Publications

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Biomedical Natural Language Processing Lab

Publications

2016
  1. Xu J, Wu Y, Zhang Y, Wang J, Lee HJ, Xu H. CD-REST: a system for extracting chemical-induced disease relation in literature. Database (Oxford). 2016 Mar 25;2016. pii: baw036. doi: 10.1093/database/baw036. Print 2016. PubMed PMID: 27016700; PubMed Central PMCID: PMC4808251.
  2. Lee H, Zhang Y, Xu J, Moon S, Wang J, Wu Y, Xu H. UTHealth at SemEval-2016 Task 12: an End-to-End System for Temporal Information Extraction from Clinical Notes. Proceedings of 10th workshop on semantic evaluation (SemEval-2016). 2016; NIHMSID: NIHMS803355
  3. Zhang Y, Jiang M, Wang J, Xu H. Semantic Role Labeling of Clinical Text: Comparing Syntactic Parsers and Features. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium. 2016;

2015
  1. Chen Y, Lasko TA, Mei Q, Denny JC, Xu H. A study of active learning methods for named entity recognition in clinical text. J Biomed Inform. 2015 Dec;58:11-8. doi: 10.1016/j.jbi.2015.09.010. Epub 2015 Sep 15. PubMed PMID: 26385377; PubMed Central PMCID: PMC4934373.
  2. Naidoo D, Wu AC, Brilliant MH, Denny J, Ingram C, Kitchner TE, Linneman JG, McGeachie MJ, Roden DM, Shaffer CM, Shah A, Weeke P, Weiss ST, Xu H, Medina MW. A polymorphism in HLA-G modifies statin benefit in asthma. Pharmacogenomics J. 2015 Jun;15(3):272-7. doi: 10.1038/tpj.2014.55. Epub 2014 Sep 30. PubMed PMID: 25266681; PubMed Central PMCID: PMC4379135.
  3. Xu J, Wu Y, Zhang Y, Wang J, Liu R, Wei Q, Xu H. UTH- CCB@BioCreative V CDR Task: Identifying Chemical-induced Disease Relations in Biomedical Text. Proceeding of the fifth BioCreative challenge evaluation workshop. 2015; :254. NIHMSID: NIHMS800810
  4. Wu Y, Xu J, Jiang M, Zhang Y, Xu H. A Study of Neural Word Embeddings for Named Entity Recognition in Clinical Text. AMIA Annu Symp Proc. 2015 Nov 5;2015:1326-33. eCollection 2015. PubMed PMID: 26958273; PubMed Central PMCID: PMC4765694.
  5. Xu J, Zhang Y, Wu Y, Wang J, Dong X, Xu H. Citation Sentiment Analysis in Clinical Trial Papers. AMIA Annu Symp Proc. 2015 Nov 5;2015:1334-41. eCollection 2015. PubMed PMID: 26958274; PubMed Central PMCID: PMC4765697.
  6. Wu Y, Jiang M, Lei J, Xu H. Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network. Stud Health Technology Inform. 2015;216:624-8. PubMed PMID: 26262126; PubMed Central PMCID: PMC4624324.
  7. Wu Y, Denny JC, Rosenbloom ST, Miller RA, Giuse DA, Song M, Xu H. A Preliminary Study of Clinical Abbreviation Disambiguation in Real Time. Appl Clin Inform. 2015 Jun 3;6(2):364-74. doi: 10.4338/ACI-2014-10-RA-0088. eCollection 2015. PubMed PMID: 26171081; PubMed Central PMCID: PMC4493336.
  8. Jiang M, Huang Y, Fan JW, Tang B, Denny J, Xu H. Parsing clinical text: how good are the state-of-the-art parsers? BMC Med Inform Decis Mak. 2015;15 Suppl 1:S2. doi: 10.1186/1472-6947-15-S1- S2. Epub 2015 May 20. PubMed PMID: 26045009; PubMed Central PMCID: PMC4460747.
  9. Xu H, Aldrich MC, Chen Q, Liu H, Peterson NB, Dai Q, Levy M, Shah A, Han X, Ruan X, Jiang M, Li Y, Julien JS, Warner J, Friedman C, Roden DM, Denny JC. Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J Am Med Inform Assoc. 2015 Jan;22(1):179-91. doi: 10.1136/amiajnl-2014-002649. Epub 2014 Jul 22. PubMed PMID: 25053577; PubMed Central PMCID: PMC4433365.

