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Juilee Thakar, Ph.D.


Showing all 69 journal articles & 5 books available

Journal Articles

Cornwell A, Llop JR, Salzman P, Rasmussen N, Thakar J, Samuelson AV. "The Replica Set Method is a Robust, Accurate, and High-Throughput Approach for Assessing and Comparing Lifespan in Experiments." . 2022 3:861701. Epub 2022 Apr 28.

Järvinen KM, Davis EC, Bevec E, Jackson CM, Pizzarello C, Catlin E, Klein M, Sunkara A, Diaz N, Miller J, Martina CA, Thakar J, Seppo AE, Looney RJ, . "Biomarkers of Development of Immunity and Allergic Diseases in Farming and Non-farming Lifestyle Infants: Design, Methods and 1 Year Outcomes in the "Zooming in to Old Order Mennonites" Birth Cohort Study." Frontiers in pediatrics.. 2022 10:916184. Epub 2022 Jul 06.

McCall MN, Chu CY, Wang L, Benoodt L, Thakar J, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Qiu X, Mariani TJ. "A systems genomics approach uncovers molecular associates of RSV severity." PLoS computational biology.. 2021 Dec 28; 17(12):e1009617. Epub 2021 Dec 28.

Palshikar MG, Hilchey SP, Zand MS, Thakar J. "WikiNetworks: translating manually created biological pathways for topological analysis." Bioinformatics.. 2021 Oct 12; Epub 2021 Oct 12.

Dräger A, Helikar T, Barberis M, Birtwistle M, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Rodríguez Martínez M, Saez-Rodriguez J, Thakar J. "SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems." Bioinformatics.. 2021 Jun 24; Epub 2021 Jun 24.

Seppo AE, Bu K, Jumabaeva M, Thakar J, Choudhury R, Yonemitsu C, Bode L, Martina CA, Allen M, Tamburini S, Piras E, Wallach DS, Looney RJ, Clemente JC, Järvinen KM. "Infant Gut Microbiome Is Enriched with Bifidobacteria longumssp. infantisin Old Order Mennoniteswith Traditional Farming Lifestyle." Allergy.. 2021 Apr 27; Epub 2021 Apr 27.

Cornwell A, Palli R, Singh MV, Benoodt L, Tyrell A, Abe JI, Schifitto G, Maggirwar SB, Thakar J. "Molecular characterization of atherosclerosis in HIV positive persons." Scientific reports.. 2021 Feb 5; 11(1):3232. Epub 2021 Feb 05.

Seppo AE, Choudhury R, Pizzarello C, Palli R, Fridy S, Rajani PS, Stern J, Martina C, Yonemitsu C, Bode L, Bu K, Tamburini S, Piras E, Wallach DS, Allen M, Looney RJ, Clemente JC, Thakar J, Järvinen KM. "Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition." Frontiers in immunology.. 2021 12:741513. Epub 2021 Oct 11.

Eisenhaber F, Thakar J, Ponte-Sucre A, Dandekar T. "Editorial: Innovative Strategies From Synthetic Biology and Bacterial Pathways to Master Biochemical Environmental Challenges." Frontiers in bioengineering and biotechnology.. 2021 9:828632. Epub 2022 Jan 11.

Thakar J, Qian Y, Benoodt L, Roumanes D, Qiu X, Laniewski N, Chu C, Slaunwhite C, Wang L, Mandava A, Chang I, Falsey AR, Caserta MT, Mariani TJ, Scheuermann RH, Walsh EE, Topham DJ. "Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein." . 2020 Aug 7; 5:100065. Epub 2020 Apr 21.

Palli R, Seaton KE, Piepenbrink MS, Hural J, Goepfert PA, Laher F, Buchbinder SP, Churchyard G, Gray GE, Robinson HL, Huang Y, Janes H, Kobie JJ, Keefer MC, Tomaras GD, Thakar J. "Impact of vaccine type on HIV-1 vaccine elicited antibody durability and B cell gene signature." Scientific reports.. 2020 Aug 3; 10(1):13031. Epub 2020 Aug 03.

