Alexey I. Nesvizhskii

Also affiliated with Gilbert Bain Hospital, Michigan Medicine

ChemistryBiochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 2%percentile

4.4Author DataRank

Indexed papers

3in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Proteogenomic data and resources for pan-cancer analysis

Cancer Cell(2023)10.1016/j.ccell.2023.06.009

Top 6%

3.4DataRank

Top 6%241 citations

Yongchao Dou, Felipe da Veiga Leprevost, Yifat Geffen, Anna Calinawan, François Aguet +93 more

Papers

Driven by 107 papers — median percentile 65. Top paper: “Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma”.

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

Cell(2020)10.1016/j.cell.2020.06.013

N/A

9.1DataRank · unranked

837 citations

Shankha Satpathy, Song Cao, Saravana M. Dhanasekaran, Suhas Vasaikar, Karsten Krug +95 more

Proteogenomic and metabolomic characterization of human glioblastoma

Cancer Cell(2021)10.1016/j.ccell.2021.01.006

N/A

8.7DataRank · unranked

702 citations

Alla Y. Karpova, Marina A. Gritsenko, Jennifer Kyle, Song Cao, Yize Li +95 more

Proteogenomic characterization of pancreatic ductal adenocarcinoma

Cell(2021)10.1016/j.cell.2021.08.023

N/A

7.9DataRank · unranked

606 citations

Chen Huang, Daniel Cui Zhou, Yingwei Hu, T. Mamie Lih, Sara R. Savage +95 more

A proteogenomic portrait of lung squamous cell carcinoma

Cell(2021)10.1016/j.cell.2021.07.016

N/A

7.2DataRank · unranked

392 citations

Karsten Krug, Pierre M. Jean Beltran, Sara R. Savage, Francesca Petralia, Chandan Kumar‐Sinha +95 more

Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer

Nature(2021)10.1038/s41586-021-04246-z

N/A

6.3DataRank · unranked

322 citations

Abhijit Parolia, Yuanyuan Qiao, Pushpinder Bawa, Sanjana Eyunni, Rahul Mannan +33 more

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Cancer Cell(2022)10.1016/j.ccell.2022.12.001

N/A

3.6DataRank · unranked

216 citations

T. Mamie Lih, Saravana M. Dhanasekaran, Rahul Mannan, Lijun Chen, Marcin Cieślik +95 more

Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Cell(2023)10.1016/j.cell.2023.07.013

N/A

3.5DataRank · unranked

197 citations

Shankara Anand, Yo Akiyama, Tomer M. Yaron, Yizhe Song, Jared L. Johnson +90 more

Proteogenomic data and resources for pan-cancer analysis

Cancer Cell(2023)10.1016/j.ccell.2023.06.009

Top 6%

3.4DataRank

Top 6%241 citations

Yongchao Dou, Felipe da Veiga Leprevost, Yifat Geffen, Anna Calinawan, François Aguet +93 more

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

Cancer Cell(2023)10.1016/j.ccell.2023.07.013

N/A

1.8DataRank · unranked

107 citations

Rita Jui-Hsien Lu, Reyka G. Jayasinghe, Steven M. Foltz, Eduard Porta‐Pardo, Yifat Geffen +95 more

Pan-cancer proteogenomics characterization of tumor immunity

Cell(2024)10.1016/j.cell.2024.01.027

N/A

1.7DataRank · unranked

91 citations

Weiping Ma, Tomer M. Yaron, Francesca Pia Caruso, Nicole Tignor, Joshua M. Wang +95 more

Proteogenomic insights suggest druggable pathways in endometrial carcinoma

Cancer Cell(2023)10.1016/j.ccell.2023.07.007

N/A

1.2DataRank · unranked

54 citations

Lizabeth Katsnelson, Marina A. Gritsenko, Yingwei Hu, Boris Reva, Runyu Hong +95 more

