SoumyaRaychaudhuriMDPhD

PubMed

• Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles.
  Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, , Andrew McDavid, Laura T Donlin, Alkes L Pri...> ;Nature Genetics. 2024 Apr 1
• Low-frequency and rare genetic variants associated with rheumatoid arthritis risk.
  James R Cerhan, Vanessa L Kronzer, Jeffrey A Sparks, Soumya Raychaudhuri> ;Nature Reviews. Rheumatology. 2024 Mar 27
• Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development.
  Taehyeung Kim, Marta Martínez-Bonet, Qiang Wang, Nicolaj Hackert, Jeffrey A Sparks, Yuriy Baglaenko, Byunghee Koh, Roxane Darbousset, Raquel Laza-Briviesca, Xiaoting C...> ;Nature Communications. 2024 Mar 9
• The genetic basis of autoimmunity seen through the lens of T cell functional traits.
  Lagattuta, K., Park, H., Rumker, L., Ishigaki, K., Nathan, A., Raychaudhuri, S.> ;Nature Communications. 2024 Feb 8
• Urine proteomic signatures of histological class, activity, chronicity, and treatment response in lupus nephritis.
  Andrea Fava, Jill Buyon, Laurence Magder, Jeff Hodgin, Avi Rosenberg, Dawit S Demeke, Deepak A Rao, Arnon Arazi, Alessandra Ida Celia, Chaim Putterman, Jennifer H Anol...> ;JCI Insight. 2024 Jan 23
• Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types.
  Samuel S Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price> ;Nature Communications. 2024 Jan 17
• 2 citations
  High-dimensional phenotyping to define the genetic basis of cellular morphology.
  Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta,...> ;Nature Communications. 2024 Jan 6
• Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma.
  Liu, Z., Luo, Y., Kirimunda, S., Verboom, M., Onabajo, O., Gouveia, M., Ogwang, M., Kerchan, P., Reynolds, S., Tenge, C., Were, P., Kuremu, R., Wekesa, W., Masalu, N.,...> ;Communications Biology. 2024 Jan 5
• 3 citations
  Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution.
  Joyce B Kang, Amber Z Shen, Saisriram Gurajala, Aparna Nathan, Laurie Rumker, Vitor R C Aguiar, Cristian Valencia, Kaitlyn A Lagattuta, Fan Zhang, Anna Helena Jonsson,...> ;Nature Genetics. 2023 Dec 1
• 1 citations
  Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability.
  Anika Gupta, Kathryn Weinand, Aparna Nathan, Saori Sakaue, Martin Jinye Zhang, , Laura Donlin, Kevin Wei, Alkes L Price, Tiffany Amariuta, Soumya Raychaudhuri> ;Nature Genetics. 2023 Dec 1
• Identifying genetic variants that influence the abundance of cell states in single-cell data.
  Laurie Rumker, Saori Sakaue, Joyce B Kang, Seyhan Yazar, Jose Alquicira-Hernandez, Cristian Valencia, Kaitlyn A Lagattuta, Aparna Nathan, Joseph E Powell, Po-Ru Loh, Y...> ;Biorxiv. 2023 Nov 15
• 15 citations
  Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes.
  Fan Zhang, Anna Helena Jonsson, Aparna Nathan, Nghia Millard, Michelle Curtis, Qian Xiao, Maria Gutierrez-Arcelus, William Apruzzese, Gerald F M Watts, Dana Weisenfeld...> ;Nature. 2023 Nov 1
• 1 citations
  Identification of a regulatory pathway governing TRAF1 via an arthritis-associated non-coding variant.
  Qiang Wang, Marta Martínez-Bonet, Taehyeung Kim, Jeffrey A Sparks, Kazuyoshi Ishigaki, Xiaoting Chen, Marc Sudman, Vitor Aguiar, Sangwan Sim, Marcos Chiñas Hernandez, ...> ;Cell Genomics. 2023 Nov 8
• 1 citations
  Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin.
  Qian Xiao, Joseph Mears, Aparna Nathan, Kazuyoshi Ishigaki, Yuriy Baglaenko, Noha Lim, Laura A Cooney, Kristina M Harris, Mark S Anderson, David A Fox, Dawn E Smilek, ...> ;Nature Communications. 2023 Oct 7
• 1 citations
  Associations Between Rheumatoid Arthritis Clinical Factors and Synovial Cell Types and States.
