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Identification of modified peptides using localization-aware open search
Yu, Fengchao, Teo, Guo Ci, Kong, Andy T., Haynes, Sarah E., Avtonomov, Dmitry M., Geiszler, Daniel J., Nesvizhskii, Alexey I.
Published in Nature communications (13.08.2020)
Published in Nature communications (13.08.2020)
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Journal Article
PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results
Geiszler, Daniel J., Kong, Andy T., Avtonomov, Dmitry M., Yu, Fengchao, Leprevost, Felipe da Veiga, Nesvizhskii, Alexey I.
Published in Molecular & cellular proteomics (2021)
Published in Molecular & cellular proteomics (2021)
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Journal Article
Philosopher: a versatile toolkit for shotgun proteomics data analysis
da Veiga Leprevost, Felipe, Haynes, Sarah E., Avtonomov, Dmitry M., Chang, Hui-Yin, Shanmugam, Avinash K., Mellacheruvu, Dattatreya, Kong, Andy T., Nesvizhskii, Alexey I.
Published in Nature methods (01.09.2020)
Published in Nature methods (01.09.2020)
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Journal Article
PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results
Geiszler, Daniel J, Kong, Andy T, Avtonomov, Dmitry M, Yu, Fengchao, Leprevost, Felipe da Veiga, Nesvizhskii, Alexey I
Published in Molecular & cellular proteomics (01.01.2021)
Published in Molecular & cellular proteomics (01.01.2021)
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Journal Article
DeltaMass: Automated Detection and Visualization of Mass Shifts in Proteomic Open-Search Results
Avtonomov, Dmitry M, Kong, Andy, Nesvizhskii, Alexey I
Published in Journal of proteome research (01.02.2019)
Published in Journal of proteome research (01.02.2019)
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Journal Article
BatMass: a Java Software Platform for LC–MS Data Visualization in Proteomics and Metabolomics
Avtonomov, Dmitry M, Raskind, Alexander, Nesvizhskii, Alexey I
Published in Journal of proteome research (05.08.2016)
Published in Journal of proteome research (05.08.2016)
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Journal Article
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
Pan, Jianbo, Hu, Yingwei, Krek, Azra, Li, Yize, Chen, Lin S., Vasaikar, Suhas, Wu, Yige, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Kong, Andy, Sethuraman, Sunantha, Avtonomov, Dmitry M., Colaprico, Antonio, Cao, Song, Cho, Kyung-Cho, Kalayci, Selim, Ma, Shiyong, Ruggles, Kelly, Kawaler, Emily, Wen, Bo, Chen, Feng, Edwards, Nathan, Pierorazio, Phillip M., Pavlovich, Christian P., Brominski, Gabriel, Hsieh, James J., Lubinski, Jan, Wiznerowicz, Maciej, Kinsinger, Christopher R., Thiagarajan, Mathangi, Mesri, Mehdi, Hiltke, Tara, Ding, Li, Zhang, Zhen, Omenn, Gilbert S., Cieslik, Marcin, Nesvizhskii, Alexey I., Zhang, Hui, Hashimi, Abdul Samad, Charamut, Alyssa, Druker, Brian J., Tognon, Cristina, Mani, D.R., Rohrer, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Wheeler, David, Chan, Doug, Demir, Emek, Wilson, George D., Liu, Hongwei, Zhou, Hua, Day, Jacob, Suh, James, Whiteaker, Jeffrey R., Eschbacher, Jennifer, Chen, Jin, Ketchum, Karen A., Rodland, Karin D., Krug, Karsten, Holloway, Kimberly, Sokoll, Lori J., Cornwell, MacIntosh, Loriaux, Marc, Anderson, Matthew, Ellis, Matthew J., Dyer, Maureen, Burke, Meghan C., Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Smith, Michael, Khan, Munziba, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Tignor, Nicole, Piehowski, Paul, McGarvey, Peter B., Hariharan, Pushpa, Gao, Qingsong, Thangudu, Ratna R., Montgomery, Rebecca, Bremner, Ross, Liu, Ruiyang, Hong, Runyu, Payne, Samuel H., Patel, Shalin, Satpathy, Shankha, Davies, Sherri R., Patil, Snehal, Carter, Sonya, Gabriel, Stacey, Thomas, Stefani N., Carr, Steven A., Skelly, Tara, Borate, Uma, Maruvka, Yosef, Li, Zhi
Published in Cell (31.10.2019)
Published in Cell (31.10.2019)
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Journal Article
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
Clark, David J., Petralia, Francesca, Pan, Jianbo, Hu, Yingwei, Lih, Tung-Shing M., Chang, Hui-Yin, Ma, Weiping, Krek, Azra, Li, Yize, Ozbek, Umut, Wu, Yige, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Schnaubelt, Michael, Avtonomov, Dmitry M., Kalayci, Selim, Ma, Shiyong, Ruggles, Kelly, Gümüş, Zeynep H., Kawaler, Emily, Edwards, Nathan, Chen, Xi Steven, Antczak, Andrzej, Omelchenko, Tatiana, Kinsinger, Christopher R., Thiagarajan, Mathangi, Mesri, Mehdi, Robles, Ana I., Qian, Jiang, Fenyö, David, Zhang, Bing, Zhang, Zhen, Cieslik, Marcin, Chan, Daniel W., Nesvizhskii, Alexey I., Hashimi, Abdul Samad, Charamut, Alyssa, Druker, Brian J., Tognon, Cristina, Mani, D.R., Rohrer, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Wheeler, David, Chan, Doug, Demir, Emek, Modugno, Francesmary, Getz, Gaddy, Wilson, George D., Liu, Hongwei, Zhou, Hua, Day, Jacob, Suh, James, Whiteaker, Jeffrey R., Eschbacher, Jennifer, Chen, Jin, Ketchum, Karen A., Rodland, Karin D., Krug, Karsten, Holloway, Kimberly, Sokoll, Lori J., Cornwell, MacIntosh, Loriaux, Marc, Anderson, Matthew, Ellis, Matthew J., Dyer, Maureen, Burke, Meghan C., Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Smith, Michael, Khan, Munziba, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Tignor, Nicole, Grady, Pamela, Piehowski, Paul, McGarvey, Peter B., Hariharan, Pushpa, Gao, Qingsong, Thangudu, Ratna R., Montgomery, Rebecca, Bremner, Ross, Liu, Ruiyang, Hong, Runyu, Payne, Samuel H., Patel, Shalin, Satpathy, Shankha, Davies, Sherri R., Patil, Snehal, Carter, Sonya, Gabriel, Stacey, Thomas, Stefani N., Carr, Steven A., Skelly, Tara, Borate, Uma, Maruvka, Yosef, Li, Zhi
Published in Cell (09.01.2020)
Published in Cell (09.01.2020)
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Journal Article
Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant
Yu, Fengchao, Haynes, Sarah E, Teo, Guo Ci, Avtonomov, Dmitry M, Polasky, Daniel A, Nesvizhskii, Alexey I
Published in Molecular & cellular proteomics (01.09.2020)
Published in Molecular & cellular proteomics (01.09.2020)
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Journal Article