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  4. Rong Xu

Rong Xu, PhD

Professor of Biomedical Informatics, Director
Center for AI in Drug Discovery
School of Medicine
Member
Cancer Genomics and Epigenomics Program
Case Comprehensive Cancer Center
School of Medicine

Research Information

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. Artificial Intelligence
  2. Natural language processing
  3. Machine learning, Deep learning
  4. Systems biology
  5. Data mining
  6. Graph theory
  7. Ontology, knowledge representation and engineering
  8. Imaging Informatics

My research interests in biomedical sciences include:

  1. Drug discovery, drug repositioning
  2. Disease gene discover
  3. Gene-environment-disease interactions
  4. Human gut microbiome
  5. Drug target discovery
  6. Drug toxicity prediction
  7. Cancer drug toxicity
  8. Drug addiction
  9. Neuroscience informatics
  10. Health outcomes research

Awards and Honors

Fellow of American College of Medical Informatics (FACMI)
2020
American College of Medical Informatics
Research Scholar
2016
American Cancer Society
New Investigator Award
2015
American Medical Informatics Association
AACR INNOVATOR Award
2015
Landon Foundation
Director’s Innovator Award
2014
National Institutes of Health
Siebel Scholar
2004
Siebel Foundation

Publications

View Publications

  1. Wang W, Kaelber DC, Xu R*, Berger NA* (2022). Breakthrough SARS-CoV-2 infections, hospitalizations, and mortality in vaccinated patients with cancer in the United States between December 2020 and November 2021. JAMA Oncology. Published online April 08, 2022. doi:10.1001/jamaoncol.2022.1096

  2. Wang L, Berger NA, Kaelber DC, Davis PB, Volkow ND, Xu R* (2022) Comparison of incidence rates and clinical outcomes of SARS-CoV-2 infection in Children Under 5 years old between the Omicron and the Delta Variant periods in the US. JAMA Pediatr. Published online April 01, 2022. doi:10.1001/jamapediatrics.2022.0945

  3. Wang L, Davis PD, Kaelber DC,  Xu R* (2022) COVID-19 breakthrough infections and hospitalizations among vaccinated patients with dementia in the United States between December 2020 and August 2021. Alzheimer's & Dementia, First published: 13 April 2022. http://doi.org/10.1002/alz.12669

  4. Yuanyuan Zhao, Di Hu, Rihua Wang1, Xiaoyan Sun, Philip Ropelewski, Zita Hubler, Kathleen, Lundberg,  Quanqiu Wang, Drew J. Adams, Rong Xu, and Xin Qi1,* (2022)  ATAD3A oligomerization promotes neuropathology and cognitive deficits in Alzheimer’s disease models. Nat Commun 13, 1121 (2022). https://doi.org/10.1038/s41467-022-28769-9

  5. Wang L, Kaelber DC,   Xu R* , Nathan A Berger* (2022). COVID-19 Breakthrough Infections, Hospitalizations and Mortality in Fully Vaccinated Patients with Hematologic Malignancies: A Clarion Call for Maintaining Mitigation and Ramping-Up Research. Blood Rev. 2022 Jan 31:100931. doi: 10.1016/j.blre.2022.100931. Epub ahead of print. PMID: 35120771; PMCID: PMC8802493.

  6. Wang L, Davis PD, Kaelber DC, Volkow N,  Xu R* (2022) Comparison of mRNA-1273 and BNT162b2 vaccines on breakthrough SARS-CoV-2 infections and outcomes during the Delta predominant period. JAMA. Published online January 20, 2022. doi:10.1001/jama.2022.0210

  7. Wang L, Berger NA, Kaelber DC, Davis PB, Volkow ND, Xu R* (2022) Comparison of outcomes from COVID infection in pediatric and adult patients before and after the emergence of Omicron. medRxiv [Preprint]. 2022 Jan 2:2021.12.30.21268495. doi: 10.1101/2021.12.30.21268495. PMID: 35018384; PMCID: PMC8750707.

