Superstructure Searching Algorithm for Generic Reaction Retrieval. - Qian Zhu 003; Jianhua Yao 002; Shengang Yuan; Feng Li; Haifeng Chen; Wei Cai; Quan Liao (J. Chem. Inf. Model., 2005)

Semantic Rules on Drug Discovery Data. - Sashikiran Challa; David J. Wild 001; Ying Ding 001; Qian Zhu 003 (ASWC, 2009)

Chem2Bio2RDF: A Linked Open Data Portal for Systems Chemical Biology. - Bin Chen 002; Ying Ding 001; Huijun Wang; David J. Wild 001; Xiao Dong; Yuyin Sun; Qian Zhu 003; Madhuvanthi Sankaranarayanan (Web Intelligence, 2010)

Using Web Technologies for Integrative Drug Discovery. - Qian Zhu 003; Sashikiran Challa; Prajakta Purohit; Yuyin Sun; Michael S. Lajiness; David J. Wild 001; Ying Ding 001 (Web Intelligence, 2010)

Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. - Bin Chen 002; Xiao Dong; Dazhi Jiao; Huijun Wang; Qian Zhu 003; Ying Ding 001; David J. Wild 001 (BMC Bioinform., 2010)

Chem2Bio2RDF: A Linked Open Data Portal for Chemical Biology - Bin Chen 002; David J. Wild 001; Qian Zhu 003; Ying Ding 001; Xiao Dong; Madhuvanthi Sankaranarayanan; Huijun Wang; Yuyin Sun (CoRR, 2010)

WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications. - Qian Zhu 003; Michael S. Lajiness; Ying Ding 001; David J. Wild 001 (J. Cheminformatics, 2010)

Semantic Inference using Chemogenomics Data for Drug Discovery. - Qian Zhu 003; Yuyin Sun; Sashikiran Challa; Ying Ding 001; Michael S. Lajiness; David J. Wild 001 (BMC Bioinform., 2011)

A Standardized Drug and Drug Class Universal Network. - Qian Zhu 003; Guoqian Jiang; Christopher G. Chute (AMIA, 2012)

A Semantic-Web Oriented Representation of Clinical Element Model for Secondary Use of Electronic Healthcare Data. - Cui Tao; Guoqian Jiang; Thomas A. Oniki; Robert R. Freimuth; Jyotishman Pathak; Qian Zhu 003; Deepak K. Sharma; Stanley M. Huff; Christopher G. Chute (HISB, 2012)

Training support vector machine through redundant data reduction. - Xiangjun Shen; Haoxiang Wu; Qian Zhu 003 (ICIMCS, 2012)

Integrating VA's NDF-RT Drug Terminology with PharmGKB: Preliminary Results. - Jyotishman Pathak; Laura C. Weiss; Matthew J. Durski; Qian Zhu 003; Robert R. Freimuth; Christopher G. Chute (Pacific Symposium on Biocomputing, 2012)

Profiling structured product labeling with NDF-RT and RxNorm. - Qian Zhu 003; Guoqian Jiang; Christopher G. Chute (J. Biomed. Semant., 2012)

Using standardized clinical data modeling and knowledge representation to compute pharmacogenomic data elements. - Qian Zhu 003; Jyotishman Pathak; Robert R. Freimuth; Christopher G. Chute (AMIA, 2013)

Standardized Drug and Pharmacological Class Network Construction. - Qian Zhu 003; Guoqian Jiang; Liwei Wang 010; Christopher G. Chute (VDOS+DO@ICBO, 2013)

A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. - Cui Tao; Guoqian Jiang; Thomas A. Oniki; Robert R. Freimuth; Qian Zhu 003; Deepak K. Sharma; Jyotishman Pathak; Stanley M. Huff; Christopher G. Chute (J. Am. Medical Informatics Assoc., 2013)

Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: A case study. - Qian Zhu 003; Robert R. Freimuth; Zonghui Lian; Scott Bauer; Jyotishman Pathak; Cui Tao; Matthew J. Durski; Christopher G. Chute (J. Biomed. Informatics, 2013)

Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. - Qian Zhu 003; Robert R. Freimuth; Jyotishman Pathak; Matthew J. Durski; Christopher G. Chute (J. Biomed. Informatics, 2013)

Evaluation of RxNorm for Medication Clinical Decision Support. - Robert R. Freimuth; Kelly Wix; Qian Zhu 003; Mark Siska; Christopher G. Chute (AMIA, 2014)

Evaluation of Existing Phenotype Authoring Tools for Clinical Research. - Luke V. Rasmussen; Jie Xu 011; Ruijue Liu; Qian Zhu 003; Jennifer A. Pacheco; Jyotishman Pathak; William K. Thompson; Joshua C. Denny; Huan Mo; Richard C. Kiefer; Peter Speltz; Enid N. H. Montague (AMIA, 2014)

iGenetics: An Individualized Genetic Test Recommendation System Based on EHRs. - Qian Zhu 003; Hongfang Liu; Christopher G. Chute; Matthew Ferber (AMIA, 2014)

