Soumya Raychaudhuri

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 110

Top Venues

Nature communications

Nature genetics

bioRxiv : the preprint server for biology

Communications biology

This page only lists publications with an associated author ORCID identifier.

Publications

Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Dylan Kotliar, Michelle Curtis, Ryan Agnew, Kathryn Weinand, Aparna Nathan, Yuriy Baglaenko, Yu Zhao, Pardis C Sabeti, Deepak A Rao, Soumya Raychaudhuri
Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions. bioRxiv : the preprint server for biology (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Zhiwei Liu, Yang Luo, Samuel Kirimunda, Murielle Verboom, Olusegun O Onabajo, Mateus H Gouveia, Martin D Ogwang, Patrick Kerchan, Steven J Reynolds, Constance N Tenge, Pamela A Were, Robert T Kuremu, Walter N Wekesa, Nestory Masalu, Esther Kawira, Tobias Kinyera, Isaac Otim, Ismail D Legason, Hadijah Nabalende, Herry Dhudha, Leona W Ayers, Kishor Bhatia, James J Goedert, Nathan Cole, Wen Luo, Jia Liu, Michelle Manning, Belynda D Hicks, Ludmila Prokunina-Olsson, George Chagaluka, W Thomas Johnston, Nora Mutalima, Eric Borgstein, George N Liomba, Steve Kamiza, Nyengo Mkandawire, Collins Mitambo, Elizabeth M Molyneux, Robert Newton, Ann W Hsing, James E Mensah, Anthony A Adjei, Amy Hutchinson, Mary N Carrington, Meredith Yeager, Rainer Blasczyk, Stephen J Chanock, Soumya Raychaudhuri, Sam M Mbulaiteye
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma. Communications biology 7 (1) (2024)
Zhiwei Liu, Yang Luo, Samuel Kirimunda, Murielle Verboom, Olusegun O Onabajo, Mateus H Gouveia, Martin D Ogwang, Patrick Kerchan, Steven J Reynolds, Constance N Tenge, Pamela A Were, Robert T Kuremu, Walter N Wekesa, Nestory Masalu, Esther Kawira, Tobias Kinyera, Isaac Otim, Ismail D Legason, Hadijah Nabalende, Herry Dhudha, Leona W Ayers, Kishor Bhatia, James J Goedert, Nathan Cole, Wen Luo, Jia Liu, Michelle Manning, Belynda D Hicks, Ludmila Prokunina-Olsson, George Chagaluka, W Thomas Johnston, Nora Mutalima, Eric Borgstein, George N Liomba, Steve Kamiza, Nyengo Mkandawire, Collins Mitambo, Elizabeth M Molyneux, Robert Newton, Ann W Hsing, James E Mensah, Anthony A Adjei, Amy Hutchinson, Mary N Carrington, Meredith Yeager, Rainer Blasczyk, Stephen J Chanock, Soumya Raychaudhuri, Sam M Mbulaiteye
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma. Communications biology 7 (1) (2024)
Chirag Krishna, Joshua Chiou, Saori Sakaue, Joyce B Kang, Stephen M Christensen, Isac Lee, Melis Atalar Aksit, Hye In Kim, David von Schack, Soumya Raychaudhuri, Daniel Ziemek, Xinli Hu
The influence of HLA genetic variation on plasma protein expression. Nature communications 15 (1) (2024)
Kathryn Weinand, Saori Sakaue, Aparna Nathan, Anna Helena Jonsson, Fan Zhang, Gerald F M Watts, Majd Al Suqri, Zhu Zhu, null null, Deepak A Rao, Jennifer H Anolik, Michael B Brenner, Laura T Donlin, Kevin Wei, Soumya Raychaudhuri
The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nature communications 15 (1) (2024)
Garrett S Dunlap, Aaron Wagner, Nida Meednu, Ruoqiao Huiyi Wang, Fan Zhang, Jabea Cyril Ekabe, Anna Helena Jonsson, Kevin Wei, Saori Sakaue, Aparna Nathan, null null, Vivian P Bykerk, Laura T Donlin, Susan M Goodman, Gary S Firestein, David L Boyle, V Michael Holers, Larry W Moreland, Darren Tabechian, Costantino Pitzalis, Andrew Filer, Soumya Raychaudhuri, Michael B Brenner, Juilee Thakar, Andrew McDavid, Deepak A Rao, Jennifer H Anolik
Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Zhiwei Liu, Yang Luo, Samuel Kirimunda, Murielle Verboom, Olusegun O Onabajo, Mateus H Gouveia, Martin D Ogwang, Patrick Kerchan, Steven J Reynolds, Constance N Tenge, Pamela A Were, Robert T Kuremu, Walter N Wekesa, Nestory Masalu, Esther Kawira, Tobias Kinyera, Isaac Otim, Ismail D Legason, Hadijah Nabalende, Herry Dhudha, Leona W Ayers, Kishor Bhatia, James J Goedert, Nathan Cole, Wen Luo, Jia Liu, Michelle Manning, Belynda D Hicks, Ludmila Prokunina-Olsson, George Chagaluka, W Thomas Johnston, Nora Mutalima, Eric Borgstein, George N Liomba, Steve Kamiza, Nyengo Mkandawire, Collins Mitambo, Elizabeth M Molyneux, Robert Newton, Ann W Hsing, James E Mensah, Anthony A Adjei, Amy Hutchinson, Mary N Carrington, Meredith Yeager, Rainer Blasczyk, Stephen J Chanock, Soumya Raychaudhuri, Sam M Mbulaiteye
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma. Communications biology 7 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Vanessa L Kronzer, Jeffrey A Sparks, Soumya Raychaudhuri, James R Cerhan
Low-frequency and rare genetic variants associated with rheumatoid arthritis risk. Nature reviews. Rheumatology (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Kaitlyn A Lagattuta, Hannah L Park, Laurie Rumker, Kazuyoshi Ishigaki, Aparna Nathan, Soumya Raychaudhuri
