Shesh N. Rai

Shesh N. Rai

Education:

B.Sc., Banaras Hindu University, India, 1979
M.Sc., Banaras Hindu University, India, 1981
Ph.D., University of Waterloo, Waterloo, Canada, 1993
Postdoctoral Fellowship, Health Canada, 1996

Curriculum Vitae

Current Positions:

Wendell Cherry Chair in Clinical Trial Research, University of Louisville
Director, Biostatistics Shared Facility, JB Brown Cancer Center, School of Medicine, University of Louisville
Professor, Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville
Professor, Department of Pharmacology and Toxicology (Associate Faculty), School of Medicine

Contact Information:

Clinical Translational Research Building, Room 211
University of Louisville
505 Hancock St.
Louisville, KY 40202, USA
Phone 502-852-4030
Fax 502-852-7979
Email: Shesh.Rai@louisville.edu

Website:

http://louisville.edu/sphis/directory/shesh-n-rai-phd

Research Description:

Thoroughly experienced in designing (SAMPLE SIZE) and analyzing retrospective/prospective studies in CANCER and other CLINICAL and BASIC SCIENCE researches and BEHAVIORAL INTERVENTIONS; pursue developing statistical methods with real applications in heterogeneity in CLINICAL STUDIES, threshold DOSE-RESPONSE models, SURVIVAL ANALYSIS with incomplete and correlated data, efficient estimation in MIXED effects (REPEATED measure) models, robust estimation in high-dimension data (BIOINFORMATICS), effects of SAMPLING weights in log-linear models, and characterization and estimation of POPULATION RISK.

Representative Publicatoins:

