Publications

Dokic, Anja, et al. “Mycobacterium Abscessus Biofilms Produce an Extracellular Matrix and Have a Distinct Mycolic Acid Profile.” Cell Surface (Amsterdam, Netherlands), vol. 7, Dec. 2021, p. 100051, http://doi.org/10.1016/j.tcsw.2021.100051.
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, http://doi.org/10.1111/mec.16064. Download
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, http://doi.org/10.1038/s41698-021-00185-0. Download
Park, James H., et al. “A Systems Approach to Brain Tumor Treatment.” Cancers, vol. 13, no. 13, June 2021, p. 3152, http://doi.org/10.3390/cancers13133152. Download
Turkarslan, Serdar, et al. “Synergistic Epistasis Enhances the Co-Operativity of Mutualistic Interspecies Interactions.” The ISME Journal, Feb. 2021, http://doi.org/10.1038/s41396-021-00919-9.
Otwell, Anne E., et al. “Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification.” MSystems, vol. 6, no. 1, Feb. 2021, http://doi.org/10.1128/mSystems.01025-20.
Neal, Maxwell L., et al. “A Systems-Level Gene Regulatory Network Model for Plasmodium Falciparum.” Nucleic Acids Research, Jan. 2021, http://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, http://doi.org/10.3389/fphys.2021.637999.
Lui, Lauren M., et al. “Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.” Frontiers in Microbiology, vol. 12, 2021, p. 642422, http://doi.org/10.3389/fmicb.2021.642422.
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, http://doi.org/10.1371/journal.pone.0247534. Download
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, http://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, http://doi.org/10.1016/j.tcsw.2020.100043. Download
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, http://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, http://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, http://doi.org/10.1128/mSystems.00057-20. Download
Peterson, Eliza J. R., et al. “Intricate Genetic Programs Controlling Dormancy in Mycobacterium Tuberculosis.” Cell Reports, vol. 31, no. 4, Apr. 2020, p. 107577, http://doi.org/10.1016/j.celrep.2020.107577.
Wall, Matthew A., et al. Genetic Program Activity Delineates Risk, Relapse, and Therapy Responsiveness in Multiple Myeloma. preprint, Systems Biology, 1 Apr. 2020, doi:10.1101/2020.04.01.012351.
Idso, Matthew N., et al. “Antibody-Recruiting Protein-Catalyzed Capture Agents to Combat Antibiotic-Resistant Bacteria.” Chemical Science, Feb. 2020, http://doi.org/10.1039/C9SC04842A.
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, http://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, http://doi.org/10.1038/s41598-020-69152-2. Download
Peterson, Eliza, et al. “Intricate Genetic Programs Controlling Dormancy in Mycobacterium Tuberculosis.” Cell Rep, vol. 31, no. 4, 2020, p. 107577, http://doi.org/10.1016/j.celrep.2020.107577. Download
Rothchild, Alissa, et al. “Flow Cytometry Analysis and Fluorescence-Activated Cell Sorting of Myeloid Cells from Lung and Bronchoalveolar Lavage Samples from -Infected Mice.” Bio Protoc, vol. 10, no. 10, 2020, http://doi.org/10.21769/bioprotoc.3630. Download
Plumlee, Courtney, et al. “Ultra-Low Dose Aerosol Infection of Mice with Mycobacterium Tuberculosis More Closely Models Human Tuberculosis.” Cell Host Microbe, 2020, http://doi.org/10.1016/j.chom.2020.10.003.
Ma, Shuyi, et al. “Transcriptional Regulator-Induced Phenotype Screen Reveals Drug Potentiators in Mycobacterium Tuberculosis.” Nat Microbiol, 2020, http://doi.org/10.1038/s41564-020-00810-x. Download
Rahil, Zainab, et al. “Landscape of Coordinated Immune Responses to H1N1 Challenge in Humans.” J Clin Invest, vol. 130, no. 11, 2020, pp. 5800–16, http://doi.org/10.1172/JCI137265. Download
Peters, Julian, et al. “Genetic Diversity in  Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease.” Annu Rev Genet, 2020, http://doi.org/10.1146/annurev-genet-022820-085940.
Nemeth, Johannes, et al. “Contained Mycobacterium Tuberculosis Infection Induces Concomitant and Heterologous Protection.” PLoS Pathog, vol. 16, no. 7, 2020, p. e1008655, http://doi.org/10.1371/journal.ppat.1008655. Download
Plumlee, Courtney, et al. “Ultra-Low Dose Aerosol Infection of Mice with Mycobacterium Tuberculosis More Closely Models Human Tuberculosis.” Cell Host Microbe, 2020, http://doi.org/10.1016/j.chom.2020.10.003.
Peterson, Eliza, et al. “Intricate Genetic Programs Controlling Dormancy in Mycobacterium Tuberculosis.” Cell Rep, vol. 31, no. 4, 2020, p. 107577, http://doi.org/10.1016/j.celrep.2020.107577.