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs

Molecular & Cellular Proteomics(2021)10.1016/j.mcpro.2021.100077

N/A

0.949DataRank · unranked

557 citations

Sarah E. Haynes, Alexey I. Nesvizhskii, Fengchao Yu

Comprehensive proteogenomic characterization of rare kidney tumors

Cell Reports Medicine(2024)10.1016/j.xcrm.2024.101547

N/A

0.920DataRank · unranked

46 citations

Lijun Chen, Yi Hsiao, Rahul Mannan, Yuping Zhang, Jie Luo +95 more

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Cell(2020)10.1016/j.cell.2020.10.044

N/A

0.878DataRank · unranked

347 citations

Nicole Tignor, Boris Reva, Mateusz P. Koptyra, Shrabanti Chowdhury, Dmitry Rykunov +94 more

Deep learning integrates histopathology and proteogenomics at a pan-cancer level

Cell Reports Medicine(2023)10.1016/j.xcrm.2023.101173

N/A

0.843DataRank · unranked

33 citations

Runyu Hong, Elizabeth G. Demicco, Jimin Tan, Rossana Lazcano, André L. Moreira +95 more

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer

Cell(2023)10.1016/j.cell.2023.07.004

N/A

0.680DataRank · unranked

92 citations

Jacob J. Kennedy, Richard G. Ivey, Oscar Murillo, Noshad Hosseini, Xiaoyu Song +42 more

Omics Discovery Index - Discovering and Linking Public ‘Omics’ Datasets

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/049205

Top 35%

0.563DataRank

Top 35%12 citations

Mingze Bai, Felipe da Veiga Leprevost, Silvano Squizzato, Young Mi Park, Kenneth Haug +25 more

Profiling the proteome-wide selectivity of diverse electrophiles

(2021)10.33774/chemrxiv-2021-w7rss-v2

N/A

0.510DataRank · unranked

29 citations

Fengchao Yu, Patricia Z. Musacchio, Lisa Lewald, Michael Zollo, Kristina Krauskopf +10 more

Chemoproteogenomic stratification of the missense variant cysteinome

Nature Communications(2024)10.1038/s41467-024-53520-x

N/A

0.460DataRank · unranked

13 citations

Katrina H. Andrews, Kristina V. Bergersen, Samuel Ofori, Fengchao Yu, Flowreen Shikwana +8 more

Regulation of protein abundance in normal human tissues

medRxiv(2025)10.1101/2025.01.10.25320181

Top 44%

0.427DataRank

Top 44%10 citations

Lihua Jiang, Felipe da Veiga Leprevost, Ruiqi Jian, Joanne Chan, Dafni A. Glinos +6 more

Proteome-Scale Tissue Mapping Using Mass Spectrometry Based on Label-Free and Multiplexed Workflows

Molecular & Cellular Proteomics(2024)10.1016/j.mcpro.2024.100841

N/A

0.425DataRank · unranked

16 citations

Jongmin Jacob Woo, Fengchao Yu, Sarah Williams, Lye Meng Markillie, Ronald Moore +8 more

Unraveling the glycosylated immunopeptidome with HLA-Glyco

Nature Communications(2023)10.1038/s41467-023-39270-2

N/A

0.385DataRank · unranked

12 citations

Daniel A. Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier A. Alfaro +3 more

CCN6 Suppresses Metaplastic Breast Carcinoma by Antagonizing Wnt/β-Catenin Signaling to Inhibit EZH2-Driven EMT

Cancer Research(2024)10.1158/0008-5472.can-23-4054

N/A

0.384DataRank · unranked

10 citations

Bryce Brophy, Ahmad Eido, Adele Elisabetta Leonetti, Sabra Djomehri, Giuseppina Augimeri +8 more

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer

Cell(2024)10.1016/j.cell.2024.01.016

N/A

0.373DataRank · unranked

11 citations

Jacob J. Kennedy, Richard G. Ivey, Oscar Murillo, Noshad Hosseini, Xiaoyu Song +42 more

