Rong Xu, PhD
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'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. Disease gene discovery
2. Drug repositioning
3. Drug target discovery
4. Drug toxicity prediction
5. Cancer drug toxicity
6. Medical image retrieval
7. Post-market drug surveillance
- 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 (accepted)
- Chen Y, Xu R (2014) Mining cancer-specific disease comorbidities from a large observational database, Journal of Cancer Informatics (in press).
- Chen Y, Xu R (2014) Network Analysis of Human Disease Comorbidity Patterns Based on Large-scale Data Mining. International Symposium on Bioinformatics Research and Applications (ISBRA) 2014 Conference (accepted).
- Xu R, Wang Q, (2014) Comparing a knowledge-driven approach to a supervised machine learning 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 (accepted).
- 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.
- 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, 15:17. DOI: 10.1186/10.1186/1471-2105-15-17 .
- 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), pp. 171-177. 
- 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.
- 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 .
- 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
- 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. .
- 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..
- 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. 
- 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. 
- 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).
- 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.. .
- 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. .
- Zhang GQ, Cui LC, Teagno J, Kaelber, D, Koroukian S, Xu R, (2013) Combining Ontology Browsing with Data Exploration: Moving the Needle in Medicaid Data Access, AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:285-9
- Zhang GQ, Xu R, Luo LY (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
- Lingyun Luo, James Rowbottom, John Craker, Rong Xu , GQ Zhang.(2013) VINSIA: Visual Navigator for Surgical Information Access. Military Medicine. 2013 Jul;178(7):746-52. doi: 10.7205/MILMED-D-12-00406.
- 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).
- 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).
- 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. 
- 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.
- 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.
- 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.
- 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. (Student Paper Finalist)
- 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. 
- 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.
- 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.
- 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.