Publications

2014
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.
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)
Zak DE, Tam VC, Aderem A. "Systems-level analysis of innate immunity." Annu. Rev. Immunol.. 2014;32:547-77.
Urdahl KB. "Understanding and overcoming the barriers to T cell-mediated immunity against tuberculosis." Semin. Immunol.. 2014;26(6):578-87.
2015
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)
Minch KJ, Rustad TR, Peterson EJR, et al. "The DNA-binding network of Mycobacterium tuberculosis." Nat Commun. 2015;6:5829.
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.
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.
Zak DE, Aderem A. "Systems integration of innate and adaptive immunity." Vaccine. 2015;33(40):5241-8.
Andersen P, Urdahl KB. "TB vaccines; promoting rapid and durable protection in the lung." Curr. Opin. Immunol.. 2015;35:55-62.
2016
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.
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.
2017
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.
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.
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.
Thompson EG, Du Y, Malherbe ST, et al. "Host blood RNA signatures predict the outcome of tuberculosis treatment." Tuberculosis (Edinb). 2017;107:48-58.
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.
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.
Banaei-Esfahani A, Nicod C, Aebersold R, Collins BC. "Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis." Curr. Opin. Microbiol.. 2017;39:64-72.
2018
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.
Cohen SB, Urdahl KB. "Going beyond gamma for TB protection." Nat Microbiol. 2018;3(11):1194-1195.
Hansen SG, Zak DE, Xu G, et al. "Prevention of tuberculosis in rhesus macaques by a cytomegalovirus-based vaccine." Nat. Med.. 2018;24(2):130-143.
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.