Center for Computational Biomedicine

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Center for Computational Biomedicine

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 Technol 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. Chen Y, Cao H, Mei Q, Zheng K, Xu H. Applying Active Learning to Supervised Word Sense Disambiguation in MEDLINE. J Am Med Inform Assoc. 2013, In Press. [PMID: 23364851]
  6. Wiley LK, Shah A, Xu H, Bush WS. ICD-9 Tobacco Use Codes are Effective Identifiers of Smoking Status. J Am Med Inform Assoc. 2013, In Press. [PMID: 23396545]
  7. Diane Gesty-Palmer, Ling Yuan, Bronwen Martin, William H. Wood III, Mi-Hye Lee, Michael G. Janech, Lam C. Tsoi, W. Jim Zheng, and Louis M. Luttrel, β-Arrestin Selective G Protein-Coupled Receptor Agonists Engender Unique Biological Efficacy In Vivo,Molecular Endocrinology, 27(2):296-314, 2013
  8. Tao C, Song D, Sharma D, Chute CG. Semantic Annotator for Converting Biomedical Text to Linked Data, Journal of Biomedical Informatics, 2013 pii: S1532-0464(13)00102-0. doi: 10.1016/j.jbi.2013.07.003
  9. Tao C, Li D, Shen F, Pathak J, Liu H, Chute CG, Phenotyping on EHR Data Using OWL and Semantic Web Technologies, Lecture Notes in Computer Science series 8084, International Conference of Smart Health 2013.
  10. 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)
  11. 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)
  12. Atrey R, Sun J*, Zhao Z. Exploring drug-target interaction networks of illicit drugs. 2013 BMC Genomics (in press) (*Co-first author)
  13. 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. Tingting Qin, Lam Tsoi, Kellie Sims, Xinghua Lu, W. Jim Zheng: Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network. BMC Systems Biology, 6 Suppl 3:S3, 2012.
  28. Tao C, Jiang G, Oniki TA, Freimuth RR, Zhu Q, Sharma D, Pathak J, Huff SM, Chute CG, A Semantic-Web Oriented Representation of the Clinical Element Model for Secondary Use of EHR Data, J Am Med Inform Assoc. 2012, PMID:23268487. DOI:10.1136/amiajnl-2012-001326
  29. Tao C, He Y, Yang H, Poland GA, Chute CG, Ontology-based Time Information Representation of Vaccine Adverse Events in VAERS for Temporal Analysis. J Biomedical Semantics. 2012, 3:13
  30. Tao C, Pathak J, Solbrig HR, Wei W-Q, Chute CG. Terminology representation guidelines for biomedical ontologies in the semantic web notations. J Biomed Inform. 2012 Sep 28. pii: S1532-0464(12)00150-5. doi: 10.1016/j.jbi.2012.09.003.
  31. Zhu Q, Tao C, Ding Y, Chute CG, Time-Related Patient Data Retrieval for the Case Studies from the Pharmacogenomics Research Network. Journal of Medical Systems, 2012 PMID: 23076712
  32. Tao C, He Y, Poland GA, Chute CG. Time modeling of vaccine adverse events in VAERS for temporal analysis. International Conference on Biomedical Ontology. July 2012.
  33. Tao C, Zhang Y, Jiang G, Bouamrane M, Chute CG. Optimizing Semantic MEDLINE for Translational Science Studies Using Semantic Web Technologies. International Conference on Information and Knowledge Management, (CIKM 2012). 2012.
  34. Tao C, Wongsuphasawat K, Clark K, Plaisant C, Shneiderman B, Chute CG. Towards event sequence representation, reasoning and visualization for EHR data. IHI'12 - Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium. 2012:801-5.
  35. Tao C, Noy NF, Solbrig HR, Shah NH, Musen MA, Chute CG. Proposed SKOS extensions for bioportal terminology services. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2012; 7185 LNCS:342-9.
  36. Li D, Tao C, Liu H, Chute CG. Ontology-based Temporal Relation Modeling with MapReduce Latent Dirichlet Allocations for Big EHR Data. International Symposium on Big Data and MapReduce. 2012.
  37. Bouamrane M, Tao C, Mair F. Quality Assessment of Electronic Health Information Management Systems. International Conference on Information and Knowledge Management (CIKM 2012). 2012.
