Publications

Wang, Yaxi, et al. “Genetic Manipulation of Candidate Phyla Radiation Bacteria Provides Functional Insights into Microbial Dark Matter.” BioRxiv: The Preprint Server for Biology, May 2023, p. 2023.05.02.539146, https://doi.org/10.1101/2023.05.02.539146.

Carr, Alex, et al. “Personalized Clostridioides Difficile Engraftment Risk Prediction and Probiotic Therapy Assessment in the Human Gut.” BioRxiv: The Preprint Server for Biology, May 2023, p. 2023.04.28.538771, https://doi.org/10.1101/2023.04.28.538771.

Lorenzetti, Alan P. R., et al. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” MSystems, vol. 8, no. 2, Apr. 2023, p. e0081622, https://doi.org/10.1128/msystems.00816-22.

Arrieta-Ortiz, Mario L., et al. “Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia Coli.” MSystems, vol. 8, no. 1, Feb. 2023, p. e0090422, https://doi.org/10.1128/msystems.00904-22.

Park, James H., et al. “A Single-Cell Based Precision Medicine Approach Using Glioblastoma Patient-Specific Models.” NPJ Precision Oncology, vol. 6, no. 1, Aug. 2022, p. 55, https://doi.org/10.1038/s41698-022-00294-4.

Pavao, Aidan, et al. “Reconsidering the in Vivo Functions of Clostridial Stickland Amino Acid Fermentations.” Anaerobe, vol. 76, Aug. 2022, p. 102600, https://doi.org/10.1016/j.anaerobe.2022.102600.

Xavier, Joao B., et al. “Mathematical Models to Study the Biology of Pathogens and the Infectious Diseases They Cause.” IScience, vol. 25, no. 4, Apr. 2022, p. 104079, https://doi.org/10.1016/j.isci.2022.104079.

Cooper, Charlotte, et al. “MadR Mediates Acyl CoA-Dependent Regulation of Mycolic Acid Desaturation in Mycobacteria.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 8, Feb. 2022, p. e2111059119, https://doi.org/10.1073/pnas.2111059119.

Srinivas, Vivek, et al. “Transcriptome Signature of Cell Viability Predicts Drug Response and Drug Interaction in Mycobacterium Tuberculosis.” Cell Reports Methods, vol. 1, no. 8, Dec. 2021, p. None, https://doi.org/10.1016/j.crmeth.2021.100123.

Immanuel, Selva Rupa Christinal, et al. “Quantitative Prediction of Conditional Vulnerabilities in Regulatory and Metabolic Networks Using PRIME.” NPJ Systems Biology and Applications, vol. 7, no. 1, Dec. 2021, p. 43, https://doi.org/10.1038/s41540-021-00205-6.

Arrieta-Ortiz, Mario L., et al. “Predictive Regulatory and Metabolic Network Models for Systems Analysis of Clostridioides Difficile.” Cell Host & Microbe, vol. 29, no. 11, Nov. 2021, pp. 1709-1723.e5, https://doi.org/10.1016/j.chom.2021.09.008.

Girinathan, Brintha P., et al. “In Vivo Commensal Control of Clostridioides Difficile Virulence.” Cell Host & Microbe, vol. 29, no. 11, Nov. 2021, pp. 1693-1708.e7, https://doi.org/10.1016/j.chom.2021.09.007.

Voolstra, Christian R., et al. “Contrasting Heat Stress Response Patterns of Coral Holobionts across the Red Sea Suggest Distinct Mechanisms of Thermal Tolerance.” Molecular Ecology, Aug. 2021, https://doi.org/10.1111/mec.16064.

Wall, Matthew A., et al. “Genetic Program Activity Delineates Risk, Relapse, and Therapy Responsiveness in Multiple Myeloma.” NPJ Precision Oncology, vol. 5, no. 1, June 2021, p. 60, https://doi.org/10.1038/s41698-021-00185-0.

Park, James H., et al. “A Systems Approach to Brain Tumor Treatment.” Cancers, vol. 13, no. 13, June 2021, p. 3152, https://doi.org/10.3390/cancers13133152. Download

Neal, Maxwell L., et al. “A Systems-Level Gene Regulatory Network Model for Plasmodium Falciparum.” Nucleic Acids Research, Jan. 2021, https://doi.org/10.1093/nar/gkaa1245. Download

Azer, Karim, et al. “History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications.” Frontiers in Physiology, vol. 12, 2021, p. 637999, https://doi.org/10.3389/fphys.2021.637999.

