Cathy H. Wu

According to our database1, Cathy H. Wu authored at least 150 papers between 1990 and 2019.

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Bibliography

2019
PIRSitePredict for protein functional site prediction using position-specific rules.
Database, 2019

2018
iPTMnet: an integrated resource for protein post-translational modification network discovery.
Nucleic Acids Research, 2018

Automatic gene annotation using GO terms from cellular component domain.
BMC Med. Inf. & Decision Making, 2018

Completing sparse and disconnected protein-protein network by deep learning.
BMC Bioinformatics, 2018

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature.
Database, 2018

DEXTER: Disease-Expression Relation Extraction from Text.
Database, 2018

Protein Complex Mention Recognition with Web-Based Knowledge Learning.
Proceedings of the Emerging Technologies for Education - Third International Symposium, 2018

Pattern Discovery for Wide-Window Open Information Extraction in Biomedical Literature.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

PENNER: Pattern-enhanced Nested Named Entity Recognition in Biomedical Literature.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

PTM Knowledge Networks and LINCS Multi-Omics Data for Kinase Inhibitor Drug-Analytics in Lung Cancer.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

RESTful API for iPTMnet: An Integrated Resource for Protein Post-translational Modification Network Discovery.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

Cloud-based Semantic Integration and Knowledge Discovery Systems in Precision Medicine.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017
Predicting nsSNPs that Disrupt Protein-Protein Interactions Using Docking.
IEEE/ACM Trans. Comput. Biology Bioinform., 2017

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.
Nucleic Acids Research, 2017

InterPro in 2017 - beyond protein family and domain annotations.
Nucleic Acids Research, 2017

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality.
Database, 2017

UD_GU_BioTM at TREC 2017: Precision Medicine Track.
Proceedings of The Twenty-Sixth Text REtrieval Conference, 2017

Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017

Identifying Comparative Structures in Biomedical Text.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017

2016
Inference of protein-protein interaction networks from multiple heterogeneous data.
EURASIP J. Bioinformatics and Systems Biology, 2016

Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction.
EURASIP J. Bioinformatics and Systems Biology, 2016

Protein-protein interaction prediction based on multiple kernels and partial network with linear programming.
BMC Systems Biology, 2016

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.
J. Biomedical Semantics, 2016

Computational clustering for viral reference proteomes.
Bioinformatics, 2016

Overview of the interactive task in BioCreative V.
Database, 2016

BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.
Database, 2016

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
Database, 2016

Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2015
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

miRTex: A Text Mining System for miRNA-Gene Relation Extraction.
PLoS Computational Biology, 2015

The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Research, 2015

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.
Bioinformatics, 2015

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.
Database, 2015

An extended dependency graph for relation extraction in biomedical texts.
Proceedings of the Workshop on Biomedical Natural Language Processing, BioNLP@IJCNLP 2015, 2015

Protein-protein interaction network inference from multiple kernels with optimization based on random walk by linear programming.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

Inference of protein-protein interaction networks from multiple heterogeneous data.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014
Software for pre-processing Illumina next-generation sequencing short read sequences.
Source Code for Biology and Medicine, 2014

Protein Ontology: a controlled structured network of protein entities.
Nucleic Acids Research, 2014

A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems.
BMC Bioinformatics, 2014

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.
Database, 2014

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system.
Database, 2014

BioC interoperability track overview.
Database, 2014

BioCreative-IV virtual issue.
Database, 2014

Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Docking features for predicting binding loss due to protein mutation.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

DDI2PPI: an integrated web server for protein-protein interaction and residue contact matrix predictions.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

2013
Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress.
BMC Systems Biology, 2013

A framework for biomedical figure segmentation towards image-based document retrieval.
BMC Systems Biology, 2013

Prediction of contact matrix for protein-protein interaction.
Bioinformatics, 2013

A fast Peptide Match service for UniProt Knowledgebase.
Bioinformatics, 2013

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint.
Database, 2013

BioC: a minimalist approach to interoperability for biomedical text processing.
Database, 2013

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
Database, 2013

Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach.
Proceedings of the ACM Conference on Bioinformatics, 2013

An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature.
Proceedings of the ACM Conference on Bioinformatics, 2013

ngsShoRT: A Software for Pre-processing Illumina Short Read Sequences for De Novo Genome Assembly.
Proceedings of the ACM Conference on Bioinformatics, 2013

