Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE)

by Shekhar, Karthik, Brodin, Petter, Davis, Mark M., Chakraborty, Arup K
Published 2014

Preferential targeting of co-evolving Gag residues in long-term non progressors

by Sunshine, J., Shekhar, Karthik, Heckerman, David, Frahm, Nicole, Chakraborty, Arup K
Published 2013

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

by Shekhar, Karthik, Ruberman, Claire, Ferguson, Andrew L., Kardar, Mehran, Barton, John P., Chakraborty, Arup K
Published 2014

Hydrophobic CDR3 residues promote the development of self-reactive T cells

by Stadinski, Brian D, Shekhar, Karthik, Gómez-Touriño, Iria, Jung, Jonathan, Sasaki, Katsuhiro, Sewell, Andrew K, Peakman, Mark, Chakraborty, Arup K, Huseby, Eric S
Published 2017

Continuous immunotypes describe human immune variation and predict diverse responses

by Kaczorowski, Kevin J., Shekhar, Karthik, Nkulikiyimfura, Dieudonné, Dekker, Cornelia L., Maecker, Holden, Davis, Mark M., Chakraborty, Arup K., Brodin, Petter, Kaczorowski, Kevin John, Chakraborty, Arup K
Published 2018

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

by Pereyra, Florencia, Miura, Toshiyuki, Allen, Todd M., Altfeld, Marcus, Carrington, Mary, Walker, Bruce D., Dahirel, Vincent, Shekhar, Karthik, Artyomov, Mikita, Talsania, Shiv, Irvine, Darrell J., Chakraborty, Arup K.
Published 2012

Geometry-dependent functional changes in iPSC-derived cardiomyocytes probed by functional imaging and RNA sequencing

by Gaublomme, Jellert, Shekhar, Karthik, Yi, B. Alexander, Kralj, Joel M., Bloxham, William, Cohen, Adam E., Werley, Christopher A., Chien, Miao-Ping, Butty, Vincent L G, Boyer, Laurie Ann, Regev, Aviv
Published 2017

Massively parallel single-nucleus RNA-seq with DroNc-seq

by Avraham-Davidi, Inbal, Burks, Tyler, Shekhar, Karthik, Hofree, Matan, Aguet, François, Gelfand, Ellen, Ardlie, Kristin, Weitz, David A, Rozenblatt-Rosen, Orit, Zhang, Feng, Habib, Naomi, Choudhury, Sourav, Regev, Aviv, Basu, Anindita 1978-
Published 2018

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

by Shekhar, Karthik, Lapan, Sylvain W., Whitney, Irene E., Tran, Nicholas M., Macosko, Evan Z., Kowalczyk, Monika, Adiconis, Xian, Levin, Joshua Z., Nemesh, James, Goldman, Melissa, McCarroll, Steven A., Cepko, Constance L., Regev, Aviv, Sanes, Joshua R.
Published 2018

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

by Macosko, Evan Z, Satija, Rahul, Nemesh, James, Shekhar, Karthik, Goldman, Melissa, Tirosh, Itay, Bialas, Allison R, Kamitaki, Nolan, Martersteck, Emily M, Trombetta, John J, Weitz, David A, Sanes, Joshua R, McCarroll, Steven A, Shalek, Alexander K, Regev, Aviv, Basu, Anindita 1978-
Published 2017

Magnitude and Kinetics of CD8[superscript +] T Cell Activation during Hyperacute HIV Infection Impact Viral Set Point

by Ndhlovu, Zaza M, Kamya, Philomena, Mewalal, Nikoshia, Kløverpris, Henrik N, Nkosi, Thandeka, Pretorius, Karyn, Laher, Faatima, Ogunshola, Funsho, Chopera, Denis, Ghebremichael, Musie, Ismail, Nasreen, Moodley, Amber, Malik, Amna, Leslie, Alasdair, Goulder, Philip J.R, Buus, Søren, Dong, Krista, Ndung'u, Thumbi, Walker, Bruce D, Chakraborty, Arup K, Shekhar, Karthik
Published 2017

A single-cell survey of the small intestinal epithelium

by Haber, Adam L., Biton, Moshe, Rogel, Noga, Herbst, Rebecca H., Shekhar, Karthik, Smillie, Christopher, Burgin, Grace, Delorey, Toni M., Howitt, Michael R., Katz, Yarden, Tirosh, Itay, Beyaz, Semir, Dionne, Danielle, Zhang, Mei, Raychowdhury, Raktima, Garrett, Wendy S., Rozenblatt-Rosen, Orit, Shi, Hai Ning, Yilmaz, Omer, Xavier, Ramnik J., Regev, Aviv
Published 2018

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

by Villani, Alexandra-Chloé, Satija, Rahul, Reynolds, Gary, Sarkizova, Siranush, Shekhar, Karthik, Fletcher, James, Griesbeck, Morgane, Butler, Andrew, Zheng, Shiwei, Lazo, Suzan, Jardine, Laura, Dixon, David, Stephenson, Emily, Nilsson, Emil, Grundberg, Ida, McDonald, David, Filby, Andrew, Li, Weibo, De Jager, Philip L., Rozenblatt-Rosen, Orit, Lane, Andrew A., Haniffa, Muzlifah, Regev, Aviv, Hacohen, Nir
Published 2018

Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys

by Barouch, Dan H., Whitney, James B., Moldt, Brian, Klein, Florian, Oliveira, Thiago Y., Liu, Jinyan, Stephenson, Kathryn E., Chang, Hui-Wen, Shekhar, Karthik, Gupta, Sanjana, Nkolola, Joseph P., Seaman, Michael S., Smith, Kaitlin M., Borducchi, Erica N., Cabral, Crystal, Smith, Jeffrey Y., Blackmore, Stephen, Sanisetty, Srisowmya, Perry, James R., Beck, Matthew, Lewis, Mark G., Rinaldi, William, Poignard, Pascal, Nussenzweig, Michel C., Burton, Dennis R., Chakraborty, Arup K
Published 2014

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation

by Biton, Moshe, Haber, Adam L., Rogel, Noga, Burgin, Grace, Beyaz, Semir, Schnell, Alexandra, Ashenberg, Orr, Su, Chien-Wen, Smillie, Christopher, Shekhar, Karthik, Chen, Zuojia, Wu, Chuan, Ordovas-Montanes, Jose Manuel, Alvarez, David, Herbst, Rebecca H., Zhang, Mei, Tirosh, Itay, Dionne, Danielle, Nguyen, Lan T., Xifaras, Michael, Shalek, Alexander K, von Andrian, Ulrich H., Graham, Daniel B., Rozenblatt-Rosen, Orit, Shi, Hai Ning, Kuchroo, Vijay, Yilmaz, Omer, Regev, Aviv, Xavier, Ramnik Joseph
Published 2020