Publications - Thakar Lab - University of Rochester Medical Center

URMC / Labs / Thakar Lab / Publications

1. Shaposhnikov M
2. Thakar J
3. Berk BC
Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis.; Circulation research; Vol 136(10), pp. 1147-1165. 2025 May 08.
1. Alzamareh DF
2. Meednu N
3. Nandedkar-Kulkarni N
4. Krenitsky D
5. Barnard J
6. Yasaka K
7. Durrett W
8. Thakar J
9. Rangel-Moreno J
10. Anolik JH
11. Barnas JL
Interferon activation in bone marrow long-lived plasma cells in systemic lupus erythematosus.; Frontiers in immunology; Vol 15, pp. 1499551. 2025 Jan 10.
1. Osborn RM
2. Anderson CS
3. Leach JR
4. Chu CY
5. Dewhurst S
6. Mariani TJ
7. Thakar J
Single-cell analysis of lung epithelial cells reveals age and cell population-specific responses to SARS-CoV-2 infection in ciliated cells.; Clinical and experimental immunology. 2025 Jan 09.
1. Niarakis A
2. Laubenbacher R
3. An G
4. Ilan Y
5. Fisher J
6. Flobak Å
7. Reiche K
8. Rodríguez Martínez M
9. Geris L
10. Ladeira L
11. Veschini L
12. Blinov ML
13. Messina F
14. Fonseca LL
15. Ferreira S
16. Montagud A
17. Noël V
18. Marku M
19. Tsirvouli E
20. Torres MM
21. Harris LA
22. Sego TJ
23. Cockrell C
24. Shick AE
25. Balci H
26. Salazar A
27. Rian K
28. Hemedan AA
29. Esteban-Medina M
30. Staumont B
31. Hernandez-Vargas E
32. Martis B S
33. Madrid-Valiente A
34. Karampelesis P
35. Sordo Vieira L
36. Harlapur P
37. Kulesza A
38. Nikaein N
39. Garira W
40. Malik Sheriff RS
41. Thakar J
42. Tran VDT
43. Carbonell-Caballero J
44. Safaei S
45. Valencia A
46. Zinovyev A
47. Glazier JA
Immune digital twins for complex human pathologies: applications, limitations, and challenges.; NPJ systems biology and applications; Vol 10(1), pp. 141. 2024 Nov 30.
1. Wang RH
2. Thakar J
Comparative analysis of single-cell pathway scoring methods and a novel approach.; NAR genomics and bioinformatics; Vol 6(3), pp. lqae124. 2024 Sep 24.
1. Cornwell AB
2. Zhang Y
3. Thondamal M
4. Johnson DW
5. Thakar J
6. Samuelson AV
The C. elegans Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction.; GeroScience. 2024 Jun 15.
1. Dunlap G
2. Wagner A
3. Meednu N
4. Wang R
5. Zhang F
6. Ekabe JC
7. Jonsson AH
8. Wei K
9. Sakaue S
10. Nathan A
11. Bykerk VP
12. Donlin LT
13. Goodman SM
14. Firestein GS
15. Boyle DL
16. Holers VM
17. Moreland LW
18. Tabechian D
19. Pitzalis C
20. Filer A
21. Raychaudhuri S
22. Brenner MB
23. Thakar J
24. McDavid A
25. Rao DA
26. Anolik JH
Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium.; Nature communications; Vol 15(1), pp. 4991. 2024 Jun 11.
1. Mosmann TR
2. Rebhahn JA
3. De Rosa SC
4. Keefer MC
5. McElrath MJ
6. Rouphael NG
7. Pantaleo G
8. Gilbert PB
9. Corey L
10. Kobie JJ
11. Thakar J
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.; Frontiers in immunology; Vol 15, pp. 1347926. 2024 Jun 06.
1. Kassis G
2. Palshikar MG
3. Hilchey SP
4. Zand MS
5. Thakar J
Discrete-state models identify pathway specific B cell states across diseases and infections at single-cell resolution.; Journal of theoretical biology. 2024 Feb 27.
1. Lazaro-Pena MI
2. Cornwell AB
3. Diaz-Balzac CA
4. Das R
5. Ward ZC
6. Macoretta N
7. Thakar J
8. Samuelson AV
Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal Caenorhabditis elegans aging and systemically regulates longevity from serotonergic and GABAergic neurons.; eLife; Vol 12. 2023 Jun 20.