2014
  1. Xu H, Aldrich MC, Chen Q, Liu H, Peterson NB, Dai Q, Levy M, Shah A, Han X, Ruan X, Jiang M, Li Y, Julien JS, Warner J, Friedman C, Roden DM, Denny JC. Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J Am Med Inform Assoc. 2014, in press
  2. Niadoo D, Wu AC, Brilliant MH, Denny JC, Ingram C, Kitchner TE, Linneman JG, McGeachie MJ, Roden DM, Shaffer CM, Shah A, Weeke P, Weiss ST, Xu H, Medina MW. A polymorphism in HLA-G modifiers statin benefit in asthma. The Pharmacogenomics Journal. 2014. Accepted. [PMCID pending]
  3. Gobbel GT, Garvin J, Reeves R, Cronin RM, Heavirland J, Williams J, Weaver A, Jayaramaraja S, Giuse D, Speroff T, Brown SH, Xu H, Matheny ME. Assisted annotation of medical free text using RapTAT. J Am Med Inform Assoc. 2014, 21(5): 833-41. [PMCID PMC4147611]
  4. Sun J, Huang L, Xu H, Zhao Z. Network-assisted prediction of potential drugs for addiction. BioMed Research International. 2014, doi:10.1155/2014/258784. [PMCID pending]
  5. Tang B, Cao H, Wang X, Chen Q, Xu H. Evaluating word representation features in biomedical named entity recognition tasks. BioMed Research International. 2014, doi:10.1155/2014/240403. [PMCID PMC5932722]
  6. Liu M, Cai R, Hu Y, Matheny ME, Sun J, Hu J, Xu H. Determining molecular predictors of adverse drug reactions with causality analysis based on structure learning. J Am Med Inform Assoc. 2014, 21(2):245-51. [PMCID: PMC3932464]
  7. Doan S, Lin KW, Conway M, Ohno-Machado L, Hsieh A, Feupeo SF, Garland A, Ross MK, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim HE. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. J Am Med Inform Assoc. 2014, 21(1):31-6. [PMCID: PMC3912702]

2013
  1. Sun S., Zhou X., Denny JC, Rosenbloom CT, Xu H. Messaging to Your Doctors: Understanding Patient-Provider Communications via a Portal System. Proceedings of ACM Conference on Human Factors in Computing Systems (SIG'CHI), 2013, Paris, France. In Press.
  2. Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H. A hybrid system for temporal information extraction from clinical text. J Am Med Inform Assoc. 2013, In Press.
  3. Mani S, Chen Y, Li X, Arlinghaus L, Chakravarthy AB, Abramson V, Bhave SR, Levy MA, Xu H, Yankeelov TE. Machine learning for predicting the response of breast cancer to neoadjuvant chemotherapy. J Am Med Inform Assoc. 2013, In Press.
  4. Wei W, Cronin RM, Xu H, Lasko TA, Bastarache L, Denny JC. Development and evaluation of an ensemble resource linking medications to their indications. J Am Med Inform Assoc. 2013, In Press.
  5. Zhao M, Sun J, Zhao Z. Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. Molecular BioSystems (in press)
  6. Sun J, Zhao M, Fanous AM, Zhao Z. Characterization of schizophrenia adverse drug interactions through a network approach and drug classification. BioMed Research International (in press)
  7. Atrey R, Sun J*, Zhao Z. Exploring drug-target interaction networks of illicit drugs. 2013 BMC Genomics (in press) (*Co-first author)
  8. Zhao M, Sun J, Zhao Z. TSGene: a web resource for tumor suppressor genes. Nucleic Acids Research. 2013 41(D1):D970-976

