Joseph P. McElroy

Work

The Ohio State University
Center for Biostatistics
2012 Kenny Road
Columbus, OH 43221

Tel: (614) 293-9220

Email:

Education

Postdoctoral-The Ohio State University

Fellow-Comprehensive Cancer Center

2011-Current

Postdoctoral-University of California, San Francisco, CA

Researcher-Department of Neurology

2005-2011Multiple Sclerosis Genetics

Ph.D. July2005Iowa State University, Ames, Iowa

Department of Animal Science

Major: Interdepartmental Genetics

(Specialty: Statistical, Quantitative, and Molecular Genetics)

Co-Major Professors: Jack. C. M. Dekkers, Susan J. Lamont

Thesis: Mapping QTL for Economic Traits in Chickens.

B.S. May 1998University of Rio Grande, Rio Grande, Ohio

Majors: Math, Biology; Minors: Chemistry, Physics

Employment

The Ohio State University Center for Biostatistics – Columbus, OH. June 2011 to present

  • Biostatistical Scientist

The Ohio State University Comprehensive Cancer Center – Columbus OH. June 2011 to present

  • Postdoctoral fellow with Gustavo Leone. Conduct genomic analyses to identify cancer related networks and pathways.

University of California, SF – San Francisco, California. October 2005 to May 2011

  • Postdoctoral researcher with Dr. Jorge Oksenberg. Utilize genomic analysesto identify genetic factors affecting multiple sclerosis susceptibility and severity.

Iowa State University - Ames, Iowa.

  • Graduate Research Assistant (August 1998 - July 2005). Conduct poultry breeding and genome-wide genetic analyses utilizing both quantitative, statistical, and molecular genetics principals and tools, while working toward Doctor of Philosophy degree. Dissertation: Mapping quantitative trait loci for economic traits in chickens.
  • Teaching Assistant (Jan 2002 - May 2002). Undergraduate Animal Breeding, AnSci 352. Enrollment: 25 students. Responsibilities: presenting material, instructing lab, grading homework

Research Interests

  • DNA/RNA sequence analysis
  • Genome-wide association, CNV, and RNA expression analyses

Experience

Analyses

  • Genome-wide association (SNPs, microsatellites, CNVs)
  • Data management
  • File formatting
  • Chip/array QC
  • GenotypingQC
  • Model development
  • Analysis
  • Multiple testing correction
  • Bioinformatics
  • Biological interpretation
  • Summary of results (presentation, lay summary, manuscript, tele/video conference)
  • Copy number variation (whole genome)
  • DNA sequence
  • RNA expression (whole genome)
  • Protein expression
  • Pathway/Network analyses of genome-wide data and results
  • Allele specific expression (whole genome, microarray based)
  • eQTL/genetical genomics
  • Candidate gene analysis
  • Quantitative trait loci analysis (whole genome)
  • Marker assisted selection
  • Survival analysis (disease and censored traits)
  • Line Cross QTL
  • MAS

Programs

  • R/Bioconductor (SNP, CNV, RNA whole genome analyses, data QC)
  • Ingenuity Pathway Analysis
  • Plink (genome-wide analyses, genetic analyses, data QC)
  • JMP Genomics (statistical and genetic analyses, including genome-wide analyses, data QC)
  • Nexus (genome-wide copy number analysis from Biodiscovery)
  • Affymetrix Genotyping Console (genotype calling, chip based QC for genome-wide data)
  • Illumina BeadStudio (genotype calling, chip based QC for genome-wide data)
  • Haploview (linkage disequilibrium analysis)
  • Cytoscape (network analysis of genome-wide SNP, protein, and RNA data)
  • Standard MS Windows and Linux programs (data management, displaying results of analyses, presentations, etc.)
  • MS-Dos (batch running of genomic analysis programs)
  • Bourne Again Shell (BASH) (batch running of genomic analysis programs, data management)

Microarray platforms

  • Affymetrix
  • Illumina
  • Agilent

Awards and Honors

T32fellowinCancerGenetics, 2011-Present

National MS Society Postdoctoral Research Fellowship, 2008-2010

Professional Advancement Grant, 2003

USDA National Needs International Study and Research Graduate Fellowship, 2002

President- Animal Breeding and Genetics Graduate Student Organization, 2000-2001

USDA Food and AgriculturalSciences National Needs Graduate Fellowship, 1998-2002

Activities

San Carlos Tennis Club, San Carlos CA, 2009-2010

Animal Breeding and Genetics Graduate Student Organization, IowaStateUniversity,

1998-2005.

ISU Boxing Club, Iowa State University 2000-2005 (president, 2002-2003)

Member, American Mensa, 1999-present

Professional Development

Short Courses

Applied Survival Analysis. The Ohio State University, Columbus, OH, 2011.

