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    Hong Yu PhD

    TitleProfessor
    InstitutionUniversity of Massachusetts Medical School
    DepartmentQuantitative Health Sciences
    AddressUniversity of Massachusetts Medical School
    55 Lake Avenue North, AC7-059
    Worcester MA 01655
    Phone508-856-3474
      Other Positions
      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentBioinformatics and Computational Biology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentClinical Population Health Research

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentMasters in Clinical Investigation

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentMD/PhD Program

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentBioinformatics and Integrative Biology

        Overview 
        Narrative

        Interests

        Information retrieval, extraction, natural language processing, summarization, human-computer interaction, with a focus on biomedical applications.

        Biography

        Ph.D. Biomedical Informatics, Columbia University, New York; MA and MPh, Physiology and Cellular Biophysics, Columbia University, New York; MS, Physiology, Beijing University, China; BS, Biomedical Engineering, Huazhong University of Science and Technology, China

        Research

        Professor Yu's research interests are in the areas of information retrieval, extraction, natural language processing, summarization, human-computer interaction, with a focus on biomedical applications. She has led the development of many systems, including the biomedical question answering system AskHERMES (http://www.askhermes.org), the adverse drug event pharmacovigilance system (http://www.ADErepository.org), the innovative biomedical figure search system (http://figuresearch.askhermes.org), and the NoteAid systems that help patients comprehend electronic medical records (http://ClinicalNotesAid.org).

        Awards & Activities

        Professor Yu has served as co-Chair in the biomedical natural language processing sections of the Pacific Symposium of Biocomputing and IEEE International Conference on Bioinformatics & Biomedicine. She is a member of the editorial board of the Journal of Biomedical Informatics, and is the PI of several National Institutes of Health funded projects. She was a recipient of the National Library of Medicine (NLM) pre-doctoral training grant to Columbia University and is one of the six “star trainees” selected by NLM on its celebration of 175th anniversary. Her first paper in biomedical informatics was nominated as one of the best papers in the American Medical Informatics Association Fall Symposium of 1999. Her work is included as best paper in IMIA Yearbook of Medical Informatics 2011, described in “Translational Bioinformatics 2012 Year in Review” by Russ Altman, and featured in Science, Nature, BioInform, the Pulitzer-winning Milwaukee Journal Sentinel, and the Milwaukee Public Radio.



