Omics 4 TB Publications | Omics4TB

Prevention of tuberculosis in rhesus macaques by a cytomegalovirus-based vaccine., Hansen, Scott G., Zak Daniel E., Xu Guangwu, Ford Julia C., Marshall Emily E., Malouli Daniel, Gilbride Roxanne M., Hughes Colette M., Ventura Abigail B., Ainslie Emily, et al. , Nat Med, 2018 Feb, Volume 24, Issue 2, p.130-143, (2018)

Blood RNA signatures prospectively discriminate controllers from progressors early after low-dose M. tuberculosis infection of cynomolgus macaques, Thompson, Ethan G., Shankar Smitha, Gideon Hannah P., Braun Jackie, Valvo Joe, Skinner Jason, Aderem Alan, Flynn JoAnne L., Lin Philana Ling, and Zak Daniel E. , 2018/01/08, p.jiy006 - jiy006, (2018)

Cell envelope stress in mycobacteria is regulated by the novel signal transduction ATPase IniR in response to trehalose., Boot, Maikel, van Winden Vincent J. C., Sparrius Marion, van de Weerd Robert, Speer Alexander, Ummels Roy, Rustad Tige, Sherman David R., and Bitter Wilbert , PLoS Genet, 2017 12, Volume 13, Issue 12, p.e1007131, (2017)

Host blood RNA signatures predict the outcome of tuberculosis treatment., Thompson, Ethan G., Du Ying, Malherbe Stephanus T., Shankar Smitha, Braun Jackie, Valvo Joe, Ronacher Katharina, Tromp Gerard, Tabb David L., Alland David, et al. , Tuberculosis (Edinb), 2017 Dec, Volume 107, p.48-58, (2017)

Sequential inflammatory processes define human progression from M. tuberculosis infection to tuberculosis disease., Scriba, Thomas J., Penn-Nicholson Adam, Shankar Smitha, Hraha Tom, Thompson Ethan G., Sterling David, Nemes Elisa, Darboe Fatoumatta, Suliman Sara, Amon Lynn M., et al. , PLoS Pathog, 2017 Nov, Volume 13, Issue 11, p.e1006687, (2017)

Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis., Banaei-Esfahani, Amir, Nicod Charlotte, Aebersold Ruedi, and Collins Ben C. , Curr Opin Microbiol, 2017 Oct, Volume 39, p.64-72, (2017)

Elucidation of host-pathogen protein-protein interactions to uncover mechanisms of host cell rewiring., Nicod, Charlotte, Banaei-Esfahani Amir, and Collins Ben C. , Curr Opin Microbiol, 2017 Oct, Volume 39, p.7-15, (2017)

Antigen Availability Shapes T Cell Differentiation and Function during Tuberculosis., Moguche, Albanus O., Musvosvi Munyaradzi, Penn-Nicholson Adam, Plumlee Courtney R., Mearns Helen, Geldenhuys Hennie, Smit Erica, Abrahams Deborah, Rozot Virginie, Dintwe One, et al. , Cell Host Microbe, 2017 Jun 14, Volume 21, Issue 6, p.695-706.e5, (2017)

Subunit vaccine H56/CAF01 induces a population of circulating CD4 T cells that traffic into the Mycobacterium tuberculosis-infected lung., Woodworth, J S., Cohen S B., Moguche A O., Plumlee C R., Agger E M., Urdahl K B., and Andersen P , Mucosal Immunol, 2017 Mar, Volume 10, Issue 2, p.555-564, (2017)

MiR-155-regulated molecular network orchestrates cell fate in the innate and adaptive immune response to Mycobacterium tuberculosis., Rothchild, Alissa C., Sissons James R., Shafiani Shahin, Plaisier Christopher, Min Deborah, Mai Dat, Gilchrist Mark, Peschon Jacques, Larson Ryan P., Bergthaler Andreas, et al. , Proc Natl Acad Sci U S A, 2016 Oct 11, Volume 113, Issue 41, p.E6172-E6181, (2016)

