Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
Beliveau, Brian J., Boettiger, Alistair N., Avendaño, Maier S., Jungmann, Ralf, McCole, Ruth B., Joyce, Eric F., Kim-Kiselak, Caroline, Bantignies, Frédéric, Fonseka, Chamith Y., Erceg, Jelena, Hannan, Mohammed A., Hoang, Hien G., Colognori, David, Lee, Jeannie T., Shih, William M., Yin, Peng, Zhuang, Xiaowei, Wu, Chao-ting
Published in Nature communications (12.05.2015)
Published in Nature communications (12.05.2015)
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Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes
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Published in Proceedings of the National Academy of Sciences - PNAS (26.12.2012)
Published in Proceedings of the National Academy of Sciences - PNAS (26.12.2012)
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Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells
McCole, Ruth B, Fonseka, Chamith Y, Koren, Amnon, Wu, C-Ting
Published in PLoS genetics (01.10.2014)
Published in PLoS genetics (01.10.2014)
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Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis
Rao, Deepak A., Gurish, Michael F., Marshall, Jennifer L., Slowikowski, Kamil, Fonseka, Chamith Y., Liu, Yanyan, Donlin, Laura T., Henderson, Lauren A., Wei, Kevin, Mizoguchi, Fumitaka, Teslovich, Nikola C., Weinblatt, Michael E., Massarotti, Elena M., Coblyn, Jonathan S., Helfgott, Simon M., Lee, Yvonne C., Todd, Derrick J., Bykerk, Vivian P., Goodman, Susan M., Pernis, Alessandra B., Ivashkiv, Lionel B., Karlson, Elizabeth W., Nigrovic, Peter A., Filer, Andrew, Buckley, Christopher D., Lederer, James A., Raychaudhuri, Soumya, Brenner, Michael B.
Published in Nature (London) (02.02.2017)
Published in Nature (London) (02.02.2017)
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Multimodal single-cell approaches shed light on T cell heterogeneity
Nathan, Aparna, Baglaenko, Yuriy, Fonseka, Chamith Y, Beynor, Jessica I, Raychaudhuri, Soumya
Published in Current opinion in immunology (01.12.2019)
Published in Current opinion in immunology (01.12.2019)
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Mixed-effects association of single cells identifies an expanded effector CD4 + T cell subset in rheumatoid arthritis
Fonseka, Chamith Y, Rao, Deepak A, Teslovich, Nikola C, Korsunsky, Ilya, Hannes, Susan K, Slowikowski, Kamil, Gurish, Michael F, Donlin, Laura T, Lederer, James A, Weinblatt, Michael E, Massarotti, Elena M, Coblyn, Jonathan S, Helfgott, Simon M, Todd, Derrick J, Bykerk, Vivian P, Karlson, Elizabeth W, Ermann, Joerg, Lee, Yvonne C, Brenner, Michael B, Raychaudhuri, Soumya
Published in Science translational medicine (17.10.2018)
Published in Science translational medicine (17.10.2018)
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PD-1hiCXCR5- T peripheral helper cells promote B cell responses in lupus via MAF and IL-21
Bocharnikov, Alexandra V, Keegan, Joshua, Wacleche, Vanessa S, Cao, Ye, Fonseka, Chamith Y, Wang, Guoxing, Muise, Eric S, Zhang, Kelvin X, Arazi, Arnon, Keras, Gregory, Li, Zhihan J, Qu, Yujie, Gurish, Michael F, Petri, Michelle, Buyon, Jill P, Putterman, Chaim, Wofsy, David, James, Judith A, Guthridge, Joel M, Diamond, Betty, Anolik, Jennifer H, Mackey, Matthew F, Alves, Stephen E, Nigrovic, Peter A, Costenbader, Karen H, Brenner, Michael B, Lederer, James A, Rao, Deepak A
Published in JCI insight (17.10.2019)
Published in JCI insight (17.10.2019)
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Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry
Zhang, Fan, Wei, Kevin, Slowikowski, Kamil, Fonseka, Chamith Y., Rao, Deepak A., Kelly, Stephen, Goodman, Susan M., Tabechian, Darren, Hughes, Laura B., Salomon-Escoto, Karen, Watts, Gerald F. M., Jonsson, A. Helena, Rangel-Moreno, Javier, Meednu, Nida, Rozo, Cristina, Apruzzese, William, Eisenhaure, Thomas M., Lieb, David J., Boyle, David L., Mandelin, Arthur M., Boyce, Brendan F., DiCarlo, Edward, Gravallese, Ellen M., Gregersen, Peter K., Moreland, Larry, Firestein, Gary S., Hacohen, Nir, Nusbaum, Chad, Lederer, James A., Perlman, Harris, Pitzalis, Costantino, Filer, Andrew, Holers, V. Michael, Bykerk, Vivian P., Donlin, Laura T., Anolik, Jennifer H., Brenner, Michael B., Raychaudhuri, Soumya
Published in Nature immunology (01.07.2019)
Published in Nature immunology (01.07.2019)
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Notch signalling drives synovial fibroblast identity and arthritis pathology
Wei, Kevin, Korsunsky, Ilya, Marshall, Jennifer L., Gao, Anqi, Watts, Gerald F. M., Major, Triin, Croft, Adam P., Watts, Jordan, Blazar, Philip E., Lange, Jeffrey K., Thornhill, Thomas S., Filer, Andrew, Raza, Karim, Donlin, Laura T., Siebel, Christian W., Buckley, Christopher D., Raychaudhuri, Soumya, Brenner, Michael B.