Day, Jessica A., et al. “Lettuce (Lactuca Sativa) Productivity Influenced by Microbial Inocula under Nitrogen-Limited Conditions in Aquaponics.” PloS One, vol. 16, no. 2, 2021, p. e0247534, https://doi.org/10.1371/journal.pone.0247534.

Srinivas, Vivek, et al. “PerSort Facilitates Characterization and Elimination of Persister Subpopulation in Mycobacteria.” MSystems, edited by Charles Langelier, vol. 5, no. 6, Dec. 2020, pp. e01127-20, /msystems/5/6/mSys.01127-20.atom, https://doi.org/10.1128/mSystems.01127-20.

Vega-Dominguez, Perla, et al. “Biofilms of the Non-Tuberculous Mycobacterium Chelonae Form an Extracellular Matrix and Display Distinct Expression Patterns.” Cell Surface (Amsterdam, Netherlands), vol. 6, Dec. 2020, p. 100043, https://doi.org/10.1016/j.tcsw.2020.100043.

Midha, Mukul K., et al. “A Comprehensive Spectral Assay Library to Quantify the Escherichia Coli Proteome by DIA/SWATH-MS.” Scientific Data, vol. 7, no. 1, Nov. 2020, p. 389, https://doi.org/10.1038/s41597-020-00724-7.

López García de Lomana, Adrián, et al. “Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium Salinarum.” MSystems, vol. 5, no. 4, July 2020, https://doi.org/10.1128/mSystems.00329-20. Download

Arrieta-Ortiz, Mario L., et al. “Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks.” MSystems, vol. 5, no. 3, June 2020, https://doi.org/10.1128/mSystems.00057-20.

Wall, Matthew A., et al. Genetic Program Activity Delineates Risk, Relapse, and Therapy Responsiveness in Multiple Myeloma. preprint, Systems Biology, 1 Apr. 2020, https://doi.org/10.1101/2020.04.01.012351.

Mast, Fred D., et al. “Crippling Life Support for SARS-CoV-2 and Other Viruses through Synthetic Lethality.” The Journal of Cell Biology, vol. 219, no. 10, 05 2020, https://doi.org/10.1083/jcb.202006159.

Flores-Valdez, Mario Alberto, et al. “Transcriptional Portrait of M. Bovis BCG during Biofilm Production Shows Genes Differentially Expressed during Intercellular Aggregation and Substrate Attachment.” Scientific Reports, vol. 10, no. 1, 28 2020, p. 12578, https://doi.org/10.1038/s41598-020-69152-2. Download

Abidi, Abrar A., et al. “Intricate Genetic Programs Controlling Dormancy in Mycobacterium Tuberculosis.” BioRxiv, July 2019, p. 709378, https://doi.org/10.1101/709378.

Arrieta-Ortiz, Mario L., et al. “Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor Driven Regulatory Networks.” BioRxiv, June 2019, p. 657478, https://doi.org/10.1101/657478.

Srinivas, Vivek, et al. “Characterization and Elimination of Stochastically Generated Persister Subpopulation in Mycobacteria.” BioRxiv, Nov. 2018, p. 463232, https://doi.org/10.1101/463232.

Valenzuela, Jacob J., et al. “Ocean Acidification Conditions Increase Resilience of Marine Diatoms.” Nature Communications, vol. 9, no. 1, June 2018, p. 2328, https://doi.org/10.1038/s41467-018-04742-3.

Ament, Seth A., et al. “Transcriptional Regulatory Networks Underlying Gene Expression Changes in Huntington’s Disease.” Molecular Systems Biology, vol. 14, no. 3, Mar. 2018, https://doi.org/10.15252/msb.20167435.

Flowers, Jason J., et al. “Constraint-Based Modelling Captures the Metabolic Versatility of Desulfovibrio Vulgaris.” Environmental Microbiology Reports, vol. 10, no. 2, 2018, pp. 190–201, https://doi.org/10.1111/1758-2229.12619.

Qin, Wei, et al. “Stress Response of a Marine Ammonia-Oxidizing Archaeon Informs Physiological Status of Environmental Populations.” The ISME Journal, Oct. 2017, https://doi.org/10.1038/ismej.2017.186.

Lopez Garcia de Lomana, Adrian, et al. “Adaptive Prediction Emerges Over Short Evolutionary Time Scales.” Genome Biology and Evolution, vol. in press, June 2017.

