Biomedical and Translational Informatics Laboratory

Alex Frase

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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

 

Allison Baker

Statistical Genetic Analyst II
Vanderbilt University
Nashville, TN

Becca Zuvich

Research Fellow
Vanderbilt University
Nashville, TN

Ben Grady

Graduate Student (Human Genetics)
Vanderbilt University
Nashville, TN

Binglan (Victoria) Li

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Graduate Student

A301 Richards Building 
3700 Hamilton Walk, Philadelphia, PA 19104

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Current Projects

Data integration approach to identify disease status indicating factors, including genetic factors and features from electronic heath records.

 
Education

B.S Life Sciences
Fudan University, Shanghai, China
2015

 

Carrie Moore

Graduate Student (MD/PhD)
Vanderbilt University
Nashville, TN

Daniel Wolfe

Research Assistant

Dokyoon Kim

 

Postdoctoral Fellow

Pennsylvania State University
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Curriculum Vitae

 

 

Current Projects

ATHENA
BioBin
Integrative analysis with multi-omics data

Education

Ph.D. Bioinformatics
Seoul National University
2013

B.S. Computer Science
Korea University
2006

Work Experience

Ph.D. Candidate & Researcher (PI: Ju Han Kim, M.D., Ph.D.)
Division of Biomedical Informatics, College of Medicine
Seoul National University, Seoul, Korea
Mar, 2006 – Feb, 2013

Visiting Researcher (PI: Hyunjung Shin, Ph.D.)
Department of Industrial Engineering
Ajou University, Suwon, Korea
Dec, 2009 – Aug, 2011

Intern (PI: Ju Han Kim, M.D., Ph.D.)
Division of Biomedical Informatics, College of Medicine
Seoul National University, Seoul, Korea
Jun, 2005 – Aug, 2005

Intern
Sun Microsystems, Colorado, USA
Jan, 2004 – Feb, 2004

Exchange Student
University of Colorado at Boulder, Colorado, USA
Aug, 2003 – Feb, 2004
 

Emily Holzinger

Graduate Student (Human Genetics)
Vanderbilt University
Nashville, TN

Currently Post-Doctoral fellow at NIH

Eric Torstenson

Programmer/Analyst
Vanderbilt University
Nashville, TN

Jason Miller

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Post-Doctoral Fellow

A301 Richards Building 
3700 Hamilton Walk, Philadelphia, PA 19104

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 Current Projects

Analysis of multi-omics datasets from the Pharmacogenomics of Statin Therapy (POST) center.

Education

Ph.D. in Biochemistry, Microbiology and Molecular Biology, Fall 2016
The Pennsylvania State University, University Park, PA

B.S. in Lyman Briggs Biochemistry/Biotechnology, Summer 2008
Michigan State University, East Lansing, MI

Work Experience

Undergraduate Research Assistant,
Rice Genomics Laboratory, 2007-2008
Michigan State University, East Lansing, MI

Publications

For the list of my publications please visit Google Scholar.

 

Jeff Sumrall

Project Manager
Vanderbilt University
Nashville, TN

Marta Byrska-Bishop

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Post-Doctoral Fellow (Geisinger Health System)

Current Contact Information

 

 

 

 Current Projects

Disease co-occurrence: identification of a genetic link between Electronic Health Record (EHR)-derived phenotypes that tend to co-occur in population more often than expected by random chance. 

Education

PhD, Molecular, Cellular and Integrative Biosciences
The Pennsylvania State University, University Park, PA
2015 

MS, Interdisciplinary Biological Sciences
Northwestern University, Evanston, IL
2009 

BS, Biology
Jagiellonian University, Krakow, Poland
2007

Publications

For the list of my publications please visit Google Scholar.

 

Molly Hall

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Post Doctoral Fellow with Dr. Jason Moore (University of Pennsylvania)

512 Wartik Laboratory
Pennsylvania State University

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Current Projects

Gene-Environment Interactions
Gene-Gene Interactions
Environment-Wide Association Studies
Phenome-Wide Association Studies

Education
M.S. Neuroscience and Education
Columbia University
2011

B.S. Human Development
Cornell University
2005

Work Experience

Middle School Science Teacher
Teach For America
Bronx, NY
2005-2007

Middle School Science Teacher
Uncommon Schools, Inc.
Brooklyn, NY
2007-2009

Publications

  • Hall, M. A. et al. Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network. Genet. Epidemiol. 39, 376–84 (2015).
  • Hall, M. A. et al. 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. 10, (2014).
  • Hall, M. A. et al. Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank. Pac. Symp. Biocomput. 200–11 (2014).
  • Hall, M.A. et al. Session Introduction: Characterizing the the importance of environmental exposures, interactions between the environment and genetic architecture, and genetic interactions. Pac. Symp. Biocomput. 2015.
  • Pendergrass SA, Verma SS, Hall MA et al. (2013) Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. Pac Symp Biocomput: 147-58.
  • Ritchie MD, Verma SS, Hall MA et al., (2014) Electronic medical records and genomics (eMERGE) network exploration in cataract: Several new potential susceptibility loci. Molecular Vision: 20.
  • Pendergrass SA, Verma A, Okula A, Hall MA, Crawford DC, Ritchie MD (2015) Phenome-wide association studies (PheWAS): Embracing complexity for discovery. Human Heredity 79:111- 123.
  • De R, Verma SS, Drenos F, Holzinger ER, Holmes MV, Hall MA, et al. Dissecting the obesity disease landscape: identifying gene-gene interactions that are highly associated with Body Mass Index (submitted).

