Biomedical and Translational Informatics Laboratory

Alex Frase

alex opt

 


Software Developer

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Current Projects

Biofilter
Athena
BioBin

Education

B.A. in Computer Science
University of Wisconsin – Madison
2001-2005

Work Experience


Software Developer
The Wedge Community Co-op
2007-2011

 

Anastasia Lucas

ana opt

 

Analyst

A301 Richard Building                                                                                                                                      3700 Hamilton Walk, Philadelphia, PA 19104

 

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Current Projects

Environment-Wide Association Study on autism, Copy Number Variation burden analysis

Education

BS Biostatistics
The Pennsylvania State University
2011-2015

Anurag Verma


Lead Bioinformatics Scientist

A301 Richards Building
3700 Hamilton Walk, Philadelphia, PA 19104

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Current Projects

Exploring and analyzing complex trait associations in Electronic Medical Record(EMR) linked bio-repositories using Phenome-Wide Association Studies (PheWAS).

Education

        PhD Bioinformatics and Genomics
        The Pennsylvania State University
        2014-2017

MS Bioinformatics
New Jersey Institute of Technology
2008-2010

Publications

Google Scholar

  • 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 labaratory measures and ICD-9 code diagnosis in Phenomw-Wide Association Studies. Pac Symp Biocomput. 2016;21:168-79.
  • Pendergrass SA, Verma A, Okula A, Hall MA, Crawford DC, Ritchie MD. Phenome-Wide Association Studies: Embracing Complexity for Discovery. Hum Hered. 2015;79(3-4):111-23. doi: 10.1159/000381851. Epub 2015 Jul 28. PubMed PMID: 26201697.
  • Moore CB*, Verma A*, Pendergrass S, Verma SS, Johnson DH, Daar ES, Gulick RM, Haubrich R, Robbins GK, Ritchie MD, Haas DW. Phenome-wide Association Study Relating Pretreatment Laboratory Parameters With Human Genetic Variants in AIDS Clinical Trials Group Protocols. Open Forum Infect Dis. 2015 Jan 9;2(1):ofu113. doi: 10.1093/ofid/ofu113. eCollection 2015 Jan. PubMed PMID: 25884002; PubMed Central PMCID: PMC4396430.
  • Hall MA, Verma A, Brown-Gentry KD, Goodloe R, Boston J, Wilson S, McClellan B, Sutcliffe C, Dilks HH, Gillani NB, Jin H, Mayo P, Allen M, Schnetz-Boutaud N, Crawford DC, Ritchie MD, Pendergrass SA. Detection of pleiotropy through a Phenome-wide association study (PheWAS) of epidemiologic data as part of the Environmental Architecture for Genes Linked to Environment (EAGLE) study. PLoS Genet. 2014 Dec 4;10(12):e1004678. doi: 10.1371/journal.pgen.1004678. eCollection 2014 Dec. PubMed PMID: 25474351; PubMed Central PMCID: PMC4256091.
  • Barrie ES, Weinshenker D, Verma A, Pendergrass SA, Lange LA, Ritchie MD, Wilson JG, Kuivaniemi H, Tromp G, Carey DJ, Gerhard GS, Brilliant MH, Hebbring SJ, Cubells JF, Pinsonneault JK, Norman GJ, Sadee W. Regulatory polymorphisms in human DBH affect peripheral gene expression and sympathetic activity. Circ Res. 2014 Dec 5;115(12):1017-25. doi: 10.1161/CIRCRESAHA.116.304398. Epub 2014 Oct 17. PubMed PMID: 25326128; PubMed Central PMCID: PMC4258174.
  • Kim D, Shin H, Sohn KA, Verma A, Ritchie MD, Kim JH. Incorporating inter-relationships between different levels of genomic data into cancer clinical outcome prediction. Methods. 2014 Jun 1;67(3):344-53. doi: 10.1016/j.ymeth.2014.02.003. Epub 2014 Feb 18. PubMed PMID: 24561168; PubMed Central PMCID: PMC4664202.
  • Patel V, Wang JT, Setia S, Verma A, Warden CD, Zhang K. On comparing two structured RNA multiple alignments. J Bioinform Comput Biol. 2010 Dec;8(6):967-80.

