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Publication

Peer-reviewed Articles (*  indicating mentor-mentee relationship)

2016

  1. Qin W*, Zhu Q, Network Analysis with PubChem BioAssay: Preliminary Study on Drug Abuse, 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI), Las Vegas, NV, 2016, pp. 248-251.doi: 10.1109/BHI.2016.7455881.
  2. Guo A,  et.al….., Zhu Q, He YOntology-based collection, representation and analysis of drug-associated neuropathy adverse events. Journal of Biomedical Semantics. 2016;7(1):1-12.
  3. Rupa A*, Zhu Q, GT2RDF: Semantic Representation of Genetic Testing Data. Accepted by AMIA Annual Symposium 2016 as a full paper, Nov.12-16, 2016; Chicago, IL.
  4. Zhu Q, Akkati A*, Hongwattanakul P*,  Risk feature assessment of readmission for diabetes, accepted by The IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2016 as a short paper (19% acceptance rate).
  5. Ding T, Roy A, Chen Z, Zhu Q, Pan S, Analyzing and Retrieving Illicit Drug-Related Posts from Social Media, accepted by the workshop on Data Mining in Translational Biomedical Informatics(TBI) in conjunction of The IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2016.
  6. Zhu Q, Singh S*, Semantic Representation of GeneReviews in OWL towards Diagnostic Decision Support in Genetic Medicine. Submitted to Journal of Biomedical Semantics.

2015

  1. Rasmussen L, et. al…., Zhu Q, et. al., A Modular Architecture for Electronic Health Record-Driven Phenotyping, AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science. 2015;2015:147-51. Epub 2015/08/26. PubMed PMID: 26306258; PMCID: PMC4525215.
  2. Wang L, Liu H, Chute, CG, Zhu Q, Cancer Based Pharmacogenomics Network Supported with Scientific Evidence: from the View of Drug RepurposingBioData Mining. 2015;8(1):9.
  3. Ayvaz S, Horn J, Hassanzadeh O, Zhu Q, et. al., Toward a complete dataset of drug-drug interaction information from publicly available sources, J Biomed Inform. 2015 Jun; 55:206-17.
  4. Li P*, Liu H, Zhu Q, Scientific Evidence Based Genetic Testing Ontology Development towards Individualized Medicine, Journal of Translational Medicine & Epidemiology, 3(1): 1040.
  5. Xu J, et.al…., Zhu Q, et. al., Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research, Journal of the American Medical Informatics Association Jul 2015, DOI: 10.1093/jamia/ocv070
  6. Guo A, et.al…, Zhu Q, et.al. Ontology-based collection, representation and analysis of  drug-associated neuropathy adverse events, accepted by VDOS’15 workshop in conjunction with ICBO 2015.
  7. Mo H, et. al…. Zhu Q, et. al., Desiderata for Computable Representations of Electronic Health Records-Driven Phenotype Algorithms, Journal of the American Medical Informatics Association. 2015 Sep 5. pii: ocv112. doi: 10.1093/jamia/ocv112.
  8. Zhu Q, Liu H, Chute CG, Ferber M, EHR based Genetic Testing Knowledge Base (iGTKB) Development, BMC Medical Informatics and Decision Making 2015, 15 (Suppl 4):S3  doi:10.1186/1472-6947-15-S4-S3.
  9. Odebode L*, Gangopadhyay A, Zhu Q, Acquisition of diabetes based biological associations from a motif based network: preliminary results, Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2877463: IEEE Computer Society; 2015. p. 1057-62.
  10. Zhang Y, Zhu Q, Liu H, Next generation informatics for big data in precision medicine era, BioData Mining  June 2015, 8:34.