1. Zhou T
2. Gilliam NJ
3. Li S
4. Spandau S
5. Osborn RM
6. Connor S
7. Anderson CS
8. Mariani TJ
9. Thakar J
10. Dewhurst S
11. Mathews DH
12. Huang L
13. Sun Y
Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection.; mBio. 2023 Apr 19.
1. Palshikar MG
2. Min X
3. Crystal A
4. Meng J
5. Hilchey SP
6. Zand MS
7. Thakar J
Executable Network Models of Integrated Multiomics Data.; Journal of proteome research. 2023 Mar 31.
1. Osborn RM
2. Leach J
3. Zanche M
4. Ashton JM
5. Chu C
6. Thakar J
7. Dewhurst S
8. Rosenberger S
9. Pavelka M
10. Pryhuber GS
11. Mariani TJ
12. Anderson CS
Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells.; PloS one; Vol 18(2), pp. e0281898. 2023 Feb 24.
1. Thakar J
Pillars of biology: Boolean modeling of gene-regulatory networks.; Journal of theoretical biology. 2023 Jan 24.
1. Cornwell A
2. Zhang Y
3. Thondamal M
4. Johnson DW
5. Thakar J
6. Samuelson AV
The C. elegans Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction.; bioRxiv : the preprint server for biology. 2023 Jan 22.
1. Lazaro-Pena MI
2. Cornwell AB
3. Diaz-Balzac CA
4. Das R
5. Macoretta N
6. Thakar J
7. Samuelson AV
Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal Caenorhabditis elegans aging and systemically regulates longevity from serotonergic and GABAergic neurons.; bioRxiv : the preprint server for biology. 2023 Jan 12.
1. Huang Y
2. Zhang Y
3. Seaton KE
4. De Rosa S
5. Heptinstall J
6. Carpp LN
7. Randhawa AK
8. McKinnon LR
9. McLaren P
10. Viegas E
11. Gray GE
12. Churchyard G
13. Buchbinder SP
14. Edupuganti S
15. Bekker LG
16. Keefer MC
17. Hosseinipour MC
18. Goepfert PA
19. Cohen KW
20. Williamson BD
21. McElrath MJ
22. Tomaras GD
23. Thakar J
24. Kobie JJ
Baseline host determinants of robust human HIV-1 vaccine-induced immune responses: A meta-analysis of 26 vaccine regimens.; EBioMedicine; Vol 84, pp. 104271. 2022 Sep 27.
1. Zhou T
2. Gilliam NJ
3. Li S
4. Spaudau S
5. Osborn RM
6. Anderson CS
7. Mariani TJ
8. Thakar J
9. Dewhurst S
10. Mathews DH
11. Huang L
12. Sun Y
Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection.; bioRxiv : the preprint server for biology. 2022 Sep 23.
1. Palshikar MG
2. Palli R
3. Tyrell A
4. Maggirwar S
5. Schifitto G
6. Singh MV
7. Thakar J
Executable models of immune signaling pathways in HIV-associated atherosclerosis.; NPJ systems biology and applications; Vol 8(1), pp. 35. 2022 Sep 21.
1. Hilchey SP
2. Palshikar MG
3. Mendelson ES
4. Shen S
5. Rasam S
6. Emo JA
7. Qu J
8. Thakar J
9. Zand MS
Cyclosporine A Modulates LSP1 Protein Levels in Human B Cells to Attenuate B Cell Migration at Low O2 Levels.; Life (Basel, Switzerland); Vol 12(8). 2022 Aug 22.
1. Järvinen KM
2. Davis EC
3. Bevec E
4. Jackson CM
5. Pizzarello C
6. Catlin E
7. Klein M
8. Sunkara A
9. Diaz N
10. Miller J
11. Martina CA
12. Thakar J
13. Seppo AE
14. 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; Vol 10, pp. 916184. 2022 Jul 06.
1. Cornwell A
2. Llop JR
3. Salzman P
4. Rasmussen N
5. Thakar J
6. Samuelson AV
The Replica Set Method is a Robust, Accurate, and High-Throughput Approach for Assessing and Comparing Lifespan in C. elegans Experiments.; Frontiers in aging; Vol 3, pp. 861701. 2022 Apr 28.
1. Beck LA
2. Pesonen M
3. Thakar J
4. Georas SN
5. Järvinen KM
IgE Sensitization Drives the Atopic March.; American journal of respiratory and critical care medicine. 2022 Jan 08.
1. McCall MN
2. Chu CY
3. Wang L
4. Benoodt L
5. Thakar J
6. Corbett A
7. Holden-Wiltse J
8. Slaunwhite C
9. Grier A
10. Gill SR
11. Falsey AR
12. Topham DJ
13. Caserta MT
14. Walsh EE
15. Qiu X
16. Mariani TJ
A systems genomics approach uncovers molecular associates of RSV severity.; PLoS computational biology; Vol 17(12). 2021 Dec 28.
