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Juilee Thakar, Ph.D.

Juilee Thakar, Ph.D.

Contact

Office (585) 276-6925

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About Me

Faculty Appointments

Associate Professor - Department of Microbiology and Immunology (SMD)

Associate Professor - Department of Biomedical Genetics (SMD) - Joint

Credentials

Post-doctoral Training & Residency

Associate Research Scientist, Department of Pathology, Yale School of Medicine, USA 2011 - 2013

Cancer Research Institute fellow, Department of Physics, Pennsylvania State University, USA 2006 - 2010

Education

PhD | Germany-U Wurzburg. Bioinformatics. 2006

MSc with certificate | India-Univ of Pune, Pune. Microbiology and Computational Biology. 2003

BSc | India-Univ of Pune, Pune. Microbiology and Mathematics. 2001

Awards

Novel Biostatistical and Epidemiologic Methods (NBEM) Awards. 2016 - 2017

PhRMA research starter award in informatics. 2015 - 2016

Beutner Speaker. 2014

Cancer-Research-Institute fellowship. 2008 - 2010

Shankar Subramaniam award in systems biology research. 2007

The Association for the Study of Animal Behavior fellowship. 2001

Research

Thakar lab uses systems biology approaches to identify immune signatures that can predict outcome of an immune response to infections or vaccinations. We develop computational tools to model probable trajectories of the immune r...
Thakar lab uses systems biology approaches to identify immune signatures that can predict outcome of an immune response to infections or vaccinations. We develop computational tools to model probable trajectories of the immune response which then allows us to identify parameters that can predict future outcomes of the disease. This has direct implications in early diagnosis. The models also reveal the mechanisms of pathogenesis. This work is based on multi-parameter datasets including gene expression, serum cytokine levels and known information about signaling and metabolic pathways.

Publications

Journal Articles

Immune digital twins for complex human pathologies: applications, limitations, and challenges.

Niarakis A, Laubenbacher R, An G, Ilan Y, Fisher J, Flobak Å, Reiche K, Rodríguez Martínez M, Geris L, Ladeira L, Veschini L, Blinov ML, Messina F, Fonseca LL, Ferreira S, Montagud A, Noël V, Marku M, Tsirvouli E, Torres MM, Harris LA, Sego TJ, Cockrell C, Shick AE, Balci H, Salazar A, Rian K, Hemedan AA, Esteban-Medina M, Staumont B, Hernandez-Vargas E, Martis B S, Madrid-Valiente A, Karampelesis P, Sordo Vieira L, Harlapur P, Kulesza A, Nikaein N, Garira W, Malik Sheriff RS, Thakar J, Tran VDT, Carbonell-Caballero J, Safaei S, Valencia A, Zinovyev A, Glazier JA

NPJ systems biology and applications.. 2024 November 3010 (1):141. Epub 11/30/2024.

The C. elegans Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction.

Cornwell AB, Zhang Y, Thondamal M, Johnson DW, Thakar J, Samuelson AV

GeroScience.. 2024 October 46 (5):4827-4854. Epub 06/15/2024.

Comparative analysis of single-cell pathway scoring methods and a novel approach.

Wang RH, Thakar J

NAR genomics and bioinformatics.. 2024 September 6 (3):lqae124. Epub 09/24/2024.

Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium.

Dunlap G, Wagner A, Meednu N, Wang R, Zhang F, Ekabe JC, Jonsson AH, Wei K, Sakaue S, Nathan A, , Bykerk VP, Donlin LT, Goodman SM, Firestein GS, Boyle DL, Holers VM, Moreland LW, Tabechian D, Pitzalis C, Filer A, Raychaudhuri S, Brenner MB, Thakar J, McDavid A, Rao DA, Anolik JH

Nature communications.. 2024 June 1115 (1):4991. Epub 06/11/2024.

Discrete-state models identify pathway specific B cell states across diseases and infections at single-cell resolution.

Kassis G, Palshikar MG, Hilchey SP, Zand MS, Thakar J

Journal of theoretical biology.. 2024 April 21583 :111769. Epub 02/28/2024.

Pillars of biology: Boolean modeling of gene-regulatory networks.

Thakar J

Journal of theoretical biology.. 2024 February 7578 :111682. Epub 11/25/2023.