  1. Li X, Wu D, Cooper NGF, Rai SN.  Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model.   Statistical Applications in Genetcis & Molecular Biology 2019 Jan 22. pii: /j/sagmb.ahead-of-print/sagmb-2018-0021/sagmb-2018-0021.xml. doi: 10.1515/sagmb-2018-0021. [Epub ahead of print] PMID: 30667368.
  2. Gill A, Gosain R, Gragg H, Bycroft R, Rai SN, Pan J, Chesney JA, Miller DM.  5-(3,3-dimethyle-1-triazeno) imidazole-4-carboxamide and interleukin-2 adjuvant therapy in resected high-risk primary and regionally metastatic m elanoma. American Journal of Medical Science 2019 Jan;357(1):43-8. doi: 10.1016/j.amjms.2018.10.009. Epub 2018 Oct 25. PMID: 30611319.
  3. Breaux A, Turner B, Wu X, Rai SN, Riley EC, Mandadi M, Sanders MA.  Impact of 21-gene expression assay on staging estrogen receptor-positive HER2-negative breast cancer.  Clinical Breast Cancer 2019 Feb;19(1):e261-e269. doi: 10.1016/j.clbc.2018.10.005. Epub 2018 Oct 29. PMID: 30509870.
  4. Al-Eryani L, Jenkins SF, States VA, Pan J, Malone JC, Rai SN, Galandiuk S, Giri AK, States JC.  miRNA expression profiles of premalignant and malignant arsenic-induced skin lesions.  PLoS One 2018 Aug 16;13(8):e0202579. doi: 10.1371/journal.pone.0202579. eCollection 2018. PMID: 30114287; PMCID: PMC6095593.
  5. Zafar N, Krishnasamy SS, Shah J, Rai SN, Riggs DW, Bhatnagar A, O'Toole TE.  Circulating angiogenic stem cells in type 2 diabetes are associated with glycemic control and endothelial dysfunction.  PLoS One 2018 Oct 15;13(10):e0205851. doi: 10.1371/journal.pone.0205851. PMID: 30321232; PMCID: PMC6188890.
  6. Khanal S, Shumway BS, Zahin M, Redman RA, Strickley JD, Trainor PJ, Rai SN, Ghim SJ, Jenson AB, Joh J.  Viral DNA integration and methylation of human papillomavirus type 16 in high-grade oral epithelial dysplasia and head and neck squamous cell carcinoma.  Oncotarget 2018 Jul 13;9(54):30419-33. doi: 10.18632/oncotarget.25754. PMID: 30100997; PMCID: PMC6084396
  7. Malovichko MV, Zeller I, Krivokhizhina TV, Xie Z, Lorkiewicz P, Agarwal A, Wickramasinghe N, Sithu SD, Shah J, O'Toole T, Rai SN, Bhatnagar A, Conklin DJ, Srivastava S.  Systemic toxicity of smokeless tobacco products in mice.  Nicotine & Tobacco Research 2019 Jan 1:21(1):101-110. doi: 10.1093/ntr/ntx230. PMID: 30085294; PMCID: PMC6329408.
  8. Clair HB, Pinkston CM, Rai SN, Pavuk M, Dutton ND, Brock GN, Prough RA, Falkner KC, McClain CJ, Cave MC.  Liver disease in a residential cohort with elevated polychlorinated biphenyl exposures.  Toxicological Sciences 2018 Jul 1;164(1):39-49. doi: 10.1093/toxsci/kfy076. PMID: 29684222; PMCID: PMC6016643.
  9. Jones DZ, Schmidt ML, Suman S, Hobbing KR, Barve SS, Gobejishvili L, Brock G, Klinge CM, Rai SN, Park J, Clark GJ, Agarwal R, Kidd LR.  Micro-RNA-186-5p inhibition attenuates proliferation, anchorage independent growth and invasion in metastatic prostate cancer cells.  BMC Cancer 2018 Apr 13;18(1):421. doi: 10.1186/s12885-018-4258-0. PMID: 29653561; PMCID: PMC5899400.
  10. Al-Eryani L, Jenkins SF, States VA, Pan J, Malone JC, Rai SN, Galandiuk S, Giri AK, States JC.  miRNA expressions profile of premalignant and malignant arsenic-induced skin lesions.  PLoS One 2018 Aug 16;13(8):e0202579. doi: 10.1371/journal.pone.0202579. eCollection2018. PMID: 30114287; PMCID: PMC695593.
  11. Shah JS, Rai SN, DeFilippis AP, Hill BG, Bhatnagar A, Brock GN.  Distribution based nearest neighbor imputation for truncated high-dimensional data with applications to pre-clinical and clinical metabolomics studies.  BMC Bioinformatics 2017 Feb 20;18:114. doi: 10.1186/s12859-017-1547-6. PMID: 28219348; PMCID: PMC5319174.