1. Palshikar MG
2. Hilchey SP
3. Zand MS
4. Thakar J
WikiNetworks: translating manually created biological pathways for topological analysis.; Bioinformatics (Oxford, England). 2021 Oct 12.
1. Dräger A
2. Helikar T
3. Barberis M
4. Birtwistle M
5. Calzone L
6. Chaouiya C
7. Hasenauer J
8. Karr JR
9. Niarakis A
10. Rodríguez Martínez M
11. Saez-Rodriguez J
12. Thakar J
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.; Bioinformatics (Oxford, England). 2021 Jun 24.
1. Seppo AE
2. Bu K
3. Jumabaeva M
4. Thakar J
5. Choudhury R
6. Yonemitsu C
7. Bode L
8. Martina CA
9. Allen M
10. Tamburini S
11. Piras E
12. Wallach DS
13. Looney RJ
14. Clemente JC
15. Järvinen KM
Infant Gut Microbiome Is Enriched with Bifidobacteria longumssp. infantisin Old Order Mennoniteswith Traditional Farming Lifestyle.; Allergy. 2021 Apr 27.
1. Cornwell A
2. Palli R
3. Singh MV
4. Benoodt L
5. Tyrell A
6. Abe JI
7. Schifitto G
8. Maggirwar SB
9. Thakar J
Molecular characterization of atherosclerosis in HIV positive persons.; Scientific reports; Vol 11(1). 2021 Feb 05.
1. Eisenhaber F
2. Thakar J
3. Ponte-Sucre A
4. Dandekar T
Editorial: Innovative Strategies From Synthetic Biology and Bacterial Pathways to Master Biochemical Environmental Challenges.; Frontiers in bioengineering and biotechnology; Vol 9. 2021.
1. Seppo AE
2. Choudhury R
3. Pizzarello C
4. Palli R
5. Fridy S
6. Rajani PS
7. Stern J
8. Martina C
9. Yonemitsu C
10. Bode L
11. Bu K
12. Tamburini S
13. Piras E
14. Wallach DS
15. Allen M
16. Looney RJ
17. Clemente JC
18. Thakar J
19. Järvinen KM
Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition.; Frontiers in immunology; Vol 12. 2021.
1. Thakar J
2. Qian Y
3. Benoodt L
4. Roumanes D
5. Qiu X
6. Laniewski N
7. Chu C
8. Slaunwhite C
9. Wang L
10. Mandava A
11. Chang I
12. Falsey AR
13. Caserta MT
14. Mariani TJ
15. Scheuermann RH
16. Walsh EE
17. Topham DJ
Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein.; Vaccine: X; Vol 5. 2020 Aug 07.
1. Palli R
2. Seaton KE
3. Piepenbrink MS
4. Hural J
5. Goepfert PA
6. Laher F
7. Buchbinder SP
8. Churchyard G
9. Gray GE
10. Robinson HL
11. Huang Y
12. Janes H
13. Kobie JJ
14. Keefer MC
15. Tomaras GD
16. Thakar J
Impact of vaccine type on HIV-1 vaccine elicited antibody durability and B cell gene signature.; Scientific reports; Vol 10(1). 2020 Aug 03.
1. Hilchey SP
2. Palshikar MG
3. Emo JA
4. Li D
5. Garigen J
6. Wang J
7. Mendelson ES
8. Cipolla V
9. Thakar J
10. Zand MS
Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 αdependent, o2 sensing, molecular switch.; BMC immunology; Vol 21(1). 2020 Mar 18.
1. Benoodt L
2. Thakar J
Network Analysis of Large-Scale Data and Its Application to Immunology.; Methods in molecular biology (Clifton, N.J.); Vol 2131. 2020.
1. Nakaya HI
2. Thakar J
3. Maracaja-Coutinho V
Editorial: User-Friendly Tools Applied to Genetics or Systems Biology.; Frontiers in genetics; Vol 11. 2020.
1. Rivera-Escalera F
2. Pinney JJ
3. Owlett L
4. Ahmed H
5. Thakar J
6. Olschowka JA
7. Elliott MR
8. O'Banion MK
IL-1β-driven amyloid plaque clearance is associated with an expansion of transcriptionally reprogrammed microglia.; Journal of neuroinflammation; Vol 16(1). 2019 Dec 10.
