Molly Hall, PhD, M.S.

Molly Hall, PhD, M.S.

  • Assistant Professor
  • Dr. Frances Keesler Graham Early Career Professor
Veterinary and Biomedical Sciences
College of Agricultural Sciences
Huck Institutes of the Life Sciences
512A Wartik Lab

University Park, PA 16802

Areas of Expertise

  • Genomics
  • Human Genetics
  • Exposome
  • Genetic Interactions (Epistasis)
  • Gene-Environment Interactions
  • Complex Disease
  • Precision Medicine
  • Biomedical Informatics
  • Metabolomics

Education

  • Postdoctoral Fellowship - University of Pennsylvania School of Medicine
  • PhD - Penn State University, Biochemistry & Molecular Biology
  • MS - Columbia University, Neuroscience & Education
  • BS - Cornell University, Human Development

Research:

The Hall Lab is focused on building tools to elucidate the complex genetic and environmental underpinnings of human disease. We integrate genetic (genotype, sequence, structural variation) and exposure (derived from surveys and metabolomics methods) big data to predict disease status. The ultimate goals of this work are to 1) enrich our understanding of the complex mechanisms that lead to common disease and 2) provide methods to identify those most at risk of disease (based on their genetic and exposure backgrounds) in a clinical setting.

 Select Publications:

Lucas AM, Palmiero NE, McGuigan J, Passero K, Zhou J, Orie D, Ritchie MD and Hall MA (2019) CLARITE Facilitates the Quality Control and Analysis Process for EWAS of Metabolic-Related Traits. Front. Genet. 10:1240. doi: 10.3389/fgene.2019.01240 

Hall MA, Wallace J, Lucas A, et al. (2017) PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies. Nature Communications: 8 1167

Hall MA, Moore JH, Ritchie MD (2016) Embracing complex associations in common traits: Critical considerations for precision medicineTrends in Genetics: 32, 470-484

Hall MA, Verma SS, Wallace J, Lucas A, et al. (2015) Biology-driven gene-gene interaction analysis of age-related cataract in the eMERGE NetworkGenetic Epidemiology: 39 376-384

Hall MA, Verma A, Brown-Gentry KD, Goodloe R, et al. (2014) Detection of pleiotropy through and phenome-wide association study (PheWAS) of epidemiologic data as part of the Environmental Architecture for Genes Linked to Environment (EAGLE) studyPLoS Genetics: 10.

Hall MA, Dudek SM, Goodloe R, Crawford DC, Pendergrass SA, et al. (2014) Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project BiobankPac Symp Biocomput: 200-211

Publications

Hypothalamic-pituitary-adrenal axis attenuation and obesity risk in sexually abused females
Psychoneuroendocrinology, Li, Jacinda C., Hall, Molly A., Shalev, Idan, Schreier, Hannah M.C., Zarzar, Tomás González, Marcovici, Isabel, Putnam, Frank W., Noll, Jennie G., 2021

Novel EDGE encoding method enhances ability to identify genetic interactions
PLoS Genetics, Hall, Molly A., Wallace, John, Lucas, Anastasia M., Bradford, Yuki, Verma, Shefali S., Müller-Myhsok, Bertram, Passero, Kristin, Zhou, Jiayan, McGuigan, John, Jiang, Beibei, Pendergrass, Sarah A., Zhang, Yanfei, Peissig, Peggy, Brilliant, Murray, Sleiman, Patrick, Hakonarson, Hakon, Harley, John B., Kiryluk, Krzysztof, van Steen, Kristel, Moore, Jason H., Ritchie, Marylyn D., 2021

Semi-automated NMR Pipeline for Environmental Exposures: New Insights on the Metabolomics of Smokers versus Non-smokers
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Aguilar, Morris A., McGuigan, John, Hall, Molly A., 2021

What About the Environment? Leveraging Multi-Omic Datasets to Characterize the Environment’s Role in Human Health.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Passero, K, Setia-Verma, S, McAllister, K, Manrai, A, Patel, C, Hall, Molly, 2021

Investigation of gene-gene interactions in cardiac diseases and serum fatty acid levels in LURIC cohort
PLoS One, Zhou, Jiayan, Passero, Kristin, Palmiero, Nicole E., Müller-Myhsok, Bertram, Kleber, Marcus E., Maerz, Winfried, Hall, Molly A., 2020

Phenome-wide association studies on cardiovascular health and fatty acids considering phenotype quality control practices for epidemiological data
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Passero, Kristin, He, Xi, Zhou, Jiayan, Mueller-Myhsok, Bertram, Kleber, Marcus E., Maerz, Winfried, Hall, Molly A., 2020

CLARITE Facilitates the Quality Control and Analysis Process for EWAS of Metabolic-Related Traits
Frontiers in Genetics, Lucas, Anastasia M., Palmiero, Nicole E., McGuigan, John, Passero, Kristin, Zhou, Jiayan, Orie, Deven, Ritchie, Marylyn D., Hall, Molly A., 2019

