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Rong Xu is an Assistant Professor in the Division of Medical Informatics. Rong Xu received her Ph.D. in Biomedical Informatics and M.S in Computer Science from Stanford University, and B.S in Biology from Peking University. Rong Xu was selected as a Siebel Scholar in 2004 for her outstanding academic performance and leadership. Rong Xu received the 2014 NIH Director's Innovator Award.

Research Interests

Rong's research goal is to facilitate biomedical discovery and to improve health care delivery by promoting efficient biomedical knowledge flow among biomedical researchers, physicians and patients.

My research interests in computer science include:
1. Natural language processing
2. Systems biology
3. Machine learning
4. Data mining
5. Graph theory
6. Ontology, knowledge representation and engineering
7. Imaging Informatics

My research interests in biomedical sciences include:
1. Drug repositioning
2. Disease gene discovery
3. Host-microbiome interactions in human disease
4. Drug target discovery
5. Drug toxicity prediction
6. Cancer drug toxicity
7. Post-market drug surveillance


Positions Available

We are looking for graduate students, post-doctoral fellows, and research associates with strong background in computer science and strong program skills.

Peer-reviewed Publications (2014-present)

  1. Xu R, Wang Q, Li L, (2015) genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat. BMC Genomics (accepted).
  2. Chen Y, Xu R (2015) Network-based Gene Prediction for Plasmodium falciparum Malaria Towards Genetics-based Drug Discovery. BMC Genomics (accepted).
  3. Xu R, Wang Q, (2015) Comparing a knowledge-driven approach to a aupervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature. BMC Bioinformatics (accepted)
  4. Chen Y, Li L, Xu R (2015) Disease Comorbidity Network Guides the Detection of Molecular Evidence for the Link Between Colorectal Cancer and Obesity AMIA Summits Transl Sci Proc, 2015 (accepted)
  5. Xu R, Wang Q, (2014) Combining automatic table classification and relationship extraction in extracting anticancer drug-side effect pairs from full-text articles. Journal of Biomedical Informatics, DOI: 10.1016/j.jbi.2014.10.002.[1]
  6. Chen Y, Xiang Zhang, GQ Zhang, Xu R (2014) Comparative Analysis of A Novel Disease Phenotype Network Based on Clinical Manifestations, Journal of Biomedical Informatics, 2014 Sep 30. pii: S1532-0464(14)00217-2. doi: 10.1016/j.jbi.2014.09.007. PMID 25277758. [2]
  7. Jiang R, Chen R, Cheng S, Jiang X, Shen B, Xu R, Yi S. (2014) Introductory Editorial: Computational Advances in Cancer Informatics (A) Journal of Cancer Informatics, 2014:Suppl. 1 45-48 doi: 10.4137/CIN.S19243.[3]
  8. Chen Y, Xu R (2014) Mining cancer-specific disease comorbidities from a large observational database, Cancer Informatics 2014:Suppl. 1 37-44. doi: 10.4137/CIN.S13893. [4].
  9. Chen Y, Xu R (2014) Network Analysis of Human Disease Comorbidity Patterns Based on Large-scale Data Mining. In Bioinformatics Research and Applications (pp. 243-254). Springer International Publishing [5].
  10. Xu R, Wang Q, (2014) Automatic construction of a large-scale and accurate drug-side-effect association knowledge base from biomedical literature. Journal of Biomedical Informatics, J Biomed Inform. 2014 Oct;51:191-9. doi: 10.1016/j.jbi.2014.05.013. Epub 2014 Jun 10. PMID 24928448.[6].
  11. Xu R, Wang Q, (2014) A knowledge-Driven Approach in Constructing a Large-Scale Drug-Side Effect Relationship Knowledge Base for Computational Drug Discovery. International Symposium on Bioinformatics Research and Applications (ISBRA) 2014 Conference.
  12. Xu R, Li L, Wang Q, (2014) dRiskKB: a large-scale disease-disease risk (causal) relationship knowledge base constructed from biomedical text, BMC Bioinformatics 2014, 15:105, doi:10.1186/1471-2105-15-105. PMID 24725842. [7].
  13. Xu R, Wang Q, (2014) Large-scale combining signals from both biomedical literature and the FDA Adverse Event Reporting System (FAERS) to improve post-marketing drug safety signal detection. BMC Bioinformatics 2014 Jan 15;15:17. doi: 10.1186/1471-2105-15-17. PMID 24428898 [8].
  14. Xu R, Wang Q, (2014) Automatic signal prioritizing and filtering approaches in detecting post-marketing cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS). Journal of Biomedical Informatics (2014), Feb;47:171-7. doi: 10.1016/j.jbi.2013.10.008. Epub 2013 Oct 28. PMID 24177320. [9]
  15. Cui L, Xu R, Luo Z, Wentz S, Scarberry K, Zhang GQ. Multi-topic assignment for exploratory navigation of consumer health information in NetWellness using formal concept analysis. BMC Med Inform Decis Mak 2014;14:63 PMID 25086916.
  16. Luo J, Zhang GQ, Wentz S, Cui L, Xu R, SimQ: Real-Time Retrieval of Similar Consumer Health Questions J Med Internet Res, doi:10.2196/jmir.3388 (in press) [10]
  17. Ogbuji C, Xu R (2014) Lattices for Representing and Analyzing Organogenesis, Conference on Semantics in Healthcare and Life Sciences (CSHALS 2014), February 26-28, 2014, Boston, MA.