SWIFT clustering analysis of intracellular cytokine staining flow cytometry data of the HVTN 105 vaccine trial reveals high frequencies of HIV-specific CD4+ T cell responses and associations with humoral responses.

Mosmann TR, Rebhahn JA, De Rosa SC, Keefer MC, McElrath MJ, Rouphael NG, Pantaleo G, Gilbert PB, Corey L, Kobie JJ, Thakar J

Frontiers in immunology.. 2024 15 :1347926. Epub 06/06/2024.

The Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction.

Cornwell A, Zhang Y, Thondamal M, Johnson DW, Thakar J, Samuelson AV

bioRxiv : the preprint server for biology.. 2023 November 22 Epub 11/22/2023.

Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection.

Zhou T, Gilliam NJ, Li S, Spandau S, Osborn RM, Connor S, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y

mBio.. 2023 June 2714 (3):e0025023. Epub 04/19/2023.

Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal aging and systemically regulates longevity from serotonergic and GABAergic neurons.

Lazaro-Pena MI, Cornwell AB, Diaz-Balzac CA, Das R, Ward ZC, Macoretta N, Thakar J, Samuelson AV

eLife.. 2023 June 2012 Epub 06/20/2023.

Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal aging and systemically regulates longevity from serotonergic and GABAergic neurons.

Lazaro-Pena MI, Cornwell AB, Diaz-Balzac CA, Das R, Macoretta N, Thakar J, Samuelson AV

bioRxiv : the preprint server for biology.. 2023 June 14 Epub 06/14/2023.

Executable Network Models of Integrated Multiomics Data.

Palshikar MG, Min X, Crystal A, Meng J, Hilchey SP, Zand MS, Thakar J

Journal of proteome research.. 2023 May 522 (5):1546-1556. Epub 03/31/2023.

IgE Sensitization Drives the Atopic March.

Beck LA, Pesonen M, Thakar J, Georas SN, Järvinen KM

American journal of respiratory and critical care medicine.. 2023 March 1207 (5):632-633. Epub 1900 01 01.

Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells.

Osborn RM, Leach J, Zanche M, Ashton JM, Chu C, Thakar J, Dewhurst S, Rosenberger S, Pavelka M, Pryhuber GS, Mariani TJ, Anderson CS

PloS one.. 2023 18 (2):e0281898. Epub 02/24/2023.

Baseline host determinants of robust human HIV-1 vaccine-induced immune responses: A meta-analysis of 26 vaccine regimens.

Huang Y, Zhang Y, Seaton KE, De Rosa S, Heptinstall J, Carpp LN, Randhawa AK, McKinnon LR, McLaren P, Viegas E, Gray GE, Churchyard G, Buchbinder SP, Edupuganti S, Bekker LG, Keefer MC, Hosseinipour MC, Goepfert PA, Cohen KW, Williamson BD, McElrath MJ, Tomaras GD, Thakar J, Kobie JJ,

EBioMedicine.. 2022 October 84 :104271. Epub 09/27/2022.

Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection.

Zhou T, Gilliam NJ, Li S, Spaudau S, Osborn RM, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y

bioRxiv : the preprint server for biology.. 2022 September 23 Epub 09/23/2022.

Executable models of immune signaling pathways in HIV-associated atherosclerosis.

Palshikar MG, Palli R, Tyrell A, Maggirwar S, Schifitto G, Singh MV, Thakar J

NPJ systems biology and applications.. 2022 September 218 (1):35. Epub 09/21/2022.

Cyclosporine A Modulates LSP1 Protein Levels in Human B Cells to Attenuate B Cell Migration at Low O Levels.

Hilchey SP, Palshikar MG, Mendelson ES, Shen S, Rasam S, Emo JA, Qu J, Thakar J, Zand MS

Life.. 2022 August 2212 (8)Epub 08/22/2022.

WikiNetworks: translating manually created biological pathways for topological analysis.

Palshikar MG, Hilchey SP, Zand MS, Thakar J

Bioinformatics.. 2022 January 1238 (3):869-871. Epub 1900 01 01.

The Replica Set Method is a Robust, Accurate, and High-Throughput Approach for Assessing and Comparing Lifespan in Experiments.

Cornwell A, Llop JR, Salzman P, Rasmussen N, Thakar J, Samuelson AV

Frontiers in aging.. 2022 3 :861701. Epub 04/28/2022.

