D Kirschner

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. pmc NF-κB Signaling Dynamics Play a Key Role in Infection Control in Tuberculosis
    Mohammad Fallahi-Sichani
    Department of Chemical Engineering, University of Michigan Ann Arbor, MI, USA
    Front Physiol 3:170. 2012
  2. pmc Multi-scale modeling predicts a balance of tumor necrosis factor-α and interleukin-10 controls the granuloma environment during Mycobacterium tuberculosis infection
    Nicholas A Cilfone
    Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
    PLoS ONE 8:e68680. 2013
  3. pmc Resistance, remission, and qualitative differences in HIV chemotherapy
    D E Kirschner
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    Emerg Infect Dis 3:273-83. 1997
  4. ncbi request reprint On the global dynamics of a model for tumor immunotherapy
    Denise Kirschner
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    Math Biosci Eng 6:573-83. 2009
  5. ncbi request reprint Mycobacterium tuberculosis as viewed through a computer
    Denise Kirschner
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0260, USA
    Trends Microbiol 13:206-11. 2005
  6. ncbi request reprint Influence of backward bifurcation on interpretation of r(0) in a model of epidemic tuberculosis with reinfection
    Benjamin H Singer
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109 0620
    Math Biosci Eng 1:81-93. 2004
  7. ncbi request reprint Toward a multiscale model of antigen presentation in immunity
    Denise E Kirschner
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Immunol Rev 216:93-118. 2007
  8. pmc Mathematical and computational approaches can complement experimental studies of host-pathogen interactions
    Denise E Kirschner
    Department of Microbiology and Immunology, 6730 Medical Science Bldg II, University of Michigan Medical School, Ann Arbor, MI, USA
    Cell Microbiol 11:531-9. 2009
  9. ncbi request reprint Role of the thymus in pediatric HIV-1 infection
    D E Kirschner
    Department of Microbiology, University of Michigan Medical School, Ann Arbor 48109 0620, USA
    J Acquir Immune Defic Syndr Hum Retrovirol 18:95-109. 1998
  10. ncbi request reprint Model of HIV-1 disease progression based on virus-induced lymph node homing and homing-induced apoptosis of CD4+ lymphocytes
    D Kirschner
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
    J Acquir Immune Defic Syndr 24:352-62. 2000

Research Grants

Collaborators

Detail Information

Publications42

  1. pmc NF-κB Signaling Dynamics Play a Key Role in Infection Control in Tuberculosis
    Mohammad Fallahi-Sichani
    Department of Chemical Engineering, University of Michigan Ann Arbor, MI, USA
    Front Physiol 3:170. 2012
    ..Because we incorporate intracellular signaling pathways explicitly, our analysis also elucidates NF-κB-associated signaling molecules and processes that may be new targets for infection control...
  2. pmc Multi-scale modeling predicts a balance of tumor necrosis factor-α and interleukin-10 controls the granuloma environment during Mycobacterium tuberculosis infection
    Nicholas A Cilfone
    Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
    PLoS ONE 8:e68680. 2013
    ....
  3. pmc Resistance, remission, and qualitative differences in HIV chemotherapy
    D E Kirschner
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    Emerg Infect Dis 3:273-83. 1997
    ..Also the virus population rapidly rebounds when treatment is stopped even after extended periods of remission...
  4. ncbi request reprint On the global dynamics of a model for tumor immunotherapy
    Denise Kirschner
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    Math Biosci Eng 6:573-83. 2009
    ..This model was extensively studied using numerical simulation, however no global analytical results were originally presented. In this work we explore the global dynamics to show under what conditions tumor clearance can be achieved...
  5. ncbi request reprint Mycobacterium tuberculosis as viewed through a computer
    Denise Kirschner
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0260, USA
    Trends Microbiol 13:206-11. 2005
    ..tuberculosis as a human pathogen. Our goal is to stimulate experimentation and foster collaborations between theoretical and experimental scientists...