Design and Economics of Animal Breeding Strategies Short Course. IowaState

University, Ames, IA. 2003.

Markov Chain Monte Carlo methods for Quantitative Geneticists Short Course. Iowa

StateUniversity, Ames, IA. June 2000.

Conference Participation

Conference on New Statistical Methods for Next Generation Sequencing Data

Analysis. Iowa State University. May 11, 2012.

Statistical Analyses for Next Generation Sequencing, Birmingham, AL. 2011.

NMSS Tykeson Fellows Conference. San Antonio, TX. 2010.

NMSS Tykeson Fellows Conference. Chicago, IL. 2008.

Genomics of Common Diseases. Broad Institute. Boston, MA. 2008.

Fishman Symposium UCSF, San Francisco, CA. 2007.

Poultry Science Association, Annual Meeting. Madison, WI. 2003.

John M. Airy Beef Cattle Symposium, Visions for Genetics and Breeding, Johnston, IA.

2003.

American Society of Animal Science, Midwest Section meeting. Des Moines, IA, 2003.

Poultry Breeders of American National Breeders Roundtable. St. Louis, MO, 2001, 2002,

2003, 2004.

Seventh World Congress on Genetics Applied to Livestock Production, Montpellier,

France, 2002.

American Society of Animal Science, Midwest Section meeting. Des Moines, IA, 2000,

2002, 2002.

Plant and Animal Genome VIII. San Diego, CA. 2000.

From Jay L. Lush to Genomics: Visions for Animal Breeding and Genetics. Ames, IA,

1999.

Publications

Refereed Articles

Meng, Wei; McElroy, Joseph; Volinia, Stefano; Palatini, Jeff; Warner, Sarah; Ayers, Leona; Palanichamy, Kamalakannan; Chakravarti, Arnab; Lautenschlaeger, Tim. Comparison of MicroRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues. Plos One. Under Revision.

J.P.McElroy,L.Krupp,B.Johnson,J.McCauley,Z.Qi,S.Caillier,P.A.Gourraud,J.Yu,L.Nathanson,A.Belman,S.Hauser,E.Waubant,D.Hedges,J.Oksenberg.2012 CopyNumberVariationinPediatricMultipleSclerosis.Mult. Scler. Dec. 13 [Epub ahead of print]

McElroy,J.P.,NorikoIsobe,Pierre-AntoineF.D.Gourraud,StacyJ.Caillier,TakuyaMatsushita,TatsuoKohriyama,KatsuichiMiyamoto,YujiNakatsuji,TetsuroMiki,StephenL.Hauser,JorgeR.Oksenberg,andJun-ichiKira.2011.SNPBasedAnalysisoftheHLALocusinJapaneseMultipleSclerosisPatients. Genes.Immun.12(7):523-30.

Gelfand,J.M.,B.A.Cree,J.P.McElroy,J.R.Oksenberg,E.Mowry,S.L.Hauser,A.J.Green. 2011.VitaminDinAfrican-AmericanswithMultipleSclerosis. Neurology76(21):1824-30.

Gourraud,P.A.,J.P.McElroy,S.J.Caillier,B.A.Johnson,A.Santaniello,S.L.Hauser,J.R.Oksenberg. 2011.AggregationofMSgeneticriskvariantsinmultipleandsinglecasefamilies.Ann.Neurol69(1):65-74.

McElroy,J.P.andJ.R.Oksenberg. MultipleSclerosisGenetics2010. Neurol.Clinics.29(2):219-31.

Cree, B. A. C., J. D. Rioux, J. L. McCauley, P. A. F. D. Gourraud, P. Goyette, J. P. McElroy, P. De Jager, A. Santaniello, T. J. Vyse, P. K. Gregersen, D. Mirel, D. A. Hafler, J. L. Haines, M. A. Pericak-Vance, A. Compston, S. J. Sawcer, J. R. Oksenerg, S. L. Hauser, IMAGEN, IMSGC. 2010. A Major Histocompatibility Class I Locus Contributes to Multiple Sclerosis Susceptibility Independently from HLA-DRB1*15:01. Plos One5: e11296.

McElroy, J. P., B. A. C. Cree, S. J. Caillier, P. K. Gregersen, J. Herbert, O. A. Khan, J. Freudenberg, A. Lee, S. L. Bridges, Jr., S. L. Hauser, J. R. Oksenberg, and P. A. Gourraud. 2010. Refining the association of MHC with multiple sclerosis in African Americans. Hum. Mol. Genet. 19 (15): 3080-8.

