Hongfang Liu

According to our database1, Hongfang Liu
  • authored at least 241 papers between 1999 and 2018.
  • has a "Dijkstra number"2 of four.

Timeline

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On csauthors.net:

Bibliography

2018
Clinical information extraction applications: A literature review.
Journal of Biomedical Informatics, 2018

CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines.
JAMIA, 2018

Clinical documentation variations and NLP system portability: a case study in asthma birth cohorts across institutions.
JAMIA, 2018

Natural language processing of clinical notes for identification of critical limb ischemia.
I. J. Medical Informatics, 2018

A Deep Representation Empowered Distant Supervision Paradigm for Clinical Information Extraction.
CoRR, 2018

Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes.
CoRR, 2018

A Comparison of Word Embeddings for the Biomedical Natural Language Processing.
CoRR, 2018

2017
Intrainstitutional EHR collections for patient-level information retrieval.
JASIST, 2017

Need of informatics in designing interoperable clinical registries.
I. J. Medical Informatics, 2017

Generalized ensemble model for document ranking in information retrieval.
Comput. Sci. Inf. Syst., 2017

Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts.
Database, 2017

BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences.
Database, 2017

Leveraging both Structured and Unstructured Data for Precision Information Retrieval.
Proceedings of The Twenty-Sixth Text REtrieval Conference, 2017

MayoNLP at SemEval 2017 Task 10: Word Embedding Distance Pattern for Keyphrase Classification in Scientific Publications.
Proceedings of the 11th International Workshop on Semantic Evaluation, 2017

Aligned-Layer Text Search in Clinical Notes.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Analysis of Clinical Variations in Asthma Care Documented in Electronic Health Records Between Staff and Resident Physicians.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Using Human Phenotype Ontology for Phenotypic Analysis of Clinical Notes.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Using Unstructured Data to Identify Readmitted Patients.
Proceedings of the 2017 IEEE International Conference on Healthcare Informatics, 2017

On Mapping Textual Queries to a Common Data Model.
Proceedings of the 2017 IEEE International Conference on Healthcare Informatics, 2017

Locally Generated Bayesian Network Prediction of Colorectal Surgical Site Infections.
Proceedings of the Summit on Clinical Research Informatics, 2017

Prediction of Organ Space Colorectal Surgical Site Infections Using Prognostic Bayesian Networks.
Proceedings of the Summit on Clinical Research Informatics, 2017

Content Analysis of Free-Text Family History.
Proceedings of the Summit on Clinical Research Informatics, 2017

Populating Physician Biographical Pages Based on EMR Data.
Proceedings of the Summit on Clinical Research Informatics, 2017

Using ensembles of NLP engines without a common type system to improve abbreviation disambiguation.
Proceedings of the Summit on Clinical Research Informatics, 2017

Mortality Prognostic Model for Peripheral Arterial Disease.
Proceedings of the Summit on Clinical Research Informatics, 2017

Surveillance of Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes.
Proceedings of the Summit on Clinical Research Informatics, 2017

Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose.
Proceedings of the Summit on Clinical Research Informatics, 2017

Medical concept intersection between outside medical records and consultant notes: A case study in transferred cardiovascular patients.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Literature.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

Recommending education materials for diabetic questions using information retrieval approaches.
Proceedings of the AMIA 2017, 2017

Semantic Representations of Medical Terms: A Comparison Study of Word Embeddings Trained on Clinical Notes and PubMed Articles.
Proceedings of the AMIA 2017, 2017

Bayesian Prediction of Asthma Exacerbation in Children.
Proceedings of the AMIA 2017, 2017

Accelerating Rare Disease Diagnosis with Collaborative Filtering.
Proceedings of the AMIA 2017, 2017

Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis.
Proceedings of the AMIA 2017, 2017

Mining Hierarchies and Similarity Clusters from Value Set Repositories.
Proceedings of the AMIA 2017, 2017

Identification of Clinically Meaningful Plasma Transfusion Subgroups Using Unsupervised Random Forest Clustering.
Proceedings of the AMIA 2017, 2017

Distinction between medical and non-medical usages of short forms in clinical narratives.
Proceedings of the AMIA 2017, 2017

Guideline Based Recommended Therapies in PAD Patients Identified by NLP: A Quality Assessment Project.
Proceedings of the AMIA 2017, 2017