2014

  1. Zhu Q, Tao C, Shen F, Chute CG. Exploring the pharmacogenomics knowledge base (pharmgkb) for repositioning breast cancer drugs by leveraging web ontology language (owl) and cheminformatics approaches. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2014:172-82. Epub 2013/12/04. PubMed PMID: 24297544; PMCID: PMC3909178.
  2. Freimuth RR, Zhu Q, Pathak J, Chute CG, Simplifying Complex Clinical Element Models to Encourage Adoption, AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science. 2014;2014:26-31. Epub 2014/01/01. PubMed PMID: 25954573; PMCID: PMC4419759. Outstanding CRI Paper Award Winner.
  3. Wang L, Liu H, Chute C, Zhu Q. Cancer Based Pharmacogenomics Network for Drug Repurposing. In: Peng W-C, Wang H, Bailey J, et al., eds. Trends and Applications in Knowledge Discovery and Data Mining: Springer International Publishing; 2014:639-651.
  4. Freimuth RR, Wix K, Zhu Q, Siska M, Chute CG, Evaluation of RxNorm for Clinical Decision Support, AMIA Annual Symposium proceedings / AMIA Symposium AMIA Symposium. 2014; 2014:554-63. Epub 2014/01/01. PubMed PMID: 25954360; PMCID: PMC4419908.
  5. Zhu, Q, Liu, H, Chute, CG, & Ferber, M. (2014, November). Genetic testing knowledge base (GTKB) towards individualized genetic test recommendation—An experimental study. In Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on (pp. 574-577). IEEE (19% acceptance rate) .
  6. Zhu Q, Liu H, Zhang Y, Wang J. Evidence based computational drug repositioning candidate screening pipeline design: Case Study. 2014 8th International Conference on Systems Biology (ISB), Qingdao, 2014, pp. 210-218. doi: 10.1109/ISB.2014.6990757
  7. Wang L, Wang J, Zhu Q, Evidence Based Disease Network Construction towards Drug Repositioning, 2014 8th International Conference on Systems Biology (ISB), Qingdao, 2014, pp. 219-225. doi: 10.1109/ISB.2014.6990758
  8. Zhu Q,  Tao C. Pharmacological class data representation in the Web Ontology Language (OWL). Big Data (Big Data), 2014 IEEE International Conference on, Washington, DC, 2014, pp. 77-84. doi: 10.1109/BigData.2014.7004397

2013

  1. Zhu Q, Jiang G, Wang L, Chute CG. Standardized Drug and Pharmacological Class Network Construction. Proceedings of ICBO – International Conference on Biomedical Ontology. July 6 – 12, 2013.
  2. Zhu Q, Freimuth RR, Pathak J, Chute CG. Using clinical element models for pharmacogenomic study data standardization. AMIA Summits Transl Sci Proc. 2013; 2013:292-6. Epub 2013 Mar 18 PMID:24303283. PMCID:3845787.
  3. Hassanzadeh O, Zhu Q, Freimuth R, Boyce R. Extending the “web of drug identity” with knowledge extracted from United States product labels. AMIA Summits Transl Sci Proc. 2013; 2013:64-8. Epub 2013 Mar 18. PMID:24303301. PMCID:3814463.
  4. Jiang G, Wang C, Zhu Q, Chute CG. A Framework of Knowledge Integration and Discovery for Supporting Pharmacogenomics Target Predication of Adverse Drug Events: A Case Study of Drug-Induced Long QT Syndrome. AMIA Summits Transl Sci Proc. 2013; 2013:88-92. Epub 2013 Mar 18. PMID:24303306. PMCID:3814489.
  5.  Zhu Q, Freimuth RR, Pathak J, Durski MJ, Chute CG. Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. J Biomed Inform. 2013 Aug; 46(4):690-6. Epub 2013 May 29. PMID:23727027. PMCID:3746070. DOI:10.1016/j.jbi.2013.05.005.