Precision proteogenomics reveals pan-cancer impact of germline variants

Cell(2025)10.1016/j.cell.2025.03.026

N/A

0.341DataRank · unranked

8 citations

Nadezhda V. Terekhanova, Kathleen J. Imbach, Karl R. Clauser, Myvizhi Esai Selvan, Isabel Mendizabal +132 more

Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets

Cell Genomics(2025)10.1016/j.xgen.2025.100851

N/A

0.254DataRank · unranked

4 citations

Renan Simões, Emerson de Souza Santos, Elizabeth G. Demicco, Rossana N. Lazcano Segura, Ma Weiping +95 more

Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.27.656447

N/A

0.104DataRank · unranked

1 citations

Yamei Deng, Ruo‐hong Li, Dmitry M. Avtonomov, Bo Wen, Sarah E. Haynes +5 more

Integrating Alternative Fragmentation Techniques into Standard LC-MS Workflows Using a Single Deep Learning Model Enhances Proteome Coverage

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.28.656555

N/A

0.104DataRank · unranked

1 citations

Cemil Can Saylan, Joel Lapin, Yana Demyanenko, Kevin Yang, John D. Sidda +4 more

Identification of multiple novel procoagulant plasma ligands for stabilin-2

Journal of Thrombosis and Haemostasis(2025)10.1016/j.jtha.2025.01.023

N/A

0.104DataRank · unranked

1 citations

Felipe da Veiga Leprevost, Venkatesha Basrur, Alexey I. Nesvizhskii, Orla Rawley, Krista Golden +4 more

Recent advances in computational algorithms and software for large-scale glycoproteomics

Current Opinion in Chemical Biology(2022)10.1016/j.cbpa.2022.102238

N/A

0DataRank · unranked

43 citations

Alexey I. Nesvizhskii, Daniel A. Polasky

EML2-S constitutes a new class of proteins that recognizes and regulates the dynamics of tyrosinated microtubules

Current Biology(2022)10.1016/j.cub.2022.07.027

N/A

0DataRank · unranked

27 citations

Thomas S. McAlear, Yue Yang, Takumi Higaki, Sarah E. Haynes, Alexey I. Nesvizhskii +5 more

Identification of secreted proteins by comparison of protein abundance in conditioned media and cell lysates

Analytical Biochemistry(2022)10.1016/j.ab.2022.114846

N/A

0DataRank · unranked

18 citations

Vi T. Tang, Felipe da Veiga Leprevost, Venkatesha Basrur, Jie Xiang, Alexey I. Nesvizhskii +2 more

Implementing the MSFragger Search Engine as a Node in Proteome Discoverer

(2022)10.1021/acs.jproteome.2c00485

N/A

0DataRank · unranked

1 citations

Sarah E. Haynes, Fengchao Yu, Alexey I. Nesvizhskii, Hui-Yin Chang

MSBooster: Improving Peptide Identification Rates using Deep Learning-Based Features

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.19.512904

N/A

0DataRank · unranked

28 citations

Fengchao Yu, Guo Ci Teo, Vadim Demichev, Markus Ralser, Alexey I. Nesvizhskii +1 more

Mining for ions: diagnostic feature detection in MS/MS spectra of post-translationally modified peptides

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.12.507594

N/A

0DataRank · unranked

8 citations

Daniel A. Polasky, Fengchao Yu, Alexey I. Nesvizhskii, Daniel Geiszler

MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.12.511963

N/A

0DataRank · unranked

4 citations

Daniel Geiszler, Fengchao Yu, Kai Li, Guo Ci Teo, Alexey I. Nesvizhskii +1 more

HLA-Glyco: A large-scale interrogation of the glycosylated immunopeptidome

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.05.519200

N/A

0DataRank · unranked

1 citations

Daniel A. Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier A. Alfaro +3 more