  8. Wang L, Berger NA, Kaelber DC, Davis PB, Volkow ND, Xu R* (2022) COVID infection severity in children under 5 years old before and after Omicron emergence in the US. medRxiv [Preprint]. 2022 Jan 13:2022.01.12.22269179. doi: 10.1101/2022.01.12.22269179. PMID: 35043116; PMCID: PMC8764724.

  9. Wang L, Berger NA*, Xu R* (2021) Risks of SARS-CoV-2 breakthrough infection and hospitalization in fully vaccinated patients with multiple myeloma. JAMA Netw Open. 2021;4(11):e2137575. doi:10.1001/jamanetworkopen.2021.37575

  10. Wang Q, Davis PB, Qi X, Chen SG, Gurney ME, Perry G, Doraiswamy MP, Xu R* (2021) Gut-microbiota-microglia-brain interactions in Alzheimer’s disease: knowledge-based, multi-dimensional characterization. Alzheimers Res Ther. 2021 Oct 20;13(1):177. doi: 10.1186/s13195-021-00917-1. PMID: 34670619; PMCID: PMC8529734.

  11. Wang L, Wang Q, Davis PB, Volkow ND, Xu R* (2021)  Increased risk for COVID-19 breakthrough infection in fully vaccinated patients with substance use disorders in the United States between December 2020 and August 2021. World Psychiatry. 2021 Oct 5. doi: 10.1002/wps.20921. Epub ahead of print. PMID: 34612005. (Impact factor: 49.55).

  12. Davis PB, Wang QQ, Xu R* (2021) Reply to “Post-COVID 19 neurological syndrome: a new risk factor that modifies the prognosis of patients with dementia”. Alzheimers Dement. In press.

  13. Zheng C, Fillmore NR, Ramos-Cejudo J, Brophy M, Osorio R, Gurney ME, Qiu WQ, Au R, Perry G, Dubreuil M, Chen SG, Qi X, Davis PB, Do N, Xu R*. Potential long-term effect of tumor necrosis factor inhibitors on dementia risk: A propensity score matched retrospective cohort study in US veterans. Alzheimers Dement. 2021 Sep 27. doi: 10.1002/alz.12465. Epub ahead of print. PMID: 34569707.

  14. Connor Bargar; Chiara Maria Giulia De Luca; Grazia Devigili; Antonio Emanuele Elia; Roberto Cilia; Sara Maria Portaleone; Wen Wang; Irene Tramacere; Edoardo Bistaffa; Federico Angelo Cazzaniga; Giovanni Felisati; Giuseppe Legname; Alessio Di Fonzo; Rong Xu; Steven Alexander Gunzler; Giorgio Giaccone; Roberto Eleopra; Shu Guang Chen; Fabio Moda (2021). Discrimination of MSA-P and MSA-C by RT-QuIC analysis of olfactory mucosa: the first assessment of assay reproducibility between two specialized laboratories. Molecular Neurodegeneration (2021) 16:82 https://doi.org/10.1186/s13024-021-00491-y

  15. Pan YH, Xu R* (2021) Mining Comorbidities of Opioid Use Disorder from FDA Adverse Event Reporting System and Patient Electronic Health Records. ICIBM 2021,  BMC Medical Informatics (accepted).

  16. Sreevani Katabathula; Qinyong Wang, Xu R* (2021) Predict Alzheimer’s disease using hippocampus MRI data: a light weight 3D deep convolutional network model with visual and global shape representations. Alzheimer's Research & Therapy 13 (1), 1-9. https://alzres.biomedcentral.com/articles/10.1186/s13195-021-00837-0

  17. Zheng CL, Xu R* (2021) Molecular Subtyping of Alzheimer’s Disease with Consensus Non-Negative Matrix Factorization. PLOS ONE, Published: May 20, 2021. https://doi.org/10.1371/journal.pone.0250278

  18. Bargar C, Wang W, Gunzler SA, LeFevre A, Wang Z, Lerner AJ, Singh N, Tatsuoka C, Appleby B, Zhu X, Xu R, Haroutunian V, Zou WQ, Ma J, Chen SG (2021). Streamlined alpha-synuclein RT-QuIC assay for various biospecimens in Parkinson's disease and dementia with Lewy bodies. Acta Neuropathol Commun. 2021 Apr 7;9(1):62. doi: 10.1186/s40478-021-01175-w. PMID: 33827706; PMCID: PMC8028088.

