Nathan Edwards
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View article: Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer Open
View article: Figure 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Figure 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
PDC study summary page offering a comprehensive overview of both data and metadata.
View article: Data from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Data from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Proteomics has emerged as a powerful tool for studying cancer biology, developing diagnostics, and therapies. With the continuous improvement and widespread availability of high-throughput proteomic technologies, the generation of large-sc…
View article: Table 1 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Table 1 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Available data types in the proteomic data commons
View article: Figure 3 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Figure 3 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Cross referencing to genomic and imaging resources for individual cases. Example of cross-referencing (A) on the Clinical tab of PDC’s Explore page; B, on the Clinical tab and External References section of PDC study summary …
View article: Table 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Table 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Documentation resources in the PDC
View article: Figure 3 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Figure 3 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Cross referencing to genomic and imaging resources for individual cases. Example of cross-referencing (A) on the Clinical tab of PDC’s Explore page; B, on the Clinical tab and External References section of PDC study summary …
View article: Data from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Data from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Proteomics has emerged as a powerful tool for studying cancer biology, developing diagnostics, and therapies. With the continuous improvement and widespread availability of high-throughput proteomic technologies, the generation of large-sc…
View article: Figure 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Figure 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
PDC study summary page offering a comprehensive overview of both data and metadata.
View article: Table 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Table 2 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Documentation resources in the PDC
View article: Table 1 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
Table 1 from NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Available data types in the proteomic data commons
View article: NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data
NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data Open
Proteomics has emerged as a powerful tool for studying cancer biology, developing diagnostics, and therapies. With the continuous improvement and widespread availability of high-throughput proteomic technologies, the generation of large-sc…
View article: scSNViz: Visualization and Analysis of Cell-Specific Expressed SNVs
scSNViz: Visualization and Analysis of Cell-Specific Expressed SNVs Open
Summary Accurately characterizing expressed genetic variation at the single-cell level is essential for understanding transcriptional heterogeneity, allelic regulation, and mutational dynamics within complex tissues. However, few tools ena…
View article: Comprehensive proteogenomic characterization of rare kidney tumors
Comprehensive proteogenomic characterization of rare kidney tumors Open
View article: Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy Open
Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information focus primarily on the macromolecules within the central dogma of molecular bio…
View article: Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin
Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin Open
DNA methylation plays a critical role in establishing and maintaining cellular identity. However, it is frequently dysregulated during tumor development and is closely intertwined with other genetic alterations. Here, we leveraged multi-om…
View article: Pan-cancer proteogenomics connects oncogenic drivers to functional states
Pan-cancer proteogenomics connects oncogenic drivers to functional states Open
View article: Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation Open
View article: Cataloging natural sialic acids and other nonulosonic acids (NulOs), and their representation using the Symbol Nomenclature for Glycans
Cataloging natural sialic acids and other nonulosonic acids (NulOs), and their representation using the Symbol Nomenclature for Glycans Open
Nonulosonic acids or non-2-ulosonic acids (NulOs) are an ancient family of 2-ketoaldonic acids (α-ketoaldonic acids) with a 9-carbon backbone. In nature, these monosaccharides occur either in a 3-deoxy form (referred to as “sialic acids”) …
View article: SCExecute: custom cell barcode-stratified analyses of scRNA-seq data
SCExecute: custom cell barcode-stratified analyses of scRNA-seq data Open
Motivation In single-cell RNA-sequencing (scRNA-seq) data, stratification of sequencing reads by cellular barcode is necessary to study cell-specific features. However, apart from gene expression, the analyses of cell-specific features are…
View article: Extracellular Heparan 6-O-Endosulfatases SULF1 and SULF2 in Head and Neck Squamous Cell Carcinoma and Other Malignancies
Extracellular Heparan 6-O-Endosulfatases SULF1 and SULF2 in Head and Neck Squamous Cell Carcinoma and Other Malignancies Open
Pan-cancer analysis of TCGA and CPTAC (proteomics) data shows that SULF1 and SULF2 are oncogenic in a number of human malignancies and associated with poor survival outcomes. Our studies document a consistent upregulation of SULF1 and SULF…
View article: Extracellular heparan 6-O-endosulfatases SULF1 and SULF2 in HNSC and other malignancies
Extracellular heparan 6-O-endosulfatases SULF1 and SULF2 in HNSC and other malignancies Open
SULF1 and SULF2 are oncogenic in a number of human malignancies, including head and neck squamous cell carcinoma (HNSC). The function of these two heparan sulfate editing enzymes was previously considered largely redundant but the biology …
View article: A wealth of novel cell-specific expressed SNVs from tumor and normal scRNA-seq datasets
A wealth of novel cell-specific expressed SNVs from tumor and normal scRNA-seq datasets Open
We demonstrate a novel variant calling strategy using barcode-stratified alignments on 25 tumor and normal 10XGenomics scRNA-seq datasets (>200,000 cells). Our approach identified 24,528 exonic non-dbSNP single cell expressed (sce)SNVs, a …
View article: SCExecute: cell barcode-stratified analyses of scRNA-seq data
SCExecute: cell barcode-stratified analyses of scRNA-seq data Open
Motivation In single-cell RNA-sequencing (scRNA-seq) data, stratification of sequencing reads by cellular barcode is necessary to study cell-specific features. However, apart from gene expression, the analyses of cell-specific features are…
View article: Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis
Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis Open
International audience
View article: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis Open
Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted thr…
View article: SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data Open
View article: GNOme - Glycan Naming and Subsumption Ontology
GNOme - Glycan Naming and Subsumption Ontology Open
<p>The Glycan Naming and Subsumption Ontology (GNOme) is an OBOFoundry ontology that organizes the stable glycan accessions of GlyTouCan glycan sequence registry for reasoning and browsing by subsumption. The ontology enables the fas…
View article: Proteogenomic characterization of pancreatic ductal adenocarcinoma
Proteogenomic characterization of pancreatic ductal adenocarcinoma Open
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 1…
View article: Corrigendum to: The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application
Corrigendum to: The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application Open