2012
  1. Huang Y, Zhao Z, Xu H, Shyr Y, Zhang B (2012) Advances in Intelligent Biology and Medicine: Selected papers from 2012 ICIBM Conference. BMC Systems Biology 6 (Suppl S2):S1 (in press)
  2. Zhao Z, Zhang B, Shyr Y, Huang Y, Xu H, (2012) Genomics in 2012: challenges and opportunities in the next generation sequencing era. BMC Genomics 13 (Suppl S7):S1 (in press)
  3. Zhao Z, Xu H, Zhang B, Huang Y (2012) Advances in Intelligent Biology and Medicine: Selected papers from 2012 ICIBM Conference. International Journal of Computational Biology and Drug Design (IJCBDD) 5(4): (in press)
  4. Liu M, Matheny ME, Hu Y, Xu H. Data mining methodologies for pharmacovigilance. ACM SIGKDD Explorations Newsletter. 2012, 14(1), 35-42.
  5. Tang B, Can H, Wu Y, Jiang M, Xu H. Clinical Entity Recognition using Structural Support Vector Machines with Rich Features. ACM Sixth International Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO), 2012, In Press.
  6. Xu H, Stetson PD, Friedman C. Combining corpus-derived sense profiles with estimated frequency information to disambiguate clinical abbreviations. AMIA Annu Symp Proc. 2012. In Press.
  7. Wu Y, Denny JC, Rosenbloom ST, Miller RA, Giuse DA, Xu H. A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries. AMIA Annu Symp Proc. 2012. In Press.
  8. Liu M, Shah A, Min J, Peterson NB, Dai Q, Aldrich MC, Chen Q, Bowton EA, Liu H, Denny JC, Xu H. A study of transportability of an existing smoking status detection module across institutions. AMIA Annu Symp Proc. 2012. In Press.
  9. Jiang M, Denny JC, Tang B, Cao H, Xu H. Extracting semantic lexicons from discharge summaries using machine learning and c-value method. AMIA Annu Symp Proc. 2012. In Press.
  10. Wu Y, Liu M, Zheng W, Zhao Z, Xu H. Ranking gene-drug relationships in biomedical literature using latent dirichlet allocation. Pac Symp Biocomput. 2012: 422-33. [PMID: 22174297]
  11. Liu M, McPeek Hinz ER, Matheny ME, Denny JC, Schildcrout JS, Miller RA, Xu H. Comparative Analysis of Pharmacovigilance Methods in Detection of Adverse Drug Reactions from Electronic Medical Records. J Am Med Inform Assoc. 2012, In Press. [PMID: 23161894]
  12. Xu H, Wu Y, Elhadad N, Stetson PD, Friedman C. A new clustering method for detecting rare sense of abbreviations in clinical notes. J Biomed Inform. 2012, 45(6):1075-83. [PMID: 22742938]
  13. Liu M, Wu Y, Chen Y, Sun J, Zhao Z, Chen X, and Xu H. Large-scale prediction of adverse drug reaction by integrating chemical, biological, and phenotypic properties of drugs. J Am Med Inform Assoc. 2012. 19(e1): e28-e35. [PMCID:PMC3392844]
  14. Denny JC, Schildcrout JS, Bowton EA, Gregg W, Pulley JM, Basford MA, Cowan J, Xu H, Ramirez AH, Crawford DC, Ritchie MD, Peterson JF, Masys DR, Wilke RA, Roden DM. Optimizing drug outcomes through pharmacogenetics: A case for preemptive genotyping. Clin Pharmacol Ther. 2012. 92(2):235-42. [PMID: 22739144]
  15. Wu Y, Levy MA, Micheel CM, Yeh P, Tang B, Cantrell MJ, Cooreman SM, Xu H. Identifying the status of genetic lesions in cancer clinical trial documents using machine learning. BMC Genomics. 2012, 13 Suppl 8:S21 [PMCID: PMC3535695]
  16. Han B, Chen XW, Talebizadeh Z, Xu H. Genetic studies of complex human diseases: characterizing SNP-disease associations using Bayesian networks. BMC Syst Biol. 2012. 6 Suppl 3: S14 [PMCID: PMC3524021]
  17. Lu Y, Xu H, Peterson NB, Dai Q, Jiang M, Denny JC, Liu M. Extracting epidemiological exposure and outcome terms from literature using machine learning approaches. Int J Data Min Bioinform. 2012; 6(4):447-59. [PMID: 23155773]
  18. Roden DM, Xu H, Denny JC, Wilke RA. Electronic Medical Records as a Tool in Clinical Pharmacology: Opportunities and Challenges. Clin Pharmacol Ther. 2012, Apr 25. [PMID:22534870]
  19. Delaney JT, Ramirez AH, Bowton EA, Pulley JM, Basford MA, Schildcrout JS, Shi Y, Zink R, Oetjens M, Xu H, Cleator JH, Jahangir E, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Predicting clopidogrel response using DNA samples linked to an electronic health record. Clin Pharmacol Ther. 2012 Feb;91(2):257-63. [PMID: 22190063]
  20. Birdwell KA, Grady B, Choi L, Xu H, Bian A, Denny JC, Jiang M, Vranic G, Basford M, Cowan JD, Richardson DM, Robinson MP, Ikizler TA, Ritchie MD, Stein CM, Haas DW. The use of a DNA biobank linked to electronic medical records to characterize pharmacogenomic predictors of tacrolimus dose requirement in kidney transplant recipients. Pharmacogenet Genomics. 2012 22(1):32-42. [PMCID: PMC3237759]
  21. Ramirez AH, Shi Y, Schildcrout JS, Delaney JT, Xu H, Oetjens MT, Zuvich RL, Basford MA, Bowton EA, Jiang M, Speltz P, Zink R, Cowan J, Pulley JM, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Predicting warfarin dosage in European and African Americans using DNA samples linked to an electronic health record. Pharmacogenomics. 2012, 13(4):407-18. [PMCID: PMC3361510]
  22. Sun J, Xu H, Zhao Z Network-assisted investigation of antipsychotic drugs and their targets. Chem Biodivers. 2012, 9(5): 900-10. [PMID:22589091]
  23. Sun J, Wu Y, Xu H, Zhao Z. DTome: a web-based tool for drug-target interactome construction, BMC Bioinformatics. 2012, 13(Suppl 9): 57.
  24. Carroll RJ, Thompson WK, Eyler AE, Mandelin AM, Cai T, Zink RM, Pacheco JA, Boomershine CS, Lasko TA, Xu H, Karlson EW, Perez RG, Gainer VS, Murphy SN, Ruderman EM, Pope RM, Plenge RM, Kho AN, Liao KP, Denny JC. Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J Am Med Inform Assoc. 2012 Feb 28. [PMID: 22374935]
  25. Doan S, Collier N, Xu H, Pham HD, and Tu MP. Recognition of medication information from discharge summaries using ensembles of classifiers. BMC Medical Informatics and Decision Making. 2012, 12(1):36. [PMID: 22564405]
  26. Chen Y, Mani S, Xu H. Applying active learning to assertion classification of concepts in clinical text. J Biomed Inform 2012, 45(2): 265-272. [PMCID: PMC3306548]
  27. Sun J, Gong X, Purow B, Zhao Z. Uncovering microRNA and transcription factor mediated regulatory networks in glioblastoma. PLoS Computational Biology. 2012 8(7): e1002488
  28. Sun J, Wu Y, Xu H, Zhao Z. DTome: a web-based tool for drug-target interactome construction. BMC Bioinformatics. 2012 13 (Suppl 9): 57
  29. Sun J, Jayathilake K, Zhao Z, Meltzer H. Investigating association of four gene regions (GABRB3, MAOB, PAH, and SLC6A4) with five symptoms in schizophrenia. Psychiatry Research. 2012 198(2):202-206
  30. Xu J, Sun J*, Chen J, Helm M, Li Anna, Zhao Z, Chen X. RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia. BMC Genomics. 2012 13(Suppl 8):S2. (*Co-first author)
  31. Sun J, Xu H, Zhao Z. Network-assisted investigation of antipsychotic drugs and their targets. Chemistry & Biodiversity. 2012 9(5):900-910
  32. Zhao M, Sun J, Zhao Z. Distinct and competitive regulatory patterns of tumor suppressor genes and oncogenes in ovarian cancer. PLoS One. 2012 7(8):e44175
  33. Schleker S, Sun J, Raghavan B, Srnec M, Müller N, Koepfinger M, Murthy L, Zhao Z, Klein-Seetharaman J. The current Salmonella-host interactome. Proteomics - Clinical Applications. 2012 6(1-2):117-133
  34. Zhao M, Sun J, Zhao Z. Comprehensive analyses of tumor suppressor genes and oncogenes in protein-protein interaction networks: a topological perspective. GENSIPS 2012:101-102.

