Alex Frase

he/they

frase@umn.edu

LATIS

110 Anderson Hall

257 19th Ave. SE
Minneapolis, MN 55455

Collegiate Affiliation

Software Developer,

LATIS

Educational Background & Specialties
Publications

Educational Background & Specialties

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Educational Background

B.A.: Computer Science, Integrated Liberal Studies, University of Wisconsin, 2005

Specialties

Software Development (Python, Lua, PHP, Java, C#, C, OpenCL)
Web Application Development (Javascript, CSS, HTML, Rails)
Database and Query Development (Oracle, MySQL, SQLite, MSSQL)
High Performance Cluster Computing Support
Advanced Spreadsheet Programming (LibreOffice, Google Sheets, Excel)

Publications

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Publications

Singhal P, Veturi Y, Dudek SM, Lucas A, Frase A, van Steen K, Schrodi SJ, Fasel D, Weng C, Pendergrass R, Schaid DJ, Kullo IJ, Dikilitas O, Sleiman PMA, Hakonarson H, Moore JH, Williams SM, Ritchie MD, Verma SS. Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets. Am J Hum Genet. 2023 Apr 6;110(4):575-591. doi: 10.1016/j.ajhg.2023.03.007. PMID: 37028392; PMCID: PMC10119154.
Pendergrass SA, Buyske S, Jeff JM, Frase A, Dudek S, Bradford Y, Ambite JL, Avery CL, Buzkova P, Deelman E, Fesinmeyer MD, Haiman C, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Lin Y, Le Marchand L, Matise TC, Monroe KR, Moreland L, North KE, Park SL, Reiner A, Wallace R, Wilkens LR, Kooperberg C, Ritchie MD, Crawford DC. A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. PLoS One. 2019 Dec 31;14(12):e0226771. doi: 10.1371/journal.pone.0226771. PMID: 31891604; PMCID: PMC6938343.
Basile AO, Byrska-Bishop M, Wallace J, Frase AT, Ritchie MD. Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants. Bioinformatics. 2018 Feb 1;34(3):527-529. doi: 10.1093/bioinformatics/btx559. PMID: 28968757; PMCID: PMC5860358.
Kim D, Lucas A, Glessner J, Verma SS, Bradford Y, Li R, Frase AT, Hakonarson H, Peissig P, Brilliant M, Ritchie MD. Biofilter as a functional annotation pipeline for common and rare copy number burden. Pac Symp Biocomput. 2016;21:357-68. PMID: 26776200; PMCID: PMC4722964.
Verma A, Leader JB, Verma SS, Frase A, Wallace J, Dudek S, Lavage DR, Van Hout CV, Dewey FE, Penn J, Lopez A, Overton JD, Carey DJ, Ledbetter DH, Kirchner HL, Ritchie MD, Pendergrass SA. Integrating clinical laboratory measures and ICD-9 code diagnoses in phenome-wide association studies. Pac Symp Biocomput. 2016;21:168-79. PMID: 26776183; PMCID: PMC4718547.
Verma SS, Frase AT, Verma A, Pendergrass SA, Mahony S, Haas DW, Ritchie MD. Phenome-wide interaction study (PheWIS) in AIDS Clinical Trials Group data (ACTG). Pac Symp Biocomput. 2016;21:57-68. PMID: 26776173; PMCID: PMC4722952.
Moore CCB, Basile AO, Wallace JR, Frase AT, Ritchie MD. A biologically informed method for detecting rare variant associations. BioData Min. 2016 Aug 30;9(1):27. doi: 10.1186/s13040-016-0107-3. PMID: 27582876; PMCID: PMC5006419.
Butkiewicz M, Cooke Bailey JN, Frase A, Dudek S, Yaspan BL, Ritchie MD, Pendergrass SA, Haines JL. Pathway analysis by randomization incorporating structure-PARIS: an update. Bioinformatics. 2016 Aug 1;32(15):2361-3. doi: 10.1093/bioinformatics/btw130. Epub 2016 Mar 7. PMID: 27153576; PMCID: PMC4965631.
Kim D, Li R, Dudek SM, Frase AT, Pendergrass SA, Ritchie MD. Knowledge-driven genomic interactions: an application in ovarian cancer. BioData Min. 2014 Sep 9;7:20. doi: 10.1186/1756-0381-7-20. PMID: 25214892; PMCID: PMC4161273.
Holzinger ER, Dudek SM, Frase AT, Pendergrass SA, Ritchie MD. ATHENA: the analysis tool for heritable and environmental network associations. Bioinformatics. 2014 Mar 1;30(5):698-705. doi: 10.1093/bioinformatics/btt572. Epub 2013 Oct 21. PMID: 24149050; PMCID: PMC3933870.
Pendergrass SA, Frase A, Wallace J, Wolfe D, Katiyar N, Moore C, Ritchie MD. Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development. BioData Min. 2013 Dec 30;6(1):25. doi: 10.1186/1756-0381-6-25. PMID: 24378202; PMCID: PMC3917600.
Holzinger ER, Dudek SM, Frase AT, Krauss RM, Medina MW, Ritchie MD. ATHENA: a tool for meta-dimensional analysis applied to genotypes and gene expression data to predict HDL cholesterol levels. Pac Symp Biocomput. 2013:385-96. PMID: 23424143; PMCID: PMC3587764.
Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD. Using BioBin to explore rare variant population stratification. Pac Symp Biocomput. 2013:332-43. PMID: 23424138; PMCID: PMC3638724.
Moore CB, Wallace JR, Wolfe DJ, Frase AT, Pendergrass SA, Weiss KM, Ritchie MD. Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PLoS Genet. 2013;9(12):e1003959. doi: 10.1371/journal.pgen.1003959. Epub 2013 Dec 26. PMID: 24385916; PMCID: PMC3873241.
Pendergrass SA, Brown-Gentry K, Dudek S, Frase A, Torstenson ES, Goodloe R, Ambite JL, Avery CL, Buyske S, Bůžková P, Deelman E, Fesinmeyer MD, Haiman CA, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Kooperberg C, Le Marchand L, Lin Y, Matise TC, Monroe KR, Moreland L, Park SL, Reiner A, Wallace R, Wilkens LR, Crawford DC, Ritchie MD. Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network. PLoS Genet. 2013;9(1):e1003087. doi: 10.1371/journal.pgen.1003087. Epub 2013 Jan 31. PMID: 23382687; PMCID: PMC3561060.
Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD. BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. BMC Med Genomics. 2013;6 Suppl 2(Suppl 2):S6. doi: 10.1186/1755-8794-6-S2-S6. Epub 2013 May 7. PMID: 23819467; PMCID: PMC3654874.