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.

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,

Frontiers in pediatrics.. 2022 10 :916184. Epub 07/06/2022.

A systems genomics approach uncovers molecular associates of RSV severity.

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

PLoS computational biology.. 2021 December 17 (12):e1009617. Epub 12/28/2021.

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.

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

Bioinformatics.. 2021 November 537 (21):3702-3706. Epub 1900 01 01.

Infant gut microbiome is enriched with Bifidobacterium longum ssp. infantis in Old Order Mennonites with traditional farming lifestyle.

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

Allergy.. 2021 November 76 (11):3489-3503. Epub 05/14/2021.

Molecular characterization of atherosclerosis in HIV positive persons.

Cornwell A, Palli R, Singh MV, Benoodt L, Tyrell A, Abe JI, Schifitto G, Maggirwar SB, Thakar J

Scientific reports.. 2021 February 511 (1):3232. Epub 02/05/2021.

Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition.

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

Frontiers in immunology.. 2021 12 :741513. Epub 10/11/2021.

Editorial: Innovative Strategies From Synthetic Biology and Bacterial Pathways to Master Biochemical Environmental Challenges.

Eisenhaber F, Thakar J, Ponte-Sucre A, Dandekar T

Frontiers in bioengineering and biotechnology.. 2021 9 :828632. Epub 01/11/2022.

Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein.

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

Vaccine: X.. 2020 August 75 :100065. Epub 04/21/2020.

Impact of vaccine type on HIV-1 vaccine elicited antibody durability and B cell gene signature.

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

Scientific reports.. 2020 August 310 (1):13031. Epub 08/03/2020.

Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 ?dependent, o sensing, molecular switch.

Hilchey SP, Palshikar MG, Emo JA, Li D, Garigen J, Wang J, Mendelson ES, Cipolla V, Thakar J, Zand MS

BMC immunology.. 2020 March 1821 (1):13. Epub 03/18/2020.

Network Analysis of Large-Scale Data and Its Application to Immunology.

Benoodt L, Thakar J

Methods in molecular biology.. 2020 2131 :199-211. Epub 1900 01 01.

Editorial: User-Friendly Tools Applied to Genetics or Systems Biology.

Nakaya HI, Thakar J, Maracaja-Coutinho V

Frontiers in genetics.. 2020 11 :985. Epub 09/09/2020.

IL-1?-driven amyloid plaque clearance is associated with an expansion of transcriptionally reprogrammed microglia.

Rivera-Escalera F, Pinney JJ, Owlett L, Ahmed H, Thakar J, Olschowka JA, Elliott MR, O'Banion MK

Journal of neuroinflammation.. 2019 December 1016 (1):261. Epub 12/10/2019.

Use of Biomarkers to Assess Environmental Exposures and Health Outcomes in Deployed Troops.

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

Journal of occupational and environmental medicine. 2019 December 61 Suppl 12 :S1-S4. Epub 1900 01 01.

Advances in Comprehensive Exposure Assessment: Opportunities for the US Military.

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

Journal of occupational and environmental medicine. 2019 December 61 Suppl 12 :S5-S14. Epub 1900 01 01.

Analysis of Postdeployment Serum Samples Identifies Potential Biomarkers of Exposure to Burn Pits and Other Environmental Hazards.

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

Journal of occupational and environmental medicine. 2019 December 61 Suppl 12 (Suppl 12):S45-S54. Epub 1900 01 01.

Machine Learning Approach for Predicting Past Environmental Exposures From Molecular Profiling of Post-Exposure Human Serum Samples.

Khan A, Thatcher TH, Woeller CF, Sime PJ, Phipps RP, Hopke PK, Utell MJ, Krahl PL, Mallon TM, Thakar J

Journal of occupational and environmental medicine. 2019 December 61 Suppl 12 (Suppl 12):S55-S64. Epub 1900 01 01.

Integrative Network Analysis Linking Clinical Outcomes With Environmental Exposures and Molecular Variations in Service Personnel Deployed to Balad and Bagram.

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

Journal of occupational and environmental medicine. 2019 December 61 Suppl 12 (Suppl 12):S65-S72. Epub 1900 01 01.

Exposure to Heptachlorodibenzo-p-dioxin (HpCDD) Regulates microRNA Expression in Human Lung Fibroblasts.

