List of works - Cathy H. Wu

A comparison study of biomedical short form definition detection algorithms

A comparison study on algorithms of detecting long forms for short forms in biomedical text

scientific article

A comprehensive protein-centric ID mapping service for molecular data integration

scientific article

A crowdsourcing open platform for literature curation in UniProt

scientific article published on 6 December 2021

A fast Peptide Match service for UniProt Knowledgebase

scientific article published on 19 August 2013

A framework for biomedical figure segmentation towards image-based document retrieval

scientific article

A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems.

scientific article

Aberrant iron homeostasis, oxidative fiber enrichment, and activation of ketogenesis in muscle tissue of ISCU Myopathy patients.

scientific article published in June 2012

Accomplishments and challenges in literature data mining for biology

scientific article

An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature

An integrated approach for analyzing clinical genomic variant data from next-generation sequencing.

scientific article

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

scientific article published on 17 January 2013

Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature

scientific article published on January 2017

Artificial neural networks for molecular sequence analysis

scientific article

Automatic gene annotation using GO terms from cellular component domain

article

BioC interoperability track overview

scientific article

BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph

scientific article published on 11 May 2016

BioC: a minimalist approach to interoperability for biomedical text processing

scientific article

BioCreative III interactive task: an overview

scientific article

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.

scientific article published in September 2016

BioCreative-2012 virtual issue

scientific article published on 5 December 2012

BioCreative-IV virtual issue

scientific article published on 22 May 2014

BioTagger-GM: a gene/protein name recognition system.

scientific article published on 11 December 2008

BioThesaurus: a web-based thesaurus of protein and gene names

scientific article published on 02 November 2005

Bioinformatic Databases

Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer

scientific article published on 28 October 2015

Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia

Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees

scientific article

Community annotation in biology

scientific article (publication date: 18 February 2010)

Completing sparse and disconnected protein-protein network by deep learning.

scientific article

Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines.

scientific article published on 17 May 2007

Computational clustering for viral reference proteomes.

scientific article published on 26 February 2016

Computational identification of strain-, species- and genus-specific proteins

scientific article

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system

scientific article

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint

scientific article

Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition

scientific article published on 08 February 2019

Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework

scientific article published on 18 June 2015

DEXTER: Disease-Expression Relation Extraction from Text.

scientific article published in January 2018

Dependence network modeling for biomarker identification

scientific article published on 31 October 2006

Development of Bioinformatics Pipeline for Analyzing Clinical Pediatric NGS Data.

scientific article

Document Classification for Mining Host Pathogen Protein-Protein Interactions

Document classification for mining host pathogen protein-protein interactions

scientific article published on 15 May 2010

DynGO: a tool for visualizing and mining of Gene Ontology and its associations

scientific article

Elevated FGF21 secretion, PGC-1α and ketogenic enzyme expression are hallmarks of iron-sulfur cluster depletion in human skeletal muscle

scientific article published on 13 August 2013

Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction.

scientific article published on 22 October 2016

Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm

scientific article

Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space

scientific article published on 8 September 2017

Framework for a protein ontology

scientific article

Framework for a protein ontology

Human RhoGAP domain-containing proteins: structure, function and evolutionary relationships

scientific article (publication date: 25 September 2002)

Inference of protein-protein interaction networks from multiple heterogeneous data

scientific article

Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data

scientific article

Integration of bioinformatics resources for functional analysis of gene expression and proteomic data

scientific article

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources.

scientific article

InterPro in 2011: new developments in the family and domain prediction database

scientific article

InterPro in 2011: new developments in the family and domain prediction database

scientific article published on 19 May 2012

InterPro in 2017-beyond protein family and domain annotations

scientific article

InterPro, progress and status in 2005

scientific article

InterPro: the integrative protein signature database

scientific article

Mapping Gene/Protein Names in Free Text to Biomedical Databases

article

New developments in the InterPro database

scientific article

Omics-based molecular target and biomarker identification.

scientific article published on January 2011

Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing

scientific article

Overview of the BioCreative III Workshop

scientific article

Overview of the interactive task in BioCreative V

scientific article (publication date: 2016)

