Rong Xu, PhD

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1. Zhou MS, Kaelber D, Xu R*, Gurney M*. (2020) Tumor Necrosis Factor (TNF)Blocking Agents are Associated with Lower Risk for Alzheimer’s Disease in Patients with Rheumatoid Arthritis and Psoriasis. PlosOne Published: March 23, 2020, https://doi.org/10.1371/journal.pone.0229819
2. 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.
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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.
9. 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
10. 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.
11. 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.
12. 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.
13. 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
14. 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.
15. 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.
16. 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.
17. 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 [6] PMID:28600026.
18. 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).
19. 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 [7].
20. 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
21. 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 [8]
22. 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. [9]
23. 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. [10].
24. 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  [11].
25. 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 [12].
26. 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. [13].
27. Jingchao Ni, Mehmet Koyuturk, Hanghang Tong, Jonathan Haines, Rong Xu, 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.  [14].
28. 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.
29. 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 [15].
30. 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  [16]
31. 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  [17]
32. 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 [18]
33. 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 [19].
34. 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. [20].
35. 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.  [21]
36. 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 [22]
37. 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  [23].
38. 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 [24]
39. 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 [25]
40. 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 [26]
41. 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 [27]
42. 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. [28]
43. 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.[29]
44. 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. [30]
45. 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 [31]
46. 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.[32].
47. 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.
48. 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. [33].
49. 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. [34].
50. 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. [35]
51. 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[36].
52. 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 [37]
53. 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. [38]
54. 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 [39].
55. 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. [40]
56. 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  [41].
57. 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[42].
58. 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. [43]
59. 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. [44]
60. 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).
61. 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[45].
62. 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 [46].
63. 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. [47]
64. 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 [48]
65. 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.[49]
66. 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).[50]
67. 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).[51]
68. 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 [52]
69. 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.[53]
70. 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. [54]
71. 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. [55]
72. 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. [56] (Student Paper Finalist)
73. 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. [57]
74. 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. [58]
75. 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. [59]
76. 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. [60]