  38. 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
  39. 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
  40. 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
  41. 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)
  42. Sun J, Xu H, Zhao Z. Network-assisted investigation of antipsychotic drugs and their targets. Chemistry & Biodiversity. 2012 9(5):900-910
  43. 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
  44. 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
  45. 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. Lam C. Tsoi, Tingting Qin, Elizabeth H. Slate, W. Jim Zheng: Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. BMC Bioinformatics, Nov. 11, 12:438, 2011.
  11. Muhammad Nazmus Sakib, Jijun Tang, W. Jim Zheng, Chin-Tser Huang: Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files. PLoS One, Dec. 2, 6(12):e28251, 2011
  12. Kaushlendra Tripathi, Nabil Matmati, W. Jim Zheng, Yusuf A. Hannun, Bidyut K. Mohanty: Cellular Morphogenesis Under Stress Is Influenced by the Sphingolipid Pathway gene ISC1 and DNA Integrity Checkpoint Genes in Saccharomyces cerevisiae. Genetics, Oct, 189(2):533-47, 2011
  13. Tao C, Jiang G, Clark KK, Sharma DK, Chute CG. Toward Answering Time-Related Questions from Adverse Event Reports Using Ontology-based Approaches. International Conference on Biomedical Ontologies: Representing Adverse. 2011 Jul.
  14. Tao C, Solbrig HR, Chute CG. CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inference in Clinical Narratives. AMIA Summits Transl Sci Proc. 2011; 2011:64-8. Epub 2011 Mar 07. PMID:22211182. PMCID:3248753.
  15. Tao C, Pathak J, Welch SR, Bouamrane MM, Huff SM, Chute CG. Toward semantic web based knowledge representation and extraction from electronic health records. International Conference on Information and Knowledge Management (CIKM 2011). 2011:75-8.
  16. Tao C, Parker CG, Oniki TA, Pathak J, Huff SM, Chute CG. An OWL meta-ontology for representing the Clinical Element Model. AMIA Annual Symposium. 2011; 2011:1372-81. Epub 2011 Oct 22. PMID:22195200. PMCID:3243162.
  17. Tao C, Jiang G, Wei W, Solbrig HR, Chute CG. Towards Semantic-Web Based Representation and Harmonization of Standard Meta-data Models for Clinical Studies. AMIA Summits Transl Sci Proc. 2011; 2011:59-63. Epub 2011 Mar 07. PMID:22211181. PMCID:3248749.
  18. 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
  19. 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
  20. 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
  21. 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. Tao C, Wei WQ, Solbrig HR, Savova G, Chute CG. CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. AMIA Annual Symposium. 2010; 2010:787-91. Epub 2010 Nov 13. PMID:21347086. PMCID:3041418.
  11. Tao C, Solbrig HR, Sharma DK, Wei WQ, Savova GK, Chute CG. Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques. Lecture Notes in Computer Science. 2010; 6497:241-56. PMID:22025812. PMCID:3198866. DOI:10.1007/978-3-642-17749-1_16.
  12. Embley DW, Liddle SW, Lonsdale DW, Steward A, Tao C. KBB: A Knowledge-Bundle Builder for Research Studies. International Workshop on Active Conceptual Modeling of Learning in conjunction with ER 2009, Lecture Notes in Computer Science. 2010; 6413:148-157. DOI:10.1007/978-3-642-16385-2_19.
  13. 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
  14. Sun J, Zhao Z. Functional features, biological pathways and protein interaction networks of addiction-related genes. Chemistry & Biodiversity. 2010 7(5):1153-1161
  15. Sun J, Zhao Z. A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics. 2010 11 (Suppl 3):S5
  16. 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
  17. Jia P, Sun J, Guo AY, Zhao Z. SZGR: A comprehensive schizophrenia gene resource. Molecular Psychiatry. 2010 15(5):453-462
  18. 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
  19. 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. Hiroshi Kitagaki, Lauren A Cowart, Nabil Matmati, David Montefusco, Jason Gandy, Silvia Vaena de Avalos, Sergei A Novgorodov, Jim Zheng, Lina M Obeid, and Yusuf A Hannun: ISC1-Dependent Metabolic Adaptation Reveals an Indispensable Role for Mitochondria in Induction of Nuclear Genes During the Diauxic Shift in S. cerevisiae. J. Biol. Chem., 284(16):10818-30, 2009.