Analysis of Gene-Gene Interactions
Current Protocols in Human Genetics, Cole, B, Hall, Molly, Urbanowicz, R, Gilbert-Diamond, D, Moore, J, 2018

Gene-gene interactions, Hall, Molly A., Cole, Brian S., Moore, Jason H., 2018

Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Manduchi, Elisabetta, Chesi, Alessandra, Hall, Molly A., Grant, Struan F.A., Moore, Jason H., 2018

PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies
Nature Communications, Hall, Molly A., Wallace, John, Lucas, Anastasia, Kim, Dokyoon, Basile, Anna O., Verma, Shefali S., McCarty, Cathy A., Brilliant, Murray H., Peissig, Peggy L., Kitchner, Terrie E., Verma, Anurag, Pendergrass, Sarah A., Dudek, Scott M., Moore, Jason H., Ritchie, Marylyn D., 2017

Analysis of Gene-Gene Interactions
Current Protocols in Human Genetics, Cole, Brian S., Hall, Molly A., Urbanowicz, Ryan J., Gilbert-Diamond, Diane, Moore, Jason H., 2017

The joint effect of air pollution exposure and copy number variation on risk for autism
Autism Research, Kim, Dokyoon, Volk, Heather, Girirajan, Santhosh, Pendergrass, Sarah, Hall, Molly A., Verma, Shefali S., Schmidt, Rebecca J., Hansen, Robin L., Ghosh, Debashis, Ludena-Rodriguez, Yunin, Kim, Kyoungmi, Ritchie, Marylyn D., Hertz-Picciotto, Irva, Selleck, Scott B., 2017

Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals
BioData Mining, Holzinger, Emily R., Verma, Shefali S., Moore, Carrie B., Hall, Molly, De, Rishika, Gilbert-Diamond, Diane, Lanktree, Matthew B., Pankratz, Nathan, Amuzu, Antoinette, Burt, Amber, Dale, Caroline, Dudek, Scott, Furlong, Clement E., Gaunt, Tom R., Kim, Daniel Seung, Riess, Helene, Sivapalaratnam, Suthesh, Tragante, Vinicius, Van Iperen, Erik P.A., Brautbar, Ariel, Carrell, David S., Crosslin, David R., Jarvik, Gail P., Kuivaniemi, Helena, Kullo, Iftikhar J., Larson, Eric B., Rasmussen-Torvik, Laura J., Tromp, Gerard, Baumert, Jens, Cruickshanks, Karen J., Farrall, Martin, Hingorani, Aroon D., Hovingh, G. K., Kleber, Marcus E., Klein, Barbara E., Klein, Ronald, Koenig, Wolfgang, Lange, Leslie A., MOrz, Winfried, North, Kari E., Charlotte Onland-Moret, N., Reiner, Alex P., Talmud, Philippa J., Van Der Schouw, Yvonne T., Wilson, James G., Kivimaki, Mika, Kumari, Meena, Moore, Jason H., Drenos, Fotios, Asselbergs, Folkert W., Keating, Brendan J., Ritchie, Marylyn D., 2017

Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health
Annual Review of Public Health, Manrai, Arjun K., Cui, Yuxia, Bushel, Pierre R., Hall, Molly, Karakitsios, Spyros, Mattingly, Carolyn J., Ritchie, Marylyn, Schmitt, Charles, Sarigiannis, Denis A., Thomas, Duncan C., Wishart, David, Balshaw, David M., Patel, Chirag J., 2017

Identifying gene–gene interactions that are highly associated with four quantitative lipid traits across multiple cohorts
Human Genetics, De, Rishika, Verma, Shefali S., Holzinger, Emily, Hall, Molly, Burt, Amber, Carrell, David S., Crosslin, David R., Jarvik, Gail P., Kuivaniemi, Helena, Kullo, Iftikhar J., Lange, Leslie A., Lanktree, Matthew B., Larson, Eric B., North, Kari E., Reiner, Alex P., Tragante, Vinicius, Tromp, Gerard, Wilson, James G., Asselbergs, Folkert W., Drenos, Fotios, Moore, Jason H., Ritchie, Marylyn D., Keating, Brendan, Gilbert-Diamond, Diane, 2017

Epistatic Gene-Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium
PLoS Genetics, Verma, Shefali Setia, Cooke Bailey, Jessica N., Lucas, Anastasia, Bradford, Yuki, Linneman, James G., Hauser, Michael A., Pasquale, Louis R., Peissig, Peggy L., Brilliant, Murray H., McCarty, Catherine A., Haines, Jonathan L., Wiggs, Janey L., Vrabec, Tamara R., Tromp, Gerard, Ritchie, Marylyn D., Bickel, Jonathan, Chandler, Ariel, Holm, Ingrid, Kohane, Isaac, Manzi, Shannon, Markianos, Kyriacos, Palmer, Nathan, Perry, Cassandra, Savova, Guergana, Wolf, Wendy, Wong Kong, Sek, Antommaria, Armand, Cobb, Beth, Harley, John, Hutton, John, Lingren, Todd, Lynch, John, Marsolo, Keith, Myers, Melanie, Namjou, Bahram, Prows, Cindy, Solti, Imre, Vinks, Sander, Wagner, Michael, Abrams, Debbie, Almoguera, Berta, Chiavacci, Rosetta, Connolly, John, Devoto, Marcella, Hakonarson, Hakon, Keating, Brendan, Kim, Cecilia, Mentch, Frank, Qui, Haijun, Sleiman, Patrick, 2016