Baranzini S. E., J. Mudge, J. C. van Velkinburgh, P. Khankhanian, I. Khrebtukova, N. A. Miller, L. Zhang, A. D. Farmer, C. J. Bell, R. W. Kim, G. D. May, J. E. Woodward, S. J. Caillier, J. P. McElroy, R. Gomez, M. J. Pando, L. E. Clendenen, E. E. Ganusova, F. D. Schilkey, T. Ramaraj, O. A. Khan, J. J. Huntley, S. Luo, P. Y. Kwok, T. D. Wu, G. P. Schroth, J. R. Oksenberg, S. L. Hauser, and S. F. Kingsmore.2010.Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 464: 1351-1356.

McElroy, J. P., M. R. Nelson, S. J. Caillier, and J. R. Oksenberg. 2009. Copy number variation in African Americans. BMC Genet. 10:15.

McElroy, J. P., and J. R. Oksenberg. 2008. Multiple sclerosis genetics. Curr. Top. Microbiol. Immunol. 318:45-72.

McElroy, J. P., W. Zhang, K. J. Koehler, S. J. Lamont, and J. C. M. Dekkers. 2006. Comparison of methods for analysis of selective genotyping survival data. Genetics, Selection, and Evolution 38(6):637-655.

McElroy, J. P., J.-J. Kim, D. E. Harry, S. Brown, J. C. M. Dekkers, and S. J. Lamont. 2006. Identification of trait loci affecting white meat percent and other growth and carcass traits in commercial broiler chickens. Poultry Science 85:593–605.

McElroy, J. P., J. C. M. Dekkers, J. E. Fulton, N. P. O'Sullivan, M. Soller, E. Lipkin, W. Zhang, K. J. Koehler, S. J. Lamont, and H. H. Cheng. 2005. Microsatellite markers associated with resistance to Marek’s disease in layer chickens. Poultry Science 84:1678–1688.

McElroy, J. P., D. E. Harry, J. C. M. Dekkers, and S. J. Lamont. Molecular markers associated with growth and carcass traits in meat-type chickens. Proc. 7th World Congress on Genetics Applied to Livestock Production. Montpelier, France. 2002. Aug. 19-23.

Abstracts

McElroy, J. P., and J. R. Oksenberg. Genetic analysis of multiple sclerosis susceptibility in African Americans. NMSS Tykeson Fellows Conference. San Antonio, TX. 2010.

McElroy, J. P., S. L. Hauser, B. A. C. Cree, and J. R. Oksenberg. Genome-wide scan for multiple sclerosis in African Americans. First NMSS Tykeson Fellows Conference. Chicago, IL. 2008.

McElroy, J. P., S. L. Hauser, and J. R. Oksenberg. Genomic Copy Number Variation in Multiple Sclerosis. Fishman Symposium UCSF, San Francisco, CA. 2007.

McElroy, J. P., S. Baranzini, and J. R. Oksenberg. Genetic control of differential transcription between females and males. UCSF Neurology MS Conference. 2006.

McElroy, J. P., J. C. M. Dekkers, J. E. Fulton, N. P. O'Sullivan, M. Soller, E.

Lipkin, W. Zhang, K. J. Koehler, S. J. Lamont, and H. H. Cheng. Microsatellite markers associated with Marek’s disease survival in commercial layer chickens. The Third International Symposium on Genetics of Animal Health. 2005.

McElroy, J. P., W. Zhang, K. J. Koehler, S. J. Lamont, and J. C. M. Dekkers.

Comparison of Cox, Weibull, and Linear Regression Models to Detect Marker Associations with Survival Traits using Full and Selective Genotyping. Plant and Animal Genome XIII, 2005.

McElroy, J. P., H. H. Cheng, J. Fulton, M. Soller, E. Lipkin, J. C. M. Dekkers,

and S. J. Lamont. Markers Associated with Marek’s Disease Survival in Commercial Layers. Poultry Science Association 92nd Annual Meeting. P.24, #99.

McElroy, J. P., S. J. Lamont, and J. C. M. Dekkers. Marker Linkage Analysis of

Selective Genotyping Survival Data. The John M. Airy Beef Cattle Symposium: Visions for Genetics and Breeding. p. 133, #7.

McElroy, J. P., H. Zhou, J. C. M. Dekkers, and S. J. Lamont. Accuracy of DNA Pooling to Estimate Microsatellite Allele Frequency. J. Anim. Sci. 78, Suppl. 1: 77.

Current Topics of Research

  • Genetic Cross-species Ortholog Translation
  • Weighted Pathway Analysis
  • Protein Array Binding Analysis
  • DNA/RNA Sequence Analysis
  • SNP Imputation
  • C. elegans RNAi Analysis
  • Cluster Analysis
  • Copy Number Variation Analysis
  • miRNA Seq Analysis