2012

  1. Pathak J, Weiss LC, Durski MJ, Zhu Q, Freimuth RR, Chute CG. Integrating VA’s NDF-RT drug terminology with PharmGKB: preliminary results.  Pac Symp Biocomput. 2012; 400-9.  PMID:22174295.
  2. Zhu Q, Jiang G, Chute CG. Profiling Structured Product Labeling Using NDF-RT and RxNorm
    Proceedings of ICBO – International Conference on Biomedical Ontology. Graz, Austria July 21-25, 2012.
  3. Zhu Q, Tao C, Ding Y, Chute CG. Time-related patient data retrieval for the case studies from the pharmacogenomics research network.  J Med Syst. 2012 Nov; 36 Suppl 1:S37-42. Epub 2012 Oct 18.  PMID:23076712. PMCID:3600379. DOI:10.1007/s10916-012-9888-1.
  4. Zhu Q, Freimuth RR, Lian Z, Bauer S, Pathak J, Tao C, Durski MJ, Chute CG. Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study.  J Biomed Inform. 2013 Apr; 46(2):286-93. Epub 2012 Nov 29.  PMID:23201637. PMCID:3606279. DOI:10.1016/j.jbi.2012.11.004.
  5. Zhu Q, Jiang G, Chute CG. Profiling structured product labeling with NDF-RT and RxNorm. J Biomed Semantics. 2012; 3(1):16. Epub 2012 Dec 20. PMID:23256517. PMCID:3570438. DOI:10.1186/2041-1480-3-16.
  6. Tao C, Jiang G, Oniki TA, Freimuth RR, Zhu Q, Sharma D, Pathak J, Huff SM, Chute CG. A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. J Am Med Inform Assoc. 2013 May 1; 20(3):554-62. Epub 2012 Dec 25. PMID:23268487. PMCID:3628064. DOI:10.1136/amiajnl-2012-001326.

2010-2011

  1. Zhu Q, Sun Y, Challa S, Ding Y, Lajiness MS, Wild DJ. Semantic inference using chemogenomics data for drug discovery.  BMC Bioinformatics. 2011; 12:256. Epub 2011 Jun 23.  PMID:21699718. PMCID:3225082. DOI:10.1186/1471-2105-12-256.
  2. Chen B, Dong X, Jiao D, Wang H, Zhu Q, Ding Y, Wild DJ. Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data.  BMC Bioinformatics. 2010; 11:255. Epub 2010 May 17.  PMID:20478034. PMCID:2881087. DOI:10.1186/1471-2105-11-255.
  3. Zhu Q, Lajiness MS, Ding Y, Wild DJ. WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications.  J Cheminform. 2010; 2:6. Epub 2010 Aug 20.  PMID:20727184. PMCID:2933596. DOI:10.1186/1758-2946-2-6.
  4. Chen B, Ding Y, Wang H, Wild DJ, Dong X, Sun Y, Zhu Q, Sankaranarayanan M. Chem2Bio2RDF: A Linked Open Data Portal for Systems Biology.  Web Intelligence and Intelligent Agent Technology (WI-IAT), 2010 IEEE/WIC/ACM International Conference on. Sept 2010; 1:232-9.  DOI:10.1109/WI-IAT.2010.183.
  5. Zhu Q, Challa S, Purohit P, Sun Y, Lajiness MS, Wild DJ, Ding Y. Using Web Technologies for Integrative Drug Discovery.  Web Intelligence and Intelligent Agent Technology (WI-IAT), 2010 IEEE/WIC/ACM International Conference on. Sept 2010; 1:188-91.  DOI:10.1109/WI-IAT.2010.45.

Before 2010

  1. Zhu Q, Yao J, Li F, Chen H, Yuan S. A Novel Approach to Acquire Reaction Knowledge by Classification of Reaction Data.  Acta Chimica Sinica. 2004; 62:112.
  2. Zhu Q, Yao J, Li F, Chen H, Yuan S. Comparison of the R-Group Similarity.  Acta Chimica Sinica. 2004; 62:1585.
  3. Zhu Q, Yao J, Yuan S, Li F, Chen H, Cai W, Liao Q. Superstructure searching algorithm for generic reaction retrieval.  J Chem Inf Model. 2005 Sep-Oct; 45(5):1214-22.  PMID:16180898. DOI:10.1021/ci0496402.