Woeller CF, Thatcher TH, Thakar J, Cornwell A, Smith MR, Jones DP, Hopke PK, Sime PJ, Krahl P, Mallon TM, Phipps RP, Utell MJ

Journal of occupational and environmental medicine. 2019 December 61 Suppl 12 (Suppl 12):S82-S89. Epub 1900 01 01.

Executable pathway analysis using ensemble discrete-state modeling for large-scale data.

Palli R, Palshikar MG, Thakar J

PLoS computational biology.. 2019 September 15 (9):e1007317. Epub 09/03/2019.

Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study.

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

JMIR research protocols.. 2019 June 68 (6):e12907. Epub 06/06/2019.

IL-33 enhances the kinetics and quality of the antibody response to a DNA and protein-based HIV-1 Env vaccine.

Sarkar S, Piepenbrink MS, Basu M, Thakar J, Keefer MC, Hessell AJ, Haigwood NL, Kobie JJ

Vaccine.. 2019 April 1737 (17):2322-2330. Epub 03/27/2019.

The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan.

Cornwell AB, Llop JR, Salzman P, Thakar J, Samuelson AV

Journal of visualized experiments : JoVE.. 2018 June 29 (136)Epub 06/29/2018.

Some equivalence relationships of regularized regressions (PDF)

Zhang Y, Thakar J, Topham DJ, Falsey AR, Zeng D, Qiu X.

Mathematics for Applications. 2018; 7: 3-10.

Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases.

Palli R, Thakar J

Methods in molecular biology.. 2018 1819 :385-402. Epub 1900 01 01.

Association of Dynamic Changes in the CD4 T-Cell Transcriptome With Disease Severity During Primary Respiratory Syncytial Virus Infection in Young Infants.

Mariani TJ, Qiu X, Chu CY, Wang L, Thakar J, Holden-Wiltse J, Corbett A, Topham DJ, Falsey AR, Caserta MT, Walsh EE

The Journal of infectious diseases.. 2017 November 15216 (8):1027-1037. Epub 1900 01 01.

Frontline Science: c-Myc regulates P-selectin glycoprotein ligand-1 expression in monocytes during HIV-1 infection.

Connor R, Jones LD, Qiu X, Thakar J, Maggirwar SB

Journal of leukocyte biology.. 2017 October 102 (4):953-964. Epub 06/29/2017.

FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis.

Zhang Y, Topham DJ, Thakar J, Qiu X

Bioinformatics.. 2017 July 133 (13):1944-1952. Epub 1900 01 01.

Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes.

Khan A, Katanic D, Thakar J

BMC bioinformatics.. 2017 June 618 (1):295. Epub 06/06/2017.

Optimized logic rules reveal interferon-?-induced modes regulated by histone deacetylases and protein tyrosine phosphatases.

Van Twisk D, Murphy SP, Thakar J

Immunology.. 2017 May 151 (1):71-80. Epub 02/09/2017.

PathCellNet: Cell-type specific pathogen-response network explorer.

Katanic D, Khan A, Thakar J

Journal of immunological methods.. 2016 December 439 :15-22. Epub 09/20/2016.

Detection of Serum microRNAs From Department of Defense Serum Repository: Correlation With Cotinine, Cytokine, and Polycyclic Aromatic Hydrocarbon Levels.

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

Journal of occupational and environmental medicine. 2016 August 58 (8 Suppl 1):S62-71. Epub 1900 01 01.

MicroRNAs as Novel Biomarkers of Deployment Status and Exposure to Polychlorinated Dibenzo-p-Dioxins/Dibenzofurans.

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

Journal of occupational and environmental medicine. 2016 August 58 (8 Suppl 1):S89-96. Epub 1900 01 01.

Evaluating side effects of nanoparticle-mediated siRNA delivery to mesenchymal stem cells using next generation sequencing and enrichment analysis.

Malcolm DW, Sorrells JE, Van Twisk D, Thakar J, Benoit DS

Bioengineering & translational medicine.. 2016 June 1 (2):193-206. Epub 10/24/2016.

Competitive SWIFT cluster templates enhance detection of aging changes.

Rebhahn JA, Roumanes DR, Qi Y, Khan A, Thakar J, Rosenberg A, Lee FE, Quataert SA, Sharma G, Mosmann TR

Cytometry. Part A : the journal of the International Society for Analytical Cytology.. 2016 January 89 (1):59-70. Epub 10/06/2015.

