Cavan S. Reilly

Professor

Division of Biostatistics

I received a Ph.D. (2000) and an M.S. (1997) from the Department of Statistics at Columbia University, an M.A. in Economics at the New School for Social Research (1995) and a B.S. (1993) in Sociology from the University of Minnesota, Twin Cities. In the past I have focused on longitudinal analysis for high dimensional data and low level analysis of -omics data, mostly from a Bayesian perspective. Currently most of my work is in clinical trials and observational studies in infectious disease, with emphases on Ebola and HIV/AIDS. For full CV: pdf

Courses

PubH 8401-Linear Models. (Fall 2022)

Software

1 dimensional morphing software C code
2 dimensional morphing software C code
Some Bayesian microarray normalization software C code and info
max Kappa statistic info C code
nonparametric analysis of microarray time course experiments C code
Software for Bayesian inference with the Metropolis algorithm info C code e.g. file e.g. file e.g. file e.g. file
neighbor density variogram estimation in R info C code
Microarray quality assessment in R info and code
Semiparametric association tests for QTLs in structured populations in C++ C++ code C++ header file
Mass spectrometry calibration software C++ code info example data example data example data header file header file header file header file header file header file
Metagenomic taxonomic decomposition software
User guide

Executable

C++ source code

Books

"Statistics in Human Genetics and Molecular Biology" Cavan Reilly (2009), Chapman Hall/CRC Press

Supplementary Online Resources

Appendices for Determination of SIV production by infected activated and resting cells pdf
data set for the analysis of virus production (first column is activated cells, second is resting) txt
software for analysis of virus production C code
posterior modes and initial values for analysis of virus production txt

Selected research papers

Reilly, C., Gelman, A. and J. Katz (2001), "Post-stratification without population level information on the post-stratifying variable, with application to political polling", Journal of the American Statistical Association, 96, 1-11. ps
Raghavan, A., Ogilvie, R., Reilly, C., Abelson, M., Raghavan, S., Vasdewani, J., Krathwohl, M. and Bohjanen, P. (2002), "Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes", Nucleic Acids Research, 30, 5529-5538. pdf
Reilly, C., Schacker, T., Haase, A., Wietgrefe, S. and Krason, D. (2002), "The clustering of infected SIV cells in lymphatic tissue", Journal of the American Statistical Association, 97, 943-954. pdf
Reilly, C., Wang, C., and Rutherford, M. (2003), "A method for normalizing microarrays using the genes that are not differentially expressed", Journal of the American Statistical Association, 98, 868-878. pdf
Zhang, Z. Q., Wietgrefe, S., Li, Q., Shore, M., Lljie, D., Reilly, C., Lifson, J., Haase, A. (2004), "Roles of Target Cell Availability, Susceptibility and Productive Infection of Resting and Activated CD4+ T Cells in Transmission and Acute SIV Infection", Proceedings of the National Academy of the Sciences, USA, 101, 5640-5645.
Reilly, C., Price, P., Gelman, A., Sandgrathe, S. (2004), "Using image and curve registration for measuring the goodness of fit of spatial and temporal predictions", Biometrics , 60, 954-964. ps
Reilly, C. (2005), "A nonparametric approach to the analysis of longitudinal data via a set of level crossing problems with application to the analysis of microarray time course experiments" Biostatistics , 6, 271-278. html/pdf
Li Q, Duan, L, Estes, J, Ma Z-M, Rourke T, Wang Y, Reilly C, Carlis J, Miller C, Haase A (2005), "Peak SIV replication in resting memory CD4+ T cells depletes gut lamina propria CD4+ T cells", Nature, 434, 1148-1152. html
Hataye J, Moon JJ, Khoruts A, Reilly C, Jenkins MK (2006), "Naive and memory CD4+ T cell survival controlled by clonal abundance", Science, 312, 114-116.
Reilly C, Wietgrefe S, Sedgewick G, Haase A (2007), "Determination of simian immunodeficiency virus production by infected activated and resting cells", AIDS, 21, 163-168.
Larsson O, Perlman DM, Fan D, Reilly C, Peterson M, Dahlgren C, Liang Z, Li S, Polunovsky VA, Wahlestedt C, Bitterman P (2007), ``Apoptosis resistance downstream of eIF4E: posttranscriptional activation of an anti-apoptotic transcript carrying a consensus hairpin structure'', Nucleic Acids Research , 34, 4375-4392.
Reilly C, Miller MB, Liu Y, Oetting WS, King R, Blumenthal M (2007), ``Linkage analysis of a cluster-based quantitative phenotype constructed from pulmonary function test data in 27 multigenerational families with multiple asthmatic members'', Human Heredity , 64, 136-145.
Reilly, C., Gelman, A., (2007), "Weighted variogram estimation for data with clustering", Technometrics , 49, 184-195.
Xiao, G., Reilly, C., Khodursky, AB., (2009), "Improved detection of differentially expressed genes through incorporation of gene locations", Biometrics , 65, 805-814.
Li Q, Estes JD, Schlievert PM, Duan L, Brosnahan AJ, Southern PJ, Reilly CS, Peterson ML, Schultz-Darken N, Brunner KG, Nephew KR, Pambuccian S, Lifson JD, Carlis JV, Haase AT (2009),"Glycerol monolaurate prevents mucosal SIV transmission", Nature , 458, 1034-1038.
Kong X, Reilly C (2009), "A Bayesian approach to the alignment of mass spectra", Bioinformatics , 25, 3213-322.
Cavan Reilly
email: cavanr@biostat.umn.edu
phone: 612.624.9644; fax: 612.626.0660
postal address:
Coordinating Centers for Biometric Research
Division of Biostatistics
School of Public Health
2221 University Ave SE, Suite 200
Minneapolis, MN 55414