Mycobacterial Acid Tolerance Enables Phagolysosomal Survival and Establishment of Tuberculous Infection In Vivo., Levitte, Steven, Adams Kristin N., Berg Russell D., Cosma Christine L., Urdahl Kevin B., and Ramakrishnan Lalita , Cell Host Microbe, 2016 Aug 10, Volume 20, Issue 2, p.250-8, (2016)

Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis., Peterson, Eliza J. R., Ma Shuyi, Sherman David R., and Baliga Nitin S. , Nat Microbiol, 2016 Jun 06, Volume 1, Issue 8, p.16078, (2016)

Interdependence between Interleukin-1 and Tumor Necrosis Factor Regulates TNF-Dependent Control of Mycobacterium tuberculosis Infection., Di Paolo, Nelson C., Shafiani Shahin, Day Tracey, Papayannopoulou Thalia, Papayannoupoulou Thalia, Russell David W., Iwakura Yoichiro, Sherman David, Urdahl Kevin, and Shayakhmetov Dmitry M. , Immunity, 2015 Dec 15, Volume 43, Issue 6, p.1125-36, (2015)

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis., Ma, Shuyi, Minch Kyle J., Rustad Tige R., Hobbs Samuel, Zhou Suk-Lin, Sherman David R., and Price Nathan D. , PLoS Comput Biol, 2015 Nov, Volume 11, Issue 11, p.e1004543, (2015)

Systems integration of innate and adaptive immunity., Zak, Daniel E., and Aderem Alan , Vaccine, 2015 Sep 29, Volume 33, Issue 40, p.5241-8, (2015)

TB vaccines; promoting rapid and durable protection in the lung., Andersen, Peter, and Urdahl Kevin B. , Curr Opin Immunol, 2015 Aug, Volume 35, p.55-62, (2015)

ICOS and Bcl6-dependent pathways maintain a CD4 T cell population with memory-like properties during tuberculosis., Moguche, Albanus O., Shafiani Shahin, Clemons Corey, Larson Ryan P., Dinh Crystal, Higdon Lauren E., Cambier C J., Sissons James R., Gallegos Alena M., Fink Pamela J., et al. , J Exp Med, 2015 May 04, Volume 212, Issue 5, p.715-28, (2015)

Systems-level analysis of innate immunity., Zak, Daniel E., Tam Vincent C., and Aderem Alan , Annu Rev Immunol, 2014, Volume 32, p.547-77, (2014)

Understanding and overcoming the barriers to T cell-mediated immunity against tuberculosis., Urdahl, Kevin B. , Semin Immunol, 2014 Dec, Volume 26, Issue 6, p.578-87, (2014)

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis., Turkarslan, Serdar, Peterson Eliza J. R., Rustad Tige R., Minch Kyle J., Reiss David J., Morrison Robert, Ma Shuyi, Price Nathan D., Sherman David R., and Baliga Nitin S. , Sci Data, 2015, Volume 2, p.150010, (2015)

Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network., Rustad, Tige R., Minch Kyle J., Ma Shuyi, Winkler Jessica K., Hobbs Samuel, Hickey Mark, Brabant William, Turkarslan Serdar, Price Nathan D., Baliga Nitin S., et al. , Genome Biol, 2014, Volume 15, Issue 11, p.502, (2014)

The DNA-binding network of Mycobacterium tuberculosis., Minch, Kyle J., Rustad Tige R., Peterson Eliza J. R., Winkler Jessica, Reiss David J., Ma Shuyi, Hickey Mark, Brabant William, Morrison Bob, Turkarslan Serdar, et al. , Nat Commun, 2015, Volume 6, p.5829, (2015)

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis., Peterson, Eliza J. R., Reiss David J., Turkarslan Serdar, Minch Kyle J., Rustad Tige, Plaisier Christopher L., Longabaugh William J. R., Sherman David R., and Baliga Nitin S. , Nucleic Acids Res, 2014 Sep 17, (2014)

The Mycobacterium tuberculosis regulatory network and hypoxia., Galagan, James E., Minch Kyle, Peterson Matthew, Lyubetskaya Anna, Azizi Elham, Sweet Linsday, Gomes Antonio, Rustad Tige, Dolganov Gregory, Glotova Irina, et al. , Nature, 2013 Jul 11, Volume 499, Issue 7457, p.178-83, (2013)