Publications

Valenzuela, Jacob J., et al. “Origin of Biogeographically Distinct Ecotypes during Laboratory Evolution.” Nature Communications, vol. 15, no. 1, Aug. 2024, p. 7451, https://doi.org/10.1038/s41467-024-51759-y.

Park, James H., et al. “Gene Regulatory Network Topology Governs Resistance and Treatment Escape in Glioma Stem-like Cells.” Science Advances, vol. 10, no. 23, June 2024, p. eadj7706, https://doi.org/10.1126/sciadv.adj7706.

Flores-Valdez, Mario Alberto, et al. “Comparison of the Transcriptome, Lipidome, and c-Di-GMP Production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-Dependent Induction of Proinflammatory Cytokines in Murine Macrophages.” Scientific Reports, vol. 14, no. 1, May 2024, p. 11898, https://doi.org/10.1038/s41598-024-61815-8.

Gupta, Vishal K., et al. “3D Hydrogel Culture System Recapitulates Key Tuberculosis Phenotypes and Demonstrates Pyrazinamide Efficacy.” Advanced Healthcare Materials, Apr. 2024, p. e2304299, https://doi.org/10.1002/adhm.202304299.

Hunt, Kristopher A., et al. “Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide.” Environmental Science & Technology, vol. 58, no. 16, Apr. 2024, pp. 7056–65, https://doi.org/10.1021/acs.est.3c07972.

Turkarslan, Serdar, et al. “An Atlas of Causal and Mechanistic Drivers of Interpatient Heterogeneity in Glioma.” MedRxiv: The Preprint Server for Health Sciences, Apr. 2024, p. 2024.04.05.24305380, https://doi.org/10.1101/2024.04.05.24305380.

Murie, Carl, et al. “Individualized Dynamic Risk Assessment for Multiple Myeloma.” MedRxiv: The Preprint Server for Health Sciences, Apr. 2024, p. 2024.04.01.24305024, https://doi.org/10.1101/2024.04.01.24305024.

Ludwig, Claudia McLaughlin, et al. “Consequential Insights for Advancing Informal STEM Learning and Outcomes for Students from Historically Marginalized Communities.” Humanities & Social Sciences Communications, vol. 11, no. 1, 2024, p. 351, https://doi.org/10.1057/s41599-024-02797-w.

Wang, Yaxi, et al. “Genetic Manipulation of Patescibacteria Provides Mechanistic Insights into Microbial Dark Matter and the Epibiotic Lifestyle.” Cell, vol. 186, no. 22, Oct. 2023, pp. 4803-4817.e13, https://doi.org/10.1016/j.cell.2023.08.017.

Kusebauch, Ulrike, et al. “A Comprehensive Spectral Assay Library to Quantify the Halobacterium Salinarum NRC-1 Proteome by DIA/SWATH-MS.” Scientific Data, vol. 10, no. 1, Oct. 2023, p. 697, https://doi.org/10.1038/s41597-023-02590-5.

Lim, Joe J., et al. “Growth Phase Estimation for Abundant Bacterial Populations Sampled Longitudinally from Human Stool Metagenomes.” Nature Communications, vol. 14, no. 1, Sept. 2023, p. 5682, https://doi.org/10.1038/s41467-023-41424-1.

Peterson, Eliza J. R., et al. “MtrA Modulates Mycobacterium Tuberculosis Cell Division in Host Microenvironments to Mediate Intrinsic Resistance and Drug Tolerance.” Cell Reports, vol. 42, no. 8, Aug. 2023, p. 112875, https://doi.org/10.1016/j.celrep.2023.112875.

Wang, Yaxi, et al. “Discovery of a Glutathione Utilization Pathway in Francisella That Shows Functional Divergence between Environmental and Pathogenic Species.” Cell Host & Microbe, vol. 31, no. 8, Aug. 2023, pp. 1359-1370.e7, https://doi.org/10.1016/j.chom.2023.06.010.

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.