Eliza Peterson

Senior Research Scientist

401 Terry Ave N
206-732-1265
eliza.peterson@isbscience.org

Dr. Peterson’s research focuses on using network models, genome-wide assays (e.g, gene expression, Tn-seq, ChIP-Seq) and phenotype data to understand the underlying complexity of tuberculosis and its infectious agent, Mycobacterium tuberculosis. Dr. Peterson has constructed gene regulatory network models for M. tuberculosis, revealing how the pathogen responds to therapeutic, immunologic and nutritional challenges during infection. Dr. Peterson is focused on using network models to understand drug resistance and the prioritization of targets for antitubercular treatment. She is also working on developing network models for other CMNR bacteria (corynebacterium, mycobacterium, nocardia, rhodococcus) to elucidate regulatory mechanisms that allow these bacteria to alter their cell envelope composition in different environmental conditions.

Publications

Wang, Yaxi, Larry A. Gallagher, Pia A. Andrade, Andi Liu, Ian R. Humphreys, Serdar Turkarslan, Kevin J. Cutler, et al. 2023. “Genetic Manipulation of Candidate Phyla Radiation Bacteria Provides Functional Insights into Microbial Dark Matter.” BioRxiv: The Preprint Server for Biology, May, 2023.05.02.539146. https://doi.org/10.1101/2023.05.02.539146.
Xavier, Joao B., Jonathan M. Monk, Saugat Poudel, Charles J. Norsigian, Anand V. Sastry, Chen Liao, Jose Bento, et al. 2022. “Mathematical Models to Study the Biology of Pathogens and the Infectious Diseases They Cause.” IScience 25 (4): 104079. https://doi.org/10.1016/j.isci.2022.104079.
Cooper, Charlotte, Eliza J. R. Peterson, Rebeca Bailo, Min Pan, Albel Singh, Patrick Moynihan, Makoto Nakaya, Nagatoshi Fujiwara, Nitin Baliga, and Apoorva Bhatt. 2022. “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 119 (8): e2111059119. https://doi.org/10.1073/pnas.2111059119.
Srinivas, Vivek, Rene A. Ruiz, Min Pan, Selva Rupa Christinal Immanuel, Eliza J. R. Peterson, and Nitin S. Baliga. 2021. “Transcriptome Signature of Cell Viability Predicts Drug Response and Drug Interaction in Mycobacterium Tuberculosis.” Cell Reports Methods 1 (8): None. https://doi.org/10.1016/j.crmeth.2021.100123.
Immanuel, Selva Rupa Christinal, Mario L. Arrieta-Ortiz, Rene A. Ruiz, Min Pan, Adrian Lopez Garcia de Lomana, Eliza J. R. Peterson, and Nitin S. Baliga. 2021. “Quantitative Prediction of Conditional Vulnerabilities in Regulatory and Metabolic Networks Using PRIME.” NPJ Systems Biology and Applications 7 (1): 43. https://doi.org/10.1038/s41540-021-00205-6.
Neal, Maxwell L., Ling Wei, Eliza Peterson, Mario L. Arrieta-Ortiz, Samuel A. Danziger, Nitin S. Baliga, Alexis Kaushansky, and John D. Aitchison. 2021. “A Systems-Level Gene Regulatory Network Model for Plasmodium Falciparum.” Nucleic Acids Research, January. https://doi.org/10.1093/nar/gkaa1245.
Srinivas, Vivek, Mario L. Arrieta-Ortiz, Amardeep Kaur, Eliza J. R. Peterson, and Nitin S. Baliga. 2020. “PerSort Facilitates Characterization and Elimination of Persister Subpopulation in Mycobacteria.” Edited by Charles Langelier. MSystems 5 (6): e01127-20, /msystems/5/6/mSys.01127-20.atom. https://doi.org/10.1128/mSystems.01127-20.
Vega-Dominguez, Perla, Eliza Peterson, Min Pan, Alessandro Di Maio, Saumya Singh, Siva Umapathy, Deepak K. Saini, Nitin Baliga, and Apoorva Bhatt. 2020. “Biofilms of the Non-Tuberculous Mycobacterium Chelonae Form an Extracellular Matrix and Display Distinct Expression Patterns.” Cell Surface (Amsterdam, Netherlands) 6 (December): 100043. https://doi.org/10.1016/j.tcsw.2020.100043.
Flores-Valdez, Mario Alberto, Michel de Jesús Aceves-Sánchez, Eliza J. R. Peterson, Nitin Baliga, Jorge Bravo-Madrigal, Miguel Ángel De la Cruz-Villegas, Miguel A. Ares, et al. 2020. “Transcriptional Portrait of M. Bovis BCG during Biofilm Production Shows Genes Differentially Expressed during Intercellular Aggregation and Substrate Attachment.” Scientific Reports 10 (1): 12578. https://doi.org/10.1038/s41598-020-69152-2.
Abidi, Abrar A., Eliza J. R. Peterson, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, and Nitin S. Baliga. 2019. “Intricate Genetic Programs Controlling Dormancy in Mycobacterium Tuberculosis.” BioRxiv, July, 709378. https://doi.org/10.1101/709378.
Srinivas, Vivek, Mario Arrieta-Ortiz, Eliza J. R. Peterson, and Nitin S. Baliga. 2018. “Characterization and Elimination of Stochastically Generated Persister Subpopulation in Mycobacteria.” BioRxiv, November, 463232. https://doi.org/10.1101/463232.
Peterson, Eliza J. R., Shuyi Ma, David R. Sherman, and Nitin S. Baliga. 2016. “Network Analysis Identifies Rv0324 and Rv0880 as Regulators of Bedaquiline Tolerance in Mycobacterium Tuberculosis.” Nature Microbiology 1 (8): 16078. https://doi.org/10.1038/nmicrobiol.2016.78.
Turkarslan, Serdar, Eliza J. R. Peterson, Tige R. Rustad, Kyle J. Minch, David J. Reiss, Robert Morrison, Shuyi Ma, Nathan D. Price, David R. Sherman, and Nitin S. Baliga. 2015. “A Comprehensive Map of Genome-Wide Gene Regulation in Mycobacterium Tuberculosis.” Scientific Data 2: 150010. https://doi.org/10.1038/sdata.2015.10.
Minch, Kyle J., Tige R. Rustad, Eliza J. R. Peterson, Jessica Winkler, David J. Reiss, Shuyi Ma, Mark Hickey, et al. 2015. “The DNA-Binding Network of Mycobacterium Tuberculosis.” Nature Communications 6: 5829. https://doi.org/10.1038/ncomms6829.
Peterson, Eliza J. R., David J. Reiss, Serdar Turkarslan, Kyle J. Minch, Tige Rustad, Christopher L. Plaisier, William J. R. Longabaugh, David R. Sherman, and Nitin S. Baliga. 2014. “A High-Resolution Network Model for Global Gene Regulation in Mycobacterium Tuberculosis.” Nucleic Acids Research 42 (18): 11291–303. https://doi.org/10.1093/nar/gku777.
Koide, Tie, David J. Reiss, J. Christopher Bare, Wyming Lee Pang, Marc T. Facciotti, Amy K. Schmid, Min Pan, et al. 2009. “Prevalence of Transcription Promoters within Archaeal Operons and Coding Sequences.” Molecular Systems Biology 5: 285. https://doi.org/10.1038/msb.2009.42.