  19. Wang Q, Davis PB, Gurney ME, Xu R* (2021). COVID-19 and dementia: analyses of risk, disparity and outcomes from electronic health records in the US. Alzheimers Dement. 2021 Feb 9. doi: 10.1002/alz.12296. Epub ahead of print. PMID: 33559975

  20. Zhou MS† (co-first author), Wang Q† (co-first author), Zheng CL, A. John Rush, Nora D Volkow,  Xu R* (2021). Drug repurposing for opioid use disorders: integration of computational prediction, clinical corroboration, and mechanism of action analyses. Mol Psychiatry (2021). https://doi.org/10.1038/s41380-020-01011-y

  21. Wang Q, Davis PB, Xu R* (2021).COVID-19 risk, disparity and outcomes in patients with chronic liver disease in the United States. The Lancet EClinicalMedicine. DOI:https://doi.org/10.1016/j.eclinm.2020.100688

  22. Xu R*, Berger NA*, Wang Q (2021). Risk, Racial Disparity, and Outcomes Among Patients With Cancer and COVID-19 Infection-Reply. JAMA Oncology. 2021 May 6. doi: 10.1001/jamaoncol.2021.0771. Epub ahead of print. PMID: 33956054

  23. Wang Q, Nathan A Berger*, Xu R* (2020). Analyses of Risk, Racial Disparity, and Outcomes of Cancers and Coronavirus Disease 2019 From Electronic Health Records in the US. JAMA Oncology, Published online December 10, 2020. doi:10.1001/jamaoncol.2020.6178.

  24. Wang Q, Nathan A Berger*, Xu R* (2020). When Hematologic Malignancies Meet COVID-19 in the United States:  Infections, Death and Disparities. Blood Review. https://doi.org/10.1016/j.blre.2020.100775

  25. Zhang XW, Wang RH, Hu D, Sun XY, Fujioka H, Lundberg K, Chang E, Wang Q, Xu R, Fianagan ME, Pieper A, Qi X (2020). Oligodendroglial glycolytic stress triggers inflammasome activation and neuropathologyin Alzheimer’s disease. Sci Adv. 2020 Dec 4;6(49):eabb8680. doi: 10.1126/sciadv.abb8680. PMID: 33277246; PMCID: PMC7717916.

  26. Zhu XF, Li XY, Xu R, Wang T (2020). An iterative approach to detect pleiotropy and perform Mendelian Randomization analysis using GWAS summary statistics. Bioinformatics. 2020 Nov 23:btaa985. doi: 10.1093/bioinformatics/btaa985. Epub ahead of print. PMID: 33226062.

  27. Wang Q,  Xu R*, Volkow ND* (2020).  Increased risk of COVID-19 infection and mortality in people with mental disorders: analysis from electronic health records in the United States. World Psychiatry (Impact factor: 49.55). First published: 07 October 2020. https://doi.org/10.1002/wps.2080.

  28. Wang Q, Kaelber D, Xu R*, Volkow ND* (2020). COVID-19 Risk and Outcomes in patients with substance use disorders: Analyses from electronic health records in the United States. Molecular Psychiatry (2020) DOI https://doi.org/10.1038/s41380-020-00880-7

  29. Wang Q, Xu R* (2020). CoMNRank: an integrated approach to extract and prioritize human microbial metabolites from MEDLINE records. J Biomed Inform. 2020;109:103524. doi:10.1016/j.jbi.2020.103524

  30. Wang Q, Xu R* (2020). Automatic extraction, prioritization and analysis of gut microbial metabolites from biomedical literature. Sci Rep. 2020;10(1):9996. Published 2020 Jun 19. doi:10.1038/s41598-020-67075-6

  31. Wang Y, Li YS, Zheng CL, Xu R* (2020). DenseCNN: A Densely Connected CNN Model for Alzheimer's Disease Classification Based on Hippocampus MRI Data. Proceedings of 2020 AMIA Annual Symposium.