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

Nature Communications(2023)10.1038/s41467-023-39869-5

N/A

0DataRank · unranked

294 citations

Guo Ci Teo, Andy T. Kong, Klemens Fröhlich, Ginny Xiaohe Li, Vadim Demichev +2 more

MSBooster: improving peptide identification rates using deep learning-based features

Nature Communications(2023)10.1038/s41467-023-40129-9

N/A

0DataRank · unranked

239 citations

Fengchao Yu, Guo Ci Teo, Kai Li, Vadim Demichev, Markus Ralser +2 more

Autoinhibited kinesin-1 adopts a hierarchical folding pattern

eLife(2023)10.7554/elife.86776

N/A

0DataRank · unranked

51 citations

Yang Yue, Felipe da Veiga Leprevost, Sarah E. Haynes, Venkatesha Basrur, Alexey I. Nesvizhskii +3 more

MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics

Molecular & Cellular Proteomics(2023)10.1016/j.mcpro.2023.100538

N/A

0DataRank · unranked

44 citations

Daniel Geiszler, Fengchao Yu, Kai Li, Guo Ci Teo, Alexey I. Nesvizhskii +1 more

Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides

Nature Communications(2023)10.1038/s41467-023-39828-0

N/A

0DataRank · unranked

38 citations

Daniel A. Polasky, Fengchao Yu, Alexey I. Nesvizhskii, Daniel Geiszler

A hybrid breast cancer/mesenchymal stem cell population enhances chemoresistance and metastasis

JCI Insight(2023)10.1172/jci.insight.164216

N/A

0DataRank · unranked

26 citations

María E. González, Alessandro Paolì, Ahmad Eido, Yehyun Choi, Boris Burman +13 more

Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics

Analytical Chemistry(2023)10.1021/acs.analchem.2c03739

N/A

0DataRank · unranked

25 citations

Fengchao Yu, James Fulcher, Sarah Williams, Kristin Engbrecht, Ronald Moore +5 more

Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics

Journal of the American Chemical Society(2023)10.1021/jacs.3c05797

N/A

0DataRank · unranked

21 citations

Daniel A. Polasky, Flowreen Shikwana, Samuel Ofori, Tianyang Yan, Daniel Geiszler +4 more

Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling

Journal of Proteome Research(2023)10.1021/acs.jproteome.3c00155

N/A

0DataRank · unranked

14 citations

Mateusz Staniak, Felipe da Veiga Leprevost, Amanda M. Figueroa‐Navedo, Alexander R. Ivanov, Alexey I. Nesvizhskii +3 more

Sulfoproteomics Workflow with Precursor Ion Accurate Mass Shift Analysis Reveals Novel Tyrosine Sulfoproteins in the Golgi

Journal of Proteome Research(2023)10.1021/acs.jproteome.3c00323

N/A

0DataRank · unranked

9 citations

Andy T. Kong, Katherine E. Hersberger, Shijiao Huang, Alexey I. Nesvizhskii, Yanzhuang Wang +3 more

Mass Spectrometric Profiling of HLA-B44 Peptidomes Provides Evidence for Tapasin-Mediated Tryptophan Editing

The Journal of Immunology(2023)10.4049/jimmunol.2300232

N/A

0DataRank · unranked

5 citations

Avrokin Surnilla, Anita Zaitouna, Michael B. Mumphrey, Venkatesha Basrur, Irina Grigorova +5 more

Autoinhibited kinesin-1 adopts a hierarchical folding pattern

eLife(2023)10.7554/elife.86776.3

N/A

0DataRank · unranked

5 citations

Yang Yue, Felipe da Veiga Leprevost, Sarah E. Haynes, Venkatesha Basrur, Alexey I. Nesvizhskii +3 more

Multi-omic stratification of the missense variant cysteinome

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.12.553095

N/A

0DataRank · unranked

13 citations

Samuel Ofori, Lisa M. Boatner, Fengchao Yu, Miranda Villanueva, Nicholas Ung +3 more