2011
  1. Xu H, Fu Z, Shah A, Chen Y, Peterson NB, Chen Q, Mani S, Levy MA, Dai Q,Denny  JC. Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases. AMIA Annu Symp Proc. 2011, 1564-72. [PMCID: PMC3244156]
  2. Liu M, Kawai VK, Stein CM, Denny JC, Roden DM, Xu H. Modeling drug exposure data in electronic medical records: an application to warfarin. AMIA Annu Symp Proc. 2011, 815-23. [PMCID: PMC3243123]
  3. Wu Y, Rosenbloom ST, Denny JC, Miller RA, Mani S, Giuse DA, Xu H. Detecting abbreviations in discharge summaries using machine learning methods. AMIA Annu Symp Proc. 2011, 1541-9. [PMCID: PMC3243185]
  4. Xu H, AbdelRahman S, Jiang M, Fan JW, Huang Y. An Initial Study of Full Parsing of Clinical Text using the Stanford Parser. International Workshop on Biomedical and Health Informatics, IEEE Conference of Bioinformatics and Biomedicine (BIBM), 2011.
  5. Wilke RA, Xu H, Denny JC, Roden DM, Krauss RM, McCarty CA, Davis RL, Skaar T, Lamba J, and Savova G. The emerging role of electronic medical records in pharmacogenomics. Clin Pharmacol Ther. 2011, 89(3): 379-86. [PMCID: PMC3204342]
  6. Rosenbloom ST, Denny JC, Xu H, Lorenzi N, Stead WW, Johnson KB. Data from clinical notes: a perspective on the tension between structure and flexible documentation. J Am Med Inform Assoc. 2011, 18(2):181-6. [PMCID: PMC3116264]
  7. Jiang M, Chen Y, Liu M, Rosenbloom ST, Mani S, Denny JC, Xu H. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J Am Med Inform Assoc. 2011, 18(5):601-6. [PMCID: PMC3168315]
  8. Xu H, Jiang M, Oetjens M, Bowton EA, Ramirez AH, Jeff JM, Basford MA, Pulley JM, Cowan JD, Wang X, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Facilitating pharmacogenetic studies using electronic health records and natural language processing: a case study of warfarin. J Am Med Inform Assoc. 2011; 18(4): 387-91. [PMCID: PMC3128409]
  9. Xu H, AbdelRahman S, Lu Y, Denny JC, Doan S. Applying semantic-based probabilistic context free grammar to medical language processing – a preliminary study on parsing medication sentences. J Biomed Inform 2011, 44(6): 1068-75. [PMCID: PMC3226929]
  10. Sun J, Wan C, Jia P, Riley BP, Kendler KS, Zhao Z. Application of systems biology approach identifies and validates GRB2 as a risk gene for schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample. Schizophrenia Research. 2011 125(2-3):201-208
  11. Putnam D, Sun J, Zhao Z. Exploring schizophrenia drug-gene interactions through molecular network and pathway modeling. AMIA Annu. Symp. Proc. 2011 2011:1127-1133
  12. Xia J, Sun J, Jia P, Zhao Z. Do cancer proteins really interact strongly in the human protein-protein interaction network? Computational Biology and Chemistry. 2011 35(3):121-125
  13. Gong X, Sun J, Zhao Z. Gene regulation in glioblastoma: a combinatorial analysis of microRNAs and transcription factors. Int. J. Comput. Biol. Drug Des. 2011 4(2):111-126