  32. Zheng C, Xu R* (2020). Predicting cancer origins with a DNA methylation-based deep neural network model. PLoS One. 2020;15(5):e0226461. Published 2020 May 8. doi:10.1371/journal.pone.0226461

  33. Zheng C, Berger NA, Li L, Xu R* (2020).Epigenetic age acceleration and clinical outcomes in gliomas. PLoS One. 2020 Jul 21;15(7):e0236045. doi: 10.1371/journal.pone.0236045. PMID: 32692766; PMCID: PMC7373289.

  34. Zhou M, Zheng C, Xu R* (2020). Combining phenome-driven drug-target interaction prediction with patients' electronic health records-based clinical corroboration toward drug discovery. Bioinformatics. 2020;36(Supplement_1):i436-i444. doi:10.1093/bioinformatics/btaa451

  35. Zhou M, Xu R*, Kaelber DC, Gurney ME* (2020). Tumor Necrosis Factor (TNF) blocking agents are associated with lower risk for Alzheimer's disease in patients with rheumatoid arthritis and psoriasis. PLoS One. 2020;15(3):e0229819. Published 2020 Mar 23. doi:10.1371/journal.pone.0229819'

  36. Conic, R.R.; Damiani, G.; Schrom, K.P.; Ramser, A.E.; Zheng, C.; Xu, R.; McCormick, T.S.; Cooper, K.D. (2020) Psoriasis and Psoriatic Arthritis Cardiovascular Disease Endotypes Identified by Red Blood Cell Distribution Width and Mean Platelet Volume. J. Clin. Med. 2020, 9, 186.

  37. Zhen CL, Li L, Xu R* (2019) Association of epigenetic clock with consensus molecular subtypes and overall survival of colorectal cancer. Cancer Epidemiology, Biomarkers & Prevention. August 2, 2019
    doi: 10.1158/1055-9965.EPI-19-0208

  38. Wang Q, Xu R* (2019) Data-driven multiple-level analysis of gut-microbiome-immune-joint interactions in rheumatoid arthritis, BMC Genomics (2019) 20:124. https://doi.org/10.1186/s12864-019-5510-y

  39. Luo LY*, Zheng CL, Wang JL, Tan MS, Li YS, Xu R, “Analysis of disease organ as a novel phenotype towards disease genetics understanding” Journal of Biomedical Informatics. 2019 Jul;95:103235. doi: 10.1016/j.jbi.2019.103235. Epub 2019 Jun 15. PMID:31207382; PMCID:PMC6644057

  40. Zhou MS, Chen Y, Xu R* (2018) A Drug-Side Effect Context-Sensitive Network approach for Drug Target Prediction. Bioinformatics,, bty906, https://doi.org/10.1093/bioinformatics/bty906

  41. Zhen CL, Xu R* (2018) The Alzheimer’s comorbidity phenome: mining from a large patient database and phenome-driven genetics prediction. Journal of the American Medical Informatics Association Open (JAMIA Open). https://doi.org/10.1093/jamiaopen/ooy050

  42. Wang Q, Xu R* (2018) Disease comorbidity-guided drug repositioning: a case study in schizophrenia. The 2018 Annual American Medical Informatics Association Symposium, Nov 3-7, San Francisco CA.

  43. Wang Q, Xu R* (2018) Immunotherapy-related adverse events (irAEs): extraction from FDA drug labels and comparative analysis. Journal of the American Medical Informatics Association Open (JAMIA Open). JAMIA Open, ooy045, https://doi.org/10.1093/jamiaopen/ooy045

  44. Wang Q, Li L, Xu R* (2018) A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer, Scientific reports, 8(1), 6225. https://www.nature.com/articles/s41598-018-24315-0.

  45. Anil Belur Nagaraj, Ph.D; Peronne Joseph; Olga Kovalenko; QuanQiu Wang; Rong Xu, Analisa Defeo (2018) Evaluating class III antiarrhythmic agents as novel MYC targeting drugs in ovarian cancer. Gynecologic Oncology 2018 Dec;151(3):525-532. doi: 10.1016/j.ygyno.2018.09.019. Epub 2018 Oct 6.