  6. ncbi request reprint Influence of backward bifurcation on interpretation of r(0) in a model of epidemic tuberculosis with reinfection
    Benjamin H Singer
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109 0620
    Math Biosci Eng 1:81-93. 2004
    ..In particular, when reinfection is present the basic reproductive number, R(0), does not accurately describe the severity of an epidemic...
  7. ncbi request reprint Toward a multiscale model of antigen presentation in immunity
    Denise E Kirschner
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Immunol Rev 216:93-118. 2007
    ..In addition, we begin to address how such models can be used to answer questions about mechanisms of infection and new strategies for treatment and vaccines...
  8. pmc Mathematical and computational approaches can complement experimental studies of host-pathogen interactions
    Denise E Kirschner
    Department of Microbiology and Immunology, 6730 Medical Science Bldg II, University of Michigan Medical School, Ann Arbor, MI, USA
    Cell Microbiol 11:531-9. 2009
    ..g. seconds to lifetimes). In sum, when combined, these compatible approaches offer new opportunities for understanding host-pathogen interactions...
  9. ncbi request reprint Role of the thymus in pediatric HIV-1 infection
    D E Kirschner
    Department of Microbiology, University of Michigan Medical School, Ann Arbor 48109 0620, USA
    J Acquir Immune Defic Syndr Hum Retrovirol 18:95-109. 1998
    ..We find that infection in the thymus not only can supplement peripheral infection but can help explain the faster progression in pediatric cases, as well as the early and high viral burden...
  10. ncbi request reprint Model of HIV-1 disease progression based on virus-induced lymph node homing and homing-induced apoptosis of CD4+ lymphocytes
    D Kirschner
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
    J Acquir Immune Defic Syndr 24:352-62. 2000
    ..These results lead to a recalculation of the CD4+ lymphocyte dynamics during highly active antiretroviral therapy, and also suggest new targets for therapy...
  11. ncbi request reprint A model to predict cell-mediated immune regulatory mechanisms during human infection with Mycobacterium tuberculosis
    J E Wigginton
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    J Immunol 166:1951-67. 2001
    ..A balance in Th1 and Th2 immune responses governed by IFN-gamma, IL-10, and IL-4 facilitate this down-regulation. These results are further explored through virtual deletion and depletion experiments...
  12. pmc Identification of key processes that control tumor necrosis factor availability in a tuberculosis granuloma
    Mohammad Fallahi-Sichani
    Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
    PLoS Comput Biol 6:e1000778. 2010
    ..Ultimately, these modeling and experimental results can help identify new strategies for TB disease control/therapy...
  13. pmc Effect of multiple genetic polymorphisms on antigen presentation and susceptibility to Mycobacterium tuberculosis infection
    Stewart T Chang
    Program in Bioinformatics, Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Infect Immun 76:3221-32. 2008
    ..Furthermore, the model allows polymorphisms to be ranked by effect, providing a new tool for designing association studies...
  14. pmc Multiple mechanisms allow Mycobacterium tuberculosis to continuously inhibit MHC class II-mediated antigen presentation by macrophages
    Stewart T Chang
    Department of Microbiology and Immunology, University of Michigan Medical School, 6730 Medical Science Building II, Ann Arbor, MI 48109 0620, USA
    Proc Natl Acad Sci U S A 102:4530-5. 2005
    ..In addition, based on a sensitivity analysis of the model, we identify other cellular processes that may be targeted by such pathogens to accomplish the same effect, representing potentially novel mechanisms...
  15. ncbi request reprint Dendritic cell trafficking and antigen presentation in the human immune response to Mycobacterium tuberculosis
    Simeone Marino
    Department of Microbiology and Immunology, University of Michigan Medical School, 6730 Medical Science Building II, Ann Arbor, MI 48109, USA
    J Immunol 173:494-506. 2004
    ..This will induce the most protective T cell response...
  16. pmc The timing of TNF and IFN-gamma signaling affects macrophage activation strategies during Mycobacterium tuberculosis infection
    J Christian J Ray
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Theor Biol 252:24-38. 2008
    ..We examine implications of these results in establishment of latent Mtb infection...