Evaluating Side Effects of Nanoparticle-mediated siRNA Delivery to Mesenchymal Stem Cells Using Next Generation Sequencing and Enrichment Analysis

Malcolm, D. W.; Sorrells, J. E.; Van Twisk, D.; Thakar, J.; Benoit, D. S. W.

Bioengineering and Translational Medicine. 2016; DOI: 10.1002/btm2.10035.

Boolean Modeling of Cellular and Molecular Pathways Involved in Influenza Infection.

Anderson CS, DeDiego ML, Topham DJ, Thakar J

Computational and mathematical methods in medicine.. 2016 2016 :7686081. Epub 02/14/2016.

Humoral Dysregulation Associated with Increased Systemic Inflammation among Injection Heroin Users.

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

PloS one.. 2016 11 (7):e0158641. Epub 07/05/2016.

Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates.

Anderson CS, DeDiego ML, Thakar J, Topham DJ

PloS one.. 2016 11 (8):e0160510. Epub 08/05/2016.

Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses.

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

Journal of virology.. 2015 October 89 (20):10190-205. Epub 07/29/2015.

Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism.

Thakar J, Hartmann BM, Marjanovic N, Sealfon SC, Kleinstein SH

BMC immunology.. 2015 August 1416 :46. Epub 08/14/2015.

GESPA: classifying nsSNPs to predict disease association.

Khurana JK, Reeder JE, Shrimpton AE, Thakar J

BMC bioinformatics.. 2015 July 2516 :228. Epub 07/25/2015.

Aging-dependent alterations in gene expression and a mitochondrial signature of responsiveness to human influenza vaccination.

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.. 2015 January 7 (1):38-52. Epub 1900 01 01.

Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice.

Qiu X, Wu S, Hilchey SP, Thakar J, Liu ZP, Welle SL, Henn AD, Wu H, Zand MS

PloS one.. 2015 10 (9):e0138110. Epub 09/28/2015.

Immune markers associated with host susceptibility to infection with West Nile virus.

Qian F, Thakar J, Yuan X, Nolan M, Murray KO, Lee WT, Wong SJ, Meng H, Fikrig E, Kleinstein SH, Montgomery RR

Viral immunology.. 2014 March 27 (2):39-47. Epub 1900 01 01.

Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions.

Albert R, Thakar J

Wiley interdisciplinary reviews. Systems biology and medicine.. 2014 6 (5):353-69. Epub 1900 01 01.

Overcoming NS1-mediated immune antagonism involves both interferon-dependent and independent mechanisms.

Thakar J, Schmid S, Duke JL, García-Sastre A, Kleinstein SH

Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.. 2013 November 33 (11):700-8. Epub 06/17/2013.

Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.

Yaari G, Bolen CR, Thakar J, Kleinstein SH

Nucleic acids research.. 2013 October 41 (18):e170. Epub 08/05/2013.

Generating super-shedders: co-infection increases bacterial load and egg production of a gastrointestinal helminth.

Lass S, Hudson PJ, Thakar J, Saric J, Harvill E, Albert R, Perkins SE

Journal of the Royal Society, Interface. 2013 March 610 (80):20120588. Epub 12/19/2012.

Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection.

Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH

BMC bioinformatics.. 2013 14 Suppl 6 (Suppl 6):S1. Epub 04/17/2013.

Network model of immune responses reveals key effectors to single and co-infection dynamics by a respiratory bacterium and a gastrointestinal helminth.

Thakar J, Pathak AK, Murphy L, Albert R, Cattadori IM

PLoS computational biology.. 2012 January 8 (1):e1002345. Epub 01/12/2012.

Network analysis reveals cross-links of the immune pathways activated by bacteria and allergen.

Campbell C, Thakar J, Albert R

Physical review. E, Statistical, nonlinear, and soft matter physics.. 2011 September 84 (3 Pt 1):031929. Epub 09/28/2011.

Computational and experimental analysis reveals a requirement for eosinophil-derived IL-13 for the development of allergic airway responses in C57BL/6 mice.

Walsh ER, Thakar J, Stokes K, Huang F, Albert R, August A

The Journal of immunology : official journal of the American Association of Immunologists.. 2011 March 1186 (5):2936-49. Epub 02/02/2011.