2010
  1. Xu H, Doan S, Birdwell KA, Cowan JD, Vincz AJ, Haas DW, Basford MA, Denny JC. An automated approach to calculating the daily dose of tacrolimus in electronic health records. AMIA Summits Transl Sci Proc. 2010:71-5. [PMCID: PMC3041548]
  2. Denny JC, Speltz P, Maddox R, Stein G, Xu H, Spickard A. Comparing Content Coverage in Medical Curriculum to Trainee-Authored Clinical Notes. AMIA Annu Symp Proc. 2010, 157-161. [PMCID: PMC3041398]
  3. Doan S and Xu H. Recognizing Medication related Entities in Hospital Discharge Summaries using Support Vector Machine. COLING 2010, the 23rd International Conference on Computational Linguistics, 259-266.
  4. Xu H, Lu Y, Jiang M, Liu M, Denny JC, Dai Q, Peterson NB. Mining Biomedical Literature for Terms related to Epidemiologic Exposures. AMIA Annu Symp Proc. 2010, 897-901. [PMCID: PMC3041399]
  5. Xu H, Stenner SP, Doan S, Johnson KB, Waitman LR, Denny JC. MedEx – A Medication Information Extraction System for Clinical Narratives. J Am Med Inform Assoc. 2010; 17(1):19-24. [PMCID: PMC2995636]
  6. Denny JC, Peterson JF, Choma NN, Xu H, Miller RA, Bastarache L, Peterson NB. Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records. J Am Med Inform Assoc. 2010; 17(4): 393-8. [PMCID: PMC2815478]
  7. Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H. Integrating Existing NLP Tools for Medication Extraction from Discharge Summaries. J Am Med Inform Assoc. 2010, 17:528-31. [PMCID: PMC2995674]
  8. Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng: Genome3D: A view-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. BMC Bioinformatics, Sep 2; 11:444, 2010 (Highly Accessed).
  9. Wei WQ, Tao C, Jiang G, Chute CG. A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes. AMIA Annual Symposium. 2010; 2010:857-61. Epub 2010 Nov 13. PMID:21347100. PMCID:3041302.
  10. Sun J, Jia P, Fanous AH, van den Oord EJCG, Chen X, Riley BP, Amdur RL, Kendler KS, Zhao Z. Schizophrenia gene networks and pathways and their applications for novel candidate gene selection. PLoS One. 2010 5(6): e11351
  11. Sun J, Zhao Z. Functional features, biological pathways and protein interaction networks of addiction-related genes. Chemistry & Biodiversity. 2010 7(5):1153-1161
  12. Sun J, Zhao Z. A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics. 2010 11 (Suppl 3):S5
  13. Sun J, Han L, Zhao Z. Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis. Artificial Intelligence in Medicine. 2010 48(2-3):99-106
  14. Jia P, Sun J, Guo AY, Zhao Z. SZGR: A comprehensive schizophrenia gene resource. Molecular Psychiatry. 2010 15(5):453-462
  15. Guo AY, Sun J, Jia P, Zhao Z. A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Systems Biology. 2010 4:10
  16. Guo AY, Sun J, Jia P, Zhao Z. Network analysis of ethanol-related candidate genes. Chemistry & Biodiversity. 2010 7(5):1142-1152