Hilchey SP, Palshikar MG, Emo JA, Li D, Garigen J, Wang J, Mendelson ES, Cipolla V, Thakar J, Zand MS. "Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 ?dependent, o sensing, molecular switch." BMC immunology. 2020 Mar 18; 21(1):13. Epub 2020 Mar 18.

Benoodt L, Thakar J. "Network Analysis of Large-Scale Data and Its Application to Immunology." Methods in molecular biology.. 2020 2131:199-211.

Nakaya HI, Thakar J, Maracaja-Coutinho V. "Editorial: User-Friendly Tools Applied to Genetics or Systems Biology." Frontiers in genetics.. 2020 11:985. Epub 2020 Sep 09.

Rivera-Escalera F, Pinney JJ, Owlett L, Ahmed H, Thakar J, Olschowka JA, Elliott MR, O'Banion MK. "IL-1?-driven amyloid plaque clearance is associated with an expansion of transcriptionally reprogrammed microglia." Journal of neuroinflammation.. 2019 Dec 10; 16(1):261. Epub 2019 Dec 10.

Mallon TM, Krahl PK, Haines KM, Walker DI, Thatcher T, Woeller CF, Thakar J, Hopke PK, Gaydos JC, Smith MR, Uppal K, Go YM, Jones DP, Utell M. "Use of Biomarkers to Assess Environmental Exposures and Health Outcomes in Deployed Troops." Journal of occupational and environmental medicine. 2019 Dec 0; 61 Suppl 12:S1-S4.

Krahl PL, Benchoff E, Go YM, Jones DP, Smith MR, Walker DI, Uppal K, Woeller CF, Thatcher TH, Thakar J, Phipps RP, Hopke P, Utell MJ, Mallon TM. "Advances in Comprehensive Exposure Assessment: Opportunities for the US Military." Journal of occupational and environmental medicine. 2019 Dec 0; 61 Suppl 12:S5-S14.

Thatcher TH, Woeller CF, Thakar J, Khan A, Hopke PK, Smith MR, Uppal K, Walker DI, Go YM, Jones DP, Krahl PL, Mallon TM, Sime PJ, Phipps RP, Utell MJ. "Analysis of Postdeployment Serum Samples Identifies Potential Biomarkers of Exposure to Burn Pits and Other Environmental Hazards." Journal of occupational and environmental medicine. 2019 Dec 0; 61 Suppl 12:S45-S54.

Khan A, Thatcher TH, Woeller CF, Sime PJ, Phipps RP, Hopke PK, Utell MJ, Krahl PL, Mallon TM, Thakar J. "Machine Learning Approach for Predicting Past Environmental Exposures From Molecular Profiling of Post-Exposure Human Serum Samples." Journal of occupational and environmental medicine. 2019 Dec 0; 61 Suppl 12:S55-S64.

Thakar J, Thatcher TH, Smith MR, Woeller CF, Walker DI, Utell MJ, Hopke PK, Mallon TM, Krahl PL, Rohrbeck P, Go YM, Jones DP, Uppal K. "Integrative Network Analysis Linking Clinical Outcomes With Environmental Exposures and Molecular Variations in Service Personnel Deployed to Balad and Bagram." Journal of occupational and environmental medicine. 2019 Dec 0; 61 Suppl 12:S65-S72.

Woeller CF, Thatcher TH, Thakar J, Cornwell A, Smith MR, Jones DP, Hopke PK, Sime PJ, Krahl P, Mallon TM, Phipps RP, Utell MJ. "Exposure to Heptachlorodibenzo-p-dioxin (HpCDD) Regulates microRNA Expression in Human Lung Fibroblasts." Journal of occupational and environmental medicine. 2019 Dec 0; 61 Suppl 12:S82-S89.

Palli R, Palshikar MG, Thakar J. "Executable pathway analysis using ensemble discrete-state modeling for large-scale data." PLoS computational biology.. 2019 Sep 0; 15(9):e1007317. Epub 2019 Sep 03.