Conferences

  • 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 labaratory measures and ICD-9 code diagnosis in Phenomw-Wide Association Studies. at 2016 Pacific Symposium of Biocomputing, Big Island, Hawaii, USA
  • Anurag Verma, Shefali S. Verma, Sarah A. Pendergrass, Dana C. Crawford, David R. Crosslin, Helena Kuivaniemi, William S. Bush, Yuki Bradford, Iftikhar Kullo, Sue Bielinski, Rongling Li, Joshua C. Denny, Peggy Peissig, Scott Hebbring, Elizabeth Pugh, Mariza de Andrade, Marylyn D. Ritchie, Gerard Tromp. eMERGE Phenome-Wide Association Study (PheWAS) Identifies Clinical Associations and Pleiotropy for Functional Variants at 2015 Translational Bioinformatics Conference, Tokyo, Japan (Platform Presentation)
  • Anurag Verma, Shefali S. Verma, Sarah A. Pendergrass, Dana C. Crawford, David R. Crosslin, Helena Kuivaniemi, William S. Bush, Yuki Bradford, Iftikhar Kullo, Sue Bielinski, Rongling Li, Joshua C. Denny, Peggy Peissig, Scott Hebbring, Elizabeth Pugh, Mariza de Andrade, Marylyn D. Ritchie, Gerard Tromp. eMERGE Phenome-Wide Association Study (PheWAS) Identifies Clinical Associations and Pleiotropy for Functional Variants at 2015 Biology of Genome, Cold Spring Harbor, New York, USA (Poster Presentation)
  • Anurag Verma, Shefali S. Verma, Sarah A. Pendergrass, Dana C. Crawford, David R. Crosslin, Helena Kuivaniemi, William S. Bush, Yuki Bradford, Iftikhar Kullo, Sue Bielinski, Rongling Li, Joshua C Denny, Peggy Peissig, Scott Hebbring, Elizabeth Pugh, Mariza de Andrade, Marylyn D. Ritchie, Gerard Tromp eMERGE PhenomeWide Association Study (PheWAS) Identifies Clinical Associations and Pleiotropy for Functional Variants at 2014 American Society of Human Genetics, San Diego, USA (Poster presentation)
  • Anurag Verma*, Carrie Buchanan Moore*, Dan Johnson, Sarah A. Pendergrass, David Haas, Marylyn Ritchie A Phenome-Wide Association Study of Numerous Laboratory Phenotypes in AIDS Clinical Trials Group (ACTG) Protocols at 2014 American Society of Human Genetics, San Diego, USA (Poster presentation)
  • Anurag Verma*, Carrie Buchanan Moore*, Dan Johnson, Sarah A. Pendergrass, David Haas, Marylyn Ritchie A Phenome-Wide Association Study of Numerous Laboratory Phenotypes in AIDS Clinical Trials Group (ACTG) Protocols at 2014 International Genetic Epidemiology Society conference, Vienna, Austria (Platform presentation)
  • Carrie Buchanan Moore, Anurag Verma, Dan Johnson, Sarah A. Pendergrass, David Haas, Marylyn Ritchie An exploration of multiple traits within the AIDS Clinical Trials Group (ACTG) Using A Phenome-Wide Association Study (PheWAS) at 2013 P-STAR Analysis Workshop , Nashville, TN (Platform Presentation)
  • Carrie Buchanan Moore, Anurag Verma, Dan Johnson, Sarah A. Pendergrass, David Haas, Marylyn Ritchie An exploration of multiple traits within the AIDS Clinical Trials Group (ACTG) Using A Phenome-Wide Association Study (PheWAS) at 2013 American Society for Human Genetics(ASHG) Conference, Boston, MA (Poster Presentation)
  • Anurag Verma, Helena Kuivaniemi , Gerard Tromp, David J. Carey, Glenn S. Gerhard, James E. Crowe, Jr., Marylyn D. Ritchie, Sarah A. Pendergrass Exploring the relationship between Immune System Related Genetic Loci And Complex Traits and Diseases through a Phenome-Wide Association Studies(PheWAS). at 2013 American Society for Human Genetics(ASHG) Conference, Boston, MA (Poster Presentation)
  • Anurag Verma, Helena Kuivaniemi , Gerard Tromp, David J. Carey, Glenn S. Gerhard, James E. Crowe, Jr., Marylyn D. Ritchie, Sarah A. Pendergrass Exploring the relationship between Immune System Related Genetic Loci And Complex Traits and Diseases through a Phenome-Wide Association Studies(PheWAS). at 2013  International Genetic Epidemiology Society (IGES) Conference, Chicago, IL (Poster Presentation)
  • M.A. Hall, A. Verma, K.D. Brown-Gentry, R. Goodloe, J. Boston, S.A. Pendergrass, D.C. Crawford, M.D. Ritchie. 2012. A Phenome-Wide Association Study (PheWAS) using multiple National Health and Nutritional Surveys (NHANES) to identify pleiotropy. at  2012 American Society for Human Genetics (ASHG) Conference, San Fransisco,CA (Poster Presentation)
 