2009
  1. Xu H, Stetson P, Friedman C. Methods for Building Sense Inventories of Abbreviations in Clinical Notes. J Am Med Inform Assoc. 2009 16(1):103-108. [PMCID: PMC2605589]
  2. Sun J, Jia P, Fanous AH, Webb BT, van den Oord EJCG, Kendler KS, Zhao Z. A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases – schizophrenia as a case. Bioinformatics. 2009 25(19):2595-2602
  3. Guo A*, Sun J*, Riley BP, Kendler KS, Zhao Z. The dystrobrevin binding protein 1 gene: features and networks. Molecular Psychiatry. 2009 14:18-29. (*Co-first author)

2008
  1. Chen ES, Hripcsak G, Xu H, Markatou M, Friedman C. Automated Acquisition of Disease-Drug Knowledge from Biomedical and Clinical Documents. J Am Med Inform Assoc. 2008, 15(1):87-98. [PMCID: PMC2274872]
  2. Sarah Bradshaw, W. Jim Zheng, Lam C. Tsoi, Gary S. Gilkeson, Xian K. Zhang: A role for Fli-1 in B cell proliferation: implications for SLE pathogenesis. Clinical Immunology, 129(1):19-30, 2008
  3. Jingshan Huang, Jiangbo Dang, Michael N. Huhns, W. Jim Zheng: Using Artificial Neural Network to Align Biological Ontology. BMC Genomics, 9 Suppl 2:S16, 2008
  4. Sun J, Kuo PH, Riley BP, Kendler KS, Zhao Z. Candidate genes for schizophrenia: a survey of association studies and gene ranking. American Journal of Medical Genetics B: Neuropsychiatric Genetics. 2008 147B(7):1173-1181