PIRSF family classification system for protein functional and evolutionary analysis

scientific article published on January 2006

PIRSF: family classification system at the Protein Information Resource

scientific article

PIRSitePredict for protein functional site prediction using position-specific rules

Pathway curation: Application of text-mining tools eGIFT and RLIMS-P

Phylogenomic analysis of marine Roseobacters

scientific article

Plant protein annotation in the UniProt knowledgebase

scientific article

Predicting ligand binding residues and functional sites using multipositional correlations with graph theoretic clustering and kernel CCA.

scientific article published in July 2012

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties

scientific article

Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.

scientific article published on 6 June 2016

Prepublication data sharing

scientific article

Protein Bioinformatics Databases and Resources.

scientific article

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data

scientific article

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

scientific article

Protein Ontology: a controlled structured network of protein entities

scientific article

Protein bioinformatics databases and resources

scientific article published on 01 January 2011

Protein classification artificial neural system ⬇️

scientific article published on May 1, 1992

Protein family classification and functional annotation

scientific article

Protein name tagging guidelines: lessons learned

scientific article published on January 2005

Protein ontology on the semantic web for knowledge discovery

scientific article published on 12 October 2020

Protein sequence databases

Protein-centric data integration for functional analysis of comparative proteomics data

scientific article

Protein-protein interaction prediction based on multiple kernels and partial network with linear programming.

scientific article published in August 2016

Proteomic analysis of pathways involved in estrogen-induced growth and apoptosis of breast cancer cells.

scientific article

Quantitative assessment of dictionary-based protein named entity tagging

scientific article

RESTful API for iPTMnet: a resource for protein post-translational modification network discovery

scientific article published on 01 January 2020

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information

scientific article

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information

scientific article

RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism

scientific article

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference

scientific article (publication date: 2012)

Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

scientific article

Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology

scientific article published on August 2016

Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes.

scientific article

SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

scientific article

Software for pre-processing Illumina next-generation sequencing short read sequences.

scientific article

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach

scientific article

Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase

scientific article

Substring selection for biomedical document classification

scientific article published on 12 July 2006

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets

scientific article (publication date: 25 September 2009)

TGF-beta signaling proteins and the Protein Ontology

scientific article

Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach

Text mining for the biocuration workflow

scientific article

The InterPro protein families and domains database: 20 years on

scientific article published on 06 November 2020

The InterPro protein families database: the classification resource after 15 years

scientific article

The Protein Information Resource

scientific article

The Protein Information Resource: an integrated public resource of functional annotation of proteins

scientific article

The Protein Ontology: a structured representation of protein forms and complexes

scientific article

The Universal Protein Resource (UniProt)

scientific article

The Universal Protein Resource (UniProt): an expanding universe of protein information

scientific article

The eFIP system for text mining of protein interaction networks of phosphorylated proteins

scientific article

The human proteome project: Current state and future direction.

scientific article published on 29 April 2011

The iProClass integrated database for protein functional analysis

scientific article published on February 2004

The representation of protein complexes in the Protein Ontology (PRO).

scientific article

TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis

scientific article published on 14 September 2021

Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.

scientific article

Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress.

scientific article

Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus)

scientific article published on 21 September 2018

Tunable synthetic extracellular matrices to investigate breast cancer response to biophysical and biochemical cues

scientific article published on 08 February 2019

Understanding ER+ Breast Cancer Dormancy Using Bioinspired Synthetic Matrices for Long-Term 3D Culture and Insights into Late Recurrence

scientific article published on 30 June 2020

UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants

UniProt genomic mapping for deciphering functional effects of missense variants.

scientific article published on 3 April 2019

UniProt: the Universal Protein knowledgebase

scientific article from 2004

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

scientific article

UniRef: comprehensive and non-redundant UniProt reference clusters

scientific article (publication date: 15 May 2007)

Update on genome completion and annotations: Protein Information Resource

scientific article

Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint

scientific article published on 26 April 2013

Using distant supervision to augment manually annotated data for relation extraction

scientific article published on 30 July 2019

eFIP: a tool for mining functional impact of phosphorylation from literature

scientific article published on January 2011

eGARD: Extracting associations between genomic anomalies and drug responses from text.