  46. Chen Y, Xu R* (2018) Context-sensitive Network Analysis Identifies Food Metabolites Associated with Alzheimer’s Disease: An Exploratory Study, BMC Genomics. DOI : 10.1186/s12920-018-0459-2 MGNM-D-10-00077.

  47. Zheng CL, Xu R* (2018) Large-scale mining disease comorbidity relationships from post-market drug adverse events surveillance data. BMC Bioinformatics 2018 19 (Suppl 17) :500. https://doi.org/10.1186/s12859-018-2468-8

  48. Nagaraj AB (co-first author), Wang Q (co-first author), Joseph P, Zheng CL, Chen Y, Kovalenko O, Singh S, Armstrong A, Resnick K, Zanotti K, Waggoner S, Xu R* (co-corresponding author), Difeo A* (co-corresponding author) (2017) Using a novel computational drug repositioning approach (DrugPredict) to Rapidly Identify Potent Drug Candidates for Cancer Treatment. Oncogene advance online publication 2 October 2017; doi: 10.1038/onc.2017.328. http://www.nature.com/onc/journal/vaop/ncurrent/full/onc2017328a.html?WT.feed_name=subjects_genetics.

  49. Wang Q, McCormick TS, Ward NL, Cooper KD, Xu R* (2017) Combining mechanism-based prediction with patient-based profiling for psoriasis metabolomics biomarker discovery. The 2017 Annual American Medical Informatics Association Symposium, Nov 14-18, Wahshington DC.

  50. Wang Q, Xu R* (2017) Drug repositioning for prostate cancer: using a data-driven approach to gain new insights. The 2017 Annual American Medical Informatics Association Symposium, Nov 14-18, Wahshington DC.

  51. Wang Q, Xu R* (2017) MetabolitePredict: a de-novo human metabolomics prediction system and its applications in rheumatoid arthritis. Journal of Biomedical Informatics, 2017 Jul;71:222-228. doi: 10.1016/j.jbi.2017.06.002. Epub 2017 Jun 7  PMID:28600026.

  52. Cai, XS, Chen Y, Zhen CL, Xu R* (2017) Interrogating Patient-level Genomics and Mouse Phenomics towards Understanding Cytokines in Colorectal Cancer Metastasis. 2017 AMIA Joint Summits on Translational Science (Student paper competition finalist).

  53. Chen Y, Xu R* (2017) Context-sensitive network based disease genetics prediction and its implications in drug discovery. Bioinformatics (2017) 33 (7): 1031-1039.PMID:28062449. DOI:https://doi.org/10.1093/bioinformatics/btw737

  54. Gao Z, Chen Y, Cai XS, Xu R* (2017) Predict Drug Permeability to Blood-Brain-Barrier from Clinical Phenotypes. Bioinformatics (2017) 33 (6): 901-908.PMID:27993785. DOI: https://doi.org/10.1093/bioinformatics/btw713

  55. Chen Y, Xu R* (2016) Personalized drug repurposing for glioblastoma based on molecular subtypes. Journal of Biomedical Informatics (2016), pp. 131-138. DOI information: 10.1016/j.jbi.2016.09.019).PMID:27697594

  56. Cai, XS, Chen Y, Gao Z, Xu R* (2016) Explore Small Molecule-induced Genome-wide Transcriptional Profiles for Novel Inflammatory Bowel Disease Drug Discovery. AMIA 2016 Joint Summits on Translational Science (Marco Ramoni Distinguished Paper Award Finalist).PMID:27570643; PMCID:PMC5001780.

  57. Chen Y, Xu R* (2016) Phenome-based Gene Discovery Provides Information about Parkinson Disease Drug Targets. BMC Genomics, 2016, 17:493, DOI: 10.1186/s12864-016-2820-1.PMID:27586503; PMCID:PMC5009520.