The genetic basis of autoimmunity seen through the lens of T cell functional traits. Nature communications 15 (1) (2024)
Kaitlyn A Lagattuta, Hannah L Park, Laurie Rumker, Kazuyoshi Ishigaki, Aparna Nathan, Soumya Raychaudhuri
The genetic basis of autoimmunity seen through the lens of T cell functional traits. Nature communications 15 (1) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Kaitlyn A Lagattuta, Hannah L Park, Laurie Rumker, Kazuyoshi Ishigaki, Aparna Nathan, Soumya Raychaudhuri
The genetic basis of autoimmunity seen through the lens of T cell functional traits. Nature communications 15 (1) (2024)
Garrett S Dunlap, Aaron Wagner, Nida Meednu, Ruoqiao Huiyi Wang, Fan Zhang, Jabea Cyril Ekabe, Anna Helena Jonsson, Kevin Wei, Saori Sakaue, Aparna Nathan, null null, Vivian P Bykerk, Laura T Donlin, Susan M Goodman, Gary S Firestein, David L Boyle, V Michael Holers, Larry W Moreland, Darren Tabechian, Costantino Pitzalis, Andrew Filer, Soumya Raychaudhuri, Michael B Brenner, Juilee Thakar, Andrew McDavid, Deepak A Rao, Jennifer H Anolik
Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Kathryn Weinand, Saori Sakaue, Aparna Nathan, Anna Helena Jonsson, Fan Zhang, Gerald F M Watts, Majd Al Suqri, Zhu Zhu, null null, Deepak A Rao, Jennifer H Anolik, Michael B Brenner, Laura T Donlin, Kevin Wei, Soumya Raychaudhuri
The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nature communications 15 (1) (2024)
Alice Horisberger, Alec Griffith, Joshua Keegan, Arnon Arazi, John Pulford, Ekaterina Murzin, Kaitlyn Howard, Brandon Hancock, Andrea Fava, Takanori Sasaki, Tusharkanti Ghosh, Jun Inamo, Rebecca Beuschel, Ye Cao, Katie Preisinger, Maria Gutierrez-Arcelus, Thomas M Eisenhaure, Joel M Guthridge, Paul J Hoover, Maria Dall'Era, David Wofsy, Diane L Kamen, Kenneth C Kalunian, Richard Furie, Michael Belmont, Peter Izmirly, Robert Clancy, David A Hildeman, E Steve Woodle, William Apruzzese, Maureen A McMahon, Jennifer Grossman, Jennifer L Barnas, Fernanda Payan-Schober, Mariko Ishimori, Michael Weisman, Matthias Kretzler, Celine C Berthier, Jeffrey B Hodgin, Dawit S Demeke, Chaim Putterman, null null, Michael B Brenner, Jennifer H Anolik, Soumya Raychaudhuri, Nir Hacohen, Judith A James, Anne Davidson, Michelle A Petri, Jill P Buyon, Betty Diamond, Fan Zhang, James A Lederer, Deepak A Rao
Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis. bioRxiv : the preprint server for biology (2024)
Dylan Kotliar, Michelle Curtis, Ryan Agnew, Kathryn Weinand, Aparna Nathan, Yuriy Baglaenko, Yu Zhao, Pardis C Sabeti, Deepak A Rao, Soumya Raychaudhuri
Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions. bioRxiv : the preprint server for biology (2024)
Garrett S Dunlap, Aaron Wagner, Nida Meednu, Ruoqiao Huiyi Wang, Fan Zhang, Jabea Cyril Ekabe, Anna Helena Jonsson, Kevin Wei, Saori Sakaue, Aparna Nathan, null null, Vivian P Bykerk, Laura T Donlin, Susan M Goodman, Gary S Firestein, David L Boyle, V Michael Holers, Larry W Moreland, Darren Tabechian, Costantino Pitzalis, Andrew Filer, Soumya Raychaudhuri, Michael B Brenner, Juilee Thakar, Andrew McDavid, Deepak A Rao, Jennifer H Anolik
Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nature communications 15 (1) (2024)
Kathryn Weinand, Saori Sakaue, Aparna Nathan, Anna Helena Jonsson, Fan Zhang, Gerald F M Watts, Majd Al Suqri, Zhu Zhu, null null, Deepak A Rao, Jennifer H Anolik, Michael B Brenner, Laura T Donlin, Kevin Wei, Soumya Raychaudhuri
The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Kaitlyn A Lagattuta, Hannah L Park, Laurie Rumker, Kazuyoshi Ishigaki, Aparna Nathan, Soumya Raychaudhuri
The genetic basis of autoimmunity seen through the lens of T cell functional traits. Nature communications 15 (1) (2024)
Chirag Krishna, Joshua Chiou, Saori Sakaue, Joyce B Kang, Stephen M Christensen, Isac Lee, Melis Atalar Aksit, Hye In Kim, David von Schack, Soumya Raychaudhuri, Daniel Ziemek, Xinli Hu
The influence of HLA genetic variation on plasma protein expression. Nature communications 15 (1) (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Zhiwei Liu, Yang Luo, Samuel Kirimunda, Murielle Verboom, Olusegun O Onabajo, Mateus H Gouveia, Martin D Ogwang, Patrick Kerchan, Steven J Reynolds, Constance N Tenge, Pamela A Were, Robert T Kuremu, Walter N Wekesa, Nestory Masalu, Esther Kawira, Tobias Kinyera, Isaac Otim, Ismail D Legason, Hadijah Nabalende, Herry Dhudha, Leona W Ayers, Kishor Bhatia, James J Goedert, Nathan Cole, Wen Luo, Jia Liu, Michelle Manning, Belynda D Hicks, Ludmila Prokunina-Olsson, George Chagaluka, W Thomas Johnston, Nora Mutalima, Eric Borgstein, George N Liomba, Steve Kamiza, Nyengo Mkandawire, Collins Mitambo, Elizabeth M Molyneux, Robert Newton, Ann W Hsing, James E Mensah, Anthony A Adjei, Amy Hutchinson, Mary N Carrington, Meredith Yeager, Rainer Blasczyk, Stephen J Chanock, Soumya Raychaudhuri, Sam M Mbulaiteye
