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Juilee Thakar, Ph.D.

Publications

Showing all 39 journal articles & 0 books available

Journal Articles

5/2017
Van Twisk D, Murphy SP, Thakar J. "Optimized logic rules reveal interferon-?-induced modes regulated by histone deacetylases and protein tyrosine phosphatases." Immunology.. 2017 May 0; 151(1):71-80. Epub 2017 Feb 09.

2/21/2017
Zhang Y, Topham DJ, Thakar J, Qiu X. "FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis." Bioinformatics.. 2017 Feb 21; Epub 2017 Feb 21.

12/2016
Katanic D, Khan A, Thakar J. "PathCellNet: Cell-type specific pathogen-response network explorer." Journal of immunological methods.. 2016 Dec 0; 439:15-22. Epub 2016 Sep 20.

8/2016
Woeller CF, Thatcher TH, Van Twisk D, Pollock SJ, Croasdell A, Kim N, Hopke PK, Xia X, Thakar J, Mallon CT, Utell MJ, Phipps RP. "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. 2016 Aug 0; 58(8 Suppl 1):S62-71.

8/2016
Woeller CF, Thatcher TH, Van Twisk D, Pollock SJ, Croasdell A, Hopke PK, Xia X, Thakar J, Sime PJ, Mallon TM, Utell MJ, Phipps RP. "MicroRNAs as Novel Biomarkers of Deployment Status and Exposure to Polychlorinated Dibenzo-p-Dioxins/Dibenzofurans." Journal of occupational and environmental medicine. 2016 Aug 0; 58(8 Suppl 1):S89-96.

6/2016
Malcolm DW, Sorrells JE, Van Twisk D, Thakar J, Benoit DS. "Evaluating side effects of nanoparticle-mediated siRNA delivery to mesenchymal stem cells using next generation sequencing and enrichment analysis." Bioengineering & translational medicine.. 2016 Jun 0; 1(2):193-206. Epub 2016 Oct 24.

1/2016
Rebhahn JA, Roumanes DR, Qi Y, Khan A, Thakar J, Rosenberg A, Lee FE, Quataert SA, Sharma G, Mosmann TR. "Competitive SWIFT cluster templates enhance detection of aging changes." Cytometry. Part A : the journal of the International Society for Analytical Cytology.. 2016 Jan 0; 89(1):59-70. Epub 2015 Oct 06.

2016
Malcolm, D. W.; Sorrells, J. E.; Van Twisk, D.; Thakar, J.; Benoit, D. S. W. "Evaluating Side Effects of Nanoparticle-mediated siRNA Delivery to Mesenchymal Stem Cells Using Next Generation Sequencing and Enrichment Analysis". Bioengineering and Translational Medicine. 2016; DOI: 10.1002/btm2.10035.

2016
Anderson CS, DeDiego ML, Topham DJ, Thakar J. "Boolean Modeling of Cellular and Molecular Pathways Involved in Influenza Infection." Computational and mathematical methods in medicine.. 2016 2016:7686081. Epub 2016 Feb 14.

2016
Piepenbrink MS, Samuel M, Zheng B, Carter B, Fucile C, Bunce C, Kiebala M, Khan AA, Thakar J, Maggirwar SB, Morse D, Rosenberg AF, Haughey NJ, Valenti W, Keefer MC, Kobie JJ. "Humoral Dysregulation Associated with Increased Systemic Inflammation among Injection Heroin Users." PloS one. 2016 11(7):e0158641. Epub 2016 Jul 05.

2016
Anderson CS, DeDiego ML, Thakar J, Topham DJ. "Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates." PloS one. 2016 11(8):e0160510. Epub 2016 Aug 05.

10/2015
Hartmann BM, Thakar J, Albrecht RA, Avey S, Zaslavsky E, Marjanovic N, Chikina M, Fribourg M, Hayot F, Schmolke M, Meng H, Wetmur J, García-Sastre A, Kleinstein SH, Sealfon SC. "Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses." Journal of virology.. 2015 Oct 0; 89(20):10190-205. Epub 2015 Jul 29.

8/14/2015
Thakar J, Hartmann BM, Marjanovic N, Sealfon SC, Kleinstein SH. "Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism." BMC immunology. 2015 Aug 14; 16:46. Epub 2015 Aug 14.

7/25/2015
Khurana JK, Reeder JE, Shrimpton AE, Thakar J. "GESPA: classifying nsSNPs to predict disease association." BMC bioinformatics. 2015 Jul 25; 16:228. Epub 2015 Jul 25.

1/2015
Thakar J, Mohanty S, West AP, Joshi SR, Ueda I, Wilson J, Blevins TP, Tsang S, Trentalange M, Siconolfi B, Park K, Gill TM, Belshe RB, Kaech SM, Shadel GS, Kleinstein SH, Shaw AC. "Aging-dependent alterations in gene expression and a mitochondrial signature of responsiveness to human influenza vaccination." Aging. 2015 Jan 0; 7(1):38-52.

2015
Qiu X, Wu S, Hilchey SP, Thakar J, Liu ZP, Welle SL, Henn AD, Wu H, Zand MS. "Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice." PloS one. 2015 10(9):e0138110. Epub 2015 Sep 28.