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

ChemRxiv(2023)10.26434/chemrxiv-2023-n8h29

N/A

0DataRank · unranked

2 citations

Daniel A. Polasky, Flowreen Shikwanna, Samuel Ofori, Tianyang Yan, Daniel Geiszler +4 more

Efficient Analysis of Proteome-wide FPOP Data by FragPipe

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.01.543263

N/A

0DataRank · unranked

2 citations

Jessica A. Espino, Lisa M. Jones, Daniel A. Polasky, Alexey I. Nesvizhskii, Carolina Rojas Ramírez

Identification of LMAN1 and SURF4 dependent secretory cargoes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.06.535922

N/A

0DataRank · unranked

1 citations

Prabhodh S. Abbineni, Felipe da Veiga Leprevost, Venkatesha Basrur, Brian T. Emmer, Alexey I. Nesvizhskii +2 more

Mass spectrometric profiling of HLA-B44 peptidomes provides evidence for tapasin-mediated tryptophan editing

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.26.530125

N/A

0DataRank · unranked

0 citations

Avrokin Surnilla, Anita Zaitouna, Venkatesha Basrur, Michael B. Mumphrey, Irina Grigorova +5 more

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

ChemRxiv(2023)10.26434/chemrxiv-2023-n8h29-v2

N/A

0DataRank · unranked

0 citations

Daniel A. Polasky, Flowreen Shikwanna, Samuel Ofori, Tianyang Yan, Daniel Geiszler +4 more

Enhancing multiplexed cysteine chemoproteomics by uniting FragPipe with solid-phase compatible dialkoxydiphenylsilane reagents

ChemRxiv(2023)10.26434/chemrxiv-2023-n8h29-v3

N/A

0DataRank · unranked

0 citations

Daniel A. Polasky, Flowreen Shikwanna, Samuel Ofori, Tianyang Yan, Daniel Geiszler +4 more

Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst

Journal of Proteome Research(2024)10.1021/acs.jproteome.4c00294

N/A

0DataRank · unranked

114 citations

Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood +4 more

Integrated proteogenomic characterization of glioblastoma evolution

Cancer Cell(2024)10.1016/j.ccell.2023.12.015

N/A

0DataRank · unranked

95 citations

Simona Migliozzi, Harim Koo, Jun-Hee Hong, Seung Min Park, Sooheon Kim +34 more

An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing

Nature Protocols(2024)10.1038/s41596-024-01000-3

N/A

0DataRank · unranked

13 citations

Mateusz Staniak, Fengchao Yu, Alexey I. Nesvizhskii, Olga Vitek, Devon Kohler

Are Internal Fragments Observable in Electron Based Top-Down Mass Spectrometry?

Molecular & Cellular Proteomics(2024)10.1016/j.mcpro.2024.100814

N/A

0DataRank · unranked

12 citations

Carolina Rojas Ramírez, Steven A. DeFiglia, Carson W. Szot, Jessie Le, Carter Lantz +10 more

Quantitative proteome-wide O-glycoproteomics analysis with FragPipe

Analytical and Bioanalytical Chemistry(2024)10.1007/s00216-024-05382-x

N/A

0DataRank · unranked

11 citations

Lei Lü, Fengchao Yu, Kai Li, Michael R. Shortreed, Lloyd M. Smith +2 more

Light‐Activated Reactivity of Nitrones with Amino Acids and Proteins

Angewandte Chemie International Edition(2024)10.1002/anie.202415976

N/A

0DataRank · unranked

4 citations

Maximilian Iglhaut, Qian Shao, F. García, Bo‐Yang Huang, Scott M. Brittain +5 more

Analysis and visualization of quantitative proteomics data using FragPipe-Analyst