2007
  1. Fan JW, Xu H, Friedman C. Using Distributional Analysis to Semantically Classify UMLS Concepts. In Proceedings of Medinfo. 2007; 519-23. [PMID: 17911771]
  2. Xu H, Fan JW, Friedman C. Combine multiple evidence for gene symbol disambiguation. ACL 2007, BioNLP Workshop, p41-48.
  3. Xu H, Stetson P, Friedman C. A Study of Abbreviations in Clinical Notes. AMIA Annu Symp Proc. 2007; 821-5.
  4. Tulipano KP, Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier YA, Friedman C. Natural language processing and visualization in the molecular imaging domain. J Biomed Inform. 2007; 40:3, 270-281. [PMID: 17084109]
  5. Fan JW, Xu H, Friedman C. Using Contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinformatics. 2007; 8: 264. [PMCID: PMC2014782]
  6. Xu H, Fan JW, Hripcsak G, Mendonça EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics, 2007 23(8):1015-1022. [PMID: 17314123]
  7. Sun J, Sun Y, Ding G, Liu Q, Wang C, He Y, Shi T, Li Y, Zhao Z. InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics. 2007 8:414
  8. Sun J, Zhao Z. Construction of phylogenetic profiles based on genetic distance of hundreds of genomes. Biochemical and Biophysical Research Communications. 2007 355(3):849-853
  9. Sun J, Li Y, Zhao Z. Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? Biochemical and Biophysical Research Communications. 2007 353(4):985-991

2006
  1. Xu H, Markatou M, Dimova R, Liu H, Friedman C. Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. BMC Bioinformatics. 2006; 7:334. [PMCID: PMC1550263]
  2. Sun J, Xu J, Cao J, Liu Q, Guo X, Shi T, Li Y. Prediction and systematic study of protein-protein interaction networks of Leptospira interrogans. Chinese Science Bulletin. 2006 51:1296-1305

2005
  1. Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y. Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics. 2005 21(16):3409-3415
  2. Sun J, Chen M, Xu J, Luo J. Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes. Journal of Molecular Evolution 2005 61(4):437-444
  3. Sun J, Xu J, Li Y. Analysis and application of large-scale protein-protein interaction data sets. Chinese Science Bulletin. 2005 50:2267-2272

2004
  1. Xu, H, Anderson, K, Grann, V, Friedman, C. Facilitating Cancer Research using Natural Language Processing of Pathology Reports. In Proceedings of Medinfo. 2004; 565-72. [PMID: 15360876]
  2. Lee HT, Krichevsky IE, Xu H, Ota-Setlik A, D'Agati VD, Emala CW. Local anesthetics worsen renal function after ischemia-reperfusion injury in rats. Am J Physiol Renal Physiol. 2004; 286(1):F111-9. [PMID: 14519592]
  3. Lee HT, Xu H, Nasr SH, Schnermann J, Emala CW. A1 adenosine receptor knockout mice exhibit increased renal injury following ischemia and reperfusion. Am J Physiol Renal Physiol. 2004; 286(2):F298-306. [PMID: 14600029]
  4. Lee HT, Xu H, Ota-Setlik A, Emala CW. Oxidant preconditioning protects human proximal tubular cells against lethal oxidant injury via p38 MAPK and heme oxygenase-1. Am J Nephrol. 2003; 23(5):324-33. [PMID: 12915776]
  5. Lee HT, Ota-Setlik A, Xu H, D'Agati VD, Jacobson MA, Emala CW. A3 adenosine receptor knockout mice are protected against ischemia- and myoglobinuria-induced renal failure. Am J Physiol Renal Physiol. 2003; 284(2):F267-73. [PMID: 12388399]
  6. Lee HT, Xu H, Siegel CD, Krichevsky IE. Local anesthetics induce human renal cell apoptosis. Am J Nephrol. 2003; 23(3):129-39. [PMID: 12586958]