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Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases

Publication: Journal Article

Korsunsky, Ilya, Kevin Wei, Mathilde Pohin, Edy Kim, Francesca Barone, Triin Major, Emily Taylor, et al. 2022. “Cross-Tissue, Single-Cell Stromal Atlas Identifies Shared Pathological Fibroblast Phenotypes in Four Chronic Inflammatory Diseases”. Med (N Y) 3 (7): 481-518.e14.

Single-cell eQTL models reveal dynamic T cell state dependence of disease loci

Publication: Journal Article

Nathan, Aparna, Samira Asgari, Kazuyoshi Ishigaki, Cristian Valencia, Tiffany Amariuta, Yang Luo, Jessica Beynor, et al. 2022. “Single-Cell EQTL Models Reveal Dynamic T Cell State Dependence of Disease Loci”. Nature 606 (7912): 120-28.

Rheumatoid Arthritis Synovial Inflammation Quantification Using Computer Vision

Publication: Journal Article

Guan, Steven, Bella Mehta, David Slater, James Thompson, Edward DiCarlo, Tania Pannellini, Diyu Pearce-Fisher, et al. 2022. “Rheumatoid Arthritis Synovial Inflammation Quantification Using Computer Vision”. ACR Open Rheumatol 4 (4): 322-31.

Aparna Nathan

Person: Research Associate, Department of Biomedical Informatics, Harvard Medical School

I am a research associate at Harvard, and recently completed my PhD in Bioinformatics and Integrative Genomics in Raychaudhuri Lab. My dissertation focused on the integration of multimodal T cell data—RNA, surface proteins, genetics—to better understand their roles in infectious and autoimmune...

Higher native Peruvian genetic ancestry proportion is associated with tuberculosis progression risk

Publication: Journal Article

Asgari, Samira, Yang Luo, Chuan-Chin Huang, Zibiao Zhang, Roger Calderon, Judith Jimenez, Rosa Yataco, et al. 2022. “Higher Native Peruvian Genetic Ancestry Proportion Is Associated With Tuberculosis Progression Risk”. Cell Genom 2 (7).

Urine Proteomics and Renal Single-Cell Transcriptomics Implicate Interleukin-16 in Lupus Nephritis

Publication: Journal Article

Fava, Andrea, Deepak Rao, Chandra Mohan, Ting Zhang, Avi Rosenberg, Paride Fenaroli, Michael Belmont, et al. 2022. “Urine Proteomics and Renal Single-Cell Transcriptomics Implicate Interleukin-16 in Lupus Nephritis”. Arthritis Rheumatol 74 (5): 829-39.

Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics

Publication: Journal Article

Reshef, Yakir, Laurie Rumker, Joyce Kang, Aparna Nathan, Ilya Korsunsky, Samira Asgari, Megan Murray, Branch Moody, and Soumya Raychaudhuri. 2022. “Co-Varying Neighborhood Analysis Identifies Cell Populations Associated With Phenotypes of Interest from Single-Cell Transcriptomics”. Nat Biotechnol 40 (3): 355-63.

Mujin Kwun

Person: Harvard University, Undergraduate Student

A framework for employing longitudinally collected multicenter electronic health records to stratify heterogeneous patient populations on disease history

Publication: Journal Article

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

Publication: Journal Article

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.