Gregory R. Warnes, Ph.D.
firstname.lastname@example.org – 585-678-6661
Computational Biostatistician – Statistical Analyst – Statistical Methods Developer – Computational Scientist
Skilled biostatistical analyst, statistical methods developer, software developer, and expert in the R statistical analysis system with a broad scientific background, deep technical understanding of advanced biomedical technologies, and solid experience in pre-clinical pharmaceutical and academic research environments. A fascination with biomedical research problems results in collaborative relationships with scientists that extend beyond statistical support to focus on solving the underlying scientific research problems. Excels at communication across scientific, technical, business, and cultural communities, and a demonstrated record of improving efficiency and scientific impact by developing and improving tools and processes. Experience in leadership, organizational development, and management of diverse technical and scientific teams.
Native English, Fluent French, Survival German
Hulin Wu; Hongyu Miao; Warnes, G.R.; Canglin Wu; LeBlanc, A.; Dykes, C.; Demeter, L.M. "DEDiscover: A Computation and Simulation Tool for HIV Viral Fitness Research," BioMedical Engineering and Informatics, 2008. BMEI 2008. International Conference on , vol.1, no., pp.687-694, 27-30 May 2008
Kooner JS, Chambers JC, Aguilar-Salina CA, et al. "Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides in man,” Nature Genetics, 40, 149 - 151 (2008).
Burrows RB, Warnes GR, Hanumara RC. "Statistical Modeling of Biochemical Pathways,” IET Systems Biology, IET Syst. Biol. 1, 353 (2007)
Mank-Seymour AR, Richmond JL, Wood LS, Reynolds JM, Fan Y, Warnes GR, Milos MP, Thompson JF. "Association of torsades de pointes with novel and known single nucleotide polymorphisms in long QT syndrome genes," American Heart Journal, Volume 152, Issue 6, Pages 1116-1122, August 2006
Warnes GR. “Sample Size Estimation for Microarray Experiments using the SSIZE package,” R News, Volume 6, Issue 5, pp. 64-68, December 2006.
Caba E, Dickinson DA, Warnes GR, Aubrecht J. “Differentiating mechanisms of toxicity using global gene expression analysis in Saccharomyces cerevisiae,” Special Issue on EEMS 2004, Mutation Research, Volume 575, Issues 1-2, Aug. 2005, Pages 34-46.
DEDiscover: High-quality software application that enables biologists and physicians to model biological processes using systems of ordinary and delay differential equations. - https://cbim.urmc.rochester.edu/software/dediscover
MiDAS: Web-based system based on the scientific workflow that allows scientists, lab staff, and statisticians to store, manage, process, and analyze mRNA microarray data using best-available statistical, graphical, and computational technologies based on R, Zope, and RStatServer
RStatServer: System for quickly developing and deploying web applications that integrate statistical computations and graphics using R. Includes Python, R & Zope packages RSessionDA, Rpy, RSOAP, SOAPpy, and fpconst.
R Packages: General tools: gregmisc, gtools, gdata, gmodels, gplots, namespace, SASxport, session – Statistical genetics & genomics: genetics, GeneticsBase, GeneticsDesign, GeneticsPed, GeneticsQC, fbat, ssize, qvalue - Parallel computing: fork, Rlsf - Audiology: SII - MCMC Diagnostics: mcgibbsit.