Walsh EE, Mariani TJ, Chu C, Grier A, Gill SR, Qiu X, Wang L, Holden-Wiltse J, Corbett A, Thakar J, Benoodt L, McCall MN, Topham DJ, Falsey AR, Caserta MT. "Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study." JMIR research protocols. 2019 Jun 6; 8(6):e12907. Epub 2019 Jun 06.

Sarkar S, Piepenbrink MS, Basu M, Thakar J, Keefer MC, Hessell AJ, Haigwood NL, Kobie JJ. "IL-33 enhances the kinetics and quality of the antibody response to a DNA and protein-based HIV-1 Env vaccine." Vaccine.. 2019 Apr 17; 37(17):2322-2330. Epub 2019 Mar 27.

Cornwell AB, Llop JR, Salzman P, Thakar J, Samuelson AV. "The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan." Journal of visualized experiments : JoVE.. 2018 Jun 29; (136)Epub 2018 Jun 29.

Zhang Y, Thakar J, Topham DJ, Falsey AR, Zeng D, Qiu X. "Some equivalence relationships of regularized regressions" . Mathematics for Applications. 2018; 7: 3-10.

Palli R, Thakar J. "Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases." Methods in molecular biology.. 2018 1819:385-402.

Mariani TJ, Qiu X, Chu CY, Wang L, Thakar J, Holden-Wiltse J, Corbett A, Topham DJ, Falsey AR, Caserta MT, Walsh EE. "Association of Dynamic Changes in the CD4 T-Cell Transcriptome With Disease Severity During Primary Respiratory Syncytial Virus Infection in Young Infants." The Journal of infectious diseases.. 2017 Nov 15; 216(8):1027-1037.

Connor R, Jones LD, Qiu X, Thakar J, Maggirwar SB. "Frontline Science: c-Myc regulates P-selectin glycoprotein ligand-1 expression in monocytes during HIV-1 infection." Journal of leukocyte biology.. 2017 Oct 0; 102(4):953-964. Epub 2017 Jun 29.

Zhang Y, Topham DJ, Thakar J, Qiu X. "FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis." Bioinformatics.. 2017 Jul 1; 33(13):1944-1952.

Khan A, Katanic D, Thakar J. "Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes." BMC bioinformatics.. 2017 Jun 6; 18(1):295. Epub 2017 Jun 06.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

Books & Chapters

Book Title: Occupational Health and the Service Member
Author List: Timothy M. Mallon*, Richard Phipps, Juilee Thakar, Collynn Woeller, Dean P. Jones, Douglas I. Walker, Karan Uppal, Mark Utell and Thomas Thatcher
Edited By: Timothy M. Mallon
Published By: Office of The Surgeon General Borden Institute US Army Medical Department Center2019

Chapter Title: Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases.
Book Title: Computational Cell Biology
Author List: Rohith Palli and Juilee Thakar
Edited By: Louise von Stechow and Alberto Santos Delgado
Published By: Springer Science and Humana Press2018 in New York

Chapter Title: Mathematical Models as Tools to Enable Infectious Diseases Research
Book Title: Emerging Trends in Antibacterial Discovery
Author List: Juilee Thakar and Eric Harvill
Edited By: Alita A. Miller and Paul F. Miller
Published By: Caister Academic Press2011

Chapter Title: Toward understanding the structure and function of cellular interaction networks
Book Title: Handbook of Large-Scale Random Networks
Author List: Juilee Thakar, Claire Christensen and Réka Albert
Edited By: Bella Bollobas, Robert Kozma and Dezso Miklos
Published By: Springer Verlag and Bolyai Mathematical Society2009

Chapter Title: Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological Level
Book Title: Handbook on Biological Networks
Author List: Juilee Thakar and Réka Albert
Edited By: Stefano Boccaletti, Vito Latora and Yamir Moreno
Published By: World Scientific publishing group2009