  58. Chen Y, Cai XS, Gao Z, Wang BC, Xu R* (2016) Towards precision medicine-based therapies for glioblastoma: interrogating human disease genomics and mouse phenotypes. BMC Genomics, 17(7), 516.PMID:27557118; PMCID:PMC5001238

  59. Xu R*, Wang Q.(2016) A genomics-based systems approach towards drug repositioning for rheumatoid arthritis. BMC Genomics 2016, 17(Suppl 7):518. DOI: 10.1186/s12864-016-2910-0.PMID:27557330; PMCID:PMC5001200

  60. Xu R*, Wang Q, (2016) Towards understanding brain-gut-microbiome connections in Alzheimer’s disease. BMC Systems Biology 2016, 10:63 DOI: 10.1186/s12918-016-0307-y. PMID:27585440; PMCID:PMC5009560.

  61. Jingchao Ni, Mehmet Koyuturk, Hanghang Tong, Jonathan Haines, Xu R, and Xiang Zhang (2016). Disease Gene Prioritization by Integrating Tissue-Specific Molecular Networks Using a Robust Multi-Network Model, BMC Bioinformatics, 17 (1), 453, 2016.PMID:27829360; PMCID:PMC5103411.

  62. Stephane Meystre ; Hongfang Liu ; Rong Xu ; Sivaram Arabandi ; Kavishwar Wagholikar ; Jon Patrick ; Guergana Savova ; Chunhua Weng ; Pierre Zweigenbaum ; Dina Demner-Fushman ; Ozlem Uzuner ; Hua Xu, (2016) Natural Language Processing Working Group Pre-Symposium: Graduate Student Consortium and ‘Hackathon’ 2016 Annual American Medical Informatics Association Symposium, Chicago, IL, Nov 12-16.

  63. Xu R*, Wang Q (2015) A genome-wide drug repositioning approach toward prostate cancer drug discovery. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). (Vol. 9096, pp. 435-437). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9096). Springer Verlag. DOI: 10.1007/978-3-319-19048-8

  64. Xu R*, Wang Q (2015) PhenoPredict: a disease phenome-wide drug repositioning approach towards schizophrenia drug discovery. Journal of Biomedical Informatics, pp. 348-355. DOI information: 10.1016/j.jbi.2015.06.027.PMID:26151312; PMCID:PMC4589865

  65. Xu R*, Wang Q, (2015) tcTKB: an integrated cardiovascular toxicity knowledge base for targeted cancer drugs. 2015 Annual American Medical Informatics Association Symposium, San Francisco, CA, Nov 13-18. PMID:26958275; PMCID:PMC4765587

  66. Wang Q, Xu R* (2015) DenguePredict: An Integrated Drug Repositioning System Towards Drug Discovery for Dengue. 2015 Annual American Medical Informatics Association Symposium, San Francisco, CA, Nov 13-18.PMID:26958268; PMCID:PMC4765554

  67. Chen Y, Cai XS, Xu R* (2015) Combing Human Disease Genetics and Mouse Model Phenotypes Towards Drug Repositioning for Parkinson’s Disease. 2015 Annual American Medical Informatics Association Symposium, San Francisco, CA, Nov 13-18.PMID:26958284; PMCID:PMC4765695

  68. Xu R*, & Wang, Q. (2015, April). A Genome-Wide Drug Repositioning Approach toward Prostate Cancer Drug Discovery. In Bioinformatics Research and Applications: 11th International Symposium, ISBRA 2015 Norfolk, USA, June 7-10, 2015 Proceedings (Vol. 9096, p. 435). Springer.

  69. Chen Y, Li L, Zhang GQ, Xu R* (2015) Phenome-driven Disease Genetics Prediction Towards Drug Discovery. Bioinformatics 2015 31 (12): i276-i283 doi: 10.1093/bioinformatics/btv245.PMID:26072493; PMCID:PMC4542779.