  12. Li X, Cooper NGF, Shyr Y, Wu D, Rouchka EC, Gill RS, O’Toole TE, Brock GN, Rai SN.  Inference and sample size calculations based on statistical tests in a negative binomial distribution for differential gene expression in RNA-seq data.  Journal of Biometrics & Biostatistics 2017;8(1):332.[https://doi.org/10.4172/2155-6180.1000332 ]
  13. Cambon AC, Baumgartner KB, Brock GN, Cooper NGF, Wu D, Rai SN.  Properties of adaptive clinical trial signature design in the presence of gene and gene–treatment interaction.  Communications in Statistics: Simulation & Computation 2017 Jun 2;46(10):8233-50. [ https://doi.org/10.1080/03610918.2016.1275690 ]
  14. Li X, Brock GN, Rouchka EC, Cooper NGF, Wu D, O’Toole TE, Gill RS. Eteleeb AM, O’Brien L, Rai SN.  A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.  PLoS One 2017 May 1;12(5):e0176185. PMID: 28459823; PMCID: PMC5411036.  [ https://doi.org/10.1371/journal.pone.0176185 ]
  15. Khanal S, Trainor P, Zahin M, Ghim SJ, Joh J, Rai SN, Jenson A, Shumway BS.  Histologic variation in high grade oral epithelial dysplasia when associated with high-risk human papillomavirus.  Oral Surgery, Oral Medicine, Oral Pathology & Oral Radiology 2017 May;123(5):566-85. PMID: 28407985. [ http://dx.doi.org/10.1016/j.oooo.2017.01.008 ]
  16. Carter JV, Roberts HL, Pan J, Rice JD, Burton JF, Galbraith NJ, Eichenberger MR, Jorden J, Deveaux P, Farmer R, Williford A, Kanaan Z, Rai SN, Galandiuk S.  A highly predictive model for diagnosis of colorectal neoplasms using plasma microRNA: Improving specificity and sensitivity.  Annals of Surgery 2016 Oct;264(4):575-84. doi: 10.1097/SLA.0000000000001873. PMID: 27471839; PMCID: PMC5115272.
  1. Egger ME, Xiao D, Hao H, Pan J, Rai SN, Cambon A, Waigel S, Zacharias W, McMasters KM.  Unique genes in the tumor-positive sentinel lymph nodes associated with non-sentinel lymph node metastases in melanoma.  Annals of Surgical Oncology 2018 May;25(5):1296-303. doi.org/10.1245/s10434-018-6377-x. Epub 2018 Mar 1.  PMID: 29497912.
  2. Das S, Rai A, Mishra DC, Rai SN.  Statistical approach for gene set analysis with trait specific quantitative trait loci.  Scientific Reports 2018 Feb 5;8(1):2391. doi: 10.1038/s41598-018-19736-w. PMID: 29402907; PMCID: PMC5799309.
  3. Das S, Rai A, Mishra DC, Rai SN.  Statistical approach for selection of biologically informative genes.  Gene 2018 May 20;655:71-83. doi: 10.1016/j.gene.2018.02.044. Epub 2018 Feb 16. PMID: 29458166.
  4. Trainor PJ, DeFilippis AP, Rai SN.  Evaluation of classifier performance for multiclass phenotype discrimination in untargeted metabolomics.  Metabolites 2017 Jun 21;7(2):E30. doi: 10.3390/metabo7020030. PMID: 28635678; PMCID: PMC5488001.
  1. Amraotkar AR, Song D, Otero D, Trainor P, Ismail I, Kothari V, Singh A, Moore J, Rai SN,  DeFilippis A. Platelet count and mean platelet volume at the time of and after acute myocardial infarction.  Clinical & Applied Thrombosis/Haemostasis 2017 Nov;23(8):1052-9. doi: 10.1177/1076029616683804. PMID: 28294633; PMCID: PMC5572529.
  2. Perez CA, Wu X, Amsbaugh MJ, Gosain R, Claudino WM, Yusuf M, Roberts T,  Jain D, Jenson A, Jenson A, Khanal S, Silverman CI, Tennant P, Bumpous JM, Dunlap NE, Rai S, Redman RA.  High-dose versus weekly cisplatin definitive chemoradiotherapy for HPV-related oropharyngeal squamous cell carcinoma of the head and neck. Oral Oncology 2017 Apr;67:24-8. PMID: 28351577
  3. Srivastava DK, Zhu L, Hudson MM, Pan J, Rai SN.  Robust estimation and inference on current status data with application to Phase IV cancer trial.  Journal of Modern Applied Statistical Methods 2018;17(1): eP2629. doi: 10.22237/jmasm/1530544863
  4. Trainor PJ, DeFilippis AP, Rai SN. Evaluation of classifier performance for multiclass phenotype discrimination in untargeted metabolomics.  Metabolites 2017 Jun 21;7(2). pii: E30. doi: 10.3390/metabo7020030.  PMID: 28635678; PMCID: PMC54488001