Peer-reviewed Publications (previous)

  1. Xu R, Li L, Wang Q, (2013) Towards building a disease-phenotype relationship knowledge base: large scale extraction of disease-manifestation relationship from literature. Bioinformatics 2013; doi: 10.1093/bioinformatics/btt359. PMID 23828786. [11].
  2. Xu R, Wang Q, (2013) A Semi-Supervised Pattern-Learning Approach to Extract Pharmacogenomics-Specific Drug-Gene Pairs from Biomedical Literature. J Pharmacogenom Pharmacoproteomics 4: 117. doi:10.4172/2153-0645.1000117.
  3. Xu R, Wang Q, (2013) Toward creation of a cancer drug toxicity knowledge base: automatically extracting cancer drug side effect relationships from literature. Journal of the American Medical Informatics Association (JAMIA), 2014;21:1 90-96. PMID 23686935. [12].
  4. Xu R, Wang Q, (2013) A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine. Journal of Biomedical Informatics 2013 Aug;46(4):585-93. doi: 10.1016/j.jbi.2013.04.001. Epub 2013 Apr 6.PMID 23570835. [13].
  5. Xu R, Wang Q, (2013) Large-scale extraction of drug-disease treatment pairs from biomedical literature for drug repurposing. BMC Bioinformatics, 2013, 14(1), 181. PMID 23742147. [14]
  6. Xu R, Wang Q, (2013) An iterative searching and ranking algorithm for prioritizing pharmacogenomics genes. Int J Comput Biol Drug Des. 2013;6(1-2):18-31. PMID 23428471. [15]
  7. Chen Y, Zhang X, Zhang GQ and Xu R, (2013) Creation and Comparative Analysis of a Novel Disease Phenotype Network Based on Clinical Manifestation. Annual American Medical Informatics Association Symposium (Accepted for Late-breaking oral presentation).
  8. Chen Y, Ren XF, Zhang GQ, Xu R, (2013) Ontology-Guided Organ Detection to Retrieve Web Images of Disease Manifestation: Towards the Construction of a Consumer-based Health Image Library. Journal of the American Medical Informatics Association(JAMIA) 2013, 20(6), 1076-1081.PMID 23792805. [16].
  9. Luo ZH, Zhang GQ, Xu R, (2013) Mining Patterns Among Adverse Events in Clinical Trials - An Exploratory Study. AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:112-6. PMID 24303317. [17].
  10. Zhang GQ, Cui LC, Teagno J, Kaelber, D, Koroukian S, Xu R, (2013) Merging Ontology Navigation with Query Construction for Web-based Medicare Data Exploration, AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:285-9. PMID 24303282. [18]
  11. Luo L1, Xu R, Zhang GQ. (2013) Dissecting the Ambiguity of FMA Concept Names Using Taxonomy and Partonomy Structural Information, AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:157-61. PMID 24303256. [19]
  12. Luo L1, Rowbottom J, Craker J, Xu R, Zhang GQ.(2013) VINSIA: Visual Navigator for Surgical Information Access. Military Medicine. 2013 Jul;178(7):746-52. doi: 10.7205/MILMED-D-12-00406.PMID 23820348.
  13. Chen Y, Ren XF, Zhang GQ, Xu R, (2012) Ontology Guided Approach to Retrieving Disease Manifestation Images for Health Image Base Construction. IEEE Healthcare Informatics, Imaging and Systems Biology (HISB) 2012 (Best Research Paper Award).[20]
  14. Ogbuji C, Xu R, (2012) Integrating large, disparate biomedical ontologies to boost organ development network connectivity. Data Integration in the Life Sciences 2012 (DILS 2012).
  15. Xu R, Wang Q, (2012) A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text, Journal of Biomedical Informatics. 2012 Oct;45(5):827-34. PMID 22561026 [21]
  16. Chen Y, Zhang GQ, Xu R, (2012) Semi-supervised Image Classification for Automatic Construction of a Health Image Library, 2nd ACM SIGHIT International Health Informatics Symposium, 2012.[22]
  17. Xu R, Musen M, Shah N, (2010) A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations. Annual American Medical Informatics Association Symposium 2010. pp. 907-911.PMID 21347110. [23]
  18. Parai, PK, Jonquet C, Xu R, Musen M, Shah N, (2010) The Lexicon Builder Web Service: Building Custom Lexicons from Two Hundred Biomedical Ontologies. Annual American Medical Informatics Association Symposium 2010. pp. 587–591. PMID 21347046. [24]
  19. Xu R, Das A, Garber AM, (2009) Unsupervised Method for Extracting Machine Understandable Medical Knowledge from a Large Free Text Collection. Annual American Medical Informatics Association Symposium, 2009. pp. 709-713. PMID 20351945. [25] (Student Paper Finalist)
  20. Xu R, Morgan A, Das A, Garber AM, (2009) Investigation of Unsupervised Pattern Learning Techniques for Bootstrap Construction of a Medical Treatment Lexicon. Association for Computational Linguistics BioNLP Workshop, 2009. pp. 63-70. [26]
  21. Xu R, Supekar K, Morgan A, Das A, Garber AM, (2008) Unsupervised Method for Automatic Construction of a Disease Dictionary from a Large Free Text Collection. Annual American Medical Informatics Association Symposium, 2008. pp. 820-824. PMID 18999169. [27]
  22. Xu R, Garten Y, Supekar K, Altman RB, Garber AM, (2007) Extracting Subject Demographics From Abstracts of Randomized Clinical Trials. World Congress on Medical and Health Informatics(MEDINFO), 2007. pp. 824-828. PMID 17911777. [28]
  23. Xu R, Supekar K, Huang Y, Das A, Garber AM, Combining Text Classification and Hidden Markov Modeling Techniques for Structuring Randomized Clinical Trial Abstracts (2006), Annual American Medical Informatics Association Symposium, 2006. pp. 824-828. PMID 17238456. [29]


Rong Xu, PhD
Assistant Professor
Division of Medical Informatics

Office: WRB
Phone: 216-368-0023
Fax: 216-368-0207