  17. pmc Predicting lymph node output efficiency using systems biology
    Chang Gong
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
    J Theor Biol 335:169-84. 2013
    ..We envision that this systems biology approach will provide novel insights for guiding vaccine development and understanding immune responses to infection. ..
  18. pmc Characterizing the dynamics of CD4+ T cell priming within a lymph node
    Jennifer J Linderman
    Department of Chemical Engineering, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    J Immunol 184:2873-85. 2010
    ..Finally, we identify several pathogen-targeted mechanisms that, if altered in their efficiency, can significantly effect the generation of primed CD4+ T cells...
  19. pmc Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection
    J Christian J Ray
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    J Immunol 182:3706-17. 2009
    ..Results suggest that bacterial numbers are a strong contributing factor to granuloma structure with TNF. Finally, TNF-dependent apoptosis may reduce inflammation at the cost of impairing mycobacterial clearance...
  20. pmc TNF and IL-10 are major factors in modulation of the phagocytic cell environment in lung and lymph node in tuberculosis: a next-generation two-compartmental model
    Simeone Marino
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Theor Biol 265:586-98. 2010
    ..Our results suggest that TNF is a major mediator of recruitment of phagocytes to the lungs. In contrast, IL-10 plays a role in balancing the dominant macrophage phenotype in LN and lung...
  21. ncbi request reprint The role of delays in innate and adaptive immunity to intracellular bacterial infection
    Simeone Marino
    Dept of Microbiology and Immunology, University of Michigan Medical School, 6730 Med Sci Bldg II, Ann Arbor, MI 48109 0620, USA
    Math Biosci Eng 4:261-88. 2007
    ..This allows us to evaluate completely the role of all parameters in the model. This includes identifying effects of stability switch parameters on infection outcome...
  22. ncbi request reprint The importance of an inter-compartmental delay in a model for human gastric acid secretion
    Simeone Marino
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109 0620, USA
    Bull Math Biol 65:963-90. 2003
    ..This suggests that gastric acid secretion homeostasis likely depends strongly on the delay in gastrin transport from the antrum to the corpus...
  23. ncbi request reprint The human immune response to Mycobacterium tuberculosis in lung and lymph node
    Simeone Marino
    Department of Microbiology and Immunology, University of Michigan Medical School, 6730 Medical Science Building II, Ann Arbor, MI 48109 0620, USA
    J Theor Biol 227:463-86. 2004
    ..Then we use the model to predict key processes determining these different disease trajectories (i.e. identify bifurcation parameters), suggesting directions for further basic science study and potential new treatment strategies...
  24. pmc Differences in reactivation of tuberculosis induced from anti-TNF treatments are based on bioavailability in granulomatous tissue
    Simeone Marino
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
    PLoS Comput Biol 3:1909-24. 2007
    ..Alternatively, the dose and timing of anti-TNF therapy could be modified. Anti-TNF therapy will likely lead to numerous incidents of primary TB if used in areas where exposure is likely...
  25. pmc A comparison of random vs. chemotaxis-driven contacts of T cells with dendritic cells during repertoire scanning
    Thomas Riggs
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Theor Biol 250:732-51. 2008
    ..Our results suggest that, within a LN T-zone, a random search strategy is optimal for a rare cognate T cell to find its DC match and maximize production of activated T cells...
  26. ncbi request reprint Contribution of CD8+ T cells to control of Mycobacterium tuberculosis infection
    Dhruv Sud
    Department of Biomedical Engineering, College of Engineering, University of Michigan, Ann Arbor, 48109, USA
    J Immunol 176:4296-314. 2006
    ..We also determined the minimum levels of effector memory cells of each T cell subset (CD4(+) and CD8(+)) in providing effective protection following vaccination...
  27. pmc The dual role of dendritic cells in the immune response to human immunodeficiency virus type 1 infection
    Ian B Hogue
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI, USA
    J Gen Virol 89:2228-39. 2008
    ....
  28. pmc The coreceptor mutation CCR5Delta32 influences the dynamics of HIV epidemics and is selected for by HIV
    A D Sullivan
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-0620, USA
    Proc Natl Acad Sci U S A 98:10214-9. 2001
    ..Also, we show that HIV can provide selective pressure for CCR5Delta32, increasing the frequency of this allele...