  Dana Weisenfeld, Fan Zhang, Laura Donlin, Anna Helena Jonsson, William Apruzzese, Debbie Campbell, , Deepak A Rao, Kevin Wei, V Michael Holers, Ellen Gravallese, Larry...> ;Arthritis & Rheumatology. 2024 Mar 1
• 5 citations
  Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease.
  Saori Sakaue, Saisriram Gurajala, Michelle Curtis, Yang Luo, Wanson Choi, Kazuyoshi Ishigaki, Joyce B Kang, Laurie Rumker, Aaron J Deutsch, Sebastian Schönherr, Lukas ...> ;Nature Protocols. 2023 Sep 1
• 1 citations
  The T cell receptor sequence influences the likelihood of T cell memory formation.
  Kaitlyn A Lagattuta, Aparna Nathan, Laurie Rumker, Michael E Birnbaum, Soumya Raychaudhuri> ;Biorxiv. 2023 Jul 23
• History of tuberculosis disease is associated with genetic regulatory variation in Peruvians.
  Sara Suliman, Victor E Nieto-Caballero, Samira Asgari, Kattya Lopez, Sarah K Iwany, Yang Luo, Aparna Nathan, Daniela Fernandez-Salinas, Marcos Chiñas, Chuan-Chin Huang...> ;Medrxiv. 2023 Jun 27
• 7 citations
  Methods and Insights from Single-Cell Expression Quantitative Trait Loci.
  Joyce B Kang, Alessandro Raveane, Aparna Nathan, Nicole Soranzo, Soumya Raychaudhuri> ;Annual Review of Genomics and Human Genetics. 2023 Aug 25
• 5 citations
  Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome.
  Alexandra Barry, Michelle T McNulty, Xiaoyuan Jia, Yask Gupta, Hanna Debiec, Yang Luo, China Nagano, Tomoko Horinouchi, Seulgi Jung, Manuela Colucci, Dina F Ahram, Ade...> ;Nature Communications. 2023 Apr 29
• 4 citations
  Identifying shared genetic architecture between rheumatoid arthritis and other conditions: a phenome-wide association study with genetic risk scores.
  Harrison G Zhang, Greg McDermott, Thany Seyok, Sicong Huang, Kumar Dahal, Sehi L'Yi, Clara Lea-Bonzel, Jacklyn Stratton, Dana Weisenfeld, Paul Monach, Soumya Raychaudh...> ;Ebiomedicine. 2023 Jun 1
• 7 citations
  Single-cell genomics meets human genetics.
  Anna S E Cuomo, Aparna Nathan, Soumya Raychaudhuri, Daniel G MacArthur, Joseph E Powell> ;Nature Reviews. Genetics. 2023 Aug 1
• 3 citations
  The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis.
  Kathryn Weinand, Saori Sakaue, Aparna Nathan, Anna Helena Jonsson, Fan Zhang, Gerald F M Watts, Zhu Zhu, , Deepak A Rao, Jennifer H Anolik, Michael B Brenner, Laura T ...> ;Biorxiv. 2023 Apr 8
• 4 citations
  Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium.
  Garrett Dunlap, Aaron Wagner, Nida Meednu, Fan Zhang, A Helena Jonsson, Kevin Wei, Saori Sakaue, Aparna Nathan, , Vivian P Bykerk, Laura T Donlin, Susan M Goodman, Gar...> ;Biorxiv. 2023 Mar 21
• 7 citations
  Mapping the dynamic genetic regulatory architecture ofgenes at single-cell resolution.
  Joyce B Kang, Amber Z Shen, Saori Sakaue, Yang Luo, Saisriram Gurajala, Aparna Nathan, Laurie Rumker, Vitor R C Aguiar, Cristian Valencia, Kaitlyn Lagattuta, Fan Zhang...> ;Medrxiv. 2023 Mar 20
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Journal Articles

• High-Throughput Identification of Noncoding Functional SNPs via Type IIS Enzyme Restriction  
  Soumya Raychaudhuri, Jing Cui, Michael B Brenner, Peter A Nigrovic, Nature
• Methods for High-Dimensonal Analysis of Cells Dissociated from Cyropreserved Synovial Tissue  
  Paul J Utz, William H Robinson, Ellen M Gravallese, Soumya Raychaudhuri, Alessandra B Pernis, Susan M Goodman, Michael B Brenner, Lionel B Ivashkiv, Brendan F Boyce, P..., BioMed Central

Other

• RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares 
  Soumya Raychaudhuri, MD, The New England Journal of Medicine
  https://www.doximity.com/articles/740ff412-66a4-4406-bb53-fe4500dd10fb
  UpToDate, Wolters Kluwer Health - 2012-06-14