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MSBooster: improving peptide identification rates using deep learning-based features
Yang, Kevin L., Yu, Fengchao, Teo, Guo Ci, Li, Kai, Demichev, Vadim, Ralser, Markus, Nesvizhskii, Alexey I.
Published in Nature communications (27.07.2023)
Published in Nature communications (27.07.2023)
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Journal Article
Recent advances in computational algorithms and software for large-scale glycoproteomics
Polasky, Daniel A., Nesvizhskii, Alexey I.
Published in Current opinion in chemical biology (01.02.2023)
Published in Current opinion in chemical biology (01.02.2023)
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Journal Article
dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts
Demichev, Vadim, Szyrwiel, Lukasz, Yu, Fengchao, Teo, Guo Ci, Rosenberger, George, Niewienda, Agathe, Ludwig, Daniela, Decker, Jens, Kaspar-Schoenefeld, Stephanie, Lilley, Kathryn S., Mülleder, Michael, Nesvizhskii, Alexey I., Ralser, Markus
Published in Nature communications (08.07.2022)
Published in Nature communications (08.07.2022)
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Journal Article
Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine
Teo, Guo Ci, Polasky, Daniel A, Yu, Fengchao, Nesvizhskii, Alexey I
Published in Journal of proteome research (01.01.2021)
Published in Journal of proteome research (01.01.2021)
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Journal Article
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
Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer
Xiao, Lanbo, Parolia, Abhijit, Qiao, Yuanyuan, Bawa, Pushpinder, Eyunni, Sanjana, Mannan, Rahul, Carson, Sandra E., Chang, Yu, Wang, Xiaoju, Zhang, Yuping, Vo, Josh N., Kregel, Steven, Simko, Stephanie A., Delekta, Andrew D., Jaber, Mustapha, Zheng, Heng, Apel, Ingrid J., McMurry, Lisa, Su, Fengyun, Wang, Rui, Zelenka-Wang, Sylvia, Sasmal, Sanjita, Khare, Leena, Mukherjee, Subhendu, Abbineni, Chandrasekhar, Aithal, Kiran, Bhakta, Mital S., Ghurye, Jay, Cao, Xuhong, Navone, Nora M., Nesvizhskii, Alexey I., Mehra, Rohit, Vaishampayan, Ulka, Blanchette, Marco, Wang, Yuzhuo, Samajdar, Susanta, Ramachandra, Murali, Chinnaiyan, Arul M.
Published in Nature (London) (20.01.2022)
Published in Nature (London) (20.01.2022)
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Journal Article
BioContainers: an open-source and community-driven framework for software standardization
da Veiga Leprevost, Felipe, Grüning, Björn A, Alves Aflitos, Saulo, Röst, Hannes L, Uszkoreit, Julian, Barsnes, Harald, Vaudel, Marc, Moreno, Pablo, Gatto, Laurent, Weber, Jonas, Bai, Mingze, Jimenez, Rafael C, Sachsenberg, Timo, Pfeuffer, Julianus, Vera Alvarez, Roberto, Griss, Johannes, Nesvizhskii, Alexey I, Perez-Riverol, Yasset
Published in Bioinformatics (Oxford, England) (15.08.2017)
Published in Bioinformatics (Oxford, England) (15.08.2017)
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Journal Article
Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides
Geiszler, Daniel J., Polasky, Daniel A., Yu, Fengchao, Nesvizhskii, Alexey I.
Published in Nature communications (12.07.2023)
Published in Nature communications (12.07.2023)
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Journal Article
Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics
Choi, Hyungwon, Fermin, Damian, Nesvizhskii, Alexey I.
Published in Molecular & cellular proteomics (01.12.2008)
Published in Molecular & cellular proteomics (01.12.2008)
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Journal Article
ProHits-viz: a suite of web tools for visualizing interaction proteomics data
Knight, James D R, Choi, Hyungwon, Gupta, Gagan D, Pelletier, Laurence, Raught, Brian, Nesvizhskii, Alexey I, Gingras, Anne-Claude
Published in Nature methods (01.07.2017)
Published in Nature methods (01.07.2017)
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Journal Article
Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors
Kacen, Assaf, Javitt, Aaron, Kramer, Matthias P., Morgenstern, David, Tsaban, Tomer, Shmueli, Merav D., Teo, Guo Ci, da Veiga Leprevost, Felipe, Barnea, Eilon, Yu, Fengchao, Admon, Arie, Eisenbach, Lea, Samuels, Yardena, Schueler-Furman, Ora, Levin, Yishai, Nesvizhskii, Alexey I., Merbl, Yifat
Published in Nature biotechnology (01.02.2023)
Published in Nature biotechnology (01.02.2023)
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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
iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates
Shteynberg, David, Deutsch, Eric W., Lam, Henry, Eng, Jimmy K., Sun, Zhi, Tasman, Natalie, Mendoza, Luis, Moritz, Robert L., Aebersold, Ruedi, Nesvizhskii, Alexey I.
Published in Molecular & cellular proteomics (01.12.2011)
Published in Molecular & cellular proteomics (01.12.2011)
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Journal Article
SAINT: probabilistic scoring of affinity purification–mass spectrometry data
Choi, Hyungwon, Larsen, Brett, Lin, Zhen-Yuan, Breitkreutz, Ashton, Mellacheruvu, Dattatreya, Fermin, Damian, Qin, Zhaohui S, Tyers, Mike, Gingras, Anne-Claude, Nesvizhskii, Alexey I
Published in Nature methods (01.01.2011)
Published in Nature methods (01.01.2011)
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Journal Article