Nesvizhskii, Alexey I.

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

Mellacheruvu, D., Wright, Z., Couzens, A. L., Lambert, J.-P., St-Denis, N. A., Li, T., Miteva, Y. V., Hauri, S., Sardiu, M. E., Low, T. Y., et al. (2013) · Nature Methods

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 1,686

Interpretation of Shotgun Proteomic Data

Nesvizhskii, A. I., & Aebersold, R. (2005) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 1,025

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

Gillette, M. A., Satpathy, S., Cao, S., Dhanasekaran, S. M., Vasaikar, S. V., Krug, K., Petralia, F., Li, Y., Liang, W.-W., Reva, B., et al. (2020) · Cell

Lung Cancer Treatments and MutationsLung Cancer Research Studies

Cited by 820

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

Choi, H., Larsen, B., Lin, Z.-Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z. S., Tyers, M., Gingras, A.-C., & Nesvizhskii, A. I. (2011) · Nature Methods

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 800

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Clark, D. J., Dhanasekaran, S. M., Petralia, F., Pan, J., Song, X., Hu, Y., da Veiga Leprevost, F., Reva, B., Lih, T.-S. M., Chang, H.-Y., et al. (2019) · Cell

Renal cell carcinoma treatmentCancer Genomics and Diagnostics

Cited by 730

Proteogenomic and metabolomic characterization of human glioblastoma

Wang, L.-B., Karpova, A., Gritsenko, M. A., Kyle, J. E., Cao, S., Li, Y., Rykunov, D., Colaprico, A., Rothstein, J. H., Hong, R., et al. (2021) · Cancer Cell

Glioma Diagnosis and TreatmentCancer Genomics and Diagnostics

Cited by 661

Proteogenomic characterization of pancreatic ductal adenocarcinoma

Cao, L., Huang, C., Cui Zhou, D., Hu, Y., Lih, T. M., Savage, S. R., Krug, K., Clark, D. J., Schnaubelt, M., Chen, L., et al. (2021) · Cell

Pancreatic and Hepatic Oncology ResearchCancer Genomics and Diagnostics

Cited by 578

Proteogenomic Characterization of Endometrial Carcinoma

Dou, Y., Kawaler, E. A., Cui Zhou, D., Gritsenko, M. A., Huang, C., Blumenberg, L., Karpova, A., Petyuk, V. A., Savage, S. R., Satpathy, S., et al. (2020) · Cell

Endometrial and Cervical Cancer TreatmentsAdvanced Proteomics Techniques and Applications

Cited by 485

Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics

Choi, H., Fermin, D., & Nesvizhskii, A. I. (2008) · Molecular & Cellular Proteomics

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 364

A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein

Goudreault, M., D'Ambrosio, L. M., Kean, M. J., Mullin, M. J., Larsen, B. G., Sanchez, A., Chaudhry, S., Chen, G. I., Sicheri, F., Nesvizhskii, A. I., et al. (2009) · Molecular & Cellular Proteomics

Protein Kinase Regulation and GTPase SignalingVascular Malformations Diagnosis and Treatment

Cited by 359

A multicenter study benchmarks software tools for label-free proteome quantification

Navarro, P., Kuharev, J., Gillet, L. C., Bernhardt, O. M., MacLean, B., Röst, H. L., Tate, S. A., Tsou, C.-C., Reiter, L., Distler, U., et al. (2016) · Nature Biotechnology

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 346

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Petralia, F., Tignor, N., Reva, B., Koptyra, M., Chowdhury, S., Rykunov, D., Krek, A., Ma, W., Zhu, Y., Ji, J., et al. (2020) · Cell

Glioma Diagnosis and TreatmentCancer Genomics and Diagnostics

Cited by 317

The functional interactome landscape of the human histone deacetylase family

Joshi, P., Greco, T. M., Guise, A. J., Luo, Y., Yu, F., Nesvizhskii, A. I., & Cristea, I. M. (2013) · Molecular Systems Biology