Hulin Wu; Hongyu Miao; Warnes, G.R.; Canglin Wu; LeBlanc, A.; Dykes, C.; Demeter, L.M. "DEDiscover: A Computation and Simulation Tool for HIV Viral Fitness Research," BioMedical Engineering and Informatics, 2008. BMEI 2008. International Conference on , vol.1, no., pp.687-694, 27-30 May 2008 http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4548758&isnumber=4548615
Kooner JS, Chambers JC, Aguilar-Salina CA, et al. “Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides in man”, Nature Genetics, 40, 149 - 151 (2008). http://www.nature.com/ng/journal/v40/n2/full/ng.2007.61.html
Burrows RB, Warnes GR, Hanumara RC. “Statistical Modeling of Biochemical Pathways”, IET Systems Biology, IET Syst. Biol. 1, 353 (2007) http://www.sciencedirect.com/science/article/B6T2C-4C4C52R-1/2/b405d51f9c53f02c012b72296796927a
Mank-Seymour AR, Richmond JL, Wood LS, Reynolds JM, Fan Y, Warnes GR, Milos MP, Thompson JF. “Association of torsades de pointes with novel and known single nucleotide polymorphisms in long QT syndrome genes.” American Heart Journal, Volume 152, Issue 6, Pages 1116-1122, August 2006 http://www.mdconsult.com/das/article/body/214469302-2/jorg=journal&source=&sp=16680575&sid=0/N/561766/s0002870306007605.pdf?issn=0002-8703
Warnes GR. “Sample Size Estimation for Microarray Experiments using the SSIZE package”, R News, Volume 6, Issue 5, pp. 64-68, December 2006. http://cran.r-project.org/doc/Rnews/Rnews_2006-5.pdf
Warnes GR, Jain N. “Balloonplot: A graphical tool for displaying tabular data”, R News, Volume 6, Issue 2, May 2006. http://cran.r-project.org/doc/Rnews/Rnews_2006-2.pdf
Warnes GR, Liu P. “Sample Size Estimation for Microarray Experiments”, Technical report 06/06, Department of Biostatistics and Computational Biology, University of Rochester, 2006. (also submitted to Bioinformatics) http://www.urmc.rochester.edu/biostat/people/faculty/documents/0606_warnes_liu.pdf
Caba E, Dickinson DA, Warnes GR, Aubrecht J. “Differentiating mechanisms of toxicity using global gene expression analysis in Saccharomyces cerevisiae,” Special Issue on EEMS 2004, Mutation Research, Volume 575, Issues 1-2, Aug. 2005, Pages 34-46. http://www.sciencedirect.com/science/article/B6T2C-4G3CX6K-1/2/b86f0d9d41a37bd2a6e805c423b4f32f
Warnes GR. “RSOAP - Using “R” with Python,” PyZine, Volume 11, Issue 05, Apr. 2004. http://www.pyzine.com/Issue005/Section_Articles/article_RSOAP.html
Dickinson DA, Warnes GR, Quievryn G, Messer J, Zhitkovich A, Rubitski E, and Jiri A. “Differentiation of DNA-reactive and non-reactive genotoxic mechanisms using gene expression profile analysis”, Mutation Research, Volume 549, Issues 1-2, May 2004, Pages 29-41. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.78.4690&rep=rep1&type=pdf#page=35
Warnes GR. “The Genetics Package,” R News, Volume 3, Issue 1, Jun. 2003. http://cran.r-project.org/doc/Rnews/Rnews_2003-1.pdf
Warnes GR. “The Gregmisc Package: Something for Everyone” submitted to R News. http://www.warnes.net/Research/Publications/gregmisc.pdf
Warnes GR. “HYDRA: A Java library for Markov Chain Monte Carlo,” Journal of Statistical Software, Volume 7, Issue 4, Mar. 2002. http://www.jstatsoft.org/v07/i04/
Warnes GR. “The Normal Kernel Coupler: An adaptive Markov Chain Monte Carlo method for efficiently sampling from multi-modal distributions,” submitted to Journal of the American Statistical Association, currently in revision.
Yanez ND, Warnes GR, and Kronmal RA. “A Univariate Measurement Error Model for Longitudinal Change,” Communications in Statistics, Volume 30, Issue 2, 2001. http://dx.doi.org/10.1081/STA-100002031
Warnes GR. “The Normal Kernel Coupler: An adaptive Markov Chain Monte Carlo method for efficiently sampling from multi-modal distributions,” Technical Report no. 395, Department of Statistics, University of Washington, Apr. 2001. http://www.stat.washington.edu/research/reports/2001/tr395.pdf
Warnes GR. “HYDRA: A Java library for Markov Chain Monte Carlo,” Technical Report no. 394, Department of Statistics, University of Washington, Apr. 2001. http://www.stat.washington.edu/research/reports/2001/tr394.pdf
Warnes GR. “The Normal Kernel Coupler: An adaptive Markov Chain Monte Carlo method for efficiently sampling from multi-modal distributions,” Ph.D. thesis, Department of Biostatistics, University of Washington, Oct. 2000. http://www.warnes.net/Research/Publications/Warnes_Thesis.