  3. Lam C. Tsoi, Ravi Patel, Wenle Zhao, W. Jim Zheng: Text Mining Approach to Evaluate Terms for Ontology Development. J. Biomedical Informatics, 42(5):824-30, 2009.
  4. Lam C. Tsoi, Ravi Patel, Wenle Zhao, W. Jim Zheng: Text Mining Approach to Evaluate Terms for Ontology Development. J. Biomedical Informatics, 42(5):824-30, 2009.
  5. Lam C. Tsoi, Michael Boehnke, Richard Klein, W. Jim Zheng: Evaluation of Genome-wide Association Study Results through Development of Ontology Fingerprint. Bioinformatics, 25(10):1314-20, 2009.
  6. Tao C, Embley DW. FOCIH: Form-based Ontology Creation, Information Harvesting. International Conference of Conceptual Modeling (ER 2009), Lecture Notes in Computer Science. 2009 Nov; 5829:346-59. DOI:10.1007/978-3-642-04840-1_26.
  7. Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG. LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies. CEUR Workshop Proc. 2009 Oct 26; 521:3. PMID:21804785. PMCID:3146261.
  8. Tao C, Pathak J, Solbrig HR, Chute CG. LexOWL: A Bridge from LexGrid to OWL. International Conference of Biomedical Ontology (ICBO 2009). 2009 Jul:131-4. DOI:1038/npre.2009.3468.1.
  9. Tao C, Embley DW. Automatic Hidden-Web Table Interpretation, Conceptualization, and Semantic Annotation. Journal of Data & Knowledge Engineering. 2009; 68(7):683-703. DOI:10.1016/j.datak.2009.02.010.
  10. 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
  11. 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. Lam C. Tsoi, W. Jim Zheng: A Method of Microarray Data Storage Using Array Data Type. Computational Biology and Chemistry. 31(2):143. 2007
  8. Tao C, Embley DW. Seed-based Generation of Personalized Bio-Ontologies for Information Extraction. International Workshop on Conceptual Modeling for Life Sciences Applications (CMLSA 2007) in conjunction with ER 2007, Lecture Notes In Computer Science. 2007 Nov; 4802:74-84. DOI:10.1007/978-3-540-76292-8_9.
  9. Tao C, Embley DW. Automatic Hidden-Web Table Interpretation by Sibling Page Comparison. International Conference on Conceptual Modeling (ER2007), Lecture Notes in Computer Science, Springer-Verlag, New York. 2007 Nov:566-81. DOI:10.1007/978-3-540-75563-0_38.
  10. 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
  11. 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
  12. 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. W. Jim Zheng: Engineering Approaches toward Biological Information Integration at the Systems Level. Current Bioinformatics. 1(1):85-93, 2006
  3. Linyong Mao, W. Jim Zheng: Combining Comparative Genomics with de novo Motif Discovery to Identify Human Transcription Factor DNA-Binding Motifs. BMC Bioinformatics. 7 (Suppl 4):S21, 2006
  4. Tao C. Toward Making Online Biological Data Machine Understandable. International Semantic Web Conference (ISWC 2006), Lecture Notes in Computer Science. 2006 Nov; 4273:992-3. DOI:10.1007/11926078_83.
  5. Tao C, Ding Y, Lonsdale D. Automatic Creation of Web Services from Extraction Ontologies. International Workshop on Semantic Web Applications: Theory and Practice (SWAT 2006) in conjunction with ER 2006, Lecture Notes in Computer Science. 2006 Nov; 4231:415-24. DOI:10.1007/11908883_49.
  6. Tao C, Embley DW. HTML Table Interpretation by Sibling Page Comparison in the Molecular Biology Domain. Proceedings of the 3rd Biotechnology and Bioinformatics Symposium (BIOT 2006) Provo, UT. 2006 Oct:116-9.
  7. 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]
  7. W. Jim Zheng, Velin Z. Spassov, Lisa Yan, Paul K. Flook and Sándor Szalma: A hidden Markov model with molecular mechanics energy scoring function for transmembrane helix prediction. Computational Biology and Chemistry. 28(4):265-74 2004
  8. Embley DW, Tao C, Liddle SW. Automating the Extraction of Data from HTML Tables with Unknown Structure. Journal of Data & Knowledge Engineering. 2005 Jul; 54(1):3-28. DOI:10.1016/j.datak.2004.10.004.