An Integrated Approach for Interpretation of Clinical NGS Genomic Variant Data.
Proceedings of the AMIA 2013, 2013

2012
Predicting Ligand Binding Residues and Functional Sites Using Multipositional Correlations with Graph Theoretic Clustering and Kernel CCA.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

InterPro in 2011: new developments in the family and domain prediction database.
Nucleic Acids Research, 2012

BioCreative-2012 Virtual Issue.
Database, 2012

Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees.
Database, 2012

The eFIP system for text mining of protein interaction networks of phosphorylated proteins.
Database, 2012

Text mining for the biocuration workflow.
Database, 2012

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.
Database, 2012

Pathway curation: Application of text-mining tools eGIFT and RLIMS-P.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

iSimp: A sentence simplification system for biomedicail text.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

Robust segmentation of biomedical figures for image-based document retrieval.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011
The Protein Ontology: a structured representation of protein forms and complexes.
Nucleic Acids Research, 2011

The Representation of Protein Complexes in the Protein Ontology (PRO).
BMC Bioinformatics, 2011

BioCreative III interactive task: an overview.
BMC Bioinformatics, 2011

Overview of the BioCreative III Workshop.
BMC Bioinformatics, 2011

A comprehensive protein-centric ID mapping service for molecular data integration.
Bioinformatics, 2011

Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

2010
Document classification for mining host pathogen protein-protein interactions.
Artificial Intelligence in Medicine, 2010

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data.
Adv. Bioinformatics, 2010

Predicting Functional Sites in Biological Sequences Using Canonical Correlation Analysis.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2010

Predicting ligand binding residues using multi-positional correlations and kernel canonical correlation analysis.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

Prediction of Catalytic Residues in Proteins Using a Consensus of Prediction (CoP) Approach.
Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010

2009
InterPro: the integrative protein signature database.
Nucleic Acids Research, 2009

Research Paper: BioTagger-GM: A Gene/Protein Name Recognition System.
JAMIA, 2009

TGF-beta signaling proteins and the Protein Ontology.
BMC Bioinformatics, 2009

Information Extraction of Protein Phosphorylation from Biomedical Literature.
Proceedings of the Information Retrieval in Biomedicine, 2009

2008
Bioinformatic Databases.
Proceedings of the Wiley Encyclopedia of Computer Science and Engineering, 2008

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.
Nucleic Acids Research, 2008

Functional Annotation of Protein Isoforms and Modified Forms.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2008

Document Classification for Mining Host Pathogen Protein-Protein Interactions.
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008

iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology.
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008

2007
New developments in the InterPro database.
Nucleic Acids Research, 2007

A comparison study on algorithms of detecting long forms for short forms in biomedical text.
BMC Bioinformatics, 2007

Framework for a Protein Ontology.
BMC Bioinformatics, 2007

UniRef: comprehensive and non-redundant UniProt reference clusters.
Bioinformatics, 2007

Dependence network modeling for biomarker identification.
Bioinformatics, 2007

Mapping Gene/Protein Names in Free Text to Biomedical Databases.
Proceedings of the Workshops Proceedings of the 7th IEEE International Conference on Data Mining (ICDM 2007), 2007

2006
The Universal Protein Resource (UniProt): an expanding universe of protein information.
Nucleic Acids Research, 2006

Research Paper: Quantitative Assessment of Dictionary-based Protein Named Entity Tagging.
JAMIA, 2006

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.
BMC Bioinformatics, 2006

An online literature mining tool for protein phosphorylation.
Bioinformatics, 2006

BioThesaurus: a web-based thesaurus of protein and gene names.
Bioinformatics, 2006

Substring selection for biomedical document classification.
Bioinformatics, 2006

2005
InterPro, progress and status in 2005.
Nucleic Acids Research, 2005

The Universal Protein Resource (UniProt).
Nucleic Acids Research, 2005

Computational identification of strain-, species- and genus-specific proteins.
BMC Bioinformatics, 2005

DynGO: a tool for visualizing and mining of Gene Ontology and its associations.
BMC Bioinformatics, 2005

Literature mining and database annotation of protein phosphorylation using a rule-based system.
Bioinformatics, 2005

Dynamically Generating a Protein Entity Dictionary Using Online Resources.
Proceedings of the ACL 2005, 2005

2004
BIO-AJAX: An Extensible Framework for Biological Data Cleaning.
SIGMOD Record, 2004

PIRSF: family classification system at the Protein Information Resource.
Nucleic Acids Research, 2004