Abstract/presentation: (* indicating mentor – mentee relationship)

2016

  1. Rupa A*,  Zhu Q, GT2RDF: a semantic representation of genetic testing data. the IEEE International Conference on Biomedical and Health Informatics (BHI2016), Las Vegas, NV, USA,  February 24-27, 2016.
  2. Rupa A*,  Singh S*, Zhu Q, Design and development of Genetic Testing Ontology (GTO2), accepted by the 2016 Bio-Ontologies SIG in conjunction with the Intelligent Systems for Molecular Biology (ISMB) 2016, Orlando, Florida, July 8 – July 12. (Poster)
  3. Singh S*, Haerian K, Zhu Q, Ontology Development for Formal Representation of GeneReviews, accepted by the 2016 Bio-Ontologies SIG in conjunction with the Intelligent Systems for Molecular Biology (ISMB) 2016, Orlando, Florida, July 8 – July 12. (Flash update)
  4. Mativo I*, Grasso M, Yesha Y, Zhu Q, Improved Mortality Prediction for Hospitalized Diabetic Patients with Comorbidities, 5th Annual Biomedical Informatics Symposium (ICBI), 2016
  5. Anam A, Wang J, Zhu Q, Gangopadhyay A, Analyzing Large-scale Drug Related Data Supported by Graph Modeling: Preliminary Results, AMIA 2016 Annual Symposium.

2015

  1. Odebode L*, Gangopadhyay A, Zhu Q, Motif-based network generation towards drug repositioning – an experimental study for Diabetes. AMIA 2015 Joint Summits on Translational Science.
  2. Wang L, Zhu J, Zhu Q, Automatically Screening Possible Chemoresistance Genes of Bladder Cancer Drugs, AMIA 2015 Annual Symposium.
  3.  Li P*, Zhu Q, A survey of automated information retrieval for genetic disorder from GeneReviews, AMIA 2015 Annual Symposium.
  4. Zhu Q, Biomedical Data Integration Toward Quality Healthcare Delivery, LINCS Data Science Research (DSR) Webinars.  (Invited talk)
  5. Rupa A*, Singh S,  Zhu Q, Patient centric meta-ontology development for genetic testing information representation, 4th Annual Biomedical Informatics Symposium (ICBI), 2015.
  6. Qin W*, Zhu Q, Bioassay based Network Generation toward Drug Repositioning, Preliminary Result of Drug Abuse, 4th Annual Biomedical Informatics Symposium (ICBI), 2015.

2014

  1. Ayvaz S, Zhu Q, Hochheiser H, Brochhausen M, Horn J, Dumontier M, Samwald M, Boyce R.  Drug-Drug Interaction Data Source Survey and Linking. AMIA Summits on Translational Science Proceedings 2014 (2014): 16.
  2. Freimuth RR, Zhu Q, Chute CG. The Pharmacogenomic Guideline Repository: A System to Facilitate Clinical Implementation. AMIA 2014 Joint Summits on Translational Science.
  3. Zhu Q, Mo H, Rasmussen Luke, et al., Qualitative evaluation of three phenotype information models to find methotrexate liver injury, AMIA Annual Symposium 2014.
  4. Rasmussen L, Xu J, Liu R, Zhu Q, et al., Evaluation of Existing Phenotype Authoring Tools for Clinical Research, AMIA Annual Symposium 2014.
  5. Zhu Q, Liu H, Chute CG, Ferber M, iGenetics: An Individualized Genetic Test Recommendation System Based on EHRs, AMIA Annual Symposium 2014.
  6. Zhu Q, Tao C, Chute CG, Standardized Pharmacological Class Profile in OWL, International Conference on Biomedical Ontologies (ICBO) 2014.
  7. Li P *, Zhu Q, Evidence based genetic testing ontology development towards individualized medicine, 3th Annual Biomedical Informatics Symposium (ICBI), 2014.
  8. Zhu Q, Pathway enrichment analysis towards drug repurposing for Alzheimer’s disease, 3th Annual Biomedical Informatics Symposium (ICBI), 2014.

2013

  1. Zhu Q, Jiang G, Wang L, Chute CG. Standardized drug and pharmacological class network construction. Stud Health Technol Inform. 2013; 192:1125. PMID:23920899.
  2. Zhu Q, Tao C, Chute CG, Standardized Pharmacological Class Profile in Ontology Representation. Semantic Technologies in Translational Medicine and Drug Discovery session at Indianapolis ACS, Sep 2013.
  3. Zhu Q, Freimuth RR, Pathak J, Chute CG. PharmGKB Drug Data Normalization with NDF-RT. AMIA Summits Transl Sci Proc. 2013; 2013:180. Epub 2013 Mar 18. PMID:24303334. PMCID:3814499.
  4. Zhu Q, Pathak J, Freimuth RR, Chute CG.  Using standardized clinical data modeling and knowledge representation to compute pharmacogenomic data elements. AMIA 2013 Annual Symposium.
  5. Freimuth RR, Zhu Q, Pathak J, Chute CG.  The Pharmacogenomic Guideline Repository. Individualized Medicine Conference 2013, Rochester, MN.
  6. Long H, Plucker J, Zhu Q, Kaufman JM. Collaboration among Creativity Researchers:A Co-Authorship Network Analysis. American Pyschological Association Annual Convention. 2013 July 31.