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.05.583643

N/A

0DataRank · unranked

33 citations

Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood +4 more

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.25.595875

N/A

0DataRank · unranked

6 citations

Guo Ci Teo, Kevin Yang, Fengchao Yu, Alexey I. Nesvizhskii, Kai Li

MSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.12.618041

N/A

0DataRank · unranked

4 citations

Yamei Deng, Alexey I. Nesvizhskii, Fengchao Yu

Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.04.583367

N/A

0DataRank · unranked

1 citations

Jongmin Jacob Woo, Fengchao Yu, Sarah Williams, Lye Meng Markillie, Ronald Moore +8 more

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data

Nature Communications(2025)10.1038/s41467-024-55448-8

N/A

0DataRank · unranked

30 citations

Guo Ci Teo, Kevin Yang, Fengchao Yu, Alexey I. Nesvizhskii, Kai Li

Profiling the proteome-wide selectivity of diverse electrophiles

Nature Chemistry(2025)10.1038/s41557-025-01902-z

N/A

0DataRank · unranked

30 citations

Fengchao Yu, Patricia Z. Musacchio, Lisa Lewald, Michael Zollo, Kristina Krauskopf +10 more

MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search

Nature Communications(2025)10.1038/s41467-025-58728-z

N/A

0DataRank · unranked

25 citations

Yamei Deng, Alexey I. Nesvizhskii, Fengchao Yu

Koina: Democratizing machine learning for proteomics research

Nature Communications(2025)10.1038/s41467-025-64870-5

N/A

0DataRank · unranked

9 citations

Kevin Yang, Tobias Kockmann, Christian Panse, Wassim Gabriel, Del Bold +20 more

Deep learning to decode sites of RNA translation in normal and cancerous tissues

Nature Communications(2025)10.1038/s41467-025-56543-0

N/A

0DataRank · unranked

10 citations

Zahra McVey, Ramneek Gupta, Ian Yannuzzi, Venkatesha Basrur, Alexey I. Nesvizhskii +3 more

Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms

Molecular & Cellular Proteomics(2025)10.1016/j.mcpro.2025.100980

N/A

0DataRank · unranked

6 citations

Kevin Yang, Wan Nur Atiqah binti Mazli, Jamison Shih, Fengchao Yu, Edwin Lo +3 more

Breaking Boundaries in Histone Modification MS-Based Detection: A Tailored Search Strategy for Unrestricted Identification of Novel Epigenetic Marks

Molecular & Cellular Proteomics(2025)10.1016/j.mcpro.2025.101080

N/A

0DataRank · unranked

3 citations

Roberta Noberini, Andrea Graziadei, Daniel A. Polasky, Fengchao Yu, Alexey I. Nesvizhskii +2 more

PAI-1 interaction with sortilin-related receptor 1 is required for lung fibrosis

JCI Insight(2025)10.1172/jci.insight.186131

N/A

0DataRank · unranked

4 citations

John J. Osterholzer, Lisa Leung, Venkatesha Basrur, Alexey I. Nesvizhskii, Natalya Subbotina +11 more

MHC1-TIP enables single-tube multimodal immunopeptidome profiling and uncovers intratumoral heterogeneity in antigen presentation

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.17.664894

N/A

0DataRank · unranked

2 citations

Diana Bocaniciu, Fraser Johnson, Rick C.P. de Jong, Fengchao Yu, Vincenzo Davide Aloi +11 more

Long-term immune reprogramming of classical monocytes with altered ontogeny mediates enhanced lung injury in sepsis survivors

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.16.654442

N/A

0DataRank · unranked

1 citations

Breanna McBean, Alan P. Boyle, Brett C. Arenberg, Matthias Mack, Bethany B. Moore +9 more

A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.28.667198

N/A

0DataRank · unranked

1 citations

Fengchao Yu, Daniel A. Polasky, Alexey I. Nesvizhskii, Carolina Rojas Ramírez

A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.07.647596

N/A

0DataRank · unranked

0 citations

Reid Wagner, Katherine Do, James E. Johnson, Fengchao Yu, Tyler Jubenville +8 more

