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Items: 1 to 50 of 80

1.

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

Palli R, Palshikar MG, Thakar J.

PLoS Comput Biol. 2019 Sep 3;15(9):e1007317. doi: 10.1371/journal.pcbi.1007317. eCollection 2019 Sep.

2.

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 Res Protoc. 2019 Jun 6;8(6):e12907. doi: 10.2196/12907.

3.

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 Apr 17;37(17):2322-2330. doi: 10.1016/j.vaccine.2019.03.044. Epub 2019 Mar 27.

4.

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

Palli R, Thakar J.

Methods Mol Biol. 2018;1819:385-402. doi: 10.1007/978-1-4939-8618-7_18.

PMID:
30421414
5.

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

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

J Vis Exp. 2018 Jun 29;(136). doi: 10.3791/57819.

PMID:
30010651
6.

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 C, Wang L, Thakar J, Holden-Wiltse J, Corbett A, Topham DJ, Falsey AR, Caserta MT, Walsh EE.

J Infect Dis. 2017 Nov 15;216(8):1027-1037. doi: 10.1093/infdis/jix400.

7.

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.

J Leukoc Biol. 2017 Oct;102(4):953-964. doi: 10.1189/jlb.6HI0217-043R. Epub 2017 Jun 29.

8.

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 Jun 6;18(1):295. doi: 10.1186/s12859-017-1669-x.

9.

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

Zhang Y, Topham DJ, Thakar J, Qiu X.

Bioinformatics. 2017 Jul 1;33(13):1944-1952. doi: 10.1093/bioinformatics/btx104.

10.

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

Van Twisk D, Murphy SP, Thakar J.

Immunology. 2017 May;151(1):71-80. doi: 10.1111/imm.12707. Epub 2017 Feb 9.

11.

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.

Bioeng Transl Med. 2016 Jun;1(2):193-206. Epub 2016 Oct 24.

12.

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

Katanic D, Khan A, Thakar J.

J Immunol Methods. 2016 Dec;439:15-22. doi: 10.1016/j.jim.2016.09.005. Epub 2016 Sep 20.

PMID:
27659011
13.

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.

J Occup Environ Med. 2016 Aug;58(8 Suppl 1):S89-96. doi: 10.1097/JOM.0000000000000769.

14.

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.

J Occup Environ Med. 2016 Aug;58(8 Suppl 1):S62-71. doi: 10.1097/JOM.0000000000000742.

15.

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 Aug 5;11(8):e0160510. doi: 10.1371/journal.pone.0160510. eCollection 2016.

16.

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 Jul 5;11(7):e0158641. doi: 10.1371/journal.pone.0158641. eCollection 2016.

17.

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

Anderson CS, DeDiego ML, Topham DJ, Thakar J.

Comput Math Methods Med. 2016;2016:7686081. doi: 10.1155/2016/7686081. Epub 2016 Feb 14.

18.

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 A. 2016 Jan;89(1):59-70. doi: 10.1002/cyto.a.22740. Epub 2015 Oct 6.

19.

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 Sep 28;10(9):e0138110. doi: 10.1371/journal.pone.0138110. eCollection 2015.

20.

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

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

BMC Immunol. 2015 Aug 14;16:46. doi: 10.1186/s12865-015-0107-y.

21.

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.

J Virol. 2015 Oct;89(20):10190-205. doi: 10.1128/JVI.01523-15. Epub 2015 Jul 29.

22.

GESPA: classifying nsSNPs to predict disease association.

Khurana JK, Reeder JE, Shrimpton AE, Thakar J.

BMC Bioinformatics. 2015 Jul 25;16:228. doi: 10.1186/s12859-015-0673-2.

23.

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, Meng H, Blevins TP, Tsang S, Trentalange M, Siconolfi B, Park K, Gill TM, Belshe RB, Kaech SM, Shadel GS, Kleinstein SH, Shaw AC.

Aging (Albany NY). 2015 Jan;7(1):38-52.

24.

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

Albert R, Thakar J.

Wiley Interdiscip Rev Syst Biol Med. 2014 Sep-Oct;6(5):353-69. Review.

PMID:
25269159
25.

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 Immunol. 2014 Mar;27(2):39-47. doi: 10.1089/vim.2013.0074.

26.

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 Res. 2013 Oct;41(18):e170. doi: 10.1093/nar/gkt660. Epub 2013 Aug 5.

27.

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

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

J Interferon Cytokine Res. 2013 Nov;33(11):700-8. doi: 10.1089/jir.2012.0113. Epub 2013 Jun 17.

28.

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:S1. doi: 10.1186/1471-2105-14-S6-S1. Epub 2013 Apr 17.

29.

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.

J R Soc Interface. 2012 Dec 19;10(80):20120588. doi: 10.1098/rsif.2012.0588. Print 2013 Mar 6.

30.

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 Comput Biol. 2012 Jan;8(1):e1002345. doi: 10.1371/journal.pcbi.1002345. Epub 2012 Jan 12.