Qualitative evaluation of three phenotype information models to find methotrexate liver injury. - Qian Zhu 003; Huan Mo; Luke V. Rasmussen; Andrew R. Post; Jennifer A. Pacheco; Jie Xu 011; Richard C. Kiefer; Peter Speltz; Enid N. H. Montague; William K. Thompson; Joshua C. Denny; Jyotishman Pathak (AMIA, 2014)

Genetic testing knowledge base (GTKB) towards individualized genetic test recommendation - An experimental study. - Qian Zhu 003; Hongfang Liu; Christopher G. Chute; Matthew Ferber (BIBM, 2014)

Pharmacological Class Data Representation in the Web Ontology Language (OWL). - Qian Zhu 003; Cui Tao (ICBO, 2014)

Cancer Based Pharmacogenomics Network for Drug Repurposing. - Liwei Wang 010; Hongfang Liu; Christopher G. Chute; Qian Zhu 003 (PAKDD Workshops, 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)

Acquisition of diabetes-related biological associations using a motif based network: Preliminary results. - Iyanuoluwa Emmanuel Odebode; Aryya Gangopadhyay; Qian Zhu 003 (BIBM, 2015)

Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing. - Liwei Wang 010; Hongfang Liu; Christopher G. Chute; Qian Zhu 003 (BioData Min., 2015)

Next generation informatics for big data in precision medicine era. - Yuji Zhang 001; Qian Zhu 003; Hongfang Liu (BioData Min., 2015)

Desiderata for computable representations of electronic health records-driven phenotype algorithms. - Huan Mo; William K. Thompson; Luke V. Rasmussen; Jennifer A. Pacheco; Guoqian Jiang; Richard C. Kiefer; Qian Zhu 003; Jie Xu 011; Enid N. H. Montague; David S. Carrell; Todd Lingren; Frank D. Mentch; et al. (J. Am. Medical Informatics Assoc., 2015)

Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research. - Jie Xu 011; Luke V. Rasmussen; Pamela L. Shaw; Guoqian Jiang; Richard C. Kiefer; Huan Mo; Jennifer A. Pacheco; Peter Speltz; Qian Zhu 003; Joshua C. Denny; Jyotishman Pathak; William K. Thompson; et al. (J. Am. Medical Informatics Assoc., 2015)

Toward a complete dataset of drug-drug interaction information from publicly available sources. - Serkan Ayvaz; John R. Horn; Oktie Hassanzadeh; Qian Zhu 003; Johann Stan; Nicholas P. Tatonetti; Santiago Vilar; Mathias Brochhausen; Matthias Samwald; Majid Rastegar-Mojarad; Michel Dumontier; Richard D. Boyce (J. Biomed. Informatics, 2015)

EHR based Genetic Testing Knowledge Base (iGTKB) Development. - Qian Zhu 003; Hongfang Liu; Christopher G. Chute; Matthew Ferber (BMC Medical Informatics Decis. Mak., 2015)

Network analysis with PubChem BioAssay: Preliminary study on drug abuse. - Weijian Qin; Qian Zhu 003 (BHI, 2016)

Analyzing and retrieving illicit drug-related posts from social media. - Tao Ding; Arpita Roy; Zhiyuan Chen 003; Qian Zhu 003; Shimei Pan (BIBM, 2016)

Risk feature assessment of readmission for diabetes. - Qian Zhu 003; Anirudh Akkati; Pornpoh Hongwattanakul (BIBM, 2016)

Building Locally Discriminative Classifier Ensemble Through Classifier Fusion Among Nearest Neighbors. - Xiangjun Shen; Wen-Chao Zhang; Wei Cai; Ben-Bright B. Benuw; Heping Song; Qian Zhu 003; Zheng-Jun Zha (PCM (1), 2016)

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. - Abra Guo; Rebecca Racz; Junguk Hur; Yu Lin; Zuoshuang Xiang; Lili Zhao; Jordan Rinder; Guoqian Jiang; Qian Zhu 003; Yongqun He (J. Biomed. Semant., 2016)

Manifold Alignment via Global and Local Structures Preserving PCA Framework. - Timothy Apasiba Abeo; Xiangjun Shen; Ernest Domanaanmwi Ganaa; Qian Zhu 003; Bing-Kun Bao; Zheng-Jun Zha (IEEE Access, 2019)

Hybrid Mortality Prediction using Multiple Source Systems. - Isaac Mativo; Yelena Yesha; Michael A. Grasso; Tim Oates 001; Qian Zhu 003 (CoRR, 2019)