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma. Communications biology 7 (1) (2024)
Zhiwei Liu, Yang Luo, Samuel Kirimunda, Murielle Verboom, Olusegun O Onabajo, Mateus H Gouveia, Martin D Ogwang, Patrick Kerchan, Steven J Reynolds, Constance N Tenge, Pamela A Were, Robert T Kuremu, Walter N Wekesa, Nestory Masalu, Esther Kawira, Tobias Kinyera, Isaac Otim, Ismail D Legason, Hadijah Nabalende, Herry Dhudha, Leona W Ayers, Kishor Bhatia, James J Goedert, Nathan Cole, Wen Luo, Jia Liu, Michelle Manning, Belynda D Hicks, Ludmila Prokunina-Olsson, George Chagaluka, W Thomas Johnston, Nora Mutalima, Eric Borgstein, George N Liomba, Steve Kamiza, Nyengo Mkandawire, Collins Mitambo, Elizabeth M Molyneux, Robert Newton, Ann W Hsing, James E Mensah, Anthony A Adjei, Amy Hutchinson, Mary N Carrington, Meredith Yeager, Rainer Blasczyk, Stephen J Chanock, Soumya Raychaudhuri, Sam M Mbulaiteye
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma. Communications biology 7 (1) (2024)
Kaitlyn A Lagattuta, Hannah L Park, Laurie Rumker, Kazuyoshi Ishigaki, Aparna Nathan, Soumya Raychaudhuri
The genetic basis of autoimmunity seen through the lens of T cell functional traits. Nature communications 15 (1) (2024)
Kathryn Weinand, Saori Sakaue, Aparna Nathan, Anna Helena Jonsson, Fan Zhang, Gerald F M Watts, Majd Al Suqri, Zhu Zhu, null null, Deepak A Rao, Jennifer H Anolik, Michael B Brenner, Laura T Donlin, Kevin Wei, Soumya Raychaudhuri
The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nature communications 15 (1) (2024)
Alice Horisberger, Alec Griffith, Joshua Keegan, Arnon Arazi, John Pulford, Ekaterina Murzin, Kaitlyn Howard, Brandon Hancock, Andrea Fava, Takanori Sasaki, Tusharkanti Ghosh, Jun Inamo, Rebecca Beuschel, Ye Cao, Katie Preisinger, Maria Gutierrez-Arcelus, Thomas M Eisenhaure, Joel M Guthridge, Paul J Hoover, Maria Dall'Era, David Wofsy, Diane L Kamen, Kenneth C Kalunian, Richard Furie, Michael Belmont, Peter Izmirly, Robert Clancy, David A Hildeman, E Steve Woodle, William Apruzzese, Maureen A McMahon, Jennifer Grossman, Jennifer L Barnas, Fernanda Payan-Schober, Mariko Ishimori, Michael Weisman, Matthias Kretzler, Celine C Berthier, Jeffrey B Hodgin, Dawit S Demeke, Chaim Putterman, null null, Michael B Brenner, Jennifer H Anolik, Soumya Raychaudhuri, Nir Hacohen, Judith A James, Anne Davidson, Michelle A Petri, Jill P Buyon, Betty Diamond, Fan Zhang, James A Lederer, Deepak A Rao
Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis. bioRxiv : the preprint server for biology (2024)
Garrett S Dunlap, Aaron Wagner, Nida Meednu, Ruoqiao Huiyi Wang, Fan Zhang, Jabea Cyril Ekabe, Anna Helena Jonsson, Kevin Wei, Saori Sakaue, Aparna Nathan, null null, Vivian P Bykerk, Laura T Donlin, Susan M Goodman, Gary S Firestein, David L Boyle, V Michael Holers, Larry W Moreland, Darren Tabechian, Costantino Pitzalis, Andrew Filer, Soumya Raychaudhuri, Michael B Brenner, Juilee Thakar, Andrew McDavid, Deepak A Rao, Jennifer H Anolik
Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nature communications 15 (1) (2024)
Chirag Krishna, Joshua Chiou, Saori Sakaue, Joyce B Kang, Stephen M Christensen, Isac Lee, Melis Atalar Aksit, Hye In Kim, David von Schack, Soumya Raychaudhuri, Daniel Ziemek, Xinli Hu
The influence of HLA genetic variation on plasma protein expression. Nature communications 15 (1) (2024)
Samuel Sungil Kim, Buu Truong, Karthik Jagadeesh, Kushal K Dey, Amber Z Shen, Soumya Raychaudhuri, Manolis Kellis, Alkes L Price
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nature communications 15 (1) (2024)
Vanessa L Kronzer, Jeffrey A Sparks, Soumya Raychaudhuri, James R Cerhan
Low-frequency and rare genetic variants associated with rheumatoid arthritis risk. Nature reviews. Rheumatology 20 (5) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Kaitlyn A Lagattuta, Hannah L Park, Laurie Rumker, Kazuyoshi Ishigaki, Aparna Nathan, Soumya Raychaudhuri
The genetic basis of autoimmunity seen through the lens of T cell functional traits. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Garrett S Dunlap, Aaron Wagner, Nida Meednu, Ruoqiao Huiyi Wang, Fan Zhang, Jabea Cyril Ekabe, Anna Helena Jonsson, Kevin Wei, Saori Sakaue, Aparna Nathan, null null, Vivian P Bykerk, Laura T Donlin, Susan M Goodman, Gary S Firestein, David L Boyle, V Michael Holers, Larry W Moreland, Darren Tabechian, Costantino Pitzalis, Andrew Filer, Soumya Raychaudhuri, Michael B Brenner, Juilee Thakar, Andrew McDavid, Deepak A Rao, Jennifer H Anolik
Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nature communications 15 (1) (2024)
Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K Dey, Karthik A Jagadeesh, Masahiro Kanai, Gerald F M Watts, Zhu Zhu, null null, Michael B Brenner, Andrew McDavid, Laura T Donlin, Kevin Wei, Alkes L Price, Soumya Raychaudhuri
Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. Nature genetics 56 (4) (2024)
Zhiwei Liu, Yang Luo, Samuel Kirimunda, Murielle Verboom, Olusegun O Onabajo, Mateus H Gouveia, Martin D Ogwang, Patrick Kerchan, Steven J Reynolds, Constance N Tenge, Pamela A Were, Robert T Kuremu, Walter N Wekesa, Nestory Masalu, Esther Kawira, Tobias Kinyera, Isaac Otim, Ismail D Legason, Hadijah Nabalende, Herry Dhudha, Leona W Ayers, Kishor Bhatia, James J Goedert, Nathan Cole, Wen Luo, Jia Liu, Michelle Manning, Belynda D Hicks, Ludmila Prokunina-Olsson, George Chagaluka, W Thomas Johnston, Nora Mutalima, Eric Borgstein, George N Liomba, Steve Kamiza, Nyengo Mkandawire, Collins Mitambo, Elizabeth M Molyneux, Robert Newton, Ann W Hsing, James E Mensah, Anthony A Adjei, Amy Hutchinson, Mary N Carrington, Meredith Yeager, Rainer Blasczyk, Stephen J Chanock, Soumya Raychaudhuri, Sam M Mbulaiteye
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma. Communications biology 7 (1) (2024)
Zhiwei Liu, Yang Luo, Samuel Kirimunda, Murielle Verboom, Olusegun O Onabajo, Mateus H Gouveia, Martin D Ogwang, Patrick Kerchan, Steven J Reynolds, Constance N Tenge, Pamela A Were, Robert T Kuremu, Walter N Wekesa, Nestory Masalu, Esther Kawira, Tobias Kinyera, Isaac Otim, Ismail D Legason, Hadijah Nabalende, Herry Dhudha, Leona W Ayers, Kishor Bhatia, James J Goedert, Nathan Cole, Wen Luo, Jia Liu, Michelle Manning, Belynda D Hicks, Ludmila Prokunina-Olsson, George Chagaluka, W Thomas Johnston, Nora Mutalima, Eric Borgstein, George N Liomba, Steve Kamiza, Nyengo Mkandawire, Collins Mitambo, Elizabeth M Molyneux, Robert Newton, Ann W Hsing, James E Mensah, Anthony A Adjei, Amy Hutchinson, Mary N Carrington, Meredith Yeager, Rainer Blasczyk, Stephen J Chanock, Soumya Raychaudhuri, Sam M Mbulaiteye
Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma. Communications biology 7 (1) (2024)
Garrett S Dunlap, Aaron Wagner, Nida Meednu, Ruoqiao Huiyi Wang, Fan Zhang, Jabea Cyril Ekabe, Anna Helena Jonsson, Kevin Wei, Saori Sakaue, Aparna Nathan, null null, Vivian P Bykerk, Laura T Donlin, Susan M Goodman, Gary S Firestein, David L Boyle, V Michael Holers, Larry W Moreland, Darren Tabechian, Costantino Pitzalis, Andrew Filer, Soumya Raychaudhuri, Michael B Brenner, Juilee Thakar, Andrew McDavid, Deepak A Rao, Jennifer H Anolik
Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nature communications 15 (1) (2024)
Kaitlyn A Lagattuta, Hannah L Park, Laurie Rumker, Kazuyoshi Ishigaki, Aparna Nathan, Soumya Raychaudhuri
The genetic basis of autoimmunity seen through the lens of T cell functional traits. Nature communications 15 (1) (2024)
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, Seyhan Yazar, Jose Alquicira-Hernandez, Hamed Khalili, Ashwin N Ananthakrishnan, Karthik A Jagadeesh, Kushal K Dey, null null, Mark J Daly, Ramnik J Xavier, Laura T Donlin, Jennifer H Anolik, Joseph E Powell, Deepak A Rao, Michael B Brenner, Maria Gutierrez-Arcelus, Yang Luo, Saori Sakaue, Soumya Raychaudhuri
Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution. Nature genetics (2023)
Anna S E Cuomo, Aparna Nathan, Soumya Raychaudhuri, Daniel G MacArthur, Joseph E Powell
Single-cell genomics meets human genetics. Nature reviews. Genetics (2023)
Alexandra Barry, Michelle T McNulty, Xiaoyuan Jia, Yask Gupta, Hanna Debiec, Yang Luo, China Nagano, Tomoko Horinouchi, Seulgi Jung, Manuela Colucci, Dina F Ahram, Adele Mitrotti, Aditi Sinha, Nynke Teeninga, Gina Jin, Shirlee Shril, Gianluca Caridi, Monica Bodria, Tze Y Lim, Nine V A M Knoers, Francesca Zanoni, Maddalena Marasà, Daniel Turudic, Mario Giordano, Loreto Gesualdo, Riccardo Magistroni, Isabella Pisani, Enrico Fiaccadori, Jana Reiterova, Silvio Maringhini, William Morello, Giovanni Montini, Patricia L Weng, Francesco Scolari, Marijan Saraga, Velibor Tasic, Domenica Santoro, Joanna A E van Wijk, Danko Milošević, Yosuke Kawai, Krzysztof Kiryluk, Martin R Pollak, Ali G Gharavi, Fangming Lin, Ana Cristina Dos Santos Lopes, Ruth J F Loos, Eimear E Kenny, Michiel F Schreuder, Aleksandra Zurowska, Claire Dossier, Gema Ariceta, Magdalena Drozynska-Duklas, Julien Hogan, Augustina Jankauskiene, Friedhelm Hildebrandt, Larisa Prikhodina, Kyuyoung Song, Arvind Bagga, Hae Il Cheong, Gian Marco Ghiggeri, Prayong Vachvanichsanong, Kandai Nozu, Dongwon Lee, Marina Vivarelli, Soumya Raychaudhuri, Katsushi Tokunaga, Simone Sanna-Cherchi, Pierre Ronco, Kazumoto Iijima, Matthew Gordon Sampson
Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome. Nature communications 14 (1) (2023)
Anika Gupta, Kathryn Weinand, Aparna Nathan, Saori Sakaue, Martin Jinye Zhang, null null, Laura Donlin, Kevin Wei, Alkes L Price, Tiffany Amariuta, Soumya Raychaudhuri
Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability. Nature genetics (2023)
Anna S E Cuomo, Aparna Nathan, Soumya Raychaudhuri, Daniel G MacArthur, Joseph E Powell
Single-cell genomics meets human genetics. Nature reviews. Genetics (2023)
Jun Inamo, Joshua Keegan, Alec Griffith, Tusharkanti Ghosh, Alice Horisberger, Kaitlyn Howard, John Pulford, Ekaterina Murzin, Brandon Hancock, Anna Helena Jonsson, Jennifer Seifert, Marie L Feser, Jill M Norris, Ye Cao, William Apruzzese, S Louis Bridges, Vivian Bykerk, Susan Goodman, Laura T Donlin, Gary S Firestein, Harris Perlman, Joan M Bathon, Laura B Hughes, Darren Tabechian, Andrew Filer, Costantino Pitzalis, Jennifer H Anolik, Larry Moreland, Joel M Guthridge, Judith A James, Michael B Brenner, Soumya Raychaudhuri, Jeffrey A Sparks, null null, V Michael Holers, Kevin D Deane, James A Lederer, Deepak A Rao, Fan Zhang
Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis. bioRxiv : the preprint server for biology (2023)
Alexandra Barry, Michelle T McNulty, Xiaoyuan Jia, Yask Gupta, Hanna Debiec, Yang Luo, China Nagano, Tomoko Horinouchi, Seulgi Jung, Manuela Colucci, Dina F Ahram, Adele Mitrotti, Aditi Sinha, Nynke Teeninga, Gina Jin, Shirlee Shril, Gianluca Caridi, Monica Bodria, Tze Y Lim, Nine V A M Knoers, Francesca Zanoni, Maddalena Marasà, Daniel Turudic, Mario Giordano, Loreto Gesualdo, Riccardo Magistroni, Isabella Pisani, Enrico Fiaccadori, Jana Reiterova, Silvio Maringhini, William Morello, Giovanni Montini, Patricia L Weng, Francesco Scolari, Marijan Saraga, Velibor Tasic, Domenica Santoro, Joanna A E van Wijk, Danko Milošević, Yosuke Kawai, Krzysztof Kiryluk, Martin R Pollak, Ali G Gharavi, Fangming Lin, Ana Cristina Dos Santos Lopes, Ruth J F Loos, Eimear E Kenny, Michiel F Schreuder, Aleksandra Zurowska, Claire Dossier, Gema Ariceta, Magdalena Drozynska-Duklas, Julien Hogan, Augustina Jankauskiene, Friedhelm Hildebrandt, Larisa Prikhodina, Kyuyoung Song, Arvind Bagga, Hae Il Cheong, Gian Marco Ghiggeri, Prayong Vachvanichsanong, Kandai Nozu, Dongwon Lee, Marina Vivarelli, Soumya Raychaudhuri, Katsushi Tokunaga, Simone Sanna-Cherchi, Pierre Ronco, Kazumoto Iijima, Matthew Gordon Sampson
Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome. Nature communications 14 (1) (2023)
Saori Sakaue, Saisriram Gurajala, Michelle Curtis, Yang Luo, Wanson Choi, Kazuyoshi Ishigaki, Joyce B Kang, Laurie Rumker, Aaron J Deutsch, Sebastian Schönherr, Lukas Forer, Jonathon LeFaive, Christian Fuchsberger, Buhm Han, Tobias L Lenz, Paul I W de Bakker, Yukinori Okada, Albert V Smith, Soumya Raychaudhuri
Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease. Nature protocols (2023)
Anna S E Cuomo, Aparna Nathan, Soumya Raychaudhuri, Daniel G MacArthur, Joseph E Powell
Single-cell genomics meets human genetics. Nature reviews. Genetics (2023)
Laurie Rumker, Saori Sakaue, Yakir Reshef, Joyce B Kang, Seyhan Yazar, Jose Alquicira-Hernandez, Cristian Valencia, Kaitlyn A Lagattuta, Annelise Mah-Som, Aparna Nathan, Joseph E Powell, Po-Ru Loh, Soumya Raychaudhuri
Identifying genetic variants that influence the abundance of cell states in single-cell data. bioRxiv : the preprint server for biology (2023)
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, Anna Helena Jonsson, Seyhan Yazar, Jose Alquicira Hernandez, Hamed Khalili, Ashwin N Ananthakrishnan, Karthik Jagadeesh, Kushal Dey, null null, Mark J Daly, Ramnik J Xavier, Laura T Donlin, Jennifer H Anolik, Joseph E Powell, Deepak A Rao, Michael B Brenner, Maria Gutierrez-Arcelus, Soumya Raychaudhuri
Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution. medRxiv : the preprint server for health sciences (2023)
Alexandra Barry, Michelle T McNulty, Xiaoyuan Jia, Yask Gupta, Hanna Debiec, Yang Luo, China Nagano, Tomoko Horinouchi, Seulgi Jung, Manuela Colucci, Dina F Ahram, Adele Mitrotti, Aditi Sinha, Nynke Teeninga, Gina Jin, Shirlee Shril, Gianluca Caridi, Monica Bodria, Tze Y Lim, Nine V A M Knoers, Francesca Zanoni, Maddalena Marasà, Daniel Turudic, Mario Giordano, Loreto Gesualdo, Riccardo Magistroni, Isabella Pisani, Enrico Fiaccadori, Jana Reiterova, Silvio Maringhini, William Morello, Giovanni Montini, Patricia L Weng, Francesco Scolari, Marijan Saraga, Velibor Tasic, Domenica Santoro, Joanna A E van Wijk, Danko Milošević, Yosuke Kawai, Krzysztof Kiryluk, Martin R Pollak, Ali G Gharavi, Fangming Lin, Ana Cristina Dos Santos Lopes, Ruth J F Loos, Eimear E Kenny, Michiel F Schreuder, Aleksandra Zurowska, Claire Dossier, Gema Ariceta, Magdalena Drozynska-Duklas, Julien Hogan, Augustina Jankauskiene, Friedhelm Hildebrandt, Larisa Prikhodina, Kyuyoung Song, Arvind Bagga, Hae Il Cheong, Gian Marco Ghiggeri, Prayong Vachvanichsanong, Kandai Nozu, Dongwon Lee, Marina Vivarelli, Soumya Raychaudhuri, Katsushi Tokunaga, Simone Sanna-Cherchi, Pierre Ronco, Kazumoto Iijima, Matthew Gordon Sampson
Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome. Nature communications 14 (1) (2023)
Kaitlyn A Lagattuta, Aparna Nathan, Laurie Rumker, Michael E Birnbaum, Soumya Raychaudhuri
The T cell receptor sequence influences the likelihood of T cell memory formation. bioRxiv : the preprint server for biology (2023)
Kathryn Weinand, Saori Sakaue, Aparna Nathan, Anna Helena Jonsson, Fan Zhang, Gerald F M Watts, Zhu Zhu, null null, Deepak A Rao, Jennifer H Anolik, Michael B Brenner, Laura T Donlin, Kevin Wei, Soumya Raychaudhuri
The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis. bioRxiv : the preprint server for biology (2023)
Anna S E Cuomo, Aparna Nathan, Soumya Raychaudhuri, Daniel G MacArthur, Joseph E Powell
Single-cell genomics meets human genetics. Nature reviews. Genetics (2023)
Fan Zhang, Anna Helena Jonsson, Aparna Nathan, Nghia Millard, Michelle Curtis, Qian Xiao, Maria Gutierrez-Arcelus, William Apruzzese, Gerald F M Watts, Dana Weisenfeld, Saba Nayar, Javier Rangel-Moreno, Nida Meednu, Kathryne E Marks, Ian Mantel, Joyce B Kang, Laurie Rumker, Joseph Mears, Kamil Slowikowski, Kathryn Weinand, Dana E Orange, Laura Geraldino-Pardilla, Kevin D Deane, Darren Tabechian, Arnoldas Ceponis, Gary S Firestein, Mark Maybury, Ilfita Sahbudin, Ami Ben-Artzi, Arthur M Mandelin, Alessandra Nerviani, Myles J Lewis, Felice Rivellese, Costantino Pitzalis, Laura B Hughes, Diane Horowitz, Edward DiCarlo, Ellen M Gravallese, Brendan F Boyce, null null, Larry W Moreland, Susan M Goodman, Harris Perlman, V Michael Holers, Katherine P Liao, Andrew Filer, Vivian P Bykerk, Kevin Wei, Deepak A Rao, Laura T Donlin, Jennifer H Anolik, Michael B Brenner, Soumya Raychaudhuri
Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes. Nature (2023)
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, James G Krueger, Soumya Raychaudhuri
Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin. Nature communications 14 (1) (2023)
Carmel Stober, Iain B McInnes, Soumya Raychaudhuri, Phillip J Mease, Stephen R Pennington, Jose U Scher, Vinod Chandran, April W Armstrong, Maarten P T de Wit, Alberto Cauli, Deepak R Jadon, Thorvardur Jon Love, Philip S Helliwell, Denis O'Sullivan, Leonieke J J van Mens, Christopher T Ritchlin, Oliver M FitzGerald
Proceedings of the 2021 GRAPPA-Collaborative Research Network (CRN) Meeting. The Journal of rheumatology 49 (6 Suppl 1) (2022)
Martin Jinye Zhang, Kangcheng Hou, Kushal K Dey, Saori Sakaue, Karthik A Jagadeesh, Kathryn Weinand, Aris Taychameekiatchai, Poorvi Rao, Angela Oliveira Pisco, James Zou, Bruce Wang, Michael J Gandal, Soumya Raychaudhuri, Bogdan Pasaniuc, Alkes L Price
Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data. Nature genetics 54 (10) (2022)
Kazuyoshi Ishigaki, Kaitlyn A Lagattuta, Yang Luo, Eddie A James, Jane H Buckner, Soumya Raychaudhuri
HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors. Nature genetics 54 (4) (2022)
Kaitlyn A Lagattuta, Joyce B Kang, Aparna Nathan, Kristen E Pauken, Anna Helena Jonsson, Deepak A Rao, Arlene H Sharpe, Kazuyoshi Ishigaki, Soumya Raychaudhuri
Repertoire analyses reveal T cell antigen receptor sequence features that influence T cell fate. Nature immunology 23 (3) (2022)
Anna Helena Jonsson, Fan Zhang, Garrett S Dunlap, Emma Gomez-Rivas, Gerald F M Watts, Heather J Faust, Karishma Vijay Rupani, Joseph R Mears, Nida Meednu, Runci Wang, Gregory Keras, Jonathan S Coblyn, Elena M Massarotti, Derrick J Todd, Jennifer H Anolik, Andrew N McDavid, null null, Kevin Wei, Deepak A Rao, Soumya Raychaudhuri, Michael B Brenner
Granzyme K + CD8 T cells form a core population in inflamed human tissue. Science translational medicine 14 (649) (2022)
Aparna Nathan, Samira Asgari, Kazuyoshi Ishigaki, Cristian Valencia, Tiffany Amariuta, Yang Luo, Jessica I Beynor, Yuriy Baglaenko, Sara Suliman, Alkes L Price, Leonid Lecca, Megan B Murray, D Branch Moody, Soumya Raychaudhuri
Single-cell eQTL models reveal dynamic T cell state dependence of disease loci. Nature 606 (7912) (2022)
