Joseph M Cicchese, Awanti Sambarey, Denise Kirschner, Jennifer J Linderman, Sriram Chandrasekaran, A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs, Sci Rep 11, 5643 (2021), DOI: 10.1038/s41598-021-84827-0, PMID: 33707554, PMCID: Pending

Joseph M. Cicchese, Véronique Dartois, Denise E. Kirschner, and Jennifer J. Linderman, Both Pharmacokinetic Variability and Granuloma Heterogeneity Impact the Ability of the First-Line Antibiotics to Sterilize Tuberculosis Granulomas, Front. Pharmacol., 24 March 2020, DOI: 10.3389/fphar.2020.00333, PMID: 32265707, PMCID: 7105635

Jansy Sarathy, Landry Blanc, Nadine Alvarez-Cabrera, Paul O'Brien, Isabela Dias-Freedman, Marizel Mina, Matthew Zimmerman, Firat Kaya, Hsin-Pin Ho Liang, Brendan Prideaux, Jillian Dietzold, Padmini Salgame, Rada Savic, Jennifer Linderman, Denise Kirschner, Elsje Pienaar, Véronique Dartois, Fluoroquinolone efficacy against tuberculosis is driven by penetration into lesions and activity against resident bacterial populations, Online 25 February 2019, Antimicrobial Agents and Chemotherapy, DOI: 10.1128/AAC.02516-18, PMID: 30803965, PMCID: 6496041

Joseph M. Cicchese, Timothy Wessler, Joshua T. Mattila, Stephanie Evans, Caitlin Hult, Louis R. Joslyn, Jess A. Millar, Simeone Marino, Nicholas A. Cilfone, Jennifer J. Linderman, Denise E. Kirschner, Dynamic balance of pro- and anti-inflammatory signals controls disease and limits pathology, Immunological Reviews. 2018; 1-21, DOI: 10.1111/imr.12671, PMID: 30129209, PMCID: 6292442

Elsje Pienaar, Jennifer J. Linderman, Denise E. Kirschner, Emergence and selection of isoniazid and rifampin resistance in tuberculosis granulomas, PLoS One. 2018 May 10;13(5):e0196322, DOI: 10.1371/journal.pone.0196322, PMID: 29746491, PMCID: 5944939

Warsinske HC, Pienaar E, Linderman JJ, Mattila JT and Kirschner DE, Deletion of TGF-β1 Increases Bacterial Clearance by Cytotoxic T Cells in a Tuberculosis Granuloma Model, Front. Immunol. 8:1843, Accepted December 2017, DOI: 10.3389/fimmu.2017.01843, PMID: 29326718, PMCID: 5742530

Elsje Pienaar, Jansy Sarathy, Brendan Prideaux, Jillian Dietzold, Véronique Dartois, Denise E. Kirschner, Jennifer J. Linderman, Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach, PLOS: Computational Biology, Published: August 17, 2017, DOI: 10.1371/journal.pcbi.1005650, PMID: 28817561, PMCID: 5560534

Biomedical Picture of the Day

Joseph M. Cicchese, Elsje Pienaar, Denise E. Kirschner, Jennifer J. Linderman, Applying Optimization Algorithms to Tuberculosis Antibiotic Treatment Regimens, Cellular and Molecular Bioengineering, pp 1-13, 30 August 2017, Pages 1-17, DOI: 10.1007/s12195-017-0507-6, PMID: 29276546, PMCID: 5737793

Article featured on Journal cover

Denise Kirschner, Elsje Pienaar, Simeone Marino, Jennifer J. Linderman, A review of computational and mathematical modeling contributions to our understanding of Mycobacterium tuberculosis within-host infection and treatment, CURRENT OPINION Systems Biology 2017, 3:170-185, DOI: 10.1016/j.coisb.2017.05.014, PMID: 30714019, PMCID: 6354243

Online Supplement

Elsje Pienaar, William M. Matern, Jennifer J. Linderman, Joel S. Bader, Denise E. Kirschner, Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions, Infect Immun. 2016 Apr 22;84(5):1650-69. Print 2016 May., DOI: 10.1128/IAI.01438-15, PMID: 26975995, PMCID: 4862722

Supplemental Information - Supplement1

Elsje Pienaar, Véronique Dartois, Jennifer J. Linderman, Denise E. Kirschner, In silico evaluation and exploration of antibiotic tuberculosis treatment regimens, BMC Systems Biology 2015, 9:79, DOI: 10.1186/s12918-015-0221-8, PMID: 26578235, PMCID: 4650854

Jennifer J. Linderman, Nicholas A. Cilfone, Elsje Pienaar, Chang Gong, Denise E. Kirschner, A Multi-scale Approach to Designing Therapeutics for Tuberculosis, Integrative Biology (2015), DOI: 10.1039/C4IB00295D, PMID: 25924949, PMCID: 4436084

Cilfone, N, Pienaar, E, Thurber, G, Kirschner, D and Linderman, JJ., A systems pharmacology approach towards the design of inhaled formulations of rifampicin and isoniazid for treatment of tuberculosis, CPT Pharmacometrics Syst. Pharmacol. (2015) 4, e22, DOI: 10.1002/psp4.22, PMID: 26225241, PMCID: 4394619

