Publications

Journal Article
Rothchild AC, Olson GS, Nemeth J, et al. "Alveolar macrophages generate a noncanonical NRF2-driven transcriptional response in vivo." Sci Immunol. 2019;4(37).
Cohen SB, Gern BH, Delahaye JL, et al. "Alveolar Macrophages Provide an Early Mycobacterium tuberculosis Niche and Initiate Dissemination." Cell Host Microbe. 2018;24(3):439-446.e4.
Moguche AO, Musvosvi M, Penn-Nicholson A, et al. "Antigen Availability Shapes T Cell Differentiation and Function during Tuberculosis." Cell Host Microbe. 2017;21(6):695-706.e5.
Delahaye JL, Gern BH, Cohen SB, et al. "BCG-induced T cells shape Mycobacterium tuberculosis infection before reducing the bacterial burden." bioRxiv. 2019.
Boot M, van Winden VJC, Sparrius M, et al. "Cell envelope stress in mycobacteria is regulated by the novel signal transduction ATPase IniR in response to trehalose." PLoS Genet.. 2017;13(12):e1007131.
Turkarslan S, Peterson EJR, Rustad TR, et al. "A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis." Scientific Data. 2015;2: - . (8.9 KB) (157.5 KB) (337.5 KB) (1.33 MB)
Nemeth J, Olson GS, Rothchild AC, et al. "Contained Mycobacterium tuberculosis infection induces concomitant and heterologous protection." PLoS Pathog. 2020;16(7):e1008655.
Delahaye JL, Gern BH, Cohen SB, et al. "Cutting Edge: Bacillus Calmette–Guérin–Induced T Cells Shape Mycobacterium tuberculosis Infection before Reducing the Bacterial Burden." The Journal of Immunology. 2019;203:807-812.
Adams KN, Verma AKumar, Gopalaswamy R, et al. "Diverse Clinical Isolates of Mycobacterium tuberculosis Develop Macrophage-Induced Rifampin Tolerance." The Journal of Infectious Diseases. 2019;219:1554-1558.
Minch KJ, Rustad TR, Peterson EJR, et al. "The DNA-binding network of Mycobacterium tuberculosis." Nat Commun. 2015;6:5829.
Nicod C, Banaei-Esfahani A, Collins BC. "Elucidation of host-pathogen protein-protein interactions to uncover mechanisms of host cell rewiring." Curr. Opin. Microbiol.. 2017;39:7-15.
Rothchild AC, Mai D, Aderem A, Diercks AH. "Flow Cytometry Analysis and Fluorescence-activated Cell Sorting of Myeloid Cells from Lung and Bronchoalveolar Lavage Samples from -infected Mice." Bio Protoc. 2020;10(10).
Peters JS, Ismail N, Dippenaar A, et al. "Genetic Diversity in Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease." Annu Rev Genet. 2020.
Cohen SB, Urdahl KB. "Going beyond gamma for TB protection." Nat Microbiol. 2018;3(11):1194-1195.
Peterson EJR, Reiss DJ, Turkarslan S, et al. "A high-resolution network model for global gene regulation in Mycobacterium tuberculosis." Nucleic Acids Res.. 2014;42(18):11291-303.
Thompson EG, Du Y, Malherbe ST, et al. "Host blood RNA signatures predict the outcome of tuberculosis treatment." Tuberculosis (Edinb). 2017;107:48-58.
Moguche AO, Shafiani S, Clemons C, et al. "ICOS and Bcl6-dependent pathways maintain a CD4 T cell population with memory-like properties during tuberculosis." J. Exp. Med.. 2015;212(5):715-28.
Duffy FJ, Weiner J, Hansen S, et al. "Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome." Front Immunol. 2019;10:527.
Ma S, Minch KJ, Rustad TR, et al. "Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis." PLoS Comput. Biol.. 2015;11(11):e1004543.
Di Paolo NC, Shafiani S, Day T, et al. "Interdependence between Interleukin-1 and Tumor Necrosis Factor Regulates TNF-Dependent Control of Mycobacterium tuberculosis Infection." Immunity. 2015;43(6):1125-36.
Peterson EJR, Abidi AA, Arrieta-Ortiz ML, et al. "Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis." Cell Rep. 2020;31(4):107577.
Rahil Z, Leylek R, Schürch CM, et al. "Landscape of coordinated immune responses to H1N1 challenge in humans." J Clin Invest. 2020;130(11):5800-5816.
Rustad TR, Minch KJ, Ma S, et al. "Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network." Genome Biol.. 2014;15(11):502. (19.36 MB) (20.15 MB)
Rothchild AC, Sissons JR, Shafiani S, et al. "MiR-155-regulated molecular network orchestrates cell fate in the innate and adaptive immune response to Mycobacterium tuberculosis." Proc. Natl. Acad. Sci. U.S.A.. 2016;113(41):E6172-E6181.
Levitte S, Adams KN, Berg RD, Cosma CL, Urdahl KB, Ramakrishnan L. "Mycobacterial Acid Tolerance Enables Phagolysosomal Survival and Establishment of Tuberculous Infection In Vivo." Cell Host Microbe. 2016;20(2):250-8.