HATK: HLA analysis toolkit
Choi, Wanson, Yang Luo, Soumya Raychaudhuri, and Buhm Han. 2020. “HATK: HLA Analysis Toolkit”. Bioinformatics.
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Genome-wide Study Identifies Association between HLA-B ∗ 55:01 and Self-Reported Penicillin Allergy
Krebs, Bovjin, Zheng, Lepamets, Censin, Jurgenson, Sarg, et al. 2020. “Genome-Wide Study Identifies Association Between HLA-B ∗ 55:01 and Self-Reported Penicillin Allergy”. American Journal of Human Genetics 107 (4): 612-21.
Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements
Amariuta, Ishigaki, Sugishita, Ohta, Koido, Dey, Matsuda, et al. 2020. “Improving the Trans-Ancestry Portability of Polygenic Risk Scores by Prioritizing Variants in Predicted Cell-Type-Specific Regulatory Elements”. Nature Genetics 52: 1346-54.
A framework for employing longitudinally collected multicenter electronic health records to stratify heterogeneous patient populations on disease history
Maurits, Marc, Ilya Korsunsky, Soumya Raychaudhuri, Shawn Murphy, Jordan Smoller, Scott Weiss, Thomas Huizinga, et al. 2022. “A Framework for Employing Longitudinally Collected Multicenter Electronic Health Records to Stratify Heterogeneous Patient Populations on Disease History”. J Am Med Inform Assoc 29 (5): 761-69.
TCR-sequencing in cancer and autoimmunity: barcodes and beyond
Pauken, Kristen, Kaitlyn Lagattuta, Benjamin Lu, Liliana Lucca, Adil Daud, David Hafler, Harriet Kluger, Soumya Raychaudhuri, and Arlene Sharpe. 2022. “TCR-Sequencing in Cancer and Autoimmunity: Barcodes and Beyond”. Trends Immunol 43 (3): 180-94.
Multimodal platform for assessing drug distribution and response in clinical trials
Lopez, Begoña, Ishwar Kohale, Ziming Du, Ilya Korsunsky, Walid Abdelmoula, Yang Dai, Sylwia Stopka, et al. 2022. “Multimodal Platform for Assessing Drug Distribution and Response in Clinical Trials”. Neuro Oncol 24 (1): 64-77.
Efficient and precise single-cell reference atlas mapping with Symphony
Kang, Nathan, Weinand, Zhang, Millard, Rumker, D. Branch Moody, Korsunsky, and Raychaudhuri. 2022. “Efficient and Precise Single-Cell Reference Atlas Mapping With Symphony”. Nature Communications 12 (5890).
HATK: HLA Analysis Toolkit
Choi, Luo, Raychaudhuri, and Han. 2021. “HATK: HLA Analysis Toolkit”. Bioinformatics 37 (3): 416-18.
Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC)
Neale, Benjamin, Jesen Fagerness, Robyn Reynolds, Lucia Sobrin, Margaret Parker, Soumya Raychaudhuri, Perciliz Tan, et al. 2010. “Genome-Wide Association Study of Advanced Age-Related Macular Degeneration Identifies a Role of the Hepatic Lipase Gene (LIPC)”. Proc Natl Acad Sci U S A 107 (16): 7395-400.
A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases
Han, Buhm#, Jennie Pouget, Kamil Slowikowski, Eli Stahl, Cue Hyunkyu Lee, Dorothee Diogo, Xinli Hu, et al. 2016. “A Method to Decipher Pleiotropy by Detecting Underlying Heterogeneity Driven by Hidden Subgroups Applied to Autoimmune and Neuropsychiatric Diseases”. Nat Genet 48 (7): 803-10.