An integrative computational approach to identify disease-specific networks from PubMed literature information. - Yuji Zhang 001; Dingcheng Li; Cui Tao; Feichen Shen; Hongfang Liu (BIBM, 2013)

Phenotyping on EHR Data Using OWL and Semantic Web Technologies. - Cui Tao; Dingcheng Li; Feichen Shen; Zonghui Lian; Jyotishman Pathak; Hongfang Liu; Christopher G. Chute (ICSH, 2013)

Reducing the Screening Burden of Systematic Review with a Multiple-level Relevance Ranking System. - Dingcheng Li; Zhen Wang; Feichen Shen; Mohammad Hassan Murad; Hongfang Liu (AMIA, 2014)

Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data. - Feichen Shen; Dingcheng Li; Hongfang Liu; Yugyung Lee; Jyotishman Pathak; Christopher G. Chute; Cui Tao (BHI, 2014)

Towards a multi-level framework for supporting systematic review - A pilot study. - Dingcheng Li; Zhen Wang; Feichen Shen; Mohammad Hassan Murad; Hongfang Liu (BIBM, 2014)

Exploring the Pharmacogenomics Knowledge Base (PharmGKB) for Repositioning Breast Cancer Drugs by Leveraging Web Ontology Language (OWL) and Cheminformatics Approaches. - Qian Zhu 003; Cui Tao; Feichen Shen; Christopher G. Chute (Pacific Symposium on Biocomputing, 2014)

SMARTSPACE: Multiagent Based Distributed Platform for Semantic Service Discovery. - Sourish Dasgupta; Anoop Aroor; Feichen Shen; Yugyung Lee (IEEE Trans. Syst. Man Cybern. Syst., 2014)

BmQGen: Biomedical query generator for knowledge discovery. - Feichen Shen; Hongfang Liu; Sunghwan Sohn; David W. Larson; Yugyung Lee (BIBM, 2015)

A pervasive framework for real-time activity patterns of mobile users. - Feichen Shen (PerCom Workshops, 2015)

SAMAF: Situation aware mobile apps framework. - Feichen Shen; Yugyung Lee (PerCom Workshops, 2015)

PEMAR: A pervasive middleware for activity recognition with smart phones. - Prakash Vaka; Feichen Shen; Mayanka Chandrashekar; Yugyung Lee (PerCom Workshops, 2015)

Collaborative Mobile-Cloud Computing for Civil Infrastructure Condition Inspection. - Zhiqiang Chen; Jianfei Chen 004; Feichen Shen; Yugyung Lee (J. Comput. Civ. Eng., 2015)

A Resource for Clinical Semantic Textual Similarity. - Naveed Afzal; Yanshan Wang; Feichen Shen; Liwei Wang 010; Hongfang Liu (AMIA, 2017)

Mining Hierarchies and Similarity Clusters from Value Set Repositories. - Kevin J. Peterson; Guoqian Jiang; Scott M. Brue; Feichen Shen; Hongfang Liu (AMIA, 2017)

Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. - Feichen Shen; Sijia Liu 002; Yanshan Wang; Liwei Wang 010; Naveed Afzal; Hongfang Liu (AMIA, 2017)

Accelerating Rare Disease Diagnosis with Collaborative Filtering. - Feichen Shen; Sijia Liu 002; Yanshan Wang; Liwei Wang 010; Naveed Afzal; Hongfang Liu (AMIA, 2017)

Semantic Representations of Medical Terms: A Comparison Study of Word Embeddings Trained on Clinical Notes and PubMed Articles. - Yanshan Wang; Naveed Afzal; Liwei Wang 010; Feichen Shen; Hongfang Liu (AMIA, 2017)

Recommending education materials for diabetic questions using information retrieval approaches. - Yuqun Zeng; Yanshan Wang; Feichen Shen; Sijia Liu 002; Liwei Wang 010; Majid Rastegar-Mojarad; Xusheng Liu; Hongfang Liu (AMIA, 2017)

Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Literature. - Yanshan Wang; Sijia Liu 002; Majid Rastegar-Mojarad; Liwei Wang 010; Feichen Shen; Fei Liu 004; Hongfang Liu (BCB, 2017)

Medical concept intersection between outside medical records and consultant notes: A case study in transferred cardiovascular patients. - Sungrim Moon; Sijia Liu 002; Paul R. Kingsbury; David Chen 003; Yanshan Wang; Feichen Shen; Rajeev Chaudhry; Hongfang Liu (BIBM, 2017)

Populating Physician Biographical Pages Based on EMR Data. - Feichen Shen; Sunghwan Sohn; Majid Rastegar-Mojarad; Sijia Liu 002; Joshua J. Pankratz; Michael Hatton; Nancy Sowada; Om Shrestha; Shawna Shurson; Hongfang Liu (CRI, 2017)

Content Analysis of Free-Text Family History. - Yanshan Wang; Liwei Wang 010; Majid Rastegar-Mojarad; Sijia Liu 002; Feichen Shen; Hongfang Liu (CRI, 2017)

On Mapping Textual Queries to a Common Data Model. - Sijia Liu 002; Yanshan Wang; Na Hong; Feichen Shen; Stephen T. Wu; William R. Hersh; Hongfang Liu (ICHI, 2017)

Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology. - Feichen Shen; Liwei Wang 010; Hongfang Liu (MedInfo, 2017)

Using Human Phenotype Ontology for Phenotypic Analysis of Clinical Notes. - Feichen Shen; Liwei Wang 010; Hongfang Liu (MedInfo, 2017)

MayoNLP at SemEval 2017 Task 10: Word Embedding Distance Pattern for Keyphrase Classification in Scientific Publications. - Sijia Liu 002; Feichen Shen; Vipin Chaudhary; Hongfang Liu (SemEval@ACL, 2017)

Need of informatics in designing interoperable clinical registries. - Majid Rastegar-Mojarad; Sunghwan Sohn; Liwei Wang 010; Feichen Shen; Troy C. Bleeker; William A. Cliby; Hongfang Liu (Int. J. Medical Informatics, 2017)

Incorporating Knowledge-Driven Insights into a Collaborative Filtering Model to Facilitate the Differential Diagnosis of Rare Diseases. - Feichen Shen; Hongfang Liu (AMIA, 2018)

Combining Knowledge and Data Driven Insights to Facilitate the Differential Diagnosis of Rare Diseases. - Feichen Shen; Hongfang Liu (AMIA, 2018)

BioCreative/OHNLP Challenge 2018. - Majid Rastegar-Mojarad; Sijia Liu 002; Yanshan Wang; Naveed Afzal; Liwei Wang 010; Feichen Shen; Sunyang Fu; Hongfang Liu (BCB, 2018)

Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome. - Su-Yuan Peng; Yadan Fan; Liwei Wang 010; Andrew Wen; Xusheng Liu; Hongfang Liu; Feichen Shen (BIBM, 2018)

Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility. - Yiqing Zhao; Yanshan Wang; Henry Wang; Benjamin Yan; Feichen Shen; Kevin J. Peterson; Walter A. Rocca; Jennifer St. Sauver; Hongfang Liu (BIBM, 2018)

Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. - Feichen Shen; Sijia Liu 002; Yanshan Wang; Liwei Wang 010; Andrew Wen; Andrew H. Limper; Hongfang Liu (ICHI Workshops, 2018)

Predicting Practice Setting Using Topic Modeling. - Liwei Wang 010; Yanshan Wang; Feichen Shen; Majid Rastegar-Mojarad; Hongfang Liu (ICHI Workshops, 2018)

Extracting chemical-protein relations using attention-based neural networks. - Sijia Liu 002; Feichen Shen; Ravikumar Komandur Elayavilli; Yanshan Wang; Majid Rastegar-Mojarad; Vipin Chaudhary; Hongfang Liu (Database J. Biol. Databases Curation, 2018)

MedTQ: Dynamic Topic Discovery and Query Generation for Medical Ontologies. - Feichen Shen; Yugyung Lee (CoRR, 2018)

