Publications

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Zak DE, Tam VC, Aderem A. "Systems-level analysis of innate immunity." Annu. Rev. Immunol.. 2014;32:547-77.
Zak DE, Aderem A. "Systems integration of innate and adaptive immunity." Vaccine. 2015;33(40):5241-8.
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Woodworth JS, Cohen SB, Moguche AO, et al. "Subunit vaccine H56/CAF01 induces a population of circulating CD4 T cells that traffic into the Mycobacterium tuberculosis-infected lung." Mucosal Immunol. 2017;10(2):555-564.
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Urdahl KB. "Understanding and overcoming the barriers to T cell-mediated immunity against tuberculosis." Semin. Immunol.. 2014;26(6):578-87.
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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)
Thompson EG, Du Y, Malherbe ST, et al. "Host blood RNA signatures predict the outcome of tuberculosis treatment." Tuberculosis (Edinb). 2017;107:48-58.
Thompson EG, Shankar S, Gideon HP, et al. "Prospective Discrimination of Controllers From Progressors Early After Low-Dose Mycobacterium tuberculosis Infection of Cynomolgus Macaques using Blood RNA Signatures." J. Infect. Dis.. 2018;217(8):1318-1322.
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Scriba TJ, Penn-Nicholson A, Shankar S, et al. "Sequential inflammatory processes define human progression from M. tuberculosis infection to tuberculosis disease." PLoS Pathog.. 2017;13(11):e1006687.
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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, 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).
Rothchild AC, Olson GS, Nemeth J, et al. "Alveolar macrophages generate a noncanonical NRF2-driven transcriptional response in vivo." Sci Immunol. 2019;4(37).
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.
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.
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Plumlee CR, Duffy FJ, Gern BH, et al. "Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis." Cell Host Microbe. 2020.
Peterson EJR, Ma S, Sherman DR, Baliga NS. "Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis." Nat Microbiol. 2016;1(8):16078.
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.
Peterson, JR E, Bailo R, Rothchild AC, et al. "Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation." Molecular Systems Biology. 2019;15:e8584.
Peterson EJR, Abidi AA, Arrieta-Ortiz ML, et al. "Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis." Cell Rep. 2020;31(4):107577.
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.
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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.
Nemeth J, Olson GS, Rothchild AC, et al. "Contained Mycobacterium tuberculosis infection induces concomitant and heterologous protection." PLoS Pathog. 2020;16(7):e1008655.
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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.
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.
Minch KJ, Rustad TR, Peterson EJR, et al. "The DNA-binding network of Mycobacterium tuberculosis." Nat Commun. 2015;6:5829.
Ma S, Morrison R, Hobbs SJ, et al. "Transcriptional regulator-induced phenotype screen reveals drug potentiators in Mycobacterium tuberculosis." Nat Microbiol. 2020.