Conferences:

  • Molly A. Hall, Scott M. Dudek, Robert Goodloe, Dana C. Crawford, Sarah A. Pendergrass, Peggy Pessig, Murray Brilliant, Catherine A. McCarty, Marylyn D. Ritchie. 2013. Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank. Manuscript accepted for the 2014 Pacific Symposium on Biocomputing journal and conference.
  • Molly A. Hall, Shefali S. Verma, Emily R. Holzinger, Richard Berg, John Connolly, Dana C. Crawford, David R. Crosslin, Mariza de Andrade, Kimberly F. Doheny, Jonathan L. Haines, John B. Harley, Gail P. Jarvik, Terrie Kitchner, Helena Kuivaniemi, Eric B. Larson, Gerard Tromp, Sarah A. Pendergrass, Catherine A. McCarty, Marylyn D. Ritchie. 2013. Replication of gene-gene interaction models associated with cataracts in the eMERGE Network. Abstract presented as oral platform talk at the 2013 American Society for Human Genetics (ASHG) Conference.
  • 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. Abstract Accepted for poster presentation at the 2012 American Society for Human Genetics (ASHG) Conference.
  • M.A. Hall, A. Verma, K.D. Brown-Gentry, R. Goodloe, J. Boston, S.A. Pendergrass, D.C. Crawford, M.D. Ritchie. 2012. Detection of Pleiotropy through a Phenome-Wide Association Study (PheWAS) in the National Health and Nutrition Examination Surveys (NHANES). Manuscript Accepted for talk at the 2012 Translational Biology Conference.

Scholarships, Awards & Fellowships

2015    Ruth L. Kirschstein National Research Service Award (NRSA) Individual Predoctoral Fellowship (Parent F31), funded through the National            Institutes of Health (NIH), National Human Genome Research Institute (NHGRI)
2013    Pacific Symposium on Biocomputing 2014 Travel Award, funded through the National Library of Medicine/National Institutes of Health
2013    Paul M. Althouse Outstanding Teaching Assistant Award
2012    Cold Spring Harbor Laboratory Programming for Biology Course Scholarship
2012    Genetic Analysis of Complex Human Disease Travel Scholarship, funded through the National Institutes of Health
2011    Braddock-Roberts Fellowship (Penn State University, Department of Biochemistry and Molecular Biology)

Neerja Katiyar

Master's  Bioinformatics and Genomics
The Pennsylvania State University
University Park, PA

Robert Goodloe

Statistical Genetic Analyst II
Vanderbilt University
Nashville, TN

Ruowang Li

 

Graduate Student

512 Wartik Laboratory
Pennsylvania State University

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Curriculum Vitae

 

Current Projects

Using an integrative approach to uncover genetic factors affected under chemotherapeutic agent,
Performing genome-wide analysis of heat-shock induced gene and protein network in yeast
 
Education

B.S Biology and Biotechnology

Minor in Computer Science
Worcester Polytechnic Institute
2011

Publications

  • Dokyoon Kim, Ruowang Li, Scott M. Dudek, Marylyn D. Ritchie. ATHENA: Identifying interactions between different levels of genomic data using grammatical evolution neural network. Translational Bioinformatics Conference (submitted)
  • Ruowang Li, E.R. Holzinger, S.M. Dudek, M.D. Ritchie. (2013). Evaluation of parameter contribution to neural network size and fitness in ATHENA for genetic analysis. Genetic Programming Theory And Practice (accepted)
  • Marylyn Ritchie, Emily Holzinger, Ruowang Li, Sarah Pendergrass. Next-generation analyses for exploring the genetic architecture of complex traits: meta-dimensional approaches. Nature Reviews Genetics (submitted)
  • Marylyn Ritchie, Sarah Pendergrass, Ruowang Li, Emily Holzinger. Meta-dimensional analysis to dissect the architecture of complex traits. Trends in Genetics (submitted)
  • Ozlem Yildirim, Ruowang Li, Jui-Hung Hung,Poshen B. Chen,Xianjun Dong,Ly-Sha Ee, Zhiping Weng,Oliver J. Rando, and Thomas G. Fazzio (2011) Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells. Cell 147, 1498–1510 (2011).
  • Benjamin R. Carone, Lucas Fauquier, Naomi Habib, Jeremy M. Shea, Caroline E.Hart, Ruowang Li, Christoph Bock, Chengjian Li, Phillip D. Zamore, Alexander Meissner, Zhiping Weng, Hans A. Hofmann, Nir Friedman, and Oliver J. Rando. (2010) Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell (1084-1096, 23 December 2010)
  • Quanqin Dai, Yingnan Wang, Yu Zhang, Xinbi Li, Ruowang Li, Bo Zou, JaeTae Seo, Yiding Wang, Manhong Liu, William W. Yu. (2009) Stability Study of PbSe Semiconductor Nanocrystals over Concentration, Size, Atmosphere, and Light Exposure. Langmuir 25 (20), 12320-12324

Shefali S. Verma

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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.

Xinyuan (Blair) Zhang

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Graduate Student

A301 Richards Building 
3700 Hamilton Walk, Philadelphia, PA 19104 

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Current Projects

Identify pleiotropy across cardiovascular and neurological diseases in electronic health record data using multivariate approaches.

 
Education

B.S Biotechnology
Northwest A&F University, Xianyang, China
2014

Work Experience

Research Assistant
Internship Agricultural Genomes Institute at Shenzhen
Chinese Academy of Agricultural Sciences
2014-2015

 

Publications

For the list of my publications please visit Google Scholar