MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies

por Taylor, Hannah B., Klaeger, Susan, Clauser, Karl R., Sarkizova, Siranush, Weingarten-Gabbay, Shira, Graham, Daniel B., Carr, Steven A., Abelin, Jennifer G.
Publicado 2021

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

por Li, Bo, Gould, Joshua, Yang, Yiming, Sarkizova, Siranush, Tabaka, Marcin, Ashenberg, Orr, Rosen, Yanay, Slyper, Michal, Kowalczyk, Monika S, Villani, Alexandra-Chloé, Tickle, Timothy, Hacohen, Nir, Rozenblatt-Rosen, Orit, Regev, Aviv
Publicado 2020

ERAP2 Increases the Abundance of a Peptide Submotif Highly Selective for the Birdshot Uveitis-Associated HLA-A29

por Venema, Wouter J., Hiddingh, Sanne, de Boer, Joke H., Claas, Frans H. J., Mulder, Arend, den Hollander, Anneke I., Stratikos, Efstratios, Sarkizova, Siranush, van der Veken, Lars T., Janssen, George M. C., van Veelen, Peter A., Kuiper, Jonas J. W.
Publicado 2021

Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples

por Klaeger, Susan, Apffel, Annie, Clauser, Karl R., Sarkizova, Siranush, Oliveira, Giacomo, Rachimi, Suzanna, Le, Phuong M., Tarren, Anna, Chea, Vipheaviny, Abelin, Jennifer G., Braun, David A., Ott, Patrick A., Keshishian, Hasmik, Hacohen, Nir, Keskin, Derin B., Wu, Catherine J., Carr, Steven A.
Publicado 2021

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

por Sarkizova, Siranush, Klaeger, Susan, Le, Phuong M., Li, Letitia W., Oliveira, Giacomo, Keshishian, Hasmik, Hartigan, Christina R., Zhang, Wandi, Braun, David A., Ligon, Keith L., Bachireddy, Pavan, Zervantonakis, Ioannis K., Rosenbluth, Jennifer M., Ouspenskaia, Tamara, Law, Travis, Justesen, Sune, Stevens, Jonathan, Lane, William J., Eisenhaure, Thomas, Zhang, Guang Lan, Clauser, Karl R., Hacohen, Nir, Carr, Steven A., Wu, Catherine J., Keskin, Derin B.
Publicado 2019

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

por Weingarten-Gabbay, Shira, Klaeger, Susan, Sarkizova, Siranush, Pearlman, Leah R., Chen, Da-Yuan, Gallagher, Kathleen M.E., Bauer, Matthew R., Taylor, Hannah B., Dunn, W. Augustine, Tarr, Christina, Sidney, John, Rachimi, Suzanna, Conway, Hasahn L., Katsis, Katelin, Wang, Yuntong, Leistritz-Edwards, Del, Durkin, Melissa R., Tomkins-Tinch, Christopher H., Finkel, Yaara, Nachshon, Aharon, Gentili, Matteo, Rivera, Keith D., Carulli, Isabel P., Chea, Vipheaviny A., Chandrashekar, Abishek, Bozkus, Cansu Cimen, Carrington, Mary, Bhardwaj, Nina, Barouch, Dan H., Sette, Alessandro, Maus, Marcela V., Rice, Charles M., Clauser, Karl R., Keskin, Derin B., Pregibon, Daniel C., Hacohen, Nir, Carr, Steven A., Abelin, Jennifer G., Saeed, Mohsan, Sabeti, Pardis C.
Publicado 2021

Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma

por Lee, Patrick C., Klaeger, Susan, Le, Phuong M., Korthauer, Keegan, Cheng, Jingwei, Ananthapadmanabhan, Varsha, Frost, Thomas C., Stevens, Jonathan D., Wong, Alan Y.L., Iorgulescu, J. Bryan, Tarren, Anna Y., Chea, Vipheaviny A., Carulli, Isabel P., Lemvigh, Camilla K., Pedersen, Christina B., Gartin, Ashley K., Sarkizova, Siranush, Wright, Kyle T., Li, Letitia W., Nomburg, Jason, Li, Shuqiang, Huang, Teddy, Liu, Xiaoxi, Pomerance, Lucas, Doherty, Laura M., Apffel, Annie M., Wallace, Luke J., Rachimi, Suzanna, Felt, Kristen D., Wolff, Jacquelyn O., Witten, Elizabeth, Zhang, Wandi, Neuberg, Donna, Lane, William J., Zhang, Guanglan, Olsen, Lars R., Thakuria, Manisha, Rodig, Scott J., Clauser, Karl R., Starrett, Gabriel J., Doench, John G., Buhrlage, Sara J., Carr, Steven A., DeCaprio, James A., Wu, Catherine J., Keskin, Derin B.
Publicado 2022

Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps

por Chen, Bob, Scurrah, Cherie’ R., McKinley, Eliot T., Simmons, Alan J., Ramirez-Solano, Marisol A., Zhu, Xiangzhu, Markham, Nicholas O., Heiser, Cody N., Vega, Paige N., Rolong, Andrea, Kim, Hyeyon, Sheng, Quanhu, Drewes, Julia L., Zhou, Yuan, Southard-Smith, Austin N., Xu, Yanwen, Ro, James, Jones, Angela L., Revetta, Frank, Berry, Lynne D., Niitsu, Hiroaki, Islam, Mirazul, Pelka, Karin, Hofree, Matan, Chen, Jonathan H., Sarkizova, Siranush, Ng, Kimmie, Giannakis, Marios, Boland, Genevieve M., Aguirre, Andrew J., Anderson, Ana C., Rozenblatt-Rosen, Orit, Regev, Aviv, Hacohen, Nir, Kawasaki, Kenta, Sato, Toshiro, Goettel, Jeremy A., Grady, William M., Zheng, Wei, Washington, M. Kay, Cai, Qiuyin, Sears, Cynthia L., Goldenring, James R., Franklin, Jeffrey L., Su, Timothy, Huh, Won Jae, Vandekar, Simon, Roland, Joseph T., Liu, Qi, Coffey, Robert J., Shrubsole, Martha J., Lau, Ken S.
Publicado 2021