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Prabhakar Chalise, Ph.D.

Associate Professor, Department of Biostatistics & Data Science

M.Sc., Statistics, Mathematics, Tribhuvan University, Kathmandu, Nepal
M.S., Statistics, University of Arkansas, Fayetteville, AR
Ph.D., Biostatistics, Florida State University, Tallahassee, FL
PostDoc, Statistical Genomics, Mayo Clinic, Rochester, MN

Research Focus

Survival Analysis, Statistical Genetics and Genomics, Computational Statistics, Methods in Biostatistics

Personal Mission Statement

My primary research interest is in the development and application of statistical methods to health sciences research. I work closely in statistical genetics and genomics, survival analysis, experimental design, clinical trial, multivariate analysis and computational statistics. Biomedical research is growing increasingly advanced in unprecedented ways due to the advent of high throughput technologies. Such high throughput experiments generate large volume of data and therefore it is essential to develop adequate modeling approaches that will be able to utilize all available information in order to explain the correct disease risk association. My research is focused in developing statistical and computational methods in analyzing such data to address frontier problems in biomedical research both in genotypic and phenotypic levels.

Top 15 Publications  

1. Chalise P and Fridley BL. Integrative clustering of multi-level ‘Omic data based on non-negative matrix factorization algorithm. PLOS ONE, 12(5), e0176278, 2017  

2. The Cancer Genome Atlas (TCGA), coauthor Chalise P. Integrated genomic and molecular characterization of cervical cancer. Nature, 543: 378-384, doi:10.1038/nature21386, 2017

3. Chalise P, Koestler DC, Bimali M, Yu Q and Fridley BL. Integrative Clustering methods for High-Dimensional Molecular Data. Translational Cancer Research,3(3): 202-216, 2014  

4. Chalise P, Raghavan R and Fridley BL. InterSIM: Simulation Tool for Multiple Integrative ‘Omic Datasets. Computer Methods and Programs in Biomedicine, 128: 69-74, 2016

5. Chalise P, Batzler A, Abo R, Wang L and Fridley B. Simultaneous analysis of multiple data types in Pharmacogenomic studies using weighted sparse canonical correlation analysis. OMICS: A Journal of Integrative Biology, 16(7-8):363-373, July/August 2012.

6. Chalise P and Fridley B. Comparison of performances of various penalty functions on Sparse Canonical Correlation Analysis. Computational Statistics and Data Analysis, 56: 245-254, 2012.

7. Chalise P, Chicken E and McGee D. Performance and Prediction for Varying Survival Time Scales. Communications in Statistics –Simulation and Computation, 42(3): 636-649, 2013

8. Chalise P, Chicken E and McGee D. Baseline Age Effect on Parameter Estimates in Cox Model.  Journal of Statistical Computation and Simulation, 82(12):1767-1774, 2012.

9. Hamilton-Reeves J, Bechtel M, Hand Lauren, Schleper A, Yankee T M, Chalise P, Lee E K, Mirza M, Wyre H, Griffin J and Holzbeierlein J. Effects of immunonutrition for cystectomy on immune response and infection rates: a pilot randomized controlled clinical trial. European Urology. 69: 389-392, 2016

10. Breheny P, Chalise P, Batzler A, Wang L and Fridley B. Genetic association studies of copy number variation: should assignment of copy number states precede testing? PLoS ONE 7(4): e34262. doi:10.1371/journal.pone.0034262, 2012.

11. Fridley BL†, Chalise P†, Tsai Y-Y, Sun Z, Vierkant RA, Larson MC, Cunningham JM, Iversen ES, Fenstermacher D, Barnholtz-Sloan J, Asmann Y, Risch HA, Schildkraut JM, Phelan CM, Sutphen R, Sellers TA and Goode EL. Germline copy number variation and ovarian cancer survival. Frontiers in Cancer Genetics, 3:142. doi:10.3389/fgene.2012.00142, 2012.

12. Koestler DC, Chalise P, Cicek MS, Cunningham JM, Armasu S, Larson MC, Chien J, Block M, Kalli KL, Sellers TA, Fridley BL and Goode EL. Integrative genomic analysis identifies epigenetic marks that mediate genetic risk for epithelial ovarian cancer.  BMC Medical Genomics, 7(1) ,8, 2014

13. Hamilton-Reeves J, Stanley A, Bechtel M, Yankee T M, Chalise P, Hand L, Lee E K, Smelser W, Mirza M, Wyre H, Hull H, Carlson SE and Holzbeierlein J. Perioperative immunonutrition modulates inflammatory response after radical cystectomy: results of a pilot randomized controlled clinical trial. Journal of Urology, 200(2), 292-301, doi: 10.1016/j.juro.2018.03.001, 2018

14. Trinca GM, Goodman ML, Papachristou EK, D’Santos CS, Chalise P, Madan R, Slawson C and Hagan C. O-GlcNAc-dependent regulation of progesterone receptor function in breast cancer. Hormones and Cancer 9:12, doi: 10.1007/s12672-017-0310-9, 2018

15. McCracken JM, Chalise P, Briley SM, Dennis KL Jiang L, Duncan FE and Pritchard MT. C57BL/6 sub-strains differentially respond to acute carbon tetrachloride exposure. The Gene Expression – The Journal of Basic Liver Research, doi: 10.3727/105221617X695050, 2017

†: Authors contributed equally to the work


Additional Sites

Department of Statistics, Florida State University,

Tribhuvan University,

American Statistical Association,

Eastern North American Region/International Biometric Society,

International Genetic Epidemiologic Society,


Last modified: Jun 28, 2021


Prabhakar Chalise, Ph.D.
Associate Professor, Department of Biostatistics & Data Science

P: (913) 945-7987