10.1109/MNANO.2023.3262431. 

Cheng YY*, Chen Z*, Cao X, Ross TD, Falbel TG, Burton BM and Venturelli OS. Programming bacteria to sense environmental DNA. Nature Communications. 14, 2001. https://doi.org/10.1038/s41467-023-37582-x.

Ostrem Loss, E., Thompson, J., Cheung, P.L.K., Qian Y and Venturelli OS. Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbation
s. Nature Ecology and Evolution doi:10.1038/s41559-022-01930-9.


Cheng YY, Zhou Z, Papadopoulos JM, Zuke JD, Falbel TG, Anantharaman K, Burton BM and Venturelli OS. Efficient plasmid transfer via natural competence in a microbial co-culture. Molecular Systems Biology e11406 doi:10.15252/msb.202211406.

*These authors contributed equally

Codes can be found on our Github page or requested via email at venturelli@wisc.edu 

 

2022

Juang, DS et al. Microbial community interactions on a chip. Submitted. bioRxiv preprint: doi:10.1101/2022.10.17.51.511674

Baranwal M*, Clark RL*, Thompson J, Sun Z, Hero AO and Venturelli OS. Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics. eLife https://doi.org/10.7554/eLife.73870.


 

Feng J, Qian Y, Zhou Z, Ertmer S, Vivas E, Lan F, Hamilton JJ, Rey FE, Anantharaman K and Venturelli OS. Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell Host & Microbe 30, 1-16.

Li C, Humayun M, Walker GM, Park KY, Connors BM, Feng J, Pellitteri-Hahn MC, Scarlett CO, Li J, Feng Y, Clark RL, Hefti H, Schrope J, Venturelli OS and Beebe DJ. Under-oil autonomously regulated oxygen microenvironments: A Goldilocks principle-based approach for microscale cell culture. Adv. Sci. 2022 2104510. 

2021

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 BM, 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 microbiomesAnnual 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

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 dropletsCell Systems 9, 1-14.

Shin S, Venturelli OS and Zavala V. Scalable Nonlinear Programming Framework for Parameter Estimation in Dynamic Biological System ModelsPLoS 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

msb.v14.6.cover-1.jpg

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

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