Sex, obesity, diabetes, and exposure to particulate matter among patients with severe asthma: Scientific insights from a comparative analysis of open clinical data sources during a five-day hackathon. - Karamarie Fecho; Stanley C. Ahalt; Saravanan Arunachalam; James Champion; Christopher G. Chute; Sarah Davis; Kenneth Gersing; Gustavo Glusman; Jennifer Hadlock; Jewel Lee; Emily R. Pfaff; Max Robinson; et al. (J. Biomed. Informatics, 2019)

Multi-layer framework of identifying placenta related research towards Placenta Curated Research Dataset (PCRD) development for the PAT project. - Qian Zhu 003; Shanna Frierson; Alicia Francis; Lydia Rogers; Daniel Lyman (J. Biomed. Informatics, 2019)

An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD). - Qian Zhu 003; Dac-Trung Nguyen; Ivan Grishagin; Noel Southall; Eric Sid; Anne Pariser (J. Biomed. Semant., 2020)

Data Normalization Improves Semantic Annotation - a Case Study of Rare Disease Name Annotation. - Charlie Tang; Yanji Xu; Qian Zhu 003 (BIBM, 2021)

Scientific Evidence Based Knowledge Graph in Rare Diseases. - Qian Zhu 003; Ruizheng Liu; Gunjan Vatas; Andrew Clough; Yanji Xu; Dac-Trung Nguyen; Ewy A. Mathé; Eric Sid (BIBM, 2021)

Better Understand Rare Disease Patients' Needs by Analyzing Social Media Data - a Case Study of Cystic Fibrosis. - Qian Zhu 003; Eric Sundstrom; Yanji Xu (BIBM, 2021)

Profiling Tox21 Bioassay Towards Drug Repurposing for Rare Diseases. - Fang Liu; Yanji Xu; Jaleal Sanjak; Andrew Patt; Ruili Huang; Chunxu Qu; Qian Zhu 003 (AMIA, 2022)

Semantic Annotation of NIH Funding Data for Supporting Rare Disease Research. - Szeling Hsu; Sue Qu; Yanji Xu; Qian Zhu 003 (BIBM, 2022)

Integrative Rare Disease Profile Creation via NormMap to Advance Rare Disease Research. - Devon Leadman; Yanji Xu; Sue Qu; Qian Zhu 003 (BIBM, 2022)

Experiments with LDA and Top2Vec for embedded topic discovery on social media data - A case study of cystic fibrosis. - Bradley A. Karas; Sue Qu; Yanji Xu; Qian Zhu 003 (Frontiers Artif. Intell., 2022)

Editorial: Biomedical informatics applications in rare diseases. - Qian Zhu 003; Yong-Zi Chen; Yanji Xu (Frontiers Artif. Intell., 2022)

Rare disease-based scientific annotation knowledge graph. - Qian Zhu 003; Chunxu Qu; Ruizheng Liu; Gunjan Vatas; Andrew Clough; Ðac-Trung Nguyen; Eric Sid; Ewy A. Mathé; Yanji Xu (Frontiers Artif. Intell., 2022)

Prediction of Drug Targets based on In Vitro Activity Profiles Toward Drug Repurposing for Rare Diseases. - Binghan Xue; Ruili Huang; Qian Zhu 003; Yanji Xu (BIBM, 2023)

User Centered Rare Disease Clinical Trial Knowledge Graph (RCTKG). - Jeremy Parker Yang; Devon Leadman; Richard M. Ballew; Eric Sid; Yanji Xu; Ewy A. Mathé; Qian Zhu 003 (MedInfo, 2023)

Multi-dictionary induced low-rank representation with multi-manifold regularization. - Jinghui Zhou; Xiangjun Shen; Sixing Liu; Liangjun Wang; Qian Zhu 003; Ping Qian (Appl. Intell., 2023)

Dual projection learning with adaptive graph smoothing for multi-label classification. - Zhifeng Liu; Rui-hang Cai; Timothy Apasiba Abeo; Qian Zhu 003; Cong-hua Zhou; Xiang-Jun Shen (Appl. Intell., 2023)

Clustering rare diseases within an ontology-enriched knowledge graph. - Jaleal Sanjak; Jessica Binder; Arjun Singh Yadaw; Qian Zhu 003; Ewy A. Mathé (J. Am. Medical Informatics Assoc., 2023)

Multi-view Representation Induced Kernel Ensemble Support Vector Machine. - Ebenezer Quayson; Ernest Domanaanmwi Ganaa; Qian Zhu 003; Xiang-Jun Shen (Neural Process. Lett., 2023)

Aligning Orphanet Classification to Identify Disease Characteristics among Rare Disease Clusters. - Sungrim Moon; Jessica Maine; Ewy A. Mathé; Qian Zhu 003 (BIBM, 2024)