Publications

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. 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. Download
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
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.
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
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.
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
“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.
Srinivas, Vivek, et al. “Characterization and Elimination of Stochastically Generated Persister Subpopulation in Mycobacteria.” BioRxiv, Nov. 2018, p. 463232, http://doi.org/10.1101/463232.
Zotero | Login. 4 Sept. 2018, https://www.zotero.org/user/login/.
Otwell, Anne E., et al. “Systems Biology Approaches towards Predictive Microbial Ecology.” Environmental Microbiology, Aug. 2018, http://doi.org/10.1111/1462-2920.14378.
Valenzuela, Jacob J., et al. “Ocean Acidification Conditions Increase Resilience of Marine Diatoms.” Nature Communications, vol. 9, no. 1, June 2018, p. 2328, http://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, http://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, http://doi.org/10.1111/1758-2229.12619.
Flores-Valdez, Mario A., et al. “The BCGΔBCG1419c Vaccine Candidate Reduces Lung Pathology, IL-6, TNF-α, and IL-10 During Chronic TB Infection.” Frontiers in Microbiology, vol. 9, 2018, p. 1281, http://doi.org/10.3389/fmicb.2018.01281.
Qin, Wei, et al. “Stress Response of a Marine Ammonia-Oxidizing Archaeon Informs Physiological Status of Environmental Populations.” The ISME Journal, Oct. 2017, http://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, http://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, http://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, http://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, http://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, http://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, http://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, http://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, http://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, http://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, http://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, http://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, http://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, http://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, http://doi.org/10.1111/1758-2229.12225.
Ludwig, Claudia, et al. “Ocean Acidification.” The Science Teacher, vol. 082, no. 06, 2015, http://doi.org/10.2505/4/tst15_082_06_41.
Lopez Garcia de Lomana, Adrian, et al. “Transcriptional Program for Nitrogen Starvation-Induced Lipid Accumulation in Chlamydomonas Reinhardtii.” Biotechnology for Biofuels, vol. 8, 2015, p. 207, http://doi.org/10.1186/s13068-015-0391-z.