Publications

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.
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.
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.
Gomes-Filho, Jose Vicente, et al. “Sense Overlapping Transcripts in IS1341-Type Transposase Genes Are Functional Non-Coding RNAs in Archaea.” RNA Biology, vol. 12, no. 5, 2015, pp. 490–500, http://doi.org/10.1080/15476286.2015.1019998.
Imam, Saheed, et al. “Data-Driven Integration of Genome-Scale Regulatory and Metabolic Network Models.” Frontiers in Microbiology, vol. 6, 2015, p. 409, http://doi.org/10.3389/fmicb.2015.00409.
Turkarslan, Serdar, et al. “A Comprehensive Map of Genome-Wide Gene Regulation in Mycobacterium Tuberculosis.” Scientific Data, vol. 2, 2015, p. 150010, http://doi.org/10.1038/sdata.2015.10.
Danziger, Samuel A., et al. “Bicluster Sampled Coherence Metric (BSCM) Provides an Accurate Environmental Context for Phenotype Predictions.” BMC Systems Biology, vol. 9 Suppl 2, 2015, p. S1, http://doi.org/10.1186/1752-0509-9-S2-S1.
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.
Minch, Kyle J., et al. “The DNA-Binding Network of Mycobacterium Tuberculosis.” Nature Communications, vol. 6, 2015, p. 5829, http://doi.org/10.1038/ncomms6829.
Ashworth, Justin, et al. “Structure-Based Predictions Broadly Link Transcription Factor Mutations to Gene Expression Changes in Cancers.” Nucleic Acids Research, vol. 42, no. 21, Dec. 2014, pp. 12973–83, http://doi.org/10.1093/nar/gku1031.
Hillesland, Kristina L., et al. “Erosion of Functional Independence Early in the Evolution of a Microbial Mutualism.” Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 41, Oct. 2014, pp. 14822–27, http://doi.org/10.1073/pnas.1407986111.
Peterson, Eliza J. R., et al. “A High-Resolution Network Model for Global Gene Regulation in Mycobacterium Tuberculosis.” Nucleic Acids Research, vol. 42, no. 18, Oct. 2014, pp. 11291–303, http://doi.org/10.1093/nar/gku777.
Bare, James Christopher, and Nitin S. Baliga. “Architecture for Interoperable Software in Biology.” Briefings in Bioinformatics, vol. 15, no. 4, July 2014, pp. 626–36, http://doi.org/10.1093/bib/bbs074.
Wurtmann, Elisabeth J., et al. “An Evolutionarily Conserved RNase-Based Mechanism for Repression of Transcriptional Positive Autoregulation.” Molecular Microbiology, vol. 92, no. 2, Apr. 2014, pp. 369–82, http://doi.org/10.1111/mmi.12564.
Beer, Karlyn D., et al. “Model Organisms Retain an ‘Ecological Memory’ of Complex Ecologically Relevant Environmental Variation.” Applied and Environmental Microbiology, vol. 80, no. 6, Mar. 2014, pp. 1821–31, http://doi.org/10.1128/AEM.03280-13.
Danziger, Samuel A., et al. “Molecular Mechanisms of System Responses to Novel Stimuli Are Predictable from Public Data.” Nucleic Acids Research, vol. 42, no. 3, Feb. 2014, pp. 1442–60, http://doi.org/10.1093/nar/gkt938.
Turkarslan, Serdar, et al. “Network Portal: A Database for Storage, Analysis and Visualization of Biological  Networks.” Nucleic Acids Research, vol. 42, no. Database issue, Jan. 2014, pp. D184-190, http://doi.org/10.1093/nar/gkt1190.
Ashworth, Justin, et al. “Inference of Expanded Lrp-like Feast/Famine Transcription Factor Targets in a Non-Model Organism Using Protein Structure-Based Prediction.” PloS One, vol. 9, no. 9, 2014, p. e107863, http://doi.org/10.1371/journal.pone.0107863.
Brooks, Aaron N., et al. “A System-Level Model for the Microbial Regulatory Genome.” Molecular Systems Biology, vol. 10, 2014, p. 740.
Zaramela, Livia S., et al. “Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life.” PloS One, vol. 9, no. 9, 2014, p. e107680, http://doi.org/10.1371/journal.pone.0107680.
Rustad, Tige R., et al. “Mapping and Manipulating the Mycobacterium Tuberculosis Transcriptome Using a Transcription Factor Overexpression-Derived Regulatory Network.” Genome Biology, vol. 15, no. 11, 2014, p. 502, http://doi.org/10.1186/PREACCEPT-1701638048134699.