3/2014
Qian F, Thakar J, Yuan X, Nolan M, Murray KO, Lee WT, Wong SJ, Meng H, Fikrig E, Kleinstein SH, Montgomery RR. "Immune markers associated with host susceptibility to infection with West Nile virus." Viral immunology.. 2014 Mar 0; 27(2):39-47.

2014
Albert R, Thakar J. "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.. 2014 6(5):353-69.

11/2013
Thakar J, Schmid S, Duke JL, García-Sastre A, Kleinstein SH. "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.. 2013 Nov 0; 33(11):700-8. Epub 2013 Jun 17.

10/2013
Yaari G, Bolen CR, Thakar J, Kleinstein SH. "Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations." Nucleic acids research.. 2013 Oct 0; 41(18):e170. Epub 2013 Aug 05.

3/6/2013
Lass S, Hudson PJ, Thakar J, Saric J, Harvill E, Albert R, Perkins SE. "Generating super-shedders: co-infection increases bacterial load and egg production of a gastrointestinal helminth." Journal of the Royal Society, Interface. 2013 Mar 6; 10(80):20120588. Epub 2012 Dec 19.

2013
Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH. "Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection." BMC bioinformatics. 2013 14 Suppl 6:S1. Epub 2013 Apr 17.

1/2012
Thakar J, Pathak AK, Murphy L, Albert R, Cattadori IM. "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.. 2012 Jan 0; 8(1):e1002345. Epub 2012 Jan 12.

9/2011
Campbell C, Thakar J, Albert R. "Network analysis reveals cross-links of the immune pathways activated by bacteria and allergen." Physical review. E, Statistical, nonlinear, and soft matter physics.. 2011 Sep 0; 84(3 Pt 1):031929. Epub 2011 Sep 28.

3/1/2011
Walsh ER, Thakar J, Stokes K, Huang F, Albert R, August A. "Computational and experimental analysis reveals a requirement for eosinophil-derived IL-13 for the development of allergic airway responses in C57BL/6 mice." The Journal of immunology : official journal of the American Association of Immunologists.. 2011 Mar 1; 186(5):2936-49. Epub 2011 Feb 02.

2011
Campbell C, Zhang R, Haley JS, Liu X, Loughran T, Schell TD, Albert R, Thakar J. "Why Do CD8+ T Cells become Indifferent to Tumors: A Dynamic Modeling Approach." Frontiers in physiology. 2011 2:32. Epub 2011 Jul 11.

8/20/2010
Thakar J, Poss M, Albert R, Long GH, Zhang R. "Dynamic models of immune responses: what is the ideal level of detail?" Theoretical biology & medical modelling. 2010 Aug 20; 7:35. Epub 2010 Aug 20.

6/2010
Thakar J, Albert R. "Boolean models of within-host immune interactions." Current opinion in microbiology.. 2010 Jun 0; 13(3):377-81. Epub 2010 May 10.

7/6/2009
Thakar J, Saadatpour-Moghaddam A, Harvill ET, Albert R. "Constraint-based network model of pathogen-immune system interactions." Journal of the Royal Society, Interface. 2009 Jul 6; 6(36):599-612. Epub 2008 Oct 24.

2009
Restif, O.; Thakar, J.;Harvill, E. "Mathematical models in microbiology". Microbe. 2009; .

12/5/2008
Kühnel M, Mayorga LS, Dandekar T, Thakar J, Schwarz R, Anes E, Griffiths G, Reich J. "Modelling phagosomal lipid networks that regulate actin assembly." BMC systems biology. 2008 Dec 5; 2:107. Epub 2008 Dec 05.

11/14/2008
Albert I, Thakar J, Li S, Zhang R, Albert R. "Boolean network simulations for life scientists." Source code for biology and medicine. 2008 Nov 14; 3:16. Epub 2008 Nov 14.

6/2007
Thakar J, Pilione M, Kirimanjeswara G, Harvill ET, Albert R. "Modeling systems-level regulation of host immune responses." PLoS computational biology.. 2007 Jun 0; 3(6):e109. Epub 2007 Apr 30.

2007
Christensen, C.; Thakar, J.;Albert, R. "Systems-level insights into cellular regulation: inferring, analyzing, and modeling intracellular networks". IET Systems Biology. 2007; 1: 61-67.

5/15/2006
Thakar J, Schleinkofer K, Borner C, Dandekar T. "RIP death domain structural interactions implicated in TNF-mediated proliferation and survival." Proteins.. 2006 May 15; 63(3):413-23.

8/2003
Thakar JD, Kunte K, Chauhan AK, Watve AV, Watve MG. "Nectarless flowers: ecological correlates and evolutionary stability." Oecologia.. 2003 Aug 0; 136(4):565-70. Epub 2003 Jun 28.

12/2002
Watve M, Thakar J, Kale A, Puntambekar S, Shaikh I, Vaze K, Jog M, Paranjape S. "Bee-eaters ( Merops orientalis) respond to what a predator can see." Animal cognition.. 2002 Dec 0; 5(4):253-9. Epub 2002 Nov 16.

2002
Gole, A.; Thakar, J.; Sastry, M. "Protein diffusion in to thermally evaporated lipid films: role of protein charge/mass ratio." Colloids and surfaces B: Biointerfaces. 2002; 28(2): 209-214.

1999
Smitha, B.; Thakar, J.; Watve, M. "Do bee-eaters have a theory of mind?". Current Science. 1999; 76(4): 574-577.