UniProt: the Universal Protein knowledgebase.
Nucleic Acids Research, 2004

The PIR integrated protein databases and data retrieval system.
Data Science Journal, 2004

The iProClass integrated database for protein functional analysis.
Computational Biology and Chemistry, 2004

iProLINK: an integrated protein resource for literature mining.
Computational Biology and Chemistry, 2004

2003
The Protein Information Resource.
Nucleic Acids Research, 2003

iProClass: an integrated database of protein family, function and structure information.
Nucleic Acids Research, 2003

Protein family classification and functional annotation.
Computational Biology and Chemistry, 2003

Linking Biomedical Language, Information and Knowledge - Session Introduction.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

The Protein Information Resource for Functional Genomics and Proteomics.
Proceedings of the Computational Biology and Genome Informatics, 2003

2002
The Protein Information Resource: an integrated public resource of functional annotation of proteins.
Nucleic Acids Research, 2002

Accomplishments and challenges in literature data mining for biology.
Bioinformatics, 2002

Literature Data Mining for Biology - Session Introduction.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001
DNA sequence classification via an expectation maximization algorithm and neural networks: a case study.
IEEE Trans. Systems, Man, and Cybernetics, Part C, 2001

iProClass: an integrated, comprehensive and annotated protein classification database.
Nucleic Acids Research, 2001

Protein Information Resource: a community resource for expert annotation of protein data.
Nucleic Acids Research, 2001

New techniques for extracting features from protein sequences.
IBM Systems Journal, 2001

2000
ProClass protein family database.
Nucleic Acids Research, 2000

The Protein Information Resource (PIR).
Nucleic Acids Research, 2000

PIR: a new resource for bioinformatics.
Bioinformatics, 2000

Application of neural networks to biological data mining: a case study in protein sequence classification.
Proceedings of the sixth ACM SIGKDD international conference on Knowledge discovery and data mining, 2000

1999
ProClass Protein Family Database.
Nucleic Acids Research, 1999

The PIR-International Protein Sequence Database.
Nucleic Acids Research, 1999

Gene Family Identification Network Design for Protein Sequence Analysis.
International Journal on Artificial Intelligence Tools, 1999

1998
GeneFIND web server for protein family identification and information retrieval.
Bioinformatics, 1998

1997
Artificial Neural Networks for Molecular Sequence Analysis.
Computers & Chemistry, 1997

Counter-Propagation Neural Networks for Molecular Sequence Classification: Supervised LVQ and Dynamic Node Allocation.
Appl. Intell., 1997

Motif neural network design for large-scale protein family identification.
Proceedings of International Conference on Neural Networks (ICNN'97), 1997

1996
A Protein Class Database Organized with ProSite Protein Groups and PIR Superfamilies.
Journal of Computational Biology, 1996

Motif identification neural design for rapid and sensitive protein family search.
Computer Applications in the Biosciences, 1996

1995
Neural Networks for Full-Scale Protein Sequence Classification: Sequence Encoding with Singular Value Decomposition.
Machine Learning, 1995

Gene Classification Artificial Neural System.
International Journal on Artificial Intelligence Tools, 1995

1993
Classification Neural Networks for Rapid Sequence Annotation and Automated Database Organization.
Computers & Chemistry, 1993

Neural Networks for Molecular Sequence Classification.
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993

1992
Classification Artificial Neural Systems for Genome Research.
Proceedings of the Proceedings Supercomputing '92, 1992

CANS: an interactive neural network system for CRAY supercomputers.
Proceedings of the 1992 ACM/SIGAPP Symposium on Applied Computing: Technological Challenges of the 1990's, 1992

1991
Protein Classification Using a Neural Network Database System.
Proceedings of the Conference on Analysis of Neural Network Applications, 1991

Neural networks for molecular sequence database management.
Proceedings of the 19th annual conference on Computer Science, 1991

1990
Using an Artificial Neural System to Determine the Knowledge Base of an Expert System.
Proceedings of the 1990 ACM SIGSMALL/PC Symposium on Small Systems, 1990

PROCANS: a protein classification system using a neural network.
Proceedings of the IJCNN 1990, 1990

Artificial Neural System for Gene Classification Using a Domain Database.
Proceedings of the ACM 18th Annual Computer Science Conference on Cooperation, 1990


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