2012

  1. Zhu Q, Freimuth RR, Durski MJ, Pathak J, Chute CG.  Standardization of Data Dictionaries: A Case Study from the Pharmacogenomics Research Network.  AMIA Summit on Clinical Research Informatics (CRI). San Francisco, CA. 2012 Mar.
  2. Zhu Q, Freimuth RR, Pathak J, Durski MJ, Lian Z, Bauer HS, Sharma DK, Chute CG.  Development of infrastructure, data standards, and best practices for the curation of pharmacogenomics data (poster).  The Fifth International Biocuration Conference. Georgetown University, Washington, DC. 2012 Apr.
  3. Zhu Q, Freimuth R, Lian Z, Bauer S, Durski M, Pathak J, Chute C. Pharmacogenomics Data Standardization using Clinical Element Models (CEMs)  Proceedings of SHARP Area 4 F2F Meeting. June 11-12, 2012.
  4. Zhu Q, Jiang G, Chute CG. A Standardized Drug and Drug Class Universal Network. AMIA 2012 Annual Symposium. Chicago, IL, 2012, Nov.

2009-2011

  1. Zhu Q, Pierce ME, Fox GC, Lajiness M, Wild DJ, Integrative Data Mining For Drug Discovery Using the Semantic Web, Microsoft eScience Workshop 2009, Oct 15-17 2009, Pittsburgh PA. US
  2. Zhu Q, Lajiness MS, Wild DJ, Using Aggregative Web Services for Drug Discovery. American Chemical Society 239th National Meeting, March 2010, San Francisco, CA. US.
  3. Zhu Q, Lajiness MS, Wild D J, Mining and Visualizing Chemical Compound-Specific Chemical-Gene/Disease/Pathway/Literature Relationships. American Chemical Society 240th National Meeting, August 2010, Boston, MA. US.
  4. Chen B, Ding Y, Wang H, Wild DJ, Dong X, Sun Y, Zhu Q, Sankaranarayanan M, Chem2Bio2RDF: Semantic Systems Chemical Biology, 239th ACS National Meeting, 2010
  5. Pandit Y, Zhu Q, Choi J, Bae SH, Qiu J, Wild DJ Exploring Activity Cliffs using Large Scale Semantic Analysis of PubChem. American Chemical Society 240th National Meeting, August 2010, Boston, MA.
  6. Freimuth RR, Pathak J, Zhu Q, Sharma DK, Bauer HS, Lian ZH, Durski MJ, Chute CG.  PGRN Ontology Network Resource.  AMIA 2011 Annual Symposium. 2011 Oct 24:1771.

Before 2009

  1. Zhu Q, Yao J, Li F, Chen H, Yuan S, A Novel Approach to Acquire Reaction Knowledge by Classification of Reaction Data.International Conference on Chemometrics and Bioinformatics in Asia (CCBA-2004) October, 2004. Shanghai, P. R. China.
  2. Zhu Q, Yao J, Li F, Chen H, Yuan S, A Novel Approach to Acquire Reaction Knowledge by Classification of Reaction Data.2004 National Doctoral Science forum. July, 2004. Beijing, P. R. China.

Patents:

  1. Yao J, Zhu Q, Li F, Chen H, Yuan S, Patent number: ZL03141642.x.
  2. Soft Copyright: Chemical Reaction Retrieval System (CISOC-ASRK). Register number: 2004SR08585
  3. Soft Copyright: Computer Aided Organic Synthesis Design System (CISOC-RetroSyn)  Register number: 2004SR08717