AMICUS: A Metasystem for Interoperation and Combination of UIMA Systems.
Proceedings of the AMIA 2017, 2017

Deep Learning Solutions for Classifying Patients on Opioid Use.
Proceedings of the AMIA 2017, 2017

A Resource for Clinical Semantic Textual Similarity.
Proceedings of the AMIA 2017, 2017

2016
A Part-Of-Speech term weighting scheme for biomedical information retrieval.
Journal of Biomedical Informatics, 2016

A computational framework for converting textual clinical diagnostic criteria into the quality data model.
Journal of Biomedical Informatics, 2016

Clinical element models in the SHARPn consortium.
JAMIA, 2016

MatLM: a Matrix Formulation for Probabilistic Language Models.
CoRR, 2016

Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.
BMC Bioinformatics, 2016

BELTracker: evidence sentence retrieval for BEL statements.
Database, 2016

The digital revolution in phenotyping.
Briefings in Bioinformatics, 2016

Exploiting HPO to Predict a Ranked List of Phenotype Categories for LiverTox Case Reports.
Proceedings of the Data Management and Analytics for Medicine and Healthcare, 2016

An Ensemble Model of Clinical Information Extraction and Information Retrieval for Clinical Decision Support.
Proceedings of The Twenty-Fifth Text REtrieval Conference, 2016

MayoNLP at SemEval-2016 Task 1: Semantic Textual Similarity based on Lexical Semantic Net and Deep Learning Semantic Model.
Proceedings of the 10th International Workshop on Semantic Evaluation, 2016

Staggered NLP-assisted refinement for Clinical Annotations of Chronic Disease Events.
Proceedings of the Tenth International Conference on Language Resources and Evaluation LREC 2016, 2016

On Developing Resources for Patient-level Information Retrieval.
Proceedings of the Tenth International Conference on Language Resources and Evaluation LREC 2016, 2016

LabLinker: Finding Links of Laboratory Test Results between Structured Records and Clinical Notes.
Proceedings of the 2016 IEEE International Conference on Healthcare Informatics, 2016

MutD - A PubMed Scale Resource for Protein Mutation-Disease Relations through Bio-Medical Literature Mining.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

POS-MRF: A Part-Of-Speech Weighted Markov Random Field Model for Clinical Information Retrieval.
Proceedings of the Summit on Clinical Research Informatics, 2016

Ascertaining Asthma Predictive Index through Natural Language Processing.
Proceedings of the Summit on Clinical Research Informatics, 2016

Exploring Gaps of Family History Documentation in EHR for Precision Medicine - A Case Study of Familial Hypercholesterolemia Ascertainment.
Proceedings of the Summit on Clinical Research Informatics, 2016

An Infinite Mixture Model for Coreference Resolution in Clinical Notes.
Proceedings of the Summit on Clinical Research Informatics, 2016

MayoNLPTeam at the 2016 CLEF eHealth Information Retrieval Task 1.
Proceedings of the Working Notes of CLEF 2016, 2016

MayoBMI at ImageCLEF 2016 Handwritten Document Retrieval Task.
Proceedings of the Working Notes of CLEF 2016, 2016

Answering diabetic patients' questions using expert-vetted online resources: A case study.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Using synthetic clinical data to train an HMM-based POS tagger.
Proceedings of the 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics, 2016

Identifying peripheral arterial disease cases using natural language processing of clinical notes.
Proceedings of the 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics, 2016

Prioritizing Adverse Drug Reaction and Drug Repositioning Candidates Generated by Literature-Based Discovery.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

Answering patients' questions using expert-vetted online resources: A case study of diabetes.
Proceedings of the AMIA 2016, 2016

Probabilistic Population-level Modeling of Disease Event Timelines.
Proceedings of the AMIA 2016, 2016

A Part-Of-Speech Weighting Scheme for Clinical Information Retrieval.
Proceedings of the AMIA 2016, 2016

Discovering Associations between Problem List and Practice Setting.
Proceedings of the AMIA 2016, 2016

Asthma Ascertainment NLP System Portability across Institutions.
Proceedings of the AMIA 2016, 2016

Leveraging Terminology Services for Extract-Transform-Load Processes: A User-Centered Approach.
Proceedings of the AMIA 2016, 2016

Natural Language Processing Working Group Pre-Symposium: Graduate Student Consortium and 'Hackathon'.
Proceedings of the AMIA 2016, 2016

