Biomedical and Translational Informatics Laboratory

Theodore Drivas

 Post-Doctoral Fellow

A301 Richards Building 
3700 Hamilton Walk, Philadelphia, PA 19104

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 Education and Clinical Training

Clinical Fellowship
Medical Genetics, Children’s Hospital of Philadelphia/Hospital of the University of Pennsylvania
Philadelphia, PA. (2017 -Present)

Internship and Residency
Internal Medicine, Columbia University Medical Center – New York Presbyterian Hospital
New York, NY (2015 – 2017)               

M.D., Ph.D.
Cellular and Molecular Biology; Gene Therapy and Vaccines, The Perelman School of Medicine at the University of Pennsylvania
Philadelphia, PA (2008 – 2015)

B.A.
Classics, and Molecular and Cellular Biology, The Johns Hopkins University
Baltimore, MD (2003 – 2007)

Research Experience

Postdoctoral Research
Laboratory of Marylyn Ritchie, Ph.D., University of Pennsylvania, Philadelphia, PA (2018-Present)
Genomic data integration into the EHR, Mendelian approaches to genomic data

Graduate School Research
Laboratory of Jean Bennett, M.D. Ph.D., University of PennsylvaniaPhiladelphia, PA (2008-2014)
Molecular mechanisms and treatment approaches to CEP290-related disorders
Cell biology, cell culture, gene therapy, molecular biology, biochemistry

Research Assistant
Laboratory of Gunter Blobel, M.D. Ph.D., Rockefeller University, New York, NY (2007-2008)
Mechanisms of association between the microtubule network and the eukaryote nucleus in S. pombe
Yeast genetics, chromatin immunoprecipitation, biochemistry

Undergraduate Research
Laboratory of Beverly Wendland, Ph.D ., Johns Hopkins University, Baltimore, MD (2005-2007)
Identification of novel endocytic pathways in S. cerevisiae
Yeast genetics, genetic screens, cell biology, molecular biology

High School Research
Laboratory of Gunter Blobel, M.D., Ph.D., Rockefeller University, New York, NY (2000-2004)
The role of nucleoporin Nup358 in nuclear export
Biophysics, cell biology, molecular biology

Publications:

For the list of my publications please visit Google Scholar

 

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.

 

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)