31.

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

Campbell C, Thakar J, Albert R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep;84(3 Pt 1):031929. Epub 2011 Sep 28.

PMID:
22060425
32.

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.

Front Physiol. 2011 Jul 11;2:32. doi: 10.3389/fphys.2011.00032. eCollection 2011.

33.

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.

J Immunol. 2011 Mar 1;186(5):2936-49. doi: 10.4049/jimmunol.1001148. Epub 2011 Feb 2.

34.

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

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

Theor Biol Med Model. 2010 Aug 20;7:35. doi: 10.1186/1742-4682-7-35.

35.

Boolean models of within-host immune interactions.

Thakar J, Albert R.

Curr Opin Microbiol. 2010 Jun;13(3):377-81. doi: 10.1016/j.mib.2010.04.003. Epub 2010 May 10. Review.

PMID:
20462786
36.

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 Syst Biol. 2008 Dec 5;2:107. doi: 10.1186/1752-0509-2-107.

37.

Boolean network simulations for life scientists.

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

Source Code Biol Med. 2008 Nov 14;3:16. doi: 10.1186/1751-0473-3-16.

38.

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

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

J R Soc Interface. 2009 Jul 6;6(36):599-612. doi: 10.1098/rsif.2008.0363. Epub 2008 Oct 24.

39.

Pyruvate dehydrogenase complex activity controls metabolic and malignant phenotype in cancer cells.

McFate T, Mohyeldin A, Lu H, Thakar J, Henriques J, Halim ND, Wu H, Schell MJ, Tsang TM, Teahan O, Zhou S, Califano JA, Jeoung NH, Harris RA, Verma A.

J Biol Chem. 2008 Aug 15;283(33):22700-8. doi: 10.1074/jbc.M801765200. Epub 2008 Jun 9.

40.

Increased lactate levels and reduced pH in postmortem brains of schizophrenics: medication confounds.

Halim ND, Lipska BK, Hyde TM, Deep-Soboslay A, Saylor EM, Herman MM, Thakar J, Verma A, Kleinman JE.

J Neurosci Methods. 2008 Mar 30;169(1):208-13. doi: 10.1016/j.jneumeth.2007.11.017. Epub 2007 Nov 29.

41.

Modeling systems-level regulation of host immune responses.

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

PLoS Comput Biol. 2007 Jun;3(6):e109. Epub 2007 Apr 30.

42.

Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks.

Christensen C, Thakar J, Albert R.

IET Syst Biol. 2007 Mar;1(2):61-77. Review.

PMID:
17441550
43.

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

Thakar J, Schleinkofer K, Borner C, Dandekar T.

Proteins. 2006 May 15;63(3):413-23.

PMID:
16470584
44.

Comparison of clarithromycin and ciprofloxacin therapy for Bacillus anthracis Sterne infection in mice with or without (60)Co gamma-photon irradiation.

Brook I, Giraldo DE, Germana A, Nicolau DP, Jackson WE, Elliott TB, Thakar JH, Shoemaker MO, Ledney GD.

J Med Microbiol. 2005 Dec;54(Pt 12):1157-62.

PMID:
16278429
45.

Clindamycin and quinolone therapy for Bacillus anthracis Sterne infection in 60Co-gamma-photon-irradiated and sham-irradiated mice.

Brook I, Germana A, Giraldo DE, Camp-Hyde TD, Bolduc DL, Foriska MA, Elliott TB, Thakar JH, Shoemaker MO, Jackson WE, Ledney GD.

J Antimicrob Chemother. 2005 Dec;56(6):1074-80. Epub 2005 Oct 20.

PMID:
16239289
46.

Nectarless flowers: ecological correlates and evolutionary stability.

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

Oecologia. 2003 Aug;136(4):565-70. Epub 2003 Jun 28.

PMID:
12838401
47.

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.

Anim Cogn. 2002 Dec;5(4):253-9. Epub 2002 Nov 16.

PMID:
12461603
48.

In vitro resistance of Bacillus anthracis Sterne to doxycycline, macrolides and quinolones.

Brook I, Elliott TB, Pryor HI 2nd, Sautter TE, Gnade BT, Thakar JH, Knudson GB.

Int J Antimicrob Agents. 2001 Dec;18(6):559-62.

PMID:
11738344
49.

Erythrocyte membrane ATP binding cassette (ABC) proteins: MRP1 and CFTR as well as CD39 (ecto-apyrase) involved in RBC ATP transport and elevated blood plasma ATP of cystic fibrosis.

Abraham EH, Sterling KM, Kim RJ, Salikhova AY, Huffman HB, Crockett MA, Johnston N, Parker HW, Boyle WE Jr, Hartov A, Demidenko E, Efird J, Kahn J, Grubman SA, Jefferson DM, Robson SC, Thakar JH, Lorico A, Rappa G, Sartorelli AC, Okunieff P.

Blood Cells Mol Dis. 2001 Jan-Feb;27(1):165-80.

PMID:
11358378
50.

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