A Deep Representation Empowered Distant Supervision Paradigm for Clinical Information Extraction. - Yanshan Wang; Sunghwan Sohn; Sijia Liu 002; Feichen Shen; Liwei Wang 010; Elizabeth J. Atkinson; Shreyasee Amin; Hongfang Liu (CoRR, 2018)

A comparison of word embeddings for the biomedical natural language processing. - Yanshan Wang; Sijia Liu 002; Naveed Afzal; Majid Rastegar-Mojarad; Liwei Wang 010; Feichen Shen; Paul R. Kingsbury; Hongfang Liu (J. Biomed. Informatics, 2018)

Clinical information extraction applications: A literature review. - Yanshan Wang; Liwei Wang 010; Majid Rastegar-Mojarad; Sungrim Moon; Feichen Shen; Naveed Afzal; Sijia Liu 002; Yuqun Zeng; Saeed Mehrabi 003; Sunghwan Sohn; Hongfang Liu (J. Biomed. Informatics, 2018)

Leveraging a Data-Driven Strategy to Enrich Rare Disease Knowledge. - Feichen Shen; Yiqing Zhao; Hongfang Liu (AMIA, 2019)

Integrating word embedding neural networks with PubMed abstracts to extract keyword proximity of chronic diseases. - Ahmad P. Tafti; Yanshan Wang; Feichen Shen; Elham Sagheb; Paul R. Kingsbury; Hongfang Liu (BHI, 2019)

CREATE: Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records using OMOP Common Data Model. - Sijia Liu 002; Yanshan Wang; Andrew Wen; Liwei Wang 010; Na Hong; Feichen Shen; Steven Bedrick; William R. Hersh; Hongfang Liu (CoRR, 2019)

Towards Semantic Big Graph Analytics for Cross-Domain Knowledge Discovery. - Feichen Shen (CoRR, 2019)

Development of Clinical Concept Extraction Applications: A Methodology Review. - Sunyang Fu; David Chen 003; Sijia Liu 002; Sungrim Moon; Kevin J. Peterson; Feichen Shen; Yanshan Wang; Liwei Wang 010; Andrew Wen; Yiqing Zhao; Sunghwan Sohn; Hongfang Liu (CoRR, 2019)

Ensembles of natural language processing systems for portable phenotyping solutions. - Cong Liu 020; Casey N. Ta; James R. Rogers; Ziran Li; Junghwan Lee; Alex M. Butler; Ning Shang; Fabricio Sampaio Peres Kury; Liwei Wang 010; Feichen Shen; Hongfang Liu; Lyudmila Ena; et al. (J. Biomed. Informatics, 2019)

HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. - Feichen Shen; Suyuan Peng; Yadan Fan; Andrew Wen; Sijia Liu 002; Yanshan Wang; Liwei Wang 010; Hongfang Liu (J. Biomed. Informatics, 2019)

An Interactive Visualization Tool for HL7 FHIR Specification Browsing and Profiling. - Na Hong; Kui Wang; Sizhu Wu; Feichen Shen; Lixia Yao; Guoqian Jiang (J. Heal. Informatics Res., 2019)

Special Issue on Healthcare Knowledge Discovery and Management. - Feichen Shen; Vipin Chaudhary; Yan Liu; Che Ngufor; Hongfang Liu (J. Heal. Informatics Res., 2019)

Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes. - Feichen Shen; David W. Larson; James M. Naessens; Elizabeth B. Habermann; Hongfang Liu; Sunghwan Sohn (J. Heal. Informatics Res., 2019)

Rare disease knowledge enrichment through a data-driven approach. - Feichen Shen; Yiqing Zhao; Liwei Wang 010; Majid Rastegar-Mojarad; Yanshan Wang; Sijia Liu 002; Hongfang Liu (BMC Medical Informatics Decis. Mak., 2019)

A clinical text classification paradigm using weak supervision and deep representation. - Yanshan Wang; Sunghwan Sohn; Sijia Liu 002; Feichen Shen; Liwei Wang 010; Elizabeth J. Atkinson; Shreyasee Amin; Hongfang Liu (BMC Medical Informatics Decis. Mak., 2019)