Kazuyoshi Ishigaki, Saori Sakaue, Chikashi C Terao, Yang Luo, Kyuto Sonehara, Kensuke Yamaguchi, Tiffany Amariuta, Chun Lai Too, Vincent A Laufer, Ian C Scott, Sebastien Viatte, Meiko Takahashi, Koichiro Ohmura, Akira Murasawa, Motomu Hashimoto, Hiromu Ito, Mohammed Hammoudeh, Samar Al Emadi, Basel K Masri, Hussein Halabi, Humeira Badsha, Imad W Uthman, Xin Wu, Li Lin, Ting Li, Darren Plant, Richard B Warren, Gisela Orozco, Suzanne M M Verstappen, John David Bowes, Alexander J MacGregor, Suguru Honda, Masaru Koido, Kohei Tomizuka, Yoichiro Kamatani, Hiroaki Tanaka, Eiichi Tanaka, Akari Suzuki, Yuichi Maeda, Kenichi Yamamoto, Satoru Miyawaki, Gang Xie, Jinyi Zhang, Christopher Ian Amos, Edward Keystone, Gertjan Wolbink, Irene van der Horst-Bruinsma, Jing Cui, Katherine P Liao, Robert J Carroll, Hye-Soon Lee, So-Young Bang, Katherine A Siminovitch, Niek De Vries, Lars Alfredsson, Solbritt Rantapää Dahlqvist, Elizabeth W Karlson, Sang-Cheol Bae, Robert P Kimberly, Jeffrey C Edberg, Xavier Mariette, Thomas Wj Huizinga, Philippe Dieude, Matthias Schneider, Martin Kerick, Joshua C Denny, null null, Koichi Matsuda, Keitaro Matsuo, Tsuneyo Mimori, Fumihiko Matsuda, Keishi Fujio, Yoshiya Tanaka, Atsushi Kumanogoh, Matthew Traylor, Cathryn M Lewis, Stephen Eyre, Huji Xu, Richa Saxena, Thurayya Arayssi, Yuta Kochi, Katsunori Ikari, Masayoshi Harigai, Peter K Gregersen, Kazuhiko Yamamoto, S Louis Bridges, Leonid Padyukov, Javier Martín, Lars Klareskog, Yukinori Okada, Soumya Raychaudhuri
Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nature genetics 54 (11) (2022)
Elaine T Lim, Yingleong Chan, Pepper Dawes, Xiaoge Guo, Serkan Erdin, Derek J C Tai, Songlei Liu, Julia M Reichert, Mannix J Burns, Ying Kai Chan, Jessica J Chiang, Katharina Meyer, Xiaochang Zhang, Christopher A Walsh, Bruce A Yankner, Soumya Raychaudhuri, Joel N Hirschhorn, James F Gusella, Michael E Talkowski, George M Church
Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder. Nature communications 13 (1) (2022)
Vijayashree Mysore, Suhail Tahir, Kazuhiro Furuhashi, Jatin Arora, Florencia Rosetti, Xavier Cullere, Pascal Yazbeck, Miroslav Sekulic, Madeleine E Lemieux, Soumya Raychaudhuri, Bruce H Horwitz, Tanya N Mayadas
Monocytes transition to macrophages within the inflamed vasculature via monocyte CCR2 and endothelial TNFR2. The Journal of experimental medicine 219 (5) (2022)
Aparna Nathan, Jessica I Beynor, Yuriy Baglaenko, Sara A Suliman, Kazuyoshi Ishigaki, Samira Asgari, Chuan-Chin Huang, Yang Luo, Zibiao Zhang, Kattya Lopez, Cecilia S Lindestam Arlehamn, Joel D Ernst, Judith Jimenez, Roger I Calderon, Leonid Lecca, Ildiko Van Rhijn, D Branch Moody, Megan B Murray, Soumya Raychaudhuri
Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease. Nature immunology 22 (6) (2021)
Huwenbo Shi, Steven Gazal, Masahiro Kanai, Evan M Koch, Armin P Schoech, Katherine M Siewert, Samuel Sungil Kim, Yang Luo, Tiffany Amariuta, Hailiang Huang, Yukinori Okada, Soumya Raychaudhuri, Shamil R Sunyaev, Alkes L Price
Population-specific causal disease effect sizes in functionally important regions impacted by selection. Nature communications 12 (1) (2021)
Yakir A Reshef, Laurie Rumker, Joyce B Kang, Aparna Nathan, Ilya Korsunsky, Samira Asgari, Megan B Murray, D Branch Moody, Soumya Raychaudhuri
Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics. Nature biotechnology (2021)
Fan Zhang, Joseph R Mears, Lorien Shakib, Jessica I Beynor, Sara Shanaj, Ilya Korsunsky, Aparna Nathan, null null, Laura T Donlin, Soumya Raychaudhuri
IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation. Genome medicine 13 (1) (2021)
Seungho Cook, Wanson Choi, Hyunjoon Lim, Yang Luo, Kunhee Kim, Xiaoming Jia, Soumya Raychaudhuri, Buhm Han
Accurate imputation of human leukocyte antigens with CookHLA. Nature communications 12 (1) (2021)
Yang Luo, Masahiro Kanai, Wanson Choi, Xinyi Li, Saori Sakaue, Kenichi Yamamoto, Kotaro Ogawa, Maria Gutierrez-Arcelus, Peter K Gregersen, Philip E Stuart, James T Elder, Lukas Forer, Sebastian Schönherr, Christian Fuchsberger, Albert Vernon Smith, Jacques Fellay, Mary N Carrington, David W Haas, Xiuqing Guo, Nicholette D D Allred, Yii-Der Ida Chen, Jerome I Rotter, Kent D Taylor, Stephen S Rich, Adolfo Correa, James G Wilson, Sekar Kathiresan, Michael H Cho, Andres Metspalu, Tõnu Esko, Yukinori Okada, Buhm Han, null null, Paul J McLaren, Soumya Raychaudhuri
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response. Nature genetics 53 (10) (2021)
Matthias Friedrich, Mathilde Pohin, Matthew A Jackson, Ilya Korsunsky, Samuel J Bullers, Kevin Christophe Rue-Albrecht, Zoe Christoforidou, Dharshan Sathananthan, Tom Thomas, Rahul Ravindran, Ruchi Tandon, Raphael Sanches Peres, Hannah R Sharpe, Kevin Wei, Gerald F M Watts, Elizabeth H Mann, Alessandra Geremia, Moustafa Attar, null null, null null, Sarah McCuaig, Lloyd Thomas, Elena Collantes, Hans Holm Uhlig, Stephen N Sansom, Alistair Easton, Soumya Raychaudhuri, Simon P L Travis, Fiona M Powrie
IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies. Nature medicine 27 (11) (2021)
