Biomedical and Translational Informatics Laboratory
The mission of the Ritchie Lab is to improve our understanding of the underlying genetic architecture of common diseases such as cancer, diabetes, cardiovascular disease, and pharmacogenomic traits among others.
David Zhang's paper "Protein-truncating variant in APOL3 increases chronic kidney disease risk in epistasis with APOL1 risk alleles" was accepted to JCI Insights. Also congrats to Latrice who is a coauthor on this paper with us.
Biofilter 2.4.3: The latest update for Biofilter is available. New in this version:
updated from Python2 to Python3
updated LOKI loaders
fixed a bug in removing redundant results
BioBin 2.3.0: The latest update for BioBin is now available. New in this version:
Improved genomic build detection and handling
Improved output formatting
New runtime options to better control the processing of sample, phenotype and VCF files
Recent Publications
Tong, B. et al. (2024). Class-Balanced Deep Learning with Adaptive Vector Scaling Loss for Dementia Stage Detection. In: Cao, X., Xu, X., Rekik, I., Cui, Z., Ouyang, X. (eds) Machine Learning in Medical Imaging. MLMI 2023. Lecture Notes in Computer Science, vol 14349. Springer, Cham. https://doi.org/10.1007/978-3-031-45676-3_15
Compher, C. W., Quinn, R., Haslam, R., Bader, E., Weaver, J., Dudek, S., Ritchie, M. D., Lewis, J. D., & Wu, G. D. (2024). Penn Healthy Diet survey: pilot validation and scoring.The British Journal of Nutrition., 131(1), 156–162. https://doi.org/10.1017/S0007114523001642
Li, R., Benz, L., Duan, R., Denny, J. C., Hakonarson, H., Mosley, J. D., Smoller, J. W., Wei, W.-Q., Ritchie, M. D., Moore, J. H., & Chen, Y. (2024). MixWAS: An efficient distributed algorithm for mixed-outcomes genome-wide association studies.Medrxiv. https://doi.org/10.1101/2024.01.09.24301073
Verma, S. S., Gudiseva, H. V., Chavali, V. R. M., Salowe, R. J., Bradford, Y., Guare, L., Lucas, A., Collins, D. W., Vrathasha, V., Nair, R. M., Rathi, S., Zhao, B., He, J., Lee, R., Zenebe-Gete, S., Bowman, A. S., McHugh, C. P., Zody, M. C., Pistilli, M., … O’Brien, J. M. (2024). A multi-cohort genome-wide association study in African ancestry individuals reveals risk loci for primary open-angle glaucoma.Cell, 187(2). https://doi.org/10.1016/j.cell.2023.12.006
Chae, A., Yao, M. S., Sagreiya, H., Goldberg, A. D., Chatterjee, N., MacLean, M. T., Duda, J., Elahi, A., Borthakur, A., Ritchie, M. D., Rader, D., Kahn, C. E., Witschey, W. R., & Gee, J. C. (2024). Strategies for implementing machine learning algorithms in the clinical practice of Radiology.Radiology, 310(1). https://doi.org/10.1148/radiol.223170