1. Thatcher TH
2. Woeller CF
3. Thakar J
4. Khan A
5. Hopke PK
6. Smith MR
7. Uppal K
8. Walker DI
9. Go YM
10. Jones DP
11. Krahl PL
12. Mallon TM
13. Sime PJ
14. Phipps RP
15. 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; Vol 61 Suppl 12. 2019 Dec.
1. Khan A
2. Thatcher TH
3. Woeller CF
4. Sime PJ
5. Phipps RP
6. Hopke PK
7. Utell MJ
8. Krahl PL
9. Mallon TM
10. 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; Vol 61 Suppl 12. 2019 Dec.
1. Thakar J
2. Thatcher TH
3. Smith MR
4. Woeller CF
5. Walker DI
6. Utell MJ
7. Hopke PK
8. Mallon TM
9. Krahl PL
10. Rohrbeck P
11. Go YM
12. Jones DP
13. 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; Vol 61 Suppl 12. 2019 Dec.
1. Woeller CF
2. Thatcher TH
3. Thakar J
4. Cornwell A
5. Smith MR
6. Jones DP
7. Hopke PK
8. Sime PJ
9. Krahl P
10. Mallon TM
11. Phipps RP
12. Utell MJ
Exposure to Heptachlorodibenzo-p-dioxin (HpCDD) Regulates microRNA Expression in Human Lung Fibroblasts.; Journal of occupational and environmental medicine; Vol 61 Suppl 12. 2019 Dec.
1. Krahl PL
2. Benchoff E
3. Go YM
4. Jones DP
5. Smith MR
6. Walker DI
7. Uppal K
8. Woeller CF
9. Thatcher TH
10. Thakar J
11. Phipps RP
12. Hopke P
13. Utell MJ
14. Mallon TM
Advances in Comprehensive Exposure Assessment: Opportunities for the US Military.; Journal of occupational and environmental medicine; Vol 61 Suppl 12. 2019 Dec.
1. Mallon TM
2. Krahl PK
3. Haines KM
4. Walker DI
5. Thatcher T
6. Woeller CF
7. Thakar J
8. Hopke PK
9. Gaydos JC
10. Smith MR
11. Uppal K
12. Go YM
13. Jones DP
14. Utell M
Use of Biomarkers to Assess Environmental Exposures and Health Outcomes in Deployed Troops.; Journal of occupational and environmental medicine; Vol 61 Suppl 12. 2019 Dec.
1. Palli R
2. Palshikar MG
3. Thakar J
Executable pathway analysis using ensemble discrete-state modeling for large-scale data.; PLoS computational biology; Vol 15(9). 2019 Sep.
1. Walsh EE
2. Mariani TJ
3. Chu C
4. Grier A
5. Gill SR
6. Qiu X
7. Wang L
8. Holden-Wiltse J
9. Corbett A
10. Thakar J
11. Benoodt L
12. McCall MN
13. Topham DJ
14. Falsey AR
15. Caserta MT
Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study.; JMIR research protocols; Vol 8(6). 2019 Jun 06.
1. Sarkar S
2. Piepenbrink MS
3. Basu M
4. Thakar J
5. Keefer MC
6. Hessell AJ
7. Haigwood NL
8. Kobie JJ
IL-33 enhances the kinetics and quality of the antibody response to a DNA and protein-based HIV-1 Env vaccine.; Vaccine; Vol 37(17). 2019 Apr 17.
1. Cornwell AB
2. Llop JR
3. Salzman P
4. Thakar J
5. Samuelson AV
The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan.; Journal of visualized experiments : JoVE. 2018 Jun 29.
1. Palli R
2. Thakar J
Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases.; Methods in molecular biology (Clifton, N.J.); Vol 1819. 2018.
1. Zhang Y
2. Thakar J
3. Topham DJ
4. Falsey AR
5. Zeng D
6. Qiu X
Some equivalence relationships of regularized regressions; Mathematics for Applications; Vol 7, pp. 3-10. 2018 Jan 01.
1. Mariani TJ
2. Qiu X
3. Chu CY
4. Wang L
5. Thakar J
6. Holden-Wiltse J
7. Corbett A
8. Topham DJ
9. Falsey AR
10. Caserta MT
11. Walsh EE
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. 2017 Aug 17.
1. Connor R
2. Jones LD
3. Qiu X
4. Thakar J
5. Maggirwar SB
Frontline Science: c-Myc regulates P-selectin glycoprotein ligand-1 expression in monocytes during HIV-1 infection.; Journal of leukocyte biology. 2017 Jun 29.