Scott Dudek

scott opt

 

Application Developer

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Current Projects

ATHENA – Platform for analyzing genetic data using evolutionary algorithms
PLATO – (PLatform for the Analysis, Translation, and Organization of large-scale data) incorporates a number of filters to select the important SNPs in a genome-wide association study.
Visualization – Developing tools for visualizing data and results for PheWAS projects

Education

B.A. Biology
Washington University

Washington University School of Medicine

Work Experience

Application Developer
Ritchie Lab
University of Pennsylvania

Software Developer
Ritchie Lab
Geisinger
2016-2017

Software Developer
Ritchie Lab
Pennsylvania State University
2011-2016

Software Developer
Ritchie Lab
Vanderbilt University
2004-2011

Software Developer
Bioinformatics Core
Center for Human Genetics Research
Vanderbilt University
2001-2004

Publications

  • Bush W.S., Dudek S.M., Ritchie M.D. 2009. Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pacific Symposium on Biocomputing. 368-79.
  • Motsinger A.A., Fanelli T.J., Dudek S.M., Ritchie M.D. 2008. Balanced accuracy as a fitness function in grammatical evolution neural networks is robust to imbalanced data. GECCO. In press.
  • Edwards T.L., Lewis K.G., Velez D.R., Dudek S.M., Ritchie M.D. 2008. Exploring the Performance of Multifactor Dimensionality Reduction in Large Scale SNP Studies and in the Presence of Genetic Heterogeneity among Epistatic Disease Models. Human Heredity. 67(3):183-92.
  • Bush W.S., Edwards T.L., Dudek S.M., McKinney B.A., Ritchie M.D. 2008. Alternative contingency table measures improves the power and detection of Multifactor Dimensionality Reduction. BMC Bioinformatics. 9:238
  • Motsinger-Reif A.A., Dudek S.M., Hahn L.W., Ritchie M.D. 2008. Comparison of approaches for machine learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiology. Genetic Epidemiology. 32(4):325-40.
  • Edwards T.L., Bush W.S., Turner S.D., Dudek S.M., Torstenson E.S., Schmidt M., Martin E., Ritchie M.D. 2008 Generating linkage disequilibrium patterns in data simulations using genomeSIMLA. Lecture Notes in Computer Science. 4973: 24-35.
  • Schwartz U.I., Ritchie M.D., Bradford Y., Dudek S., Frye-Anderson A., Kim R.B., Roden D.M., Stein C.M. 2008. Genetic determinants of response to warfarin during initial anticoagulation. NEJM. 358(10):999-1008. (PubMed)
  • Motsinger A.A., Reif D.M., Dudek S.M., Ritchie M.D. 2006. Dissecting the evolutionary process of grammatical evolution optimized neural networks. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 1-8.
  • Bush W.S., Dudek S.M., Ritchie M.D. 2006. Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. Bioinformatics. 22:2173-4. (PubMed)
  • Motsinger A.A., Hahn L.W., Dudek S.M., Ryckman K.K., Ritchie M.D. 2006. Alternative Cross-Over Strategies and Selection Techniques for Grammatical Evolution Optimized Neural Networks. Proceedings of Genetic and Evolutionary Computation Conference. 947-949.
  • Motsinger A.A., Dudek S.M., Hahn L.W., Ritchie M.D. 2006. Comparison of Neural Network Optimization Approaches for Studies of Human Genetics. Lecture Notes in Computer Science. 3907:103-114.
  • Dudek SM, Motsinger AA, Velez DR, Williams SM, Ritchie MD. Data Simulation Software for Whole-Genome Association and Other Studies in Human Genetics. Pac Symp BioComput. 2006;:499-510.
  • Reif DM, Dudek SM, Shaffer CM, Wang J, Moore JH. Exploratory visual analysis of pharmacogenomic results. Pac Symp BioComput. 2005;:296-307.
  • Glossop NR, Houl JH, Zheng H, Ng FS, Dudek SM, Hardin PE. VRILLE feeds back to control circadian transcription of Clock in the Drosophila circadian oscillator. Neuron. 2003 Jan 23;37(2):249-61.
  • Bergelson J, Stahl E, Dudek S, Kreitman M. Genetic variation within and among populations of Arabidopsis thaliana. Genetics. 1998 Mar;148(3):1311-23. (PubMed)