Drug-drug Interaction Detection with A Topic-modeling Based Framework Augmented with Distant-supervision.
Proceedings of the AMIA 2016, 2016

A Topic-modeling Based Framework for Drug-drug Interaction Classification from Biomedical Text.
Proceedings of the AMIA 2016, 2016

Ontology-Based Analysis of Adverse Drug Reactions Associated with Anti-infection Drugs in China.
Proceedings of the AMIA 2016, 2016

2015
The CHEMDNER corpus of chemicals and drugs and its annotation principles.
J. Cheminformatics, 2015

Ease of adoption of clinical natural language processing software: An evaluation of five systems.
Journal of Biomedical Informatics, 2015

DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx.
Journal of Biomedical Informatics, 2015

Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality.
JAMIA, 2015

Generalized Ensemble Model for Document Ranking.
CoRR, 2015

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.
BMC Bioinformatics, 2015

Next generation informatics for big data in precision medicine era.
BioData Mining, 2015

Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing.
BioData Mining, 2015

A bibliometric analysis on tobacco regulation investigators.
BioData Mining, 2015

Mining severe drug-drug interaction adverse events using Semantic Web technologies: a case study.
BioData Mining, 2015

Assessing the Need of Discourse-Level Analysis in Identifying Evidence of Drug-Disease Relations in Scientific Literature.
Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015

Identification of Patients with Family History of Pancreatic Cancer - Investigation of an NLP System Portability.
Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015

A Frequency-based Strategy of Obtaining Sentences from Clinical Data Repository for Crowdsourcing.
Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015

Retrieval of Semantically Similar Healthcare Questions in Healthcare Forums.
Proceedings of the 2015 International Conference on Healthcare Informatics, 2015

Temporal Pattern and Association Discovery of Diagnosis Codes Using Deep Learning.
Proceedings of the 2015 International Conference on Healthcare Informatics, 2015

Representing Clinical Diagnostic Criteria in Quality Data Model Using Natural Language Processing.
Proceedings of the Workshop on Biomedical Natural Language Processing, BioNLP@IJCNLP 2015, 2015

BmQGen: Biomedical query generator for knowledge discovery.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

A new method for prioritizing drug repositioning candidates extracted by literature-based discovery.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

A frequency-filtering strategy of obtaining PHI-free sentences from clinical data repository.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

Prediction of Colorectal Surgical Site Infections Using Risk Factors.
Proceedings of the AMIA 2015, 2015

Detection of Colorectal Surgical Site Infections Using Bayesian Network and Natural Language Processing.
Proceedings of the AMIA 2015, 2015

Automating risk score calculations and care recommendations by an EMR agnostic solution and potential time saving for providers.
Proceedings of the AMIA 2015, 2015

Natural Language Processing facilitates delivery of individualized recommendations at the point of care.
Proceedings of the AMIA 2015, 2015

Natural Language Processing facilitates delivery of individualized recommendations at the point of care.
Proceedings of the AMIA 2015, 2015

Social Media use for Drug Repurposing: Understanding the consumer perspective.
Proceedings of the AMIA 2015, 2015

Exploring Gaps of Family History Documentation in EHR for Precision Medicine - A Case Study of Familial Hypercholesterolemia Ascertainment.
Proceedings of the AMIA 2015, 2015

Evaluation of the accuracy of CDS for cervical cancer screening and surveillance.
Proceedings of the AMIA 2015, 2015

A Deep Learning Framework for Improving Medical Information Retrieval.
Proceedings of the AMIA 2015, 2015

2014
Study on Hot Topic Discovery from Chinese Texts.
JDIM, 2014

Using large clinical corpora for query expansion in text-based cohort identification.
Journal of Biomedical Informatics, 2014

Research and applications: Patient-level temporal aggregation for text-based asthma status ascertainment.
JAMIA, 2014

Research and applications: MedXN: an open source medication extraction and normalization tool for clinical text.
JAMIA, 2014

Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network.
J. Biomedical Semantics, 2014

Standardizing adverse drug event reporting data.
J. Biomedical Semantics, 2014

Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time?
J. Biomedical Semantics, 2014

Integrating information retrieval with distant supervision for Gene Ontology annotation.
Database, 2014

Overview of the gene ontology task at BioCreative IV.
Database, 2014

Towards Pathway Curation Through Literature Mining - A Case Study Using PharmGKB.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

