Biomedical and Translational Informatics Laboratory

Kia Speaks

  Administrative Assistant 

    A301 Richards Buildin

    3700 Hamilton Walk, Philadelphia, PA 19104

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Robert Goodloe

Statistical Genetic Analyst II

Vanderbilt University
Nashville, TN

 

Eric Torstenson

Programmer/Analyst

Vanderbilt University
Nashville, TN 

 

Allison Baker

Statistical Genetic Analyst II

Vanderbilt University
Nashville, TN

 

Jeff Sumrall

Project Manager

Vanderbilt University
Nashville, TN

 

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

 

Gretta D. Armstrong

Project Manager

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Suzy Unger

suzy opt

 Research Project Manager

328 Innovation Blvd. Suite 201
State College, PA 16803

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(814) 272-5092

 

 

 
 

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.

 

John Wallace

Associate Director, Research Computing
Geisinger Health System

328 Innovation Park Boulevard, Suite 210
State College

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Projects

genomeSIMLA
Biobin
PLATO

Work Experience

Research Engineer
Applied Research Lab
Pennsylvania State University
State College, PA
2009 – 2011

Graduate Teaching Assistant
Dept. of Mathematics
Virginia Tech, Blacksburg, VA
2007 – 2009

Software Engineer
White Oak Technologies
Silver Spring, MD
2004 – 2007

Software Engineer
Argon Engineering
Fairfax, VA
2004 – 2004

 

Daniel Wolfe

Research Assistant

 

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

 

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)