  70. Xu R*, Wang Q, (2015) Large-scale automatic extraction of side effects-associated with targeted anticancer drugs from full-text oncological articles. Journal of Biomedical Informatics Jun;55:64-72. doi: 10.1016/j.jbi.2015.03.009. Epub 2015 Mar 27. PMID:25817969; PMCID:PMC4582661

  71. 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 Genomics2015, 16(Suppl 7):S4 (11 June 2015).PMID:26100814; PMCID:PMC4474417

  72. 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 2015, 16(Suppl 5):S6 doi:10.1186/1471-2105-16-S5-S6. PMID:25860223; PMCID:PMC4402591

  73. Chen Y, Xu R* (2015) Network-based Gene Prediction for Plasmodium falciparum Malaria Towards Genetics-based Drug Discovery. BMC Genomics 2015, 16(Suppl 7):S9 (11 June 2015). PMID:26099491; PMCID:PMC4474419

  74. Chen Y, Li L, Xu R* (2015) Disease Comorbidity Network Guides the Detection of Molecular Evidence for the Link Between Colorectal Cancer and Obesity. 2015 AMIA Summits Transl Sci Proc, March 23, 2015 – March 27, 2015, San Francisco. CA. PMID:26306270; PMCID:PMC4525229

  75. Xu R*, Wang Q, (2015) Combining automatic table classification and relationship extraction in extracting anticancer drug-side effect pairs from full-text articles. Journal of Biomedical Informatics, Volume 53, February 2015, Pages 128–135. DOI: 10.1016/j.jbi.2014.10.002. PMID:25445920; PMCID:PMC4586056

  76. Chen Y, Xiang Zhang, GQ Zhang, Xu R* (2015) Comparative Analysis of A Novel Disease Phenotype Network Based on Clinical Manifestations. Journal of Biomedical Informatics, Feb;53:113-20. doi: 10.1016/j.jbi.2014.09.007. Epub 2014 Sep 30.PMID:25277758; PMCID:PMC4452018.

  77. Jiang R, Chen R, Cheng S, Jiang X, Shen B, Xu R*, Yi S. (2014) Introductory Editorial: Computational Advances in Cancer Informatics. Journal of Cancer Informatics, 2014:Suppl. 1 45-48 doi: 10.4137/CIN.S19243.PMID:25484572; PMCID:PMC4216040.

  78. 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.PMID:25392682; PMCID:PMC4216041.

  79. 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

  80. 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; PMCID:PMC4589180.

  81. 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.

  82. 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; PMCID:PMC3998061.

  83. 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; PMCID:PMC3906761.

  84. 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; PMCID:PMC4452013.

  85. 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; PMCID:PMC4131492

  86. 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. PMID:25689608; PMCID:PMC4376128

  87. 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.

  88. 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; PMCID:PMC4068009

  89. 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.

  90. 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; PMCID:PMC3912715

  91. 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; PMCID:PMC4452014

  92. 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; PMCID:PMC3702428.

  93. 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.

  94. Chen Y, Zhang X, Zhang GQ and Xu R*, (2013) Creation and Comparative Analysis of a Novel Disease Phenotype Network Based on Clinical Manifestation. 2013 Annual American Medical Informatics Association Symposium (Accepted for Late-breaking oral presentation).

  95. 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; PMCID:PMC3822108

  96. 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; PMCID:PMC3814483

  97. 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; PMCID:PMC3845758.

  98. Luo L1, Xu R, Zhang GQ. (2013) Dissecting the Ambiguity of FMA Concept Names Using Taxonomy and Partonomy Structural Information, 2013 AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:157-61.PMID:24303256; PMCID:PMC3845762

  99. 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.

  100. 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).

  101. 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).

  102. 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; PMCID:PMC4589154

  103. 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.

  104. 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; PMCID:PMC3041393.

  105. 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; PMCID:PMC3041331.

  106. 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; PMCID:PMC2815389.  (Student Paper Finalist)

  107. 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.

  108. 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; PMCID:PMC265608769.

  109. 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.

  110. 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; PMCID:PMC1839538.

Education

Doctor of Philosophy
Biomedical Informatics
Stanford University
Master of Science
Computer Science
Stanford University
Certificate
Entrepreneurship, Graduate School of Business
Stanford University
Master of Science
Biology
Case Western Reserve University
Bachelor of Science
Biology
Peking University

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