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Enhanced protein isoform characterization through long-read proteogenomics

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

2022

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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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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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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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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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Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

BMC genomics, 2014-08, Vol.15 (1), p.703-703, Article 703

2014

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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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Proteome-Scale Human Interactomics

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

2017

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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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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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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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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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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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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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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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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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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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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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Transcription Factors and Splice Factors—Interconnected Regulators of Stem Cell Differentiation

Current stem cell reports, 2023-06, Vol.9 (2), p.31-41

2023

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Connexin 37 sequestering of activated-ERK in the cytoplasm promotes p27-mediated endothelial cell cycle arrest

Life science alliance, 2023-08, Vol.6 (8), p.e202201685

2023

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Large-scale mass spectrometric detection of variant peptides resulting from non-synonymous nucleotide differences

Journal of proteome research, 2013-11, Vol.13 (1), p.228-240

2013

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Enhanced protein isoform characterization through long-read proteogenomics

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

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

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

Endothelial cell cycle state determines propensity for arterial-venous fate

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

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

Proteome-Scale Human Interactomics

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

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

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

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

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

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

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

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

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

Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy

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

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

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

Transcription Factors and Splice Factors—Interconnected Regulators of Stem Cell Differentiation

Connexin 37 sequestering of activated-ERK in the cytoplasm promotes p27-mediated endothelial cell cycle arrest

Large-scale mass spectrometric detection of variant peptides resulting from non-synonymous nucleotide differences

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