  29. ncbi request reprint Requirement for multiple activation signals by anti-inflammatory feedback in macrophages
    J Christian J Ray
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Theor Biol 241:276-94. 2006
    ..This model will be useful for evaluating macrophage control of intracellular pathogens in addition to the biochemical mechanisms examined here...
  30. ncbi request reprint Predicting differential responses to structured treatment interruptions during HAART
    Seema H Bajaria
    Department of Microbiology and Immunology, Department of Biomedical Engineering, The University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    Bull Math Biol 66:1093-118. 2004
    ..Simulations predict that short-term viral suppression with varying interruption strategies does not guarantee long-term clinical benefit...
  31. pmc A methodology for performing global uncertainty and sensitivity analysis in systems biology
    Simeone Marino
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Theor Biol 254:178-96. 2008
    ....
  32. ncbi request reprint Peptide length-based prediction of peptide-MHC class II binding
    Stewart T Chang
    Program in Bioinformatics, University of Michigan Ann Arbor, MI, USA
    Bioinformatics 22:2761-7. 2006
    ..We investigate whether representing one of these differences, the greater range of peptide lengths binding MHC class II, improves the performance of these algorithms...
  33. ncbi request reprint Reconstitution of thymic function in HIV-1 patients treated with highly active antiretroviral therapy
    Ping Ye
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Clin Immunol 106:95-105. 2003
    ..We further predict that protease inhibitors have high levels of efficacy directly suppressing viral replication within the thymus, while reverse transcriptase inhibitors have low efficacy...
  34. ncbi request reprint Measuring emigration of human thymocytes by T-cell receptor excision circles
    Ping Ye
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI, USA
    Crit Rev Immunol 22:483-97. 2002
    ..Our findings suggest that T-cell dynamics are key to the accuracy of TREC concentrations as a useful measurement of human RTEs...
  35. ncbi request reprint Reevaluation of T cell receptor excision circles as a measure of human recent thymic emigrants
    Ping Ye
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Immunol 168:4968-79. 2002
    ..Therefore, we suggest that T cell turnover should be examined together with TREC concentration as a measure of RTE. If peripheral T cell division remains relatively unchanged, then TREC concentration indeed reflects thymic output...
  36. ncbi request reprint New insights into mathematical modeling of the immune system
    Penelope A Morel
    Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
    Immunol Res 36:157-65. 2006
    ..These are collaborative studies between experimental immunologists, mathematicians, and computer scientists...
  37. pmc Tumor necrosis factor blockade in chronic murine tuberculosis enhances granulomatous inflammation and disorganizes granulomas in the lungs
    Soumya D Chakravarty
    Department of Medicine and Microbiology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, F406, Bronx, NY 10461, USA
    Infect Immun 76:916-26. 2008
    ....
  38. ncbi request reprint Virologic and immunologic events in hilar lymph nodes during simian immunodeficiency virus infection: development of polarized inflammation
    Beth A Fallert
    Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
    J Acquir Immune Defic Syndr 47:16-26. 2008
    ....
  39. ncbi request reprint The thymus during HIV disease: role in pathogenesis and in immune recovery
    Ping Ye
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
    Curr HIV Res 2:177-83. 2004
    ..Immunologic interventions aiming at restoring thymic function in AIDS patients are also reviewed...
  40. pmc Chemokine and cytokine mediated loss of regulatory T cells in lymph nodes during pathogenic simian immunodeficiency virus infection
    Shulin Qin
    Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
    J Immunol 180:5530-6. 2008
    ....
  41. ncbi request reprint Increased expression of interferon-inducible genes in macaque lung tissues during simian immunodeficiency virus infection
    Todd M Schaefer
    Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
    Microbes Infect 8:1839-50. 2006
    ....

Research Grants20

  1. "MSM" A multi-scale approach for understanding antigen presentation in immunity
    Denise Kirschner; Fiscal Year: 2005
    ..tuberculosis as well as for other pathogens. ..