Cancer Based Pharmacogenomics Network for Drug Repurposing.
Proceedings of the Trends and Applications in Knowledge Discovery and Data Mining, 2014

An Author Topic Analysis of Tobacco Regulation Investigators.
Proceedings of the Trends and Applications in Knowledge Discovery and Data Mining, 2014

Mining Severe Drug-Drug Interaction Adverse Events Using Semantic Web Technologies: A Case Study.
Proceedings of the Trends and Applications in Knowledge Discovery and Data Mining, 2014

Genetic testing knowledge base (GTKB) towards individualized genetic test recommendation - An experimental study.
Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

Towards a multi-level framework for supporting systematic review - A pilot study.
Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data.
Proceedings of IEEE-EMBS International Conference on Biomedical and Health Informatics, 2014

Challenges in adapting text mining for full text articles to assist pathway curation.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

An author topic analysis on NCI DCP/DCCPS PIs.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

iGenetics: An Individualized Genetic Test Recommendation System Based on EHRs.
Proceedings of the AMIA 2014, 2014

Layered Spaces for Clinical Information Retrieval.
Proceedings of the AMIA 2014, 2014

Exploration of Potential Drug Off-label Uses in Clinical Practice.
Proceedings of the AMIA 2014, 2014

Analysis of Medication and Indication Occurrences in Clinical Notes.
Proceedings of the AMIA 2014, 2014

Reducing the Screening Burden of Systematic Review with a Multiple-level Relevance Ranking System.
Proceedings of the AMIA 2014, 2014

An Automated Approach for Ranking Journals to Help in Clinician Decision Support.
Proceedings of the AMIA 2014, 2014

NLP enhances Quality Care Measures in Heart Failure.
Proceedings of the AMIA 2014, 2014

2013
Research and applications: Formative evaluation of the accuracy of a clinical decision support system for cervical cancer screening.
JAMIA, 2013

Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification.
JAMIA, 2013

Automatically extracting sentences from Medline citations to support clinicians' information needs.
JAMIA, 2013

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology.
J. Biomedical Semantics, 2013

A common type system for clinical natural language processing.
J. Biomedical Semantics, 2013

Pooling annotated corpora for clinical concept extraction.
J. Biomedical Semantics, 2013

MayoClinicNLP-CORE: Semantic representations for textual similarity.
Proceedings of the Second Joint Conference on Lexical and Computational Semantics, 2013

Automatic Identification of Comparative Effectiveness Research from Medline Citations to Support Clinicians' Treatment Information Needs.
Proceedings of the MEDINFO 2013, 2013

Standardizing Drug Adverse Event Reporting Data.
Proceedings of the MEDINFO 2013, 2013

Building a Knowledge Base of Severe Adverse Drug Events Based on AERS Reporting Data Using Semantic Web Technologies.
Proceedings of the MEDINFO 2013, 2013

Phenotyping on EHR Data Using OWL and Semantic Web Technologies.
Proceedings of the Smart Health - International Conference, 2013

Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology.
Proceedings of the ICBO2013 Workshops: International Workshop on Vaccine and Drug Ontology Studies (VDOS 2013), International Workshop on Definitions in Ontologies (DO 2013), part of the Semantic Trilogy 2013 , Montreal, Quebec, Canada, July 6th, 2013

Using Discharge Summaries to Improve Information Retrieval in Clinical Domain.
Proceedings of the Working Notes for CLEF 2013 Conference , 2013

An Incremental Approach for MEDLINE MeSH Indexing.
Proceedings of the first Workshop on Bio-Medical Semantic Indexing and Question Answering, 2013

Integrated cTAKES for Concept Mention Detection and Normalization.
Proceedings of the Working Notes for CLEF 2013 Conference , 2013

An integrative computational approach to identify disease-specific networks from PubMed literature information.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Profiling adverse drug events of cancer drug ingredients using normalized AERS data.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Towards assigning references using semantic, journal and citation relevance.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Prioritizing journals relevant to a topic for addressing clinicians' information needs.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Decision Support can Improve Time Efficiency of Healthcare Providers for Deciding Preventive Care Recommendations.
Proceedings of the AMIA 2013, 2013

Clinical Drug Extraction and Normalization from Clinical Notes.
Proceedings of the AMIA 2013, 2013

Medication Extraction and Normalization from Clinical Notes.
Proceedings of the AMIA 2013, 2013

