Biomedical and Translational Informatics Laboratory

Marta Byrska-Bishop

marta opt

 

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.

 

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

Neerja Katiyar

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

Emily Holzinger

Graduate Student (Human Genetics)
Vanderbilt University
Nashville, TN

Currently Post-Doctoral fellow at NIH

Carrie Moore

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

Ben Grady

Graduate Student (Human Genetics)
Vanderbilt University
Nashville, TN

Becca Zuvich

Research Fellow
Vanderbilt University
Nashville, TN

Jeff Sumrall

Project Manager
Vanderbilt University
Nashville, TN

Dokyoon Kim

 

Postdoctoral Fellow

Pennsylvania State University
This email address is being protected from spambots. You need JavaScript enabled to view it.

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
 

Suzy Unger

suzy opt

 

 Research Project Manager

328 Innovation Blvd. Suite 201
State College, PA 16803

This email address is being protected from spambots. You need JavaScript enabled to view it.

(814) 272-5092

 

 

 

 

 

 

 

 

 

 

Daniel Wolfe

Research Assistant

Molly Hall

MAH photo for defense edit opt

 

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

512 Wartik Laboratory
Pennsylvania State University

This email address is being protected from spambots. You need JavaScript enabled to view it.

 

 

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)

Ruowang Li

 

Graduate Student

512 Wartik Laboratory
Pennsylvania State University

This email address is being protected from spambots. You need JavaScript enabled to view it.

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