Histone Deacetylase Inhibitors ResearchGenomics and Chromatin Dynamics

Cited by 289

ProHits: integrated software for mass spectrometry–based interaction proteomics

Liu, G., Zhang, J., Larsen, B., Stark, C., Breitkreutz, A., Lin, Z.-Y., Breitkreutz, B.-J., Ding, Y., Colwill, K., Pasculescu, A., et al. (2010) · Nature Biotechnology

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 243

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

Rosenberger, G., Bludau, I., Schmitt, U., Heusel, M., Hunter, C. L., Liu, Y., MacCoss, M. J., MacLean, B. X., Nesvizhskii, A. I., Pedrioli, P. G. A., et al. (2017) · Nature Methods

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 203

Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

Liang, W.-W., Lu, R. J.-H., Jayasinghe, R. G., Foltz, S. M., Porta-Pardo, E., Geffen, Y., Wendl, M. C., Lazcano, R., Kolodziejczak, I., Song, Y., et al. (2023) · Cancer Cell

Epigenetics and DNA MethylationCancer Genomics and Diagnostics

Cited by 105

Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

Müller, M., Gräbnitz, F., Barandun, N., Shen, Y., Wendt, F., Steiner, S. N., Severin, Y., Vetterli, S. U., Mondal, M., Prudent, J. R., et al. (2021) · Nature Communications

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 101

SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments

Choi, H., Glatter, T., Gstaiger, M., & Nesvizhskii, A. I. (2012) · Journal of Proteome Research

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 68

Multiomic characterization of pancreatic cancer-associated macrophage polarization reveals deregulated metabolic programs driven by the GM-CSF-PI3K pathway

Boyer, S., Lee, H.-J., Steele, N., Zhang, L., Sajjakulnukit, P., Andren, A., Ward, M. H., Singh, R., Basrur, V., Zhang, Y., et al. (2022) · eLife

Immune cells in cancerPancreatic and Hepatic Oncology Research

Cited by 56

Autoinhibited kinesin-1 adopts a hierarchical folding pattern

Tan, Z., Yue, Y., Leprevost, F., Haynes, S., Basrur, V., Nesvizhskii, A. I., Verhey, K. J., & Cianfrocco, M. A. (2023) · eLife

Microtubule and mitosis dynamicsProtein Structure and Dynamics

Cited by 48

Constitutive release of CPS1 in bile and its role as a protective cytokine during acute liver injury

Park, M.-J., D’Alecy, L. G., Anderson, M. A., Basrur, V., Feng, Y., Brady, G. F., Kim, D.-I., Wu, J., Nesvizhskii, A. I., Lahann, J., et al. (2019) · Proceedings of the National Academy of Sciences

Drug-Induced Hepatotoxicity and ProtectionLiver physiology and pathology

Cited by 44

Profiling the Proteome-Wide Selectivity of Diverse Electrophiles

Zanon, P. R. A., Yu, F., Musacchio, P., Lewald, L., Zollo, M., Krauskopf, K., Mrdović, D., Raunft, P., Maher, T. E., Cigler, M., et al. (2021) · ChemRxiv

Click Chemistry and ApplicationsAdvanced Proteomics Techniques and Applications

Cited by 35

A solid-phase compatible silane-based cleavable linker enables custom isobaric quantitative chemoproteomics

Burton, N., Polasky, D., Shikwanna, F., Ofori, S., Yan, T., Geiszler, D., da Veiga Leprevost, F., Nesvizhskii, A., & Backus, K. (2023) · Journal of the American Chemical Society

Advanced Proteomics Techniques and ApplicationsClick Chemistry and Applications

Cited by 22

A solid-phase compatible silane-based cleavable linker enables custom isobaric quantitative chemoproteomics

Burton, N., Polasky, D., Shikwanna, F., Ofori, S., Yan, T., Geiszler, D., da Veiga Leprevost, F., Nesvizhskii, A., & Backus, K. (2023) · Journal of the American Chemical Society

Advanced Proteomics Techniques and ApplicationsClick Chemistry and Applications

Cited by 22