Coreference Resolution from Medical Corpus with Topic Modeling.
Proceedings of the AMIA 2013, 2013

Prioritize journals relevant to a clinical topic: A survey of US cardiologists about heart failure.
Proceedings of the AMIA 2013, 2013

2012
Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.
JAMIA, 2012

Clinical decision support with automated text processing for cervical cancer screening.
JAMIA, 2012

Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules.
JAMIA, 2012

Three Questions About Clinical Information Retrieval.
Proceedings of The Twenty-First Text REtrieval Conference, 2012

Clinical Decision Support for Colonoscopy Surveillance Using Natural Language Processing.
Proceedings of the 2012 IEEE Second International Conference on Healthcare Informatics, 2012

Systematic Analysis of Cross-Institutional Medication Description Patterns in Clinical Notes.
Proceedings of the 2012 IEEE Second International Conference on Healthcare Informatics, 2012

Automatically Extracting Sentences from Medline Citations to Support Clinicians' Information Needs.
Proceedings of the 2012 IEEE Second International Conference on Healthcare Informatics, 2012

Modeling UIMA type system using web ontology language: towards interoperability among UIMA-based NLP tools.
Proceedings of the 2nd International Workshop on Managing Interoperability and compleXity in Health Systems, 2012

Ontology-Based Temporal Relation Modeling with MapReduce Latent Dirichlet Allocations for Big EHR Data.
Proceedings of the 2012 Second International Conference on Cloud and Green Computing, 2012

Classifying protein complexes from candidate subgraphs using fuzzy machine learning model.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

Electronic health record data suggests metformin improves cancer survival: A new model for drug repurposing studies.
Proceedings of the AMIA 2012, 2012

Tracking Immigrant Health with Natural Language Processing.
Proceedings of the AMIA 2012, 2012

Asthma Status Identification with Natural Language Processing.
Proceedings of the AMIA 2012, 2012

A Preliminary Study on Normalizing AERS Drug Names Using RxNorm.
Proceedings of the AMIA 2012, 2012

Clinical Decision Support with Natural Language Processing for Cervical Cancer Screening.
Proceedings of the AMIA 2012, 2012

Towards a semantic lexicon for clinical natural language processing.
Proceedings of the AMIA 2012, 2012

A Study of Transportability of an Existing Smoking Status Detection Module across Institutions.
Proceedings of the AMIA 2012, 2012

Using Electronic Health Records to Identify Heart Failure Cohorts with Differentiation for Preserved and Reduced Ejection Fraction.
Proceedings of the AMIA 2012, 2012

2011
Using machine learning for concept extraction on clinical documents from multiple data sources.
JAMIA, 2011

An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics.
I. J. Medical Informatics, 2011

RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis.
BMC Bioinformatics, 2011

dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation.
BMC Bioinformatics, 2011

The gene normalization task in BioCreative III.
BMC Bioinformatics, 2011

Empirical Ontologies for Cohort Identification.
Proceedings of The Twentieth Text REtrieval Conference, 2011

Hamilton Non-holonomic Momentum Equation of the System and Conclusions.
Proceedings of the Information Computing and Applications, 2011

Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in medline abstracts.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

Human gene/protein synonym dictionary from WikiLinks.
Proceedings of the ACM International Conference on Bioinformatics, 2011

2010
LFXtractor: Text chunking for long form detection from biomedical text.
I. J. Functional Informatics and Personalised Medicine, 2010

Classification Systems for Bacterial Protein-Protein Interaction Document Retrieval.
IJCMAM, 2010

Testing the theory of relative defect proneness for closed-source software.
Empirical Software Engineering, 2010

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

Evaluating gene/protein name tagging and mapping for article retrieval.
Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine, 2010

An exploratory study of news article clustering for web-based bio-surveillance.
Proceedings of the ACM International Health Informatics Symposium, 2010

2009
An Investigation into the Functional Form of the Size-Defect Relationship for Software Modules.
IEEE Trans. Software Eng., 2009

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

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

Semi-supervised Learning of Text Classification on Bacterial Protein-Protein Interaction Documents.
Proceedings of the International Joint Conferences on Bioinformatics, 2009

Testing of the Uniformity of Color Appearance Space.
Proceedings of the CSIE 2009, 2009 WRI World Congress on Computer Science and Information Engineering, March 31, 2009

