The T cell receptor sequence influences the likelihood of T cell memory formation

por Lagattuta, Kaitlyn A., Nathan, Aparna, Rumker, Laurie, Birnbaum, Michael E., Raychaudhuri, Soumya
Publicado 2023

Maximizing statistical power to detect differentially abundant cell states with scPOST

por Millard, Nghia, Korsunsky, Ilya, Weinand, Kathryn, Fonseka, Chamith Y., Nathan, Aparna, Kang, Joyce B., Raychaudhuri, Soumya
Publicado 2021

IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 and other diseases with tissue inflammation

por Zhang, Fan, Mears, Joseph R., Shakib, Lorien, Beynor, Jessica I., Shanaj, Sara, Korsunsky, Ilya, Nathan, Aparna, Donlin, Laura T., Raychaudhuri, Soumya
Publicado 2020

IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation

por Zhang, Fan, Mears, Joseph R., Shakib, Lorien, Beynor, Jessica I., Shanaj, Sara, Korsunsky, Ilya, Nathan, Aparna, Donlin, Laura T., Raychaudhuri, Soumya
Publicado 2021

Efficient and precise single-cell reference atlas mapping with Symphony

por Kang, Joyce B., Nathan, Aparna, Weinand, Kathryn, Zhang, Fan, Millard, Nghia, Rumker, Laurie, Moody, D. Branch, Korsunsky, Ilya, Raychaudhuri, Soumya
Publicado 2021

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

por Reshef, Yakir, Rumker, Laurie, Kang, Joyce B., Nathan, Aparna, Korsunsky, Ilya, Asgari, Samira, Murray, Megan B., Moody, D. Branch, Raychaudhuri, Soumya
Publicado 2022

Repertoire analyses reveal T cell receptor sequence features that influence T cell fate

por Lagattuta, Kaitlyn A., Kang, Joyce B., Nathan, Aparna, Pauken, Kristen E., Jonsson, Anna Helena, Rao, Deepak A., Sharpe, Arlene H., Ishigaki, Kazuyoshi, Raychaudhuri, Soumya
Publicado 2022

Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin

por Xiao, Qian, Mears, Joseph, Nathan, Aparna, Ishigaki, Kazuyoshi, Baglaenko, Yuriy, Lim, Noha, Cooney, Laura A., Harris, Kristina M., Anderson, Mark S., Fox, David A., Smilek, Dawn E., Krueger, James G., Raychaudhuri, Soumya
Publicado 2023

The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis

por Weinand, Kathryn, Sakaue, Saori, Nathan, Aparna, Jonsson, Anna Helena, Zhang, Fan, Watts, Gerald F. M., Zhu, Zhu, Rao, Deepak A., Anolik, Jennifer H., Brenner, Michael B., Donlin, Laura T., Wei, Kevin, Raychaudhuri, Soumya
Publicado 2023

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions

por Gutierrez-Arcelus, Maria, Teslovich, Nikola, Mola, Alex R., Polidoro, Rafael B., Nathan, Aparna, Kim, Hyun, Hannes, Susan, Slowikowski, Kamil, Watts, Gerald F. M., Korsunsky, Ilya, Brenner, Michael B., Raychaudhuri, Soumya, Brennan, Patrick J.
Publicado 2019

Deep transcriptome sequencing of subgenual anterior cingulate cortex reveals cross-diagnostic and diagnosis-specific RNA expression changes in major psychiatric disorders

por Akula, Nirmala, Marenco, Stefano, Johnson, Kory, Feng, Ningping, Zhu, Kevin, Schulmann, Anton, Corona, Winston, Jiang, Xueying, Cross, Joanna, England, Bryce, Nathan, Aparna, Detera-Wadleigh, Sevilla, Xu, Qing, Auluck, Pavan K., An, Kwangmi, Kramer, Robin, Apud, Jose, Harris, Brent T., Harker Rhodes, C., Lipska, Barbara K., McMahon, Francis J.
Publicado 2021

Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment, and disease

por Nathan, Aparna, Beynor, Jessica I., Baglaenko, Yuriy, Suliman, Sara, Ishigaki, Kazuyoshi, Asgari, Samira, Huang, Chuan-Chin, Luo, Yang, Zhang, Zibiao, Lopez, Kattya, Arlehamn, Cecilia S. Lindestam, Ernst, Joel D., Jimenez, Judith, Calderón, Roger I., Lecca, Leonid, Van Rhijn, Ildiko, Moody, D. Branch, Murray, Megan B., Raychaudhuri, Soumya
Publicado 2021

History of tuberculosis disease is associated with genetic regulatory variation in Peruvians

por Suliman, Sara, Nieto-Caballero, Victor E., Asgari, Samira, Lopez, Kattya, Iwany, Sarah K., Luo, Yang, Nathan, Aparna, Fernandez-Salinas, Daniela, Chiñas, Marcos, Huang, Chuan-Chin, Zhang, Zibiao, León, Segundo R, Calderon, Roger I, Lecca, Leonid, Murray, Megan, Van Rhijn, Ildiko, Raychaudhuri, Soumya, Moody, D. Branch, Gutierrez-Arcelus, Maria
Publicado 2023

Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium

por Dunlap, Garrett, Wagner, Aaron, Meednu, Nida, Zhang, Fan, Jonsson, A. Helena, Wei, Kevin, Sakaue, Saori, Nathan, Aparna, Bykerk, Vivian P., Donlin, Laura T., Goodman, Susan M., Firestein, Gary S., Boyle, David L., Holers, V. Michael, Moreland, Larry W., Tabechian, Darren, Pitzalis, Costantino, Filer, Andrew, Raychaudhuri, Soumya, Brenner, Michael B., McDavid, Andrew, Rao, Deepak A., Anolik, Jennifer H.
Publicado 2023

Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

por Kang, Joyce B., Shen, Amber Z., Sakaue, Saori, Luo, Yang, Gurajala, Saisriram, Nathan, Aparna, Rumker, Laurie, Aguiar, Vitor R. C., Valencia, Cristian, Lagattuta, Kaitlyn, Zhang, Fan, Jonsson, Anna Helena, Yazar, Seyhan, Alquicira-Hernandez, Jose, Khalili, Hamed, Ananthakrishnan, Ashwin N., Jagadeesh, Karthik, Dey, Kushal, Daly, Mark J., Xavier, Ramnik J., Donlin, Laura T., Anolik, Jennifer H., Powell, Joseph E., Rao, Deepak A., Brenner, Michael B., Gutierrez-Arcelus, Maria, Raychaudhuri, Soumya
Publicado 2023

Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes

por Zhang, Fan, Jonsson, Anna Helena, Nathan, Aparna, Millard, Nghia, Curtis, Michelle, Xiao, Qian, Gutierrez-Arcelus, Maria, Apruzzese, William, Watts, Gerald F. M., Weisenfeld, Dana, Nayar, Saba, Rangel-Moreno, Javier, Meednu, Nida, Marks, Kathryne E., Mantel, Ian, Kang, Joyce B., Rumker, Laurie, Mears, Joseph, Slowikowski, Kamil, Weinand, Kathryn, Orange, Dana E., Geraldino-Pardilla, Laura, Deane, Kevin D., Tabechian, Darren, Ceponis, Arnoldas, Firestein, Gary S., Maybury, Mark, Sahbudin, Ilfita, Ben-Artzi, Ami, Mandelin, Arthur M., Nerviani, Alessandra, Lewis, Myles J., Rivellese, Felice, Pitzalis, Costantino, Hughes, Laura B., Horowitz, Diane, DiCarlo, Edward, Gravallese, Ellen M., Boyce, Brendan F., Moreland, Larry W., Goodman, Susan M., Perlman, Harris, Holers, V. Michael, Liao, Katherine P., Filer, Andrew, Bykerk, Vivian P., Wei, Kevin, Rao, Deepak A., Donlin, Laura T., Anolik, Jennifer H., Brenner, Michael B., Raychaudhuri, Soumya
Publicado 2023