  5. Netz U, Carter JV, Eichenberger MR, Dryden GW, Pan J, Rai SN, Galandiuk S.  Genetic polymorphismspredict response to anti-tumor necrosis factor treatment in Crohn’s disease, World Journal of Gastroenterology 2017 Jul 21;23(27):4958-67.  doi: 10.3748/wjg.v23.i27.4958. PMID: 28785150; PMCID: PMC5526766
  6. Netz U, Carter J, Eichenberger MR, Feagins K, Galbraith NJ, DrydenGW, Pan J, Rai S, Galandiuk S.  Plasma microRNA profile differentiates Crohn’s Colitis from Ulcerative Colitis.  Inflammatory Bowel Diseases 2017 Dec 19;24(1):159-65. doi: 10.1093/ibd/izx009.  PMID: 29272478; PMCID: PMC5858028
  7. Hao H, Xiao D, Pan J, Qu J, Egger M, Waigel S, Sanders MAG, Zacharias W, Rai SN, McMasters KM.  Sentinel lymph node genes to predict prognosis in node-positive melanoma patients,  Annals of Surgical Oncology 2017 Jan;24(1):108-16. doi: 10.1245/s10434-016-5575-7. PMID: 27663566
  8. Dragun AE, Ajkay NJ, Riley EC, Roberts TN, Pan J, Rai SN, Jain D, Quillo AR, Scoggins CR, McMasters KM, Woo SY. First results of a Phase II Trial of once-weekly hypofractionated breast irradiation (WHBI) for early-stage breast cancer.  International Journal of Radiation Oncology, Biology, Physics 2017 Jul 1;98(3):595-602. [http://dx.doi.org/10.1016/j.ijrobp.2017.01.212 ].  PMID: 28581400
  9. Conklin DJ, Malovichko MV, Zeller I, Das TP, Krivokhizhina TV, Lynch BH, Lorkiewicz P, Agarwal A, Wickramasinghe N, Haberzettl P, Sithu SD, Shah J, O'Toole TE, Rai SN, Bhatnagar A, Srivastava S.  Biomarkers of chronic acrolein inhalation exposure in mice: Implications for tobacco product-induced toxicity.  Toxicological Sciences 2017 Aug 1;158(2):263-74. PMID: 28482041; PMCID:: PMC5837482
  10. Abplanalp W, DeJarnett N, Riggs DW, Conklin DJ, McCracken JP, Srivastava S, Xie Z, Rai S, Bhatnagar A, O'Toole TE.  Benzene exposure is associated with cardiovascular disease risk.  PLoS One 2017 Sep 8;12(9):e0183602. doi: 10.1371/journal.pone.0183602. eCollection 2017. PMID: 28886060; PMCID: PMC5590846
  1. Carter JV, Pan J, Rai SN, Galandiuk S.  ROC-ing along: Evaluation and interpretation of receiver operating characteristic curves.  Surgery 2016 Jun;159(6):1638-45.PMID: 26962006. [ http://dx.doi.org/10.1016/j.surg.2015.12.029 ]
  2. Srivastava S, Lal SB, Mishra DC, Angadi UB, Chaturvedi KK, Rai SN, Rai A.  An efficient algorithm for protein structure comparison using elastic shape analysis.  Algorithms for Molecular Biology 2016 Sep 29;11:27. doi: 10.1186/s13015-016-0089-1. PMID: 27708689; PMCID: PMC5041553
  3. Diaz JA, Rai SN, Wu X, Chao JH, Dias AL, Kloecker GH.  Phase II Trial on extending the maintenance flushing interval of implanted ports.  Journal of Oncology Practice 2017 Jan;13(1):e22-8. doi: 10.1200/JOP.2016.010843. PMID: 28084883
  4. Rai SN, Trainor PJ, Khosravi F, Kloecker G, Panchapakesan B.  Classification of biosensor time series using dynamic time warping: Applications in screening cancer cells with characteristics biomarkers.  Open Access Medical Statistics 2016; 2016;6:21-9. PMID: 27942497; PMCID; PMC5147752
  5. Das TP, John AMSP, Suman S, Morris TJ, Rai SN, Messer JC, Alatassi H,  Ankem MK, Damodaran C.  MiR-301a expression: A prognostic marker for prostate cancer.  Urologic Oncology  2016 Aug;34(8):336 e13-e20. doi: 10.1016/j.urolonc.2016.03.009. PMID: 27133223; PMCID: PMC4967401
  6. Bhatnagar K, Rai S, Frahm H, Smith TD.  The Chiropteran Brain Database: Volumetric survey of the hypothysis in 165 species.  The Anatomical Record 2016 Apr;299:492-519. PMID: 26800031 [ https://onlinelibrary.wiley.com/doi/full/10.1002/ar.23321 ]
  7. Khosravi F, Trainor P, Rai S, Kloecker G, Wickstrom E, Panchapakesan B.  Static micro-array isolation, dynamic time series classification, capture and enumeration of spiked breast cancer cells in blood: the nanotube-CTC chip.  Nanotechnology 2016 Nov 4;27(44):44LT03. doi:10.1088/0957-4484/27/13/13LT02. PMID: 27680886; PMCID: PMC5374058