Why Do CD8+ T Cells become Indifferent to Tumors: A Dynamic Modeling Approach.

Campbell C, Zhang R, Haley JS, Liu X, Loughran T, Schell TD, Albert R, Thakar J

Frontiers in physiology.. 2011 2 :32. Epub 07/11/2011.

Dynamic models of immune responses: what is the ideal level of detail?

Thakar J, Poss M, Albert R, Long GH, Zhang R

Theoretical biology & medical modelling. 2010 August 207 :35. Epub 08/20/2010.

Boolean models of within-host immune interactions.

Thakar J, Albert R

Current opinion in microbiology.. 2010 June 13 (3):377-81. Epub 05/10/2010.

Constraint-based network model of pathogen-immune system interactions.

Thakar J, Saadatpour-Moghaddam A, Harvill ET, Albert R

Journal of the Royal Society, Interface. 2009 July 66 (36):599-612. Epub 10/24/2008.

Mathematical models in microbiology

Restif, O.; Thakar, J.;Harvill, E.

Microbe. 2009; .

Modelling phagosomal lipid networks that regulate actin assembly.

Kühnel M, Mayorga LS, Dandekar T, Thakar J, Schwarz R, Anes E, Griffiths G, Reich J

BMC systems biology.. 2008 December 52 :107. Epub 12/05/2008.

Boolean network simulations for life scientists.

Albert I, Thakar J, Li S, Zhang R, Albert R

Source code for biology and medicine. 2008 November 143 :16. Epub 11/14/2008.

Modeling systems-level regulation of host immune responses.

Thakar J, Pilione M, Kirimanjeswara G, Harvill ET, Albert R

PLoS computational biology.. 2007 June 3 (6):e109. Epub 04/30/2007.

Systems-level insights into cellular regulation: inferring, analyzing, and modeling intracellular networks (PDF)

Christensen, C.; Thakar, J.;Albert, R.

IET Systems Biology. 2007; 1: 61-67.

RIP death domain structural interactions implicated in TNF-mediated proliferation and survival.

Thakar J, Schleinkofer K, Borner C, Dandekar T

Proteins.. 2006 May 1563 (3):413-23. Epub 1900 01 01.

Nectarless flowers: ecological correlates and evolutionary stability.

Thakar JD, Kunte K, Chauhan AK, Watve AV, Watve MG

Oecologia.. 2003 August 136 (4):565-70. Epub 06/28/2003.

Bee-eaters ( Merops orientalis) respond to what a predator can see.

Watve M, Thakar J, Kale A, Puntambekar S, Shaikh I, Vaze K, Jog M, Paranjape S

Animal cognition.. 2002 December 5 (4):253-9. Epub 11/16/2002.

Protein diffusion in to thermally evaporated lipid films: role of protein charge/mass ratio.

Gole, A.; Thakar, J.; Sastry, M.

Colloids and surfaces B: Biointerfaces. 2002; 28(2): 209-214.

Do bee-eaters have a theory of mind?

Smitha, B.; Thakar, J.; Watve, M.

Current Science. 1999; 76(4): 574-577.

Books

Occupational Health and the Service Member (2019)

Chapter: BIOLOGICAL MONITORING

Authors: Timothy M. Mallon*, Richard Phipps, Juilee Thakar, Collynn Woeller, Dean P. Jones, Douglas I. Walker, Karan Uppal, Mark Utell and Thomas Thatcher

Publisher: Office of The Surgeon General Borden Institute US Army Medical Department Center 2019

Computational Cell Biology (2018)

Chapter: Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases.

Authors: Rohith Palli and Juilee Thakar

Publisher: Springer Science and Humana Press, New York 2018

Emerging Trends in Antibacterial Discovery (2011)

Chapter: Mathematical Models as Tools to Enable Infectious Diseases Research

Authors: Juilee Thakar and Eric Harvill

Publisher: Caister Academic Press 2011

Handbook of Large-Scale Random Networks (2009)

Chapter: Toward understanding the structure and function of cellular interaction networks

Authors: Juilee Thakar, Claire Christensen and Réka Albert

Publisher: Springer Verlag and Bolyai Mathematical Society 2009

Handbook on Biological Networks (2009)

Chapter: Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological Level

Authors: Juilee Thakar and Réka Albert

Publisher: World Scientific publishing group 2009