  2. The dynamics of granuloma formation in tuberculosis
    Denise Kirschner; Fiscal Year: 2005
    ..The ability to synthesize the data generated by the experiments in the models allows for an understanding of the dynamics of granuloma formation as more than the sum of its parts. ..
  3. Chemokine Dynamics in the HIV-1/SIV Infected Lung
    Denise Kirschner; Fiscal Year: 2005
    ..End of Abstract) ..
  4. Chemokine Dynamics in the HIV-1/SIV Infected Lung
    Denise Kirschner; Fiscal Year: 2004
    ..End of Abstract) ..
  5. Chemokine Dynamics in the HIV-1/SIV Infected Lung
    Denise Kirschner; Fiscal Year: 2003
    ..End of Abstract) ..
  6. Chemokine Dynamics in the HIV-1/SIV Infected Lung
    Denise Kirschner; Fiscal Year: 2002
    ..End of Abstract) ..
  7. The dynamics of granuloma formation in tuberculosis
    Denise Kirschner; Fiscal Year: 2002
    ..The ability to synthesize the data generated by the experiments in the models allows for an understanding of the dynamics of granuloma formation as more than the sum of its parts. ..
  8. MODELING CELLULAR IMMUNITY DURING HIV AND TB INFECTIONS
    Denise Kirschner; Fiscal Year: 2000
    ..Key parameters governing these interactions will be identified through mathematical sensitivity analyses. These results will incorporate, and be tested against, known clinical and experimental data. ..
  9. The dynamics of granuloma formation in tuberculosis
    Denise Kirschner; Fiscal Year: 2001
    ..The ability to synthesize the data generated by the experiments in the models allows for an understanding of the dynamics of granuloma formation as more than the sum of its parts. ..
  10. MODELING CELLULAR IMMUNITY DURING HIV AND TB INFECTIONS
    Denise Kirschner; Fiscal Year: 2001
    ..Key parameters governing these interactions will be identified through mathematical sensitivity analyses. These results will incorporate, and be tested against, known clinical and experimental data. ..
  11. MODELING CELLULAR IMMUNITY DURING HIV AND TB INFECTIONS
    Denise Kirschner; Fiscal Year: 2000
    ..Key parameters governing these interactions will be identified through mathematical sensitivity analyses. These results will incorporate, and be tested against, known clinical and experimental data. ..
  12. MODELING CELLULAR IMMUNITY DURING HIV AND TB INFECTIONS
    Denise Kirschner; Fiscal Year: 1999
    ..Key parameters governing these interactions will be identified through mathematical sensitivity analyses. These results will incorporate, and be tested against, known clinical and experimental data. ..
  13. "MSM" A multi-scale approach for understanding antigen presentation in immunity
    Denise Kirschner; Fiscal Year: 2007
    ..tuberculosis as well as for other pathogens. ..
  14. "MSM" A multi-scale approach for understanding antigen presentation in immunity
    Denise Kirschner; Fiscal Year: 2006
    ..tuberculosis as well as for other pathogens. ..
  15. Chemokine Dynamics in the HIV-1/SIV Infected Lung
    Denise Kirschner; Fiscal Year: 2006
    ..End of Abstract) ..
  16. MODELING CELLULAR IMMUNITY DURING HIV AND TB INFECTIONS
    Denise Kirschner; Fiscal Year: 2002
    ..Key parameters governing these interactions will be identified through mathematical sensitivity analyses. These results will incorporate, and be tested against, known clinical and experimental data. ..
  17. The dynamics of granuloma formation in tuberculosis
    Denise Kirschner; Fiscal Year: 2004
    ..The ability to synthesize the data generated by the experiments in the models allows for an understanding of the dynamics of granuloma formation as more than the sum of its parts. ..
  18. The dynamics of granuloma formation in tuberculosis
    Denise Kirschner; Fiscal Year: 2003
    ..The ability to synthesize the data generated by the experiments in the models allows for an understanding of the dynamics of granuloma formation as more than the sum of its parts. ..