Wang, Zhuo, et al. “Combining Inferred Regulatory and Reconstructed Metabolic Networks Enhances Phenotype Prediction in Yeast.” PLoS Computational Biology, vol. 13, no. 5, May 2017, p. e1005489, https://doi.org/10.1371/journal.pcbi.1005489.

Thompson, Anne W., et al. “Robustness of a Model Microbial Community Emerges from Population Structure among Single Cells of a Clonal Population.” Environmental Microbiology, Apr. 2017, https://doi.org/10.1111/1462-2920.13764.

Turkarslan, Serdar, et al. “Mechanism for Microbial Population Collapse in a Fluctuating Resource Environment.” Molecular Systems Biology, vol. 13, no. 3, Mar. 2017, p. 919.

Baliga, Nitin S., et al. “The State of Systems Genetics in 2017.” Cell Systems, vol. 4, no. 1, Jan. 2017, pp. 7–15, https://doi.org/10.1016/j.cels.2017.01.005.

Patra, Biranchi, et al. “A Genome Wide Dosage Suppressor Network Reveals Genomic Robustness.” Nucleic Acids Research, vol. 45, no. 1, Jan. 2017, pp. 255–70, https://doi.org/10.1093/nar/gkw1148.

Keller, Mark P., et al. “The Transcription Factor Nfatc2 Regulates Beta-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets.” PLoS Genetics, vol. 12, no. 12, Dec. 2016, p. e1006466, https://doi.org/10.1371/journal.pgen.1006466.

Rothchild, Alissa C., et al. “MiR-155-Regulated Molecular Network Orchestrates Cell Fate in the Innate and Adaptive Immune Response to Mycobacterium Tuberculosis.” Proceedings of the National Academy of Sciences of the United States of America, Sept. 2016, https://doi.org/10.1073/pnas.1608255113.

Plaisier, Christopher L., et al. “Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.” Cell Systems, vol. 3, no. 2, Aug. 2016, pp. 172–86, https://doi.org/10.1016/j.cels.2016.06.006.

Ashworth, Justin, et al. “Pan-Transcriptomic Analysis Identifies Coordinated and Orthologous Functional Modules in the Diatoms Thalassiosira Pseudonana and Phaeodactylum Tricornutum.” Marine Genomics, vol. 26, Apr. 2016, pp. 21–28, https://doi.org/10.1016/j.margen.2015.10.011.

Peterson, Eliza J. R., et al. “Network Analysis Identifies Rv0324 and Rv0880 as Regulators of Bedaquiline Tolerance in Mycobacterium Tuberculosis.” Nature Microbiology, vol. 1, no. 8, 2016, p. 16078, https://doi.org/10.1038/nmicrobiol.2016.78.

Toledo, Chad M., et al. “Genome-Wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells.” Cell Reports, vol. 13, no. 11, Dec. 2015, pp. 2425–39, https://doi.org/10.1016/j.celrep.2015.11.021.

Imam, Saheed, et al. “A Refined Genome-Scale Reconstruction of Chlamydomonas Metabolism Provides a Platform for Systems-Level Analyses.” The Plant Journal : For Cell and Molecular Biology, vol. 84, no. 6, Dec. 2015, pp. 1239–56, https://doi.org/10.1111/tpj.13059.

Thompson, Anne W., et al. “A Method to Analyze, Sort, and Retain Viability of Obligate Anaerobic Microorganisms from Complex Microbial Communities.” Journal of Microbiological Methods, vol. 117, Oct. 2015, pp. 74–77, https://doi.org/10.1016/j.mimet.2015.07.009.

Reiss, David J., et al. “CMonkey2: Automated, Systematic, Integrated Detection of Co-Regulated Gene Modules for Any Organism.” Nucleic Acids Research, vol. 43, no. 13, July 2015, p. e87, https://doi.org/10.1093/nar/gkv300.

Raman, Arjun V., and Nitin S. Baliga. “The Universe under a Microscope.” Environmental Microbiology Reports, vol. 7, no. 1, Feb. 2015, pp. 11–12, https://doi.org/10.1111/1758-2229.12225.

Turkarslan, Serdar, et al. “A Comprehensive Map of Genome-Wide Gene Regulation in Mycobacterium Tuberculosis.” Scientific Data, vol. 2, 2015, p. 150010, https://doi.org/10.1038/sdata.2015.10.