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Proteome-Scale Human Interactomics

Trends in biochemical sciences (Amsterdam. Regular ed.), 2017-05, Vol.42 (5), p.342-354

2017

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Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease

Human molecular genetics, 2022-10, Vol.31 (R1), p.R123-R136

2022

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Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing

Cell reports (Cambridge), 2021-11, Vol.37 (7), p.110022-110022, Article 110022

2021

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Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

Genome Biology, 2018-03, Vol.19 (1), p.46-18, Article 46

2018

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Enhanced protein isoform characterization through long-read proteogenomics

Genome Biology, 2022-03, Vol.23 (1), p.69-28, Article 69

2022

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Endothelial cell cycle state determines propensity for arterial-venous fate

Nature communications, 2022-10, Vol.13 (1), p.5891-5891, Article 5891

2022

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Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

Annual review of analytical chemistry (Palo Alto, Calif.), 2016-06, Vol.9 (1), p.521-545

2016

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Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

Molecular & cellular proteomics, 2013-08, Vol.12 (8), p.2341-2353

2013

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Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease

American journal of human genetics, 2024-09, Vol.111 (9), p.1914-1931

2024

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Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics

RNA biology, 2022-12, Vol.19 (1), p.1228-1243

2022

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ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms

Nature communications, 2020-05, Vol.11 (1), p.2326-2326, Article 2326

2020

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The lncRNA SLNCR Recruits the Androgen Receptor to EGR1-Bound Genes in Melanoma and Inhibits Expression of Tumor Suppressor p21

Cell reports (Cambridge), 2019-05, Vol.27 (8), p.2493-2507.e4

2019

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Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences

Journal of proteome research, 2014-01, Vol.13 (1), p.228-240

2014

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Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes

Circulation research, 2023-02, Vol.132 (3), p.323-338

2023

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Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy

Science translational medicine, 2024-01, Vol.16 (730), p.eade2886

2024

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Gain-of-Function Variomics and Multi-omics Network Biology for Precision Medicine

Methods in molecular biology (Clifton, N.J.), 2023, Vol.2660, p.357

2023

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Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data

Journal of proteome research, 2019-09, Vol.18 (9), p.3429-3438

2019

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IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection

Journal of the American Society for Mass Spectrometry, 2024-07

2024

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sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments

Bioinformatics (Oxford, England), 2014-11, Vol.30 (21), p.3136-3138

2014

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Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data

Genome Biology, 2023-04, Vol.24 (1), p.91-91, Article 91

2023

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The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets

PLoS genetics, 2016-12, Vol.12 (12), p.e1006466-e1006466

2016

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Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search

Journal of proteome research, 2015-11, Vol.14 (11), p.4714-4720

2015

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AD-Syn-Net: systematic identification of Alzheimer’s disease-associated mutation and co-mutation vulnerabilities via deep learning

Briefings in bioinformatics, 2023-03, Vol.24 (2)

2023

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Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy

Journal of proteome research, 2016-03, Vol.15 (3), p.800-808

2016

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Proteome-Scale Human Interactomics

Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease

Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

Enhanced protein isoform characterization through long-read proteogenomics

Endothelial cell cycle state determines propensity for arterial-venous fate

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease

Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics

ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms

The lncRNA SLNCR Recruits the Androgen Receptor to EGR1-Bound Genes in Melanoma and Inhibits Expression of Tumor Suppressor p21

Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes

Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy

Gain-of-Function Variomics and Multi-omics Network Biology for Precision Medicine

Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data

IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments

Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data

The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets

Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search

AD-Syn-Net: systematic identification of Alzheimer’s disease-associated mutation and co-mutation vulnerabilities via deep learning

Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy

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