Software Engineering Education for Bioinformatics.
Proceedings of the Proceedings 22nd Conference on Software Engineering Education and Training, 2009

Support Vector Machine-Based Mucin-Type O-linked Glycosylation Site Prediction Using Enhanced Sequence Feature Encoding.
Proceedings of the AMIA 2009, 2009

2008
Theory of relative defect proneness.
Empirical Software Engineering, 2008

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies.
BMC Bioinformatics, 2008

VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays.
BMC Bioinformatics, 2008

Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature.
Proceedings of the Linking Literature, Information, and Knowledge for Biology, 2008

Analysis of Microarray Titration Experiments.
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

Annotating breast cancer microarray samples using ontologies.
Proceedings of the AMIA 2008, 2008

2007
Identifying and characterizing change-prone classes in two large-scale open-source products.
Journal of Systems and Software, 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

SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.
BMC Bioinformatics, 2007

AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets.
Bioinformatics, 2007

Exploring Traits of Adjectives to Predict Polarity Opinion in Blogs and Semantic Filters in Genomics.
Proceedings of The Sixteenth Text REtrieval Conference, 2007

Effect of Coupling on Defect Proneness in Evolutionary Open-Source Software Development.
Proceedings of the Open Source Development, 2007

Classifier Ensemble for Biomedical Document Retrieval.
Proceedings of the Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine (LBM 2007), 2007

Modeling the Effect of Size on Defect Proneness for Open-Source Software.
Proceedings of the 29th International Conference on Software Engineering (ICSE 2007), 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

Semiparametric RMA Background-Correction for Oligonucleotide Arrays.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

Enhancing Acronym/Abbreviation Knowledge Bases with Semantic Information.
Proceedings of the AMIA 2007, 2007

2006
Terminology model discovery using natural language processing and visualization techniques.
, 2006

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

Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues.
BMC Bioinformatics, 2006

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

Headwords and Suffixes in Biomedical Names.
Proceedings of the Knowledge Discovery in Life Science Literature, 2006

2005
Building Effective Defect-Prediction Models in Practice.
IEEE Software, 2005

An investigation of the effect of module size on defect prediction using static measures.
ACM SIGSOFT Software Engineering Notes, 2005

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

Gene name ambiguity of eukaryotic nomenclatures.
Bioinformatics, 2005

Fusion of Knowledge-Intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents.
Proceedings of the Fourteenth Text REtrieval Conference, 2005

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

2004
Research Paper: A Multi-aspect Comparison Study of Supervised Word Sense Disambiguation.
JAMIA, 2004

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

Knowledge-Intensive and Statistical Approaches to the Retrieval and Annotation of Genomics MEDLINE Citations.
Proceedings of the Thirteenth Text REtrieval Conference, 2004

Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity.
Proceedings of the Biocomputing 2004, 2004

CliniViewer: A Tool for Viewing Electronic Medical Records Based on Natural Language Processing and XML.
Proceedings of the MEDINFO 2004, 2004

Combination Methods in Microarray Analysis.
Proceedings of the 7th International Symposium on Parallel Architectures, 2004

Identifying Significant Genes from Microarray Data.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004

2003
A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports.
Journal of Biomedical Informatics, 2003

Mining Terminological Knowledge in Large Biomedical Corpora.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

2002
Research Paper: Automatic Resolution of Ambiguous Terms Based on Machine Learning and Conceptual Relations in the UMLS.
JAMIA, 2002

A study of abbreviations in MEDLINE abstracts.
Proceedings of the AMIA 2002, 2002

2001
Disambiguating Ambiguous Biomedical Terms in Biomedical Narrative Text: An Unsupervised Method.
Journal of Biomedical Informatics, 2001

A study of abbreviations in the UMLS.
Proceedings of the AMIA 2001, 2001

Evaluating the UMLS as a source of lexical knowledge for medical language processing.
Proceedings of the AMIA 2001, 2001

2000
A method for vocabulary development and visualization based on medical language processing and XML.
Proceedings of the AMIA 2000, 2000

1999
Research Paper: Representing Information in Patient Reports Using Natural Language Processing and the Extensible Markup Language.
JAMIA, 1999

Generalized shuffle-exchange digraphs: Hamiltonian properties.
Proceedings of the 1999 International Symposium on Circuits and Systems, ISCAS 1999, Orlando, Florida, USA, May 30, 1999


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