Shefali S. Verma

shefali opt

 


Lead Bioinformatics Scientist

A301 Richards Building 
3700 Hamilton Walk, Philadelphia, PA 19104


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Current Projects

Analysis and Imputations for eMERGE Datasets.
GWAS and Interactions Analysis on different Phenotypes.

Education

MS Bioinformatics
New Jersey Institute of Technology
2010

Work Experience

Research Assistant-II
Bordenstein Lab
Vanderbilt University
2010-2011

Publications

Google Scholar

  • Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. Pendergrass SA, Verma SS, Holzinger ER, Moore CB, Wallace J, Dudek SM, Huggins W, Kitchner T, Waudby C, Berg R, McCarty CA, Ritchie MD.
  • Insect Innate Immunity Database (IIID): an annotation tool for identifying immune genes in insect genomes. Brucker RM, Funkhouser LJ, Setia S, Pauly R, Bordenstein SR.
  • Evolutionary genomics of a temperate bacteriophage in an obligate intracellular bacteria (Wolbachia).Kent BN, Funkhouser LJ, Setia S, Bordenstein SR.
  • On comparing two structured RNA multiple alignments. Patel V, Wang JT, Setia S, Verma A, Warden CD, Zhang K.


Conference Abstracts

  • Performance of two imputation methods on large scale data: experiences in the eMERGE network  Shefali S Verma, Gretta D Armstrong, Dana C. Crawford, Yuki Bradford, Mariza de Andrade, Iftikhar J.Kullo,Gerard Tromp, Helena Kuivaniemi, Loren L. Armstrong ,M. Geoffrey Hayes, Brendan Keating, David R. Crosslin,Gail P.Jarvik, Sarah Nelson, Bahram Namjou, Ebony B. Bookman, Rongling Li, Marylyn D Ritchie
  • Discovery and replication of genetic interactions for quantitative lipid traits E.R Holzinger, M.Farrall, F.Drenos, C.B Moore, I.B.C Lipid Working Group, S.S. Verma, H.Watkins, F.W Asselbers, B.J Keating, M.D. Ritchie
  • Merging Genomic Data for Research in Electronic MEdical Records and Genomics Network : Lessons Learned in eMERGE  Marylyn D Ritchie, Shefali S Verma, Gretta D Armstrong, Loren Armstrong, Dana C. Crawford,, David R Crosslin, Mariza de Andrade, Kimberley F. Dohney, M. Geoffery Hayes, Gail P Jarvik,Iftikhar J.Kullo,Cathy A. McCarthy, Daniel Mirel, Lana Olson, Shaun Prucell, Elizabeth W Pugh, Gerard Tromp, Helena Kuivaniemi, Vaneet Lotay, Omri Gottesman, Jonathan L Haines
  • Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. Pendergrass SA, Verma SS, Holzinger ER, Moore CB, Wallace J, Dudek SM, Huggins W, Kitchner T, Waudby C, Berg R, McCarty CA, Ritchie MD.

Yuki Bradford

yuki opt
 
 
Bioinformatician

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Current Projects
 
Genome-Wide / Phenome-Wide Association Studies using electronic medical records.
ACTG aids treatment response project.
 
Education
 
M.S. Statistics
University of Tennessee, Knoxville
 
M.S. Molecular Biology
Tennessee Technological University
 
B.S. Biology
Tennessee Technological University
 
Work Experience
 
Bioinformatician
Department of Genetics
University of Pennsylvania
2017-present
 
Bioinformatics System Analyst
Biomedical and Translational Informatics Institute
Geisinger Health System
2016-2017
 
Bioinformatics Analyst
Center for Systems Genomics
Pennsylvania State University
2014-2016
 
Statistical Genetic Analyst
Center for Human Genetics Research
Vanderbilt University Medical Center
1999-2014
 
Population Data Analyst
BlueCross BlueShield of Tennessee
1997-1999