The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis

Journal of Clinical Investigation(2025)10.1172/jci187998

N/A

0DataRank · unranked

0 citations

Karena Lin, Elizabeth Choe, Cher Sha, Zeel Shukla, Koral Campbell +28 more

Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors

Nature Communications(2020)10.1038/s41467-020-15283-z

N/A

0DataRank · unranked

171 citations

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Molecular & Cellular Proteomics(2020)10.1074/mcp.tir120.002216

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0DataRank · unranked

151 citations

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Molecular & Cellular Proteomics(2020)10.1074/mcp.tir120.002048

N/A

0DataRank · unranked

400 citations

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Nature Communications(2020)10.1038/s41467-020-17921-y

N/A

0DataRank · unranked

320 citations

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Nature Structural & Molecular Biology(2020)10.1038/s41594-020-0512-7

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0DataRank · unranked

55 citations

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Journal of Proteome Research(2020)10.1021/acs.jproteome.0c00119

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0DataRank · unranked

53 citations

Andy T. Kong, Felipe da Veiga Leprevost, Dmitry M. Avtonomov, Sarah E. Haynes, Alexey I. Nesvizhskii +1 more

Genotype‐phenotype analysis of LMNA ‐related diseases predicts phenotype‐selective alterations in lamin phosphorylation

The FASEB Journal(2020)10.1096/fj.202000500r

N/A

0DataRank · unranked

30 citations

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Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.19.999334

N/A

0DataRank · unranked

28 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.18.102665

N/A

0DataRank · unranked

23 citations

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.11.246652

N/A

0DataRank · unranked

11 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.02.365437

N/A

0DataRank · unranked

4 citations

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

Nature Communications(2021)10.1038/s41467-021-27280-x

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0DataRank · unranked

96 citations

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Current Biology(2021)10.1016/j.cub.2020.11.055

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0DataRank · unranked

35 citations

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Science Advances(2021)10.1126/sciadv.abd8407

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0DataRank · unranked

33 citations

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Science Advances(2021)10.1126/sciadv.abj9812

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0DataRank · unranked

22 citations

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Journal of Biological Chemistry(2021)10.1016/j.jbc.2021.100824

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0DataRank · unranked

22 citations

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ChemRxiv(2021)10.26434/chemrxiv-2021-w7rss-v2

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0DataRank · unranked

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High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.08.434385

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0DataRank · unranked

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ChemRxiv(2021)10.26434/chemrxiv.14186561.v1

N/A

0DataRank · unranked

36 citations

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Profiling the Proteome-Wide Selectivity of Diverse Electrophiles

ChemRxiv(2021)10.26434/chemrxiv.14186561

N/A

0DataRank · unranked

9 citations

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GRASP55 regulates mutant huntingtin unconventional secretion and aggregation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.05.463252

N/A

0DataRank · unranked

8 citations

Sarah Bui, Jianchao Zhang, Felipe da Veiga Leprevost, Lisa M. Sharkey, Whitney Reid +4 more

Viperin inhibits cholesterol biosynthesis and interacts with enzymes in the cholesterol biosynthetic pathway

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.19.431989

N/A

0DataRank · unranked

4 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.10.459752

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0DataRank · unranked

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Nature Communications(2022)10.1038/s41467-022-31492-0

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0DataRank · unranked

434 citations

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Molecular Cell(2022)10.1016/j.molcel.2022.09.025

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0DataRank · unranked

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Molecular & Cellular Proteomics(2022)10.1016/j.mcpro.2022.100205

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0DataRank · unranked

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GRASP55 regulates the unconventional secretion and aggregation of mutant huntingtin

Journal of Biological Chemistry(2022)10.1016/j.jbc.2022.102219

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0DataRank · unranked

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Molecular & Cellular Proteomics(2022)10.1016/j.mcpro.2022.100218

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0DataRank · unranked

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