MSFragger: ultrafast and comprehensive peptide identification in shotgun proteomics

por Kong, Andy T., Leprevost, Felipe V., Avtonomov, Dmitry M., Mellacheruvu, Dattatreya, Nesvizhskii, Alexey I.
Publicado 2017

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform

por Yu, Fengchao, Teo, Guo Ci, Kong, Andy T., Fröhlich, Klemens, Li, Ginny Xiaohe, Demichev, Vadim, Nesvizhskii, Alexey I.
Publicado 2023

PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results

por Geiszler, Daniel J., Kong, Andy T., Avtonomov, Dmitry M., Yu, Fengchao, Leprevost, Felipe da Veiga, Nesvizhskii, Alexey I.
Publicado 2020

Identification of modified peptides using localization-aware open search

por Yu, Fengchao, Teo, Guo Ci, Kong, Andy T., Haynes, Sarah E., Avtonomov, Dmitry M., Geiszler, Daniel J., Nesvizhskii, Alexey I.
Publicado 2020

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

por Freeberg, Mallory A, Han, Ting, Moresco, James J, Kong, Andy, Yang, Yu-Cheng, Lu, Zhi John, Yates, John R, Kim, John K
Publicado 2013

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

por Clark, David J., Dhanasekaran, Saravana M., Petralia, Francesca, Pan, Jianbo, Song, Xiaoyu, Hu, Yingwei, da Veiga Leprevost, Felipe, Reva, Boris, Lih, Tung-Shing M., Chang, Hui-Yin, Ma, Weiping, Huang, Chen, Ricketts, Christopher J., Chen, Lijun, Krek, Azra, Li, Yize, Rykunov, Dmitry, Li, Qing Kay, Chen, Lin S., Ozbek, Umut, Vasaikar, Suhas, Wu, Yige, Yoo, Seungyeul, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Ji, Jiayi, Schnaubelt, Michael, Kong, Andy, Sethuraman, Sunantha, Avtonomov, Dmitry M., Ao, Minghui, Colaprico, Antonio, Cao, Song, Cho, Kyung-Cho, Kalayci, Selim, Ma, Shiyong, Liu, Wenke, Ruggles, Kelly, Calinawan, Anna, Gümüş, Zeynep H., Geiszler, Daniel, Kawaler, Emily, Teo, Guo Ci, Wen, Bo, Zhang, Yuping, Keegan, Sarah, Li, Kai, Chen, Feng, Edwards, Nathan, Pierorazio, Phillip M., Chen, Xi Steven, Pavlovich, Christian P., Hakimi, A. Ari, Brominski, Gabriel, Hsieh, James J., Antczak, Andrzej, Omelchenko, Tatiana, Lubinski, Jan, Wiznerowicz, Maciej, Linehan, W. Marston, Kinsinger, Christopher R., Thiagarajan, Mathangi, Boja, Emily S., Mesri, Mehdi, Hiltke, Tara, Robles, Ana I., Rodriguez, Henry, Qian, Jiang, Fenyö, David, Zhang, Bing, Ding, Li, Schadt, Eric, Chinnaiyan, Arul M., Zhang, Zhen, Omenn, Gilbert S., Cieslik, Marcin, Chan, Daniel W., Nesvizhskii, Alexey I., Wang, Pei, Zhang, Hui
Publicado 2019