  8. Litvan I, Lees PS, Cunningham CR, Rai SN, Cambon AC, Standaert DG, Marras C, Juncos J, Riley D, Reich S, Hall D, Kluger B, Bordelon Y, Shprecher DR.  Environmental and occupational risk factors for progressive supranuclear palsy: Case-control study.  Movement Disorder 2016 May;31(5):644-52. doi: 10.1002/mds.26512. PMID: 26854325. PMCID: PMC4861658
  9. Basu P, Jenson AB, Majhi T, Choudhry P, Mandal R, Banerjee D, Biswas J, Pan J, Rai SN, Ghim S, Miller D.  Phase 2 randomized controlled trial of radiation therapy plus concurrent interferon-alpha and retinoic acid versus cisplatin for Stage III cervical c arcinoma. International Journal of Radiation Oncology, Biology & Physics 2016 Jan 1;94(1):102-10. PMID: 26700705
  10. Xiao D, Barry S, Kmetz D, Egger M, Pan J, Rai SN, Qu J, McMasters KM, Hao H.  Melanoma cell-derived exosomes promote epithelial-mesenchymal transition in primary melanocytes through paracrine/autocrine signaling in the tumor microenvironment.  Cancer Letters 2016 Jul 1;376(2):318-27. PMID: 27063098; PMCID: PMC4869527
  11. Amsbaugh M, Pan J, Yusuf MB, Dragun A, Dunlap N, Guan T, Boling W, Rai S, Woo S.  Dose-volume response relationship for brain metastases treated with frameless single-fraction linear accelerator-based stereotactic radiosurgery.  Cures 2016 Apr 27;8(4):e587. doi:10.7759/cureus.587
  12. Srivastava DK, Hudson MM, Robison LL, Wu S, Rai SN.  Design and analysis of cohort studies: Issues and practices.  Bioinformatics & Biostatistics International Journal 2015 Jun;2(5):44. doi:10.15406/bbji.2015.02.00044.
  13. Kendrick SK, Rai SN, Wu D.  Simulation study for the sensitivity and mean sojourn time specific lead time in cancer screening when human lifetime is a competing risk.  Journal of Biometrics and Biostatistics 2015;6:247.  doi:10.4172/2155-6180.1000247
  14. Boone SD, Baumgartner KB, Baumgartner RN, Connor AE, John EM, Giuliano AR, Hines LM, Rai SN, Riley EC, Pinkston CM, Wolff RK, Slattery ML.  Active and passive cigarette smoking and mortality among Hispanic and non-Hispanic white women diagnosed with invasive breast cancer: The Breast Cancer Health Disparities Study.  Annals of Epidemiology 2015 Nov;25(11):824-31. doi: 10.1016/j.annepidem.2015.08.007. PMID: 26387598; PMCID: PMC4609618.
  15. Amraotkar AR, Hargis CW, Cambon AC, Rai SN, Keith MCL, Ghafghazi S, Bolli R, DeFilippis AP.  Comparison of coliform contamination in non-municipal waters consumed by Mennonites versus the non-Mennonites rural populations.  Environmental Health & Preventive Medicine 2015 Sep;20(5):338-46. PMID: 26068785; PMCID: PMC4550604
  16. Rice J, Roberts H, Rai SN, Galandiuk S.  Housekeeping genes for studies of plasma microRNA: A need for more precise standardization.  Surgery 2015 Nov;158(5):1345-51. doi: 10.1016/j.surg.2015.04.025. PMID: 26094174.
  17. Rice J, Roberts H, States V, Burton J, Pan J, Rai SN, Galandiuk S.  Assay reproducibility in clinical studies of plasma miRNA.  PLoS ONE 2015 Apr 8;10(4):e0121948. doi: 10.1371/journal.pone.012194. PMID: 25853871; PMCID: PMC4390277.
  18. Cambon AC, Baumgartner KB, Brock GN, Cooper NGF, Wu D, Rai SN.  Classification of clinical outcomes using high-throughput informatics: Part 2-Parametric method reviews.  Journal of Model Assisted Statistics & Applications 2015;10(2):89-107
  19. Cambon AC, Baumgartner KB, Brock GN, Cooper NGF, Wu D, Rai SN.  Classification of clinical outcomes using high-throughput informatics: Part 1-Non-parametric method reviews.  Journal of Model Assisted Statistics & Applications 2015;10(1):3-23.

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