Warnes GR. “SII” This R package calculates ANSI S3.5-1997 Speech Intelligibility Index (SII), a standard method for computing the intelligibility of speech from acoustical measurements of speech, noise, and hearing thresholds. http://cran.r-project.org/package=SII, 2010-
Warnes GR. “SASxport”: This R package provides functions for reading, listing the contents of, and writing SAS xport format files, fully supporting translation between R “factor” objects and SAS FORMAT labels. http://cran.r-project.org/package=SASxport, 2007-
Warnes GR, Miao H, Wu C, LeBlanc, Wu H. “DEDiscover” a cross-platform software tool for differential equation model simulation and estimation, designed with special attention to the features necessary for modeling the interaction between the human immune system and viruses. https://cbim.urmc.rochester.edu/software/dediscover, 2007-
Qiu W, Lazarus R, Warnes GR, Jain N.“GeneticsQC”, a package of classes and functions for the open-source statistical package R that checks the quality of a genetics data set (as a geneSet object), such as reporting the counts of missing genotypes for markers or for subjects, checking Mendelian errors, testing Hardy-Weinberg Equilibrium (HWE), etc. This package also provides functions to filter out low-quality markers, subjects, and/or families. http://r-genetics.org, 2007-
Warnes GR, Duffy D, Man M, Qiu W, Lazarus R. “GeneticsDesign”, a package for the open-source statistical package R that provides classes and functions for designing genetics studies, including power and sample-size calculations. http://bioconductor.org/packages/2.6/bioc/html/GeneticsDesign.html, 2007-
Qiu W, Lazarus R, Warnes GR, Jain N. “fbat”, a package for the open-source statistical software package R that implements a broad class of Family Based Association Tests for genetics data, with adjustments for population admixture using the code from the 'FBAT' software program. http://bioconductor.org/packages/2.6/bioc/html/fbat.html, 2006-
Warnes GR, Lazarus R, Chasalow SD, Montana G, O'Connel M, Cheng J, Jain N. “GeneticsBase”, a package for the open-source statistical package R that provides classes and functions for handling and analyzing large scale genetic data (up to 1e6 markers) http://bioconductor.org/packages/2.6/bioc/html/GeneticsBase.html, 2005
Warnes GR. “WardListing”, a tool for downloading LDS Ward Membership information from the official LDS web site, and translating it into formats appropriate for importing into address book software. http://www.warnes.net/Software/WardListing, 2005-
Smith CR and Warnes GR. “Rlsf”, a package of functions for the open-source statistical package R that provides functions for using R with the LSF cluster/grid queuing system. http://cran.r-project.org/package=Rlsf, 2005-
Warnes GR and Li F. “ssize”, a package of functions for the open-source statistical package R that provides functions for computing and displaying sample size information for gene expression arrays. http://bioconductor.org/packages/2.6/bioc/html/ssize.html, 2004-
Warnes GR. “fork”, a package of functions for the open-source statistical package R that provide simple wrappers around the Unix process management API calls: fork, wait, waitpid, kill, and _exit. This enables construction of R programs that utilize multiple concurrent processes. http://cran.r-project.org/package=fork, 2003-
Warnes GR. “fpconst”, a Python library providing constants and functions for creating and detecting IEEE 754 the floating point special values. http://research.warnes.net/projects/RStatServer/fpconst, 2003-
Warnes GR. “CSVFile”, objects for the open-source web application development system Zope which automatically detecting and translating Microsoft Excel files into comma-delimited text files when uploaded. http://research.warnes.net/projects/RStatServer/csvfile/, 2003-
Warnes GR. “RSessionDA”, a Python module to allow Zope access to the features of the open-source statistical package/language R. http://research.warnes.net/projects/RStatServer/rsessionda/, 2003-
Warnes GR. “session”, a package of function for open-source statistical package R that permit the state of the R session to be saved and restored, as well as functions for capturing the result of evaluating strings containing R commands and capturing the output. http://cran.r-project.org/package=session, 2002-
Warnes GR. “RSOAP”, a server providing access to the features of the open-source statistical package R via the SOAP protocol. http://research.warnes.net/projects/RStatServer/rsoap/, 2002-
Warnes GR and Leisch F. “genetics”, a package for handling marker-based genetic data within the open-source statistical package R. The package includes function to compute allele frequencies, use genetic markers in statistical models, estimate disequilibrium, and test for departure from Hardy-Weinberg equilibrium. http://cran.r-project.org/package=genetics, 2002-
Warnes GR et al. “gregmisc”, a package of useful utility functions for the open-source statistical package R. Most functions in the gregmisc library fall into five general areas: permutations and combinations, tools for linear models, plots, data manipulation, and fixed or extended versions of existing functions. http://cran.r-project.org/package=gregmisc, 2001-
Warnes GR. “DistLib”, an Java library containing classes for computing features of and generating random numbers from a variety of statistical distribution functions. http://statdistlib.sourceforge.net/, 2000-
Warnes GR. “mcgibbsit”, a package for the open-source statistical package R implementing the MCGIBBSIT diagnostic software for multiple (potentially interrelated) MCMC samplers. http://cran.r-project.org/package=mcgibbsit, 2000-
Warnes GR. “HYDRA”, an open-source, platform-neutral library for performing Markov Chain Monte Carlo. It implements the logic of standard MCMC samplers within a framework designed to be easy to use and to extend while allowing integration with other software tools. http://research.warnes.net/projects/mcmc/hydra, 2000-
Warnes GR. “ClusterNFS”, an NFS server that allows diskless NFS clients to share a common file system by providing for host, user, and group-specific files within the same directory structure via interpreted file name extensions. http://ClusterNFS.sourceforge.net, 1999-