Rachel Knevel, Saskia Le Cessie, Chikashi C Terao, Kamil Slowikowski, Jing Cui, Thomas Wj Huizinga, Karen H Costenbader, Katherine P Liao, Elizabeth W Karlson, Soumya Raychaudhuri
Using genetics to prioritize diagnoses for rheumatology outpatients with inflammatory arthritis. Science translational medicine 12 (545) (2021)
Yuriy Baglaenko, Dana Macfarlane, Alexander Marson, Peter A Nigrovic, Soumya Raychaudhuri
Genome editing to define the function of risk loci and variants in rheumatic disease. Nature reviews. Rheumatology 17 (8) (2021)
Joyce B Kang, Aparna Nathan, Kathryn Weinand, Fan Zhang, Nghia Millard, Laurie Rumker, D Branch Moody, Ilya Korsunsky, Soumya Raychaudhuri
Efficient and precise single-cell reference atlas mapping with Symphony. Nature communications 12 (1) (2021)
Kazuyoshi Ishigaki, Masato Akiyama, Masahiro Kanai, Atsushi Takahashi, Eiryo Kawakami, Hiroki Sugishita, Saori Sakaue, Nana Matoba, Siew-Kee Low, Yukinori Okada, Chikashi C Terao, Tiffany Amariuta, Steven Gazal, Yuta Kochi, Momoko Horikoshi, Ken Suzuki, Kaoru Ito, Satoshi Koyama, Kouichi Ozaki, Shumpei Niida, Yasushi Sakata, Yasuhiko Sakata, Takashi Kohno, Kouya Shiraishi, Yukihide Momozawa, Makoto Hirata, Koichi Matsuda, Kyung Sue Hong, Masashi Ikeda, Shiro Ikegawa, Ikuyo Kou, Toshihiro Tanaka, Hidewaki Nakagawa, Akari Suzuki, Tomomitsu Hirota, Mayumi Tamari, Kazuaki Chayama, Daiki Miki, Masaki Mori, Satoshi Nagayama, Yataro Daigo, Yoshio Miki, Toyomasa Katagiri, Osamu Ogawa, Wataru Obara, Hidemi Ito, Teruhiko Yoshida, Issei Imoto, Takashi Takahashi, Chizu Tanikawa, Takao Suzuki, Nobuaki Sinozaki, Shiro Minami, Hiroki Yamaguchi, Satoshi Asai, Yasuo Takahashi, Ken Yamaji, Kazuhisa Takahashi, Tomoaki Fujioka, Ryo Takata, Hideki Yanai, Akihide Masumoto, Yukihiro Koretsune, Hiromu Kutsumi, Masahiko Higashiyama, Shigeo Murayama, Naoko Minegishi, Kichiya Suzuki, Kozo Tanno, Atsushi Shimizu, Taiki Yamaji, Motoki Iwasaki, Norie Sawada, Hirokazu Uemura, Keitaro Tanaka, Mariko Naito, Makoto Sasaki, Kenji Wakai, Shoichiro Tsugane, Masayuki Yamamoto, Kazuhiko Yamamoto, Yoshinori Murakami, Yusuke Nakamura, Soumya Raychaudhuri, Johji Inazawa, Toshimasa Yamauchi, Takashi Kadowaki, Michiaki Kubo, Yoichiro Kamatani
Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases. Nature genetics 52 (7) (2020)
Kevin Wei, Ilya Korsunsky, Jennifer L Marshall, Anqi Gao, Gerald F M Watts, Triin Major, Adam P Croft, Jordan Watts, Philip E Blazar, Jeffrey K Lange, Thomas S Thornhill, Andrew Filer, Karim Raza, Laura T Donlin, null null, Christian W Siebel, Christopher Dominic Buckley, Soumya Raychaudhuri, Michael B Brenner
Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582 (7811) (2020)
Tiffany Amariuta, Kazuyoshi Ishigaki, Hiroki Sugishita, Tazro Ohta, Masaru Koido, Kushal K Dey, Koichi Matsuda, Yoshinori Murakami, Alkes L Price, Eiryo Kawakami, Chikashi C Terao, Soumya Raychaudhuri
Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements. Nature genetics 52 (12) (2020)
Mattias N D Svensson, Martina Zoccheddu, Shen Yang, Gyrid Nygaard, Christian Secchi, Karen M Doody, Kamil Slowikowski, Fumitaka Mizoguchi, Frances Humby, Rebecca Hands, Eugenio Santelli, Cristiano Sacchetti, Kuninobu Wakabayashi, Dennis J Wu, Christopher Barback, Rizi Ai, Wei Wang, Gary P Sims, Piotr Mydel, Tsuyoshi Kasama, David L Boyle, Francesco Galimi, David Vera, Michel L Tremblay, Soumya Raychaudhuri, Michael B Brenner, Gary S Firestein, Costantino Pitzalis, Anna-Karin Hultgård Ekwall, Stephanie M Stanford, Nunzio Bottini
Synoviocyte-targeted therapy synergizes with TNF inhibition in arthritis reversal. Science advances 6 (26) (2020)
Eloisa S Bonfa, Laure Gossec, David Alan Isenberg, Zhan-Guo Li, Soumya Raychaudhuri
How COVID-19 is changing rheumatology clinical practice. Nature reviews. Rheumatology 17 (1) (2020)
Maria Gutierrez-Arcelus, Yuriy Baglaenko, Jatin Arora, Susan K Hannes, Yang Luo, Tiffany Amariuta, Nikola Teslovich, Deepak A Rao, Joerg Ermann, Anna Helena Jonsson, null null, Cristina Navarrete, Stephen S Rich, Kent D Taylor, Jerome I Rotter, Peter K Gregersen, Tonu Esko, Michael B Brenner, Soumya Raychaudhuri
Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci. Nature genetics 52 (3) (2020)
David Kuo, Jennifer Ding, Ian S Cohn, Fan Zhang, Kevin Wei, Deepak A Rao, Cristina Rozo, Upneet K Sokhi, Sara Shanaj, David J Oliver, Adriana P Echeverria, Edward F DiCarlo, Michael B Brenner, Vivian P Bykerk, Susan M Goodman, Soumya Raychaudhuri, Gunnar Rätsch, Lionel B Ivashkiv, Laura T Donlin
HBEGF+ macrophages in rheumatoid arthritis induce fibroblast invasiveness. Science translational medicine 11 (491) (2020)

Soumya Raychaudhuri.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Soumya Raychaudhuri