Discovering associations between problem list and practice setting. - Liwei Wang 010; Yanshan Wang; Feichen Shen; Majid Rastegar-Mojarad; Hongfang Liu (BMC Medical Informatics Decis. Mak., 2019)

Identifying Rare Disease Studies by Natural Language Processing. - Huan He; Feichen Shen; Michael Lin; Hongfang Liu (AMIA, 2020)

Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery. - Andrew Wen; Sunyang Fu; Feichen Shen; Hongfang Liu (AMIA, 2020)

Extracting Patient Genetic Information from Unstructured Clinical Notes. - Yiqing Zhao; Hanzhong Yu; Luke A. Carlson; Feichen Shen; Sunyang Fu; Hongfang Liu; Chen Wang 001 (AMIA, 2020)

Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System. - Feichen Shen; Andrew Wen; Hongfang Liu (CBMS, 2020)

Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings. - Feichen Shen; Andrew Wen; Hongfang Liu (CBMS, 2020)

A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. - Andrew Wen; Feichen Shen; Sungrim Moon; Hongfang Liu; Jungwei Fan 001 (CBMS, 2020)

The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task on clinical concept normalization for clinical records. - Sam Henry 001; Yanshan Wang; Feichen Shen; Özlem Uzuner (J. Am. Medical Informatics Assoc., 2020)

Constructing co-occurrence network embeddings to assist association extraction for COVID-19 and other coronavirus infectious diseases. - David Oniani; Guoqian Jiang; Hongfang Liu; Feichen Shen (J. Am. Medical Informatics Assoc., 2020)

Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity. - Nathan D. Seligson; Jeremy L. Warner; William S. Dalton; David Martin; Robert S. Miller; Debra Patt; Kenneth L. Kehl; Matvey B. Palchuk; Gil Alterovitz; Laura K. Wiley; Ming Huang 006; Feichen Shen; et al. (J. Am. Medical Informatics Assoc., 2020)

Clinical concept extraction: A methodology review. - Sunyang Fu; David Chen 003; Huan He; Sijia Liu 002; Sungrim Moon; Kevin J. Peterson; Feichen Shen; Liwei Wang 010; Yanshan Wang; Andrew Wen; Yiqing Zhao; Sunghwan Sohn; et al. (J. Biomed. Informatics, 2020)

MedSTS: a resource for clinical semantic textual similarity. - Yanshan Wang; Naveed Afzal; Sunyang Fu; Liwei Wang 010; Feichen Shen; Majid Rastegar-Mojarad; Hongfang Liu (Lang. Resour. Evaluation, 2020)

POKR: Building a Computable Heterogeneous Knowledge Resource for Precision Oncology. - Yanbo Guo; Chen Wang 001; Raymond M. Moore; Hongfang Liu; Feichen Shen (MedInfo, 2021)

Comparisons of Graph Neural Networks on Cancer Classification Leveraging a Joint of Phenotypic and Genetic Features. - David Oniani; Chen Wang 001; Yiqing Zhao; Andrew Wen; Hongfang Liu; Feichen Shen (CoRR, 2021)

Leveraging a Joint of Phenotypic and Genetic Features on Cancer Patient Subgrouping. - David Oniani; Chen Wang 001; Yiqing Zhao; Andrew Wen; Hongfang Liu; Feichen Shen (CoRR, 2021)

Corrigendum to: The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task on clinical concept normalization for clinical records. - Sam Henry 001; Yanshan Wang; Feichen Shen; Özlem Uzuner (J. Am. Medical Informatics Assoc., 2021)

An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. - Andrew Wen; Liwei Wang 010; Huan He; Sijia Liu 002; Sunyang Fu; Sunghwan Sohn; Jacob A. Kugel; Vinod C. Kaggal; Ming Huang 006; Yanshan Wang; Feichen Shen; Jungwei Fan 001; et al. (J. Biomed. Informatics, 2021)