CLARITE version 2 has been released. Full release notes are available in the documentation, but the main improvement is support for genotype data and simplification of the analysis functions to better support a variety of association and interaction tests.
Support for genotype data is possible though the use of Pandas-Genomics, another project of the Hall Lab.
The Hall Lab published a study in PLoS Genetics featuring the lab’s novel genetic encoding method: EDGE. Using EDGE, we identified a novel genetic interaction associated with age-related cataract that no other method identified. EDGE shows promise for identifying nonadditive genetic effects in biomedical data.
New publication from our collaboration with Dr. Jennie Noll (Human Development and Family Studies) on risk for obesity in women who have experienced sexual abuse:
Li J, Hall MA, Shalev I, Schreier H, González-Zarzar T, Marcovici I, Putnam F, Noll J. (2021) Hypothalamic-pituitary-adrenal axis dysregulation and risk for obesity in sexually abused females. Psychoneuroendocrinology: 129, 105254
Kristin Passero (Hall Lab PhD student) and Molly Hall organized the session “What about the environment? Leveraging multi-omic datasets to characterize the environment’s role in human health” for the Pacific Symposium on Biocomputing with environmental health research experts Dr. Chirag Patel (Harvard Medical School), Dr. Arjun Manrai (Harvard Medical School), Dr. Kimberly McAllister (National Institute of Environmental Health Sciences), and Dr. Shefali Setia Verma (University of Pennsylvania).
The Hall Lab is presenting at the 2020 ASHG virtual conference. Please see the following posters:
- 2045 John McGuigan Automated machine learning for rare variant analysis of response to antiretroviral therapy in persons living with HIV.
- 2418 Morris Aguilar Secondary Metabolomic Analysis of Breast Cancer Nanoparticle Chemotherapy: Fatty Acid Metabolism Perturbation With Newly Quantified Metabolites and High Fidelity Classification Models
- 2715 Jiayan Zhou Interactions between genes and fatty acids for cardiac-related traits in LURIC cohort
- 3508 Nicole Palmiero Environment-wide association study of the phenome to evaluate complexity of the exposome
- 3539 Molly Hall Metabolomics reveals novel biomarkers in children who experienced maltreatment
Jiayan Zhou’s first first-author paper titled “Investigation of gene-gene interactions in cardiac traits and serum fatty acid levels in the LURIC Health Study” was published in PLoS one.
Morris Aguilar’s paper was accepted at the Pacific Symposium on Biocomputing (PSB), which will be presented January 2021, titled “Semi-automated NMR Pipeline for Environmental Exposures: New Insights on the Metabolomics of Smokers versus Non-smokers”
The Hall Lab welcomes new Postdoc Tomás González Zarzar
Lab research areas and projects are now detailed here.
Congratulations to Morris Aguilar for being awarded a trainee fellowship: ‘Integrative Analysis of Metabolic Phenotypes (IAMP) Predoctoral Training Program’
Five posters from the Hall Lab were accepted for the 2020 NYC Exposome Symposium.
The Hall Lab original CLARITE (pronounced clarity) software and first EWAS for BMI was published in Frontiers in Genetics: CLARITE Facilitates the Quality Control and Analysis Process for EWAS of Metabolic-Related Traits
Kristin Passero’s first first-author paper was accepted at the Pacific Symposium on Biocomputing (PSB), which we will present in Hawaii January 2020, titled “Phenome-wide association studies on cardiovascular health and fatty acids considering phenotype quality control practices for epidemiological data”
Congratulations to Kristin Passero for passing her qualifying exam!
Dr. Molly Hall named recipient of the Dr. Frances Keesler Graham Early Career Professorship. Read more here.
Graduate students, Jiayan Zhou and Kristin Passero present their first posters at the American Society of Human Genetics in Houston
Molly Hall moderated ASHG 2019 Houston session: “What about the phenotype? Integrating electronic health records to drive discovery in precision health” with Anna Basile at New York Genome Center. The session included exciting talks from Dana Crawford (Case Western), Dokyoon Kim (UPenn), Marylyn Ritchie (UPenn), and Nicholas Tatonetti (Columbia).
Congratulations to Jiayan Zhou for passing his candidacy exam!
Congratulations to Kristin Passero for earning the Huck Travel Award to ASHG in Houston for her poster titled “Considering phenotype quality-control practices for phenome-wide association studies using epidemiological data”
Congratulations to Jiayan Zhou for earning the CAS Travel Award to ASHG in Houston for his poster titled “Investigation of gene-gene interactions in cardiac traits and serum fatty acid level in LURIC cohort”