Embracing Complex Associations in Common Traits
Trends in Genetics, Hall, Molly A., Moore, Jason H., Ritchie, Marylyn D., 2016

Identification of genetic interaction networks via an evolutionary algorithm evolved Bayesian network
BioData Mining, Li, Ruowang, Dudek, Scott M., Kim, Dokyoon, Hall, Molly A., Bradford, Yuki, Peissig, Peggy L., Brilliant, Murray H., Linneman, James G., McCarty, Catherine A., Bao, Le, Ritchie, Marylyn D., 2016

Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR)
BioData Mining, De, Rishika, Verma, Shefali S., Drenos, Fotios, Holzinger, Emily R., Holmes, Michael V., Hall, Molly A., Crosslin, David R., Carrell, David S., Hakonarson, Hakon, Jarvik, Gail, Larson, Eric, Pacheco, Jennifer A., Rasmussen-Torvik, Laura J., Moore, Carrie B., Asselbergs, Folkert W., Moore, Jason H., Ritchie, Marylyn D., Keating, Brendan J., Gilbert-Diamond, Diane, 2015

Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network
Genetic Epidemiology, Hall, Molly A., Verma, Shefali S., Wallace, John, Lucas, Anastasia, Berg, Richard L., Connolly, John, Crawford, Dana C., Crosslin, David R., de Andrade, Mariza, Doheny, Kimberly F., Haines, Jonathan L., Harley, John B., Jarvik, Gail P., Kitchner, Terrie, Kuivaniemi, Helena, Larson, Eric B., Carrell, David S., Tromp, Gerard, Vrabec, Tamara R., Pendergrass, Sarah A., Mccarty, Catherine A., Ritchie, Marylyn D., 2015

Phenome-Wide Association Studies
Human Heredity, Pendergrass, Sarah A., Verma, Anurag, Okula, Anna, Hall, Molly A., Crawford, Dana C., Ritchie, Marylyn D., 2015

Session introduction
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Hall, Molly A., Verma, Shefali Setia, Wall, Dennis P., Moore, Jason H., Keating, Brendan, Campbell, Daniel B., Gibson, Gregory, Asselbergs, Folkert W., Pendergrass, Sarah, 2015

Erratum: Next-generation analysis of cataracts: Determining knowledge driven gene-gene interactions using biofilter, and geneenvironment interactions using the phenx toolkit (Biocomputing (2013) (147-158))
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Pendergrass, Sarah A., Verma, Shefali S., Holzinger, Emily R., Moore, Carrie B., Wallace, John, Dudek, Scott M., Huggins, Wayne, Kitchner, Terrie, Waudby, Carol, Berg, Richard, Mccarty, Catherine A., Ritchie, Marylyn D., 2015

Electronic medical records and genomics (eMERGE) network exploration in cataract
Molecular Vision, Ritchie, Marylyn D., Verma, Shefali S., Hall, Molly A., Goodloe, Robert J., Berg, Richard L., Carrell, Dave S., Carlson, Christopher S., Chen, Lin, Crosslin, David R., Denny, Joshua C., Jarvik, Gail, Li, Rongling, Linneman, James G., Pathak, Jyoti, Peissig, Peggy, Rasmussen, Luke V., Ramirez, Andrea H., Wang, Xiaoming, Wilke, Russell A., Wolf, Wendy A., Torstenson, Eric S., Turner, Stephen D., McCarty, Catherine A., 2014

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 Genetics, Hall, Molly A., Verma, Anurag, Brown-Gentry, Kristin D., Goodloe, Robert, Boston, Jonathan, Wilson, Sarah, McClellan, Bob, Sutcliffe, Cara, Dilks, Holly H., Gillani, Nila B., Jin, Hailing, Mayo, Ping, Allen, Melissa, Schnetz-Boutaud, Nathalie, Crawford, Dana C., Ritchie, Marylyn D., Pendergrass, Sarah A., 2014

Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Hall, Molly A., Dudek, Scott M., Goodloe, Robert, Crawford, Dana C., Pendergrass, Sarah A., Peissig, Peggy, Brilliant, Murray, McCarty, Catherine A., Ritchie, Marylyn D., 2014

Next-generation analysis of cataracts
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, Pendergrass, Sarah A., Verma, Shefali S., Hall, Molly A., Holzinger, Emily R., Moore, Carrie B., Wallace, John R., Dudek, Scott M., Huggins, Wayne, Kitchner, Terrie, Waudby, Carol, Berg, Richard, McCarty, Catherine A., Ritchie, Marylyn D., 2013