URMC / Labs / Thakar Lab / Publications Publications Mariani TJQiu XChu CYWang LThakar JHolden-Wiltse JCorbett ATopham DJFalsey ARCaserta MTWalsh EE (2017 Aug 17). Dynamic changes in the CD4 T cell transcriptome are associated with disease severity during primary RSV infection in young infants. The Journal of infectious diseases. Connor RJones LDQiu XThakar JMaggirwar SB (2017 Jun 29). Frontline Science: c-Myc regulates P-selectin glycoprotein ligand-1 expression in monocytes during HIV-1 infection. Journal of leukocyte biology. Khan AKatanic DThakar J (2017 Jun 06). Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes. BMC bioinformatics. Van Twisk DMurphy SPThakar J (2017 May). Optimized logic rules reveal interferon-γ-induced modes regulated by histone deacetylases and protein tyrosine phosphatases. Immunology. Zhang YTopham DJThakar JQiu X (2017 Feb 21). FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis. Bioinformatics (Oxford, England). Katanic DKhan AThakar J (2016 Sep 19). PathCellNet: Cell-type specific pathogen-response network explorer. Journal of immunological methods. Woeller CFThatcher THVan Twisk DPollock SJCroasdell AKim NHopke PKXia XThakar JMallon CTUtell MJPhipps RP (2016 Aug). Detection of Serum microRNAs From Department of Defense Serum Repository: Correlation With Cotinine, Cytokine, and Polycyclic Aromatic Hydrocarbon Levels. Journal of occupational and environmental medicine / American College of Occupational and Environmental Medicine. Woeller CFThatcher THVan Twisk DPollock SJCroasdell AHopke PKXia XThakar JSime PJMallon TMUtell MJPhipps RP (2016 Aug). MicroRNAs as Novel Biomarkers of Deployment Status and Exposure to Polychlorinated Dibenzo-p-Dioxins/Dibenzofurans. Journal of occupational and environmental medicine / American College of Occupational and Environmental Medicine. Malcolm DWSorrells JEVan Twisk DThakar JBenoit DS (2016 Jun). Evaluating side effects of nanoparticle-mediated siRNA delivery to mesenchymal stem cells using next generation sequencing and enrichment analysis. Bioengineering & translational medicine. Rebhahn JARoumanes DRQi YKhan AThakar JRosenberg ALee FEQuataert SASharma GMosmann TR (2016 Jan). Competitive SWIFT cluster templates enhance detection of aging changes. Cytometry. Part A : the journal of the International Society for Analytical Cytology. Anderson CSDeDiego MLTopham DJThakar J (2016). Boolean Modeling of Cellular and Molecular Pathways Involved in Influenza Infection. Computational and mathematical methods in medicine. Piepenbrink MSSamuel MZheng BCarter BFucile CBunce CKiebala MKhan AAThakar JMaggirwar SBMorse DRosenberg AFHaughey NJValenti WKeefer MCKobie JJ (2016). Humoral Dysregulation Associated with Increased Systemic Inflammation among Injection Heroin Users. PloS one. Anderson CSDeDiego MLThakar JTopham DJ (2016). Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates. PloS one. Hartmann BMThakar JAlbrecht RAAvey SZaslavsky EMarjanovic NChikina MFribourg MHayot FSchmolke MMeng HWetmur JGarcía-Sastre AKleinstein SHSealfon SC (2015 Oct). Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses. Journal of virology. Thakar JMohanty SWest APJoshi SRUeda IWilson JMeng HBlevins TPTsang STrentalange MSiconolfi BPark KGill TMBelshe RBKaech SMShadel GSKleinstein SHShaw AC (2015 Jan). Aging-dependent alterations in gene expression and a mitochondrial signature of responsiveness to human influenza vaccination. Aging. Khurana JKReeder JEShrimpton AEThakar J (2015). GESPA: classifying nsSNPs to predict disease association. BMC bioinformatics. Thakar JHartmann BMMarjanovic NSealfon SCKleinstein SH (2015). Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism. BMC immunology. Qiu XWu SHilchey SPThakar JLiu ZPWelle SLHenn ADWu HZand MS (2015). Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice. PloS one. Albert RThakar J (2014 Sep). Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions. Wiley interdisciplinary reviews. Systems biology and medicine. Qian FThakar JYuan XNolan MMurray KOLee WTWong SJMeng HFikrig EKleinstein SHMontgomery RR (2014 Mar). Immune markers associated with host susceptibility to infection with West Nile virus. Viral immunology. Thakar JSchmid SDuke JLGarcía-Sastre AKleinstein SH (2013 Nov). Overcoming NS1-mediated immune antagonism involves both interferon-dependent and independent mechanisms. Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research. Yaari GBolen CRThakar JKleinstein SH (2013 Oct). Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations. Nucleic acids research. Lass SHudson PJThakar JSaric JHarvill EAlbert RPerkins SE (2013 Mar 6). Generating super-shedders: co-infection increases bacterial load and egg production of a gastrointestinal helminth. Journal of the Royal Society, Interface / the Royal Society. Zaslavsky ENudelman GMarquez SHershberg UHartmann BMThakar JSealfon SCKleinstein SH (2013). Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC bioinformatics. Thakar JPathak AKMurphy LAlbert RCattadori IM (2012 Jan). Network model of immune responses reveals key effectors to single and co-infection dynamics by a respiratory bacterium and a gastrointestinal helminth. PLoS computational biology. Campbell CThakar JAlbert R (2011 Sep). Network analysis reveals cross-links of the immune pathways activated by bacteria and allergen. Physical review. E, Statistical, nonlinear, and soft matter physics. Walsh ERThakar JStokes KHuang FAlbert RAugust A (2011 Mar 1). Computational and experimental analysis reveals a requirement for eosinophil-derived IL-13 for the development of allergic airway responses in C57BL/6 mice. Journal of immunology (Baltimore, Md. : 1950). Campbell CZhang RHaley JSLiu XLoughran TSchell TDAlbert RThakar J (2011). Why Do CD8+ T Cells become Indifferent to Tumors: A Dynamic Modeling Approach. Frontiers in physiology. Thakar JAlbert R (2010 Jun). Boolean models of within-host immune interactions. Current opinion in microbiology. Thakar JPoss MAlbert RLong GHZhang R (2010). Dynamic models of immune responses: what is the ideal level of detail? Theoretical biology & medical modelling. Thakar JSaadatpour-Moghaddam AHarvill ETAlbert R (2009 Jul 6). Constraint-based network model of pathogen-immune system interactions. Journal of the Royal Society, Interface / the Royal Society. Restif OThakar JHarvill E (2009 Jan 01). Mathematical models in microbiology Microbe. Albert IThakar JLi SZhang RAlbert R (2008). Boolean network simulations for life scientists. Source code for biology and medicine. Kühnel MMayorga LSDandekar TThakar JSchwarz RAnes EGriffiths GReich J (2008). Modelling phagosomal lipid networks that regulate actin assembly. BMC systems biology. Thakar JPilione MKirimanjeswara GHarvill ETAlbert R (2007 Jun). Modeling systems-level regulation of host immune responses. PLoS computational biology. Christensen CThakar JAlbert R (2007 Jan 01). Systems-level insights into cellular regulation: inferring, analyzing, and modeling intracellular networks IET Systems Biology. Thakar JSchleinkofer KBorner CDandekar T (2006 May 15). RIP death domain structural interactions implicated in TNF-mediated proliferation and survival. Proteins. Thakar JDKunte KChauhan AKWatve AVWatve MG (2003 Aug). Nectarless flowers: ecological correlates and evolutionary stability. Oecologia. Watve MThakar JKale APuntambekar SShaikh IVaze KJog MParanjape S (2002 Dec). Bee-eaters ( Merops orientalis) respond to what a predator can see. Animal cognition. Gole AThakar JSastry M (2002 Jan 01). Protein diffusion in to thermally evaporated lipid films: role of protein charge/mass ratio. Colloids and surfaces B: Biointerfaces. Smitha BThakar JWatve M (1999 Jan 01). Do bee-eaters have a theory of mind? Current Science.