Elsje Pienaar, Nicholas A. Cilfone, Philana Ling Lin, Veronique Dartois, Joshua T. Mattila, J. Russell Butler, JoAnne L. Flynn, Denise E. Kirschner, Jennifer J. Linderman, A computational tool integrating host immunity with antibiotic dynamics to study tuberculosis treatment, Journal of Theoretical Biology (2015), pp. 166-179, published online: 24-DEC-2014 DOI: 10.1016/j.jtbi.2014.11.021, PMID: 25497475, PMCID: 4332617

Supplemental Information - Supplement1

Ping Ye, Powel Kazanjian, Steven L. Kunkel, and Denise E. Kirschner Lack of good correlation of serum CC-chemokine levels with human immunodeficiency virus-1 disease stage and response to treatment J Lab and Clin Medicine, 143:310-319, 2004, PMID: 15122175, PMCID: (exempt)

Sud, D., Joseph, I., Kirschner, D., Predicting Efficacy of Proton Pump Inhibitors in Regulating Gastric Acid Secretion . Journal of Biological Systems, Vol. 12, No. 1, pg 1-34, 2004, PMID: n/a, PMCID: n/a, NIHMSID: n/a.

Seema H. Bajaria, Glenn Webb, Denise E. Kirschner. Predicting Differential Responses to Structured Treatment Interruptions During HAART. Bulletin of Mathematical Biology, 66:1093-1118, 2004, PMID: 15294419, PMCID: n/a, NIHMSID: n/a.

Jorge X. Velasco-Hernandez, Jose A. Garcia,Denise E. Kirschner , Remarks on Modeling Host-Viral Dynamics and Treatment. in: Volume 125: Mathematical Approaches for Emerging and Reemerging Infectious Diseases Part I: An Introduction to Models, Methods, and Theory
In: Chavez C, Blower S, Van Den Dreische P, Kirschner D, Yakubu A-A. (eds): Mathematical Approaches for Emerging and Reemerging Infectious Diseases: An Introduction to Models, Methods and Theory. Vols. 1 and 2, (Springer-Verlag, New York, 2001), PMID: n/a, PMCID: (exempt)

Kirschner D. Dynamics of co-infection with M. tuberculosis and HIV-1. Theor Popul Biol, 55: 94- 109, 1999, PMID: 9925811, PMCID: n/a, NIHMSID: n/a.

Kirschner D and Panetta JC. Modeling immunotherapy of the tumor-immune interaction. J Math Biol, 37: 235-252, 1998, PMID: 9785481, PMCID: n/a NIHMSID: n/a.

Kirschner D and Webb GF. Immunotherapy of HIV-1 infection. J Biol Systems, 6:71-83, 1998, PMID: 9785481, PMCID: n/a NIHMSID: n/a.

Kirschner D and Webb GF. A mathematical model of combined drug therapy of HIV infection. J Theor Med 1:25-34, 1998, PMID: n/a, PMCID: n/a, NIHMSID: n/a.

Butler S, Kirschner D and Lenhart S. Optimal control of Chemotherapy Affecting the Infectivity of HIV. In: Arino O, Axelrod D, Kimmel M, Langlais M (eds): Advances in Mathematical Population Dynamics: Molecules, Cells, Man. World Scientific Publishing, pp. 104-120, 1997, PMID: n/a, PMCID: n/a, NIHMSID: n/a.

Kirschner D, Lenhart S, Serbin S. Optimizing chemotherapy of HIV infection: Scheduling, amounts and initiation of treatment. J Math Biol 35:775-792, 1997, PMID: 9269736, PMCID: n/a, NIHMSID: n/a.

Kirschner D and Webb GF. Qualitative differences in HIV chemotherapy between resistance and remission outcomes. Emerging Inf Dis 3:273-283, 1997, PMID: 9284371, PMCID: PMC2627652, NIHMSID: n/a.

Kirschner D and Webb GF. Understanding drug resistance for montherapy treatment of HIV infection. Bull Math Biol 59:763-786, 1997, PMID: 9214852, PMCID: n/a, NIHMSID: n/a.

Kirschner D. Using mathematics to understand HIV immune dynamics. AMS Notices pp. 191-202, February 1996, PMID: n/a, PMCID: n/a, NIHMSID: n/a.

Kirschner D and Webb GF. A model for treatment strategy in the chemotherapy of AIDS. Bull Math Biol 58:367-390, 1996, PMID: 8713663, PMCID: n/a, NIHMSID: n/a.

Kirschner D and Perelson A. A Model for the Immune System Response to HIV: AZT Treatment Studies. In: Arino O, Axelrod D, Kimmel M, Langlais M (eds): Mathematical Population Dynamics: Analysis of Hetergeneity and Theory of Epidemics (Wuerz Publishing, Winnipeg, 1995) pp. 295-310, PMID: n/a, PMCID: n/a, NIHMSID: n/a.

Perelson A, Kirschner D, De Boer R. The dynamics of HIV infection of CD4+ T cells. Math Biosci 114:81-125, 1993, PMID: 8096155, PMCID: n/a, NIHMSID: n/a.