scientific article published on 20 December 2017

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality

scientific article published in January 2017

iPTMnet: Integrative Bioinformatics for Studying PTM Networks

scientific article published on January 2017

iPTMnet: an integrated resource for protein post-translational modification network discovery

scientific article

iProClass: an integrated database of protein family, function and structure information

scientific article

iProLINK: an integrated protein resource for literature mining

scientific article published on December 2004

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system

scientific article

iSimp: A sentence simplification system for biomedicail text

article

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature

scientific article published on 01 January 2018

miRTex: A Text Mining System for miRNA-Gene Relation Extraction

scientific article

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases

scientific article published on 29 April 2016

pGenN, a gene normalization tool for plant genes and proteins in scientific literature

scientific article published on 10 August 2015

piNET: a versatile web platform for downstream analysis and visualization of proteomics data

scientific article published on 29 May 2020

List of works by Cathy H. Wu

A comparison study of biomedical short form definition detection algorithms

A comparison study on algorithms of detecting long forms for short forms in biomedical text

A comprehensive protein-centric ID mapping service for molecular data integration

A crowdsourcing open platform for literature curation in UniProt

A fast Peptide Match service for UniProt Knowledgebase

A framework for biomedical figure segmentation towards image-based document retrieval

A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems.

Aberrant iron homeostasis, oxidative fiber enrichment, and activation of ketogenesis in muscle tissue of ISCU Myopathy patients.

Accomplishments and challenges in literature data mining for biology

An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature

An integrated approach for analyzing clinical genomic variant data from next-generation sequencing.

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature

Artificial neural networks for molecular sequence analysis

Automatic gene annotation using GO terms from cellular component domain

BioC interoperability track overview

BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph

BioC: a minimalist approach to interoperability for biomedical text processing

BioCreative III interactive task: an overview

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.

BioCreative-2012 virtual issue

BioCreative-IV virtual issue

BioTagger-GM: a gene/protein name recognition system.

BioThesaurus: a web-based thesaurus of protein and gene names

Bioinformatic Databases

Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer

Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia

Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees

Community annotation in biology

Completing sparse and disconnected protein-protein network by deep learning.

Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines.

Computational clustering for viral reference proteomes.

Computational identification of strain-, species- and genus-specific proteins

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint

Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition

Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework

DEXTER: Disease-Expression Relation Extraction from Text.

Dependence network modeling for biomarker identification

Development of Bioinformatics Pipeline for Analyzing Clinical Pediatric NGS Data.

Document Classification for Mining Host Pathogen Protein-Protein Interactions

Document classification for mining host pathogen protein-protein interactions

DynGO: a tool for visualizing and mining of Gene Ontology and its associations

Elevated FGF21 secretion, PGC-1α and ketogenic enzyme expression are hallmarks of iron-sulfur cluster depletion in human skeletal muscle

Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction.

Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm

Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space

Framework for a protein ontology

Framework for a protein ontology

Human RhoGAP domain-containing proteins: structure, function and evolutionary relationships

Inference of protein-protein interaction networks from multiple heterogeneous data

Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data

Integration of bioinformatics resources for functional analysis of gene expression and proteomic data

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources.

InterPro in 2011: new developments in the family and domain prediction database

InterPro in 2011: new developments in the family and domain prediction database

InterPro in 2017-beyond protein family and domain annotations

InterPro, progress and status in 2005

InterPro: the integrative protein signature database

Mapping Gene/Protein Names in Free Text to Biomedical Databases

New developments in the InterPro database

Omics-based molecular target and biomarker identification.

Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing

Overview of the BioCreative III Workshop

Overview of the interactive task in BioCreative V

PIRSF family classification system for protein functional and evolutionary analysis

PIRSF: family classification system at the Protein Information Resource

PIRSitePredict for protein functional site prediction using position-specific rules

Pathway curation: Application of text-mining tools eGIFT and RLIMS-P

Phylogenomic analysis of marine Roseobacters

Plant protein annotation in the UniProt knowledgebase

Predicting ligand binding residues and functional sites using multipositional correlations with graph theoretic clustering and kernel CCA.

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties

Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.

Prepublication data sharing

Protein Bioinformatics Databases and Resources.

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

Protein Ontology: a controlled structured network of protein entities