Published in Nature (London) (01.06.2020)
Published in Nature (London) (01.06.2020)
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Automated multi-scale computational pathotyping (AMSCP) of inflamed synovial tissue
Bell, Richard D., Brendel, Matthew, Konnaris, Maxwell A., Xiang, Justin, Otero, Miguel, Fontana, Mark A., Bai, Zilong, Krenitsky, Daria M., Meednu, Nida, Rangel-Moreno, Javier, Scheel-Toellner, Dagmar, Carr, Hayley, Nayar, Saba, McMurray, Jack, DiCarlo, Edward, Anolik, Jennifer H., Donlin, Laura T., Orange, Dana E., Kenney, H. Mark, Schwarz, Edward M., Filer, Andrew, Ivashkiv, Lionel B., Wang, Fei
Published in Nature communications (29.08.2024)
Published in Nature communications (29.08.2024)
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Synovial fibroblast gene expression is associated with sensory nerve growth and pain in rheumatoid arthritis
Bai, Zilong, Bartelo, Nicholas, Aslam, Maryam, Murphy, Elisabeth A, Hale, Caryn R, Blachere, Nathalie E, Parveen, Salina, Spolaore, Edoardo, DiCarlo, Edward, Gravallese, Ellen M, Smith, Melanie H, Frank, Mayu O, Jiang, Caroline S, Zhang, Haotan, Pyrgaki, Christina, Lewis, Myles J, Sikandar, Shafaq, Pitzalis, Costantino, Lesnak, Joseph B, Mazhar, Khadijah, Price, Theodore J, Malfait, Anne-Marie, Miller, Rachel E, Zhang, Fan, Goodman, Susan, Darnell, Robert B, Wang, Fei, Orange, Dana E
Published in Science translational medicine (10.04.2024)
Published in Science translational medicine (10.04.2024)
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Abnormal Dosage of Ultraconserved Elements Is Highly Disfavored in Healthy Cells but Not Cancer Cells: e1004646
McCole, Ruth B, Fonseka, Chamith Y, Koren, Amnon, Wu, C-ting
Published in PLoS genetics (01.10.2014)
Published in PLoS genetics (01.10.2014)
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Oligopaints: highly efficient, bioinformatically designed probes for fluorescence in situ hybridization
Beliveau, Brian J, Joyce, Eric F, Apostolopoulosa, Nicholas, Yilmaza, Feyza, Fonseka, Chamith Y, McCole, Ruth B, Chang, Yiming, Li, Jin Billy, Senaratne, Tharanga Niroshini, Williams, Benjamin R, Rouillard, Jean-Marie, Wu, Chao-ting
Published in Epigenetics & chromatin (18.03.2013)
Published in Epigenetics & chromatin (18.03.2013)
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Structural disruption of genomic regions containing ultraconserved elements is associated with neurodevelopmental phenotypes
Mccole, Ruth B, Saylor, Wren, Redin, Claire, Fonseka, Chamith Y, Brand, Harrison, Erceg, Jelena, Talkowski, Michael E, C-Ting, Wu
Published in bioRxiv (13.12.2017)
Published in bioRxiv (13.12.2017)
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Mixed Effects Association of Single Cells Identifies an Expanded Th1-Skewed Cytotoxic Effector CD4+ T Cell Subset in Rheumatoid Arthritis
Fonseka, Chamith Y, Rao, Deepak A, Teslovich, Nikola C, Hannes, Susan K, Slowikowski, Kamil, Gurish, Michael F, Donlin, Laura T, Weinblatt, Michael E, Massarotti, Elena M, Coblyn, Jonathan S, Helfgott, Simon M, Todd, Derrick J, Bykerk, Vivian P, Karlson, Elizabeth W, Ermann, Joerg, Lee, Yvonne C, Brenner, Michael B, Raychaudhuri, Soumya
Published in bioRxiv (14.03.2018)
Published in bioRxiv (14.03.2018)
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Paper
Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry
Zhang, Fan, Wei, Kevin, Slowikowski, Kamil, Fonseka, Chamith Y, Rao, Deepak A, Kelly, Stephen, Goodman, Susan M, Tabechian, Darren, Hughes, Laura B, Salomon-Escoto, Karen, Watts, Gerald F M, Apruzzese, William, Lieb, David J, Boyle, David L, Mandelin, Arthur M, Accelerating Medicines Partnership: Ra Phase 1, Amp Ra/sle, Boyce, Brendan F, Dicarlo, Edward, Gravallese, Ellen M, Gregersen, Peter K, Moreland, Larry, Firestein, Gary S, Hacohen, Nir, Nusbaum, Chad, Lederer, James A, Perlman, Harris, Pitzalis, Costantino, Filer, Andrew, Holers, V Michael, Bykerk, Vivian P, Donlin, Laura T, Anolik, Jennifer H, Brenner, Michael B, Raychaudhuri, Soumya
Published in bioRxiv (20.06.2018)
Published in bioRxiv (20.06.2018)
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