Nemeth, Johannes, et al. “Contained Mycobacterium Tuberculosis Infection Induces Concomitant and Heterologous Protection.” PLoS Pathog, vol. 16, no. 7, 2020, p. e1008655, http://doi.org/10.1371/journal.ppat.1008655.
Ma, Shuyi, et al. “Transcriptional Regulator-Induced Phenotype Screen Reveals Drug Potentiators in Mycobacterium Tuberculosis.” Nat Microbiol, 2020, http://doi.org/10.1038/s41564-020-00810-x.
Rahil, Zainab, et al. “Landscape of Coordinated Immune Responses to H1N1 Challenge in Humans.” J Clin Invest, vol. 130, no. 11, 2020, pp. 5800–16, http://doi.org/10.1172/JCI137265.
Peters, Julian, et al. “Genetic Diversity in  Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease.” Annu Rev Genet, 2020, http://doi.org/10.1146/annurev-genet-022820-085940.
Rothchild, Alissa, et al. “Flow Cytometry Analysis and Fluorescence-Activated Cell Sorting of Myeloid Cells from Lung and Bronchoalveolar Lavage Samples from -Infected Mice.” Bio Protoc, vol. 10, no. 10, 2020, http://doi.org/10.21769/bioprotoc.3630.
“Publications.” Baliga Lab, 27 Sept. 2019, https://baliga.systemsbiology.net/publications/.
Abidi, Abrar A., et al. “Intricate Genetic Programs Controlling Dormancy in Mycobacterium Tuberculosis.” BioRxiv, July 2019, p. 709378, http://doi.org/10.1101/709378.
Carr, Alex, et al. “Use and Abuse of Correlation Analyses in Microbial Ecology.” The ISME Journal, June 2019, http://doi.org/10.1038/s41396-019-0459-z.
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, http://doi.org/10.1101/657478.
Peterson, Eliza JR, et al. “Path‐seq Identifies an Essential Mycolate Remodeling Program for Mycobacterial Host Adaptation.” Molecular Systems Biology, vol. 15, no. 3, Mar. 2019, p. e8584, http://doi.org/10.15252/msb.20188584. Download
Zengler, Karsten, et al. “EcoFABs: Advancing Microbiome Science through Standardized Fabricated Ecosystems.” Nature Methods, vol. 16, no. 7, 2019, pp. 567–71, http://doi.org/10.1038/s41592-019-0465-0.
Duffy, Fergal, et al. “Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome.” Front Immunol, vol. 10, 2019, p. 527, http://doi.org/10.3389/fimmu.2019.00527. Download
Adams, Kristin, et al. “Diverse Clinical Isolates of Mycobacterium Tuberculosis Develop Macrophage-Induced Rifampin Tolerance.” The Journal of Infectious Diseases, vol. 219, 2019, pp. 1554–58, http://doi.org/10.1093/infdis/jiy710. Download
Ma, Shuyi, et al. “Transcriptomic Signatures Predict Regulators of Drug Synergy and Clinical Regimen Efficacy against Tuberculosis.” MBio, vol. 10, no. 6, 2019, http://doi.org/10.1128/mBio.02627-19. Download
Peterson, Eliza, et al. “Path-Seq Identifies an Essential Mycolate Remodeling Program for Mycobacterial Host Adaptation.” Molecular Systems Biology, vol. 15, 2019, p. e8584, http://doi.org/10.15252/msb.20188584. Download
Rothchild, Alissa, et al. “Alveolar Macrophages Generate a Noncanonical NRF2-Driven Transcriptional Response  in Vivo.” Sci Immunol, vol. 4, no. 37, 2019, http://doi.org/10.1126/sciimmunol.aaw6693. Download
Delahaye, Jared, et al. “Cutting Edge: Bacillus Calmette–Guérin–Induced T Cells Shape Mycobacterium Tuberculosis Infection before Reducing the Bacterial Burden.” The Journal of Immunology, vol. 203, 2019, pp. 807–812, http://doi.org/10.4049/jimmunol.1900108. Download
Delahaye, Jared, et al. “BCG-Induced T Cells Shape Mycobacterium Tuberculosis Infection before Reducing the Bacterial Burden.” BioRxiv, 2019, http://doi.org/10.1101/590554. Download
Ma, Shuyi, et al. “Transcriptomic Signatures Predict Regulators of Drug Synergy and Clinical Regimen Efficacy against Tuberculosis.” MBio, vol. 10, no. 6, 2019, http://doi.org/10.1128/mBio.02627-19.
Peterson, Eliza, et al. “Path-Seq Identifies an Essential Mycolate Remodeling Program for Mycobacterial Host Adaptation.” Molecular Systems Biology, vol. 15, 2019, p. e8584, http://doi.org/10.15252/msb.20188584.
Delahaye, Jared, et al. “Cutting Edge: Bacillus Calmette–Guérin–Induced T Cells Shape Mycobacterium Tuberculosis Infection before Reducing the Bacterial Burden.” The Journal of Immunology, vol. 203, 2019, pp. 807–812, http://doi.org/10.4049/jimmunol.1900108.