        Bibliographic 
        selected publications
        List All   |   Timeline
        1. Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. Overview of the gene ontology task at BioCreative IV. Database (Oxford). 2014; 2014.
          View in: PubMed
        2. de Regt AK, Yin Y, Withers TR, Wang X, Baker TA, Sauer RT, Yu HD. Overexpression of CupB5 activates alginate overproduction in Pseudomonas aeruginosa by a novel AlgW-dependent mechanism. Mol Microbiol. 2014 Aug; 93(3):415-25.
          View in: PubMed
        3. Cerny J, Devitt K, Yu H, Ramanathan M, Woda B, Nath R. Early relapse of Burkitt lymphoma heralded by a bone marrow necrosis and numb chin syndrome successfully treated with allogeneic stem cell transplantation. Leuk Res Rep. 2014; 3(2):51-3.
          View in: PubMed
        4. Devitt K, Cerny J, Switzer B, Ramanathan M, Nath R, Yu H, Woda BA, Chen BJ. Hemophagocytic lymphohistiocytosis secondary to T-cell/histiocyte-rich large B-cell lymphoma. Leuk Res Rep. 2014; 3(2):42-5.
          View in: PubMed
        5. Xiao R, Cerny J, Devitt K, Dresser K, Nath R, Ramanathan M, Rodig SJ, Chen BJ, Woda BA, Yu H. MYC Protein Expression Is Detected in Plasma Cell Myeloma but Not in Monoclonal Gammopathy of Undetermined Significance (MGUS). Am J Surg Pathol. 2014 Jun; 38(6):776-83.
          View in: PubMed
        6. Shi M, Xiao R, Woda BA, Yu H. Five important advances in hematopathology. Arch Pathol Lab Med. 2014 Mar; 138(3):410-9.
          View in: PubMed
        7. Hao S, Andersen M, Yu H. Detection of immune suppressive neutrophils in peripheral blood samples of cancer patients. Am J Blood Res. 2013; 3(3):239-45.
          View in: PubMed
        8. Liu W, Dong SL, Xu F, Wang XQ, Withers TR, Yu HD, Wang X. Effect of intracellular expression of antimicrobial peptide LL-37 on growth of escherichia coli strain TOP10 under aerobic and anaerobic conditions. Antimicrob Agents Chemother. 2013 Oct; 57(10):4707-16.
          View in: PubMed
        9. Shi M, Cipollini MJ, Crowley-Bish PA, Higgins AW, Yu H, Miron PM. Improved detection rate of cytogenetic abnormalities in chronic lymphocytic leukemia and other mature B-cell neoplasms with use of CpG-oligonucleotide DSP30 and interleukin 2 stimulation. Am J Clin Pathol. 2013 May; 139(5):662-9.
          View in: PubMed
        10. Yin Y, Wang Y, Zhu L, Liu W, Liao N, Jiang M, Zhu B, Yu HD, Xiang C, Wang X. Comparative analysis of the distribution of segmented filamentous bacteria in humans, mice and chickens. ISME J. 2013 Mar; 7(3):615-21.
          View in: PubMed
        11. Liu F, Moosavinasab S, Houston TK, Yu H. MedTxting: learning based and knowledge rich SMS-style medical text contraction. AMIA Annu Symp Proc. 2012; 2012:558-67.
          View in: PubMed
        12. Bockhorst JP, Conroy JM, Agarwal S, O'Leary DP, Yu H. Beyond captions: linking figures with abstract sentences in biomedical articles. PLoS One. 2012; 7(7):e39618.
          View in: PubMed
        13. Ramesh BP, Prasad R, Miller T, Harrington B, Yu H. Automatic discourse connective detection in biomedical text. J Am Med Inform Assoc. 2012 Sep-Oct; 19(5):800-8.
          View in: PubMed
        14. Liao N, Yin Y, Sun G, Xiang C, Liu D, Yu HD, Wang X. Colonization and distribution of segmented filamentous bacteria (SFB) in chicken gastrointestinal tract and their relationship with host immunity. FEMS Microbiol Ecol. 2012 Aug; 81(2):395-406.
          View in: PubMed
        15. Agarwal S, Yu H, Kohane I. BioNØT: a searchable database of biomedical negated sentences. BMC Bioinformatics. 2011; 12:420.
          View in: PubMed
        16. Miller T, Ravvaz K, Cimino JJ, Yu H. An investigation into the feasibility of spoken clinical question answering. AMIA Annu Symp Proc. 2011; 2011:954-9.
          View in: PubMed
        17. Agarwal S, Liu F, Yu H. Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. BMC Bioinformatics. 2011; 12 Suppl 8:S10.
          View in: PubMed
        18. Liu F, Antieau LD, Yu H. Toward automated consumer question answering: automatically separating consumer questions from professional questions in the healthcare domain. J Biomed Inform. 2011 Dec; 44(6):1032-8.
          View in: PubMed
        19. Liu F, Tur G, Hakkani-Tür D, Yu H. Towards spoken clinical-question answering: evaluating and adapting automatic speech-recognition systems for spoken clinical questions. J Am Med Inform Assoc. 2011 Sep-Oct; 18(5):625-30.
          View in: PubMed
        20. Kim D, Ramesh BP, Yu H. Automatic figure classification in bioscience literature. J Biomed Inform. 2011 Oct; 44(5):848-58.
          View in: PubMed
        21. Agarwal S, Yu H. Figure summarizer browser extensions for PubMed Central. Bioinformatics. 2011 Jun 15; 27(12):1723-4.
          View in: PubMed
        22. Zhang Q, Cao YG, Yu H. Parsing citations in biomedical articles using conditional random fields. Comput Biol Med. 2011 Apr; 41(4):190-4.
          View in: PubMed
        23. Cao Y, Liu F, Simpson P, Antieau L, Bennett A, Cimino JJ, Ely J, Yu H. AskHERMES: An online question answering system for complex clinical questions. J Biomed Inform. 2011 Apr; 44(2):277-88.
          View in: PubMed
        24. Kim D, Yu H. Figure text extraction in biomedical literature. PLoS One. 2011; 6(1):e15338.
          View in: PubMed
        25. Agarwal S, Choubey L, Yu H. Automatically classifying the role of citations in biomedical articles. AMIA Annu Symp Proc. 2010; 2010:11-5.
          View in: PubMed
        26. Ramesh BP, Yu H. Identifying discourse connectives in biomedical text. AMIA Annu Symp Proc. 2010; 2010:657-61.
          View in: PubMed
        27. Agarwal S, Yu H. Biomedical negation scope detection with conditional random fields. J Am Med Inform Assoc. 2010 Nov-Dec; 17(6):696-701.
          View in: PubMed
        28. Yu H, Liu F, Ramesh BP. Automatic figure ranking and user interfacing for intelligent figure search. PLoS One. 2010; 5(10):e12983.
          View in: PubMed
        29. Li Z, Liu F, Antieau L, Cao Y, Yu H. Lancet: a high precision medication event extraction system for clinical text. J Am Med Inform Assoc. 2010 Sep-Oct; 17(5):563-7.
          View in: PubMed
        30. Agarwal S, Yu H. Detecting hedge cues and their scope in biomedical text with conditional random fields. J Biomed Inform. 2010 Dec; 43(6):953-61.
          View in: PubMed
        31. Cao YG, Cimino JJ, Ely J, Yu H. Automatically extracting information needs from complex clinical questions. J Biomed Inform. 2010 Dec; 43(6):962-71.
          View in: PubMed
        32. Cao Y, Li Z, Liu F, Agarwal S, Zhang Q, Yu H. An IR-aided machine learning framework for the BioCreative II.5 Challenge. IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep; 7(3):454-61.
          View in: PubMed
        33. Agarwal S, Yu H. FigSum: automatically generating structured text summaries for figures in biomedical literature. AMIA Annu Symp Proc. 2009; 2009:6-10.
          View in: PubMed
        34. Kim D, Yu H. Hierarchical image classification in the bioscience literature. AMIA Annu Symp Proc. 2009; 2009:327-31.
          View in: PubMed
        35. Yu H, Agarwal S, Frid N. Investigating and Annotating the Role of Citation in Biomedical Full-Text Articles. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2009 Nov 1; 1-4 Nov(2009):308-313.
          View in: PubMed
        36. Agarwal S, Yu H. Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion. Bioinformatics. 2009 Dec 1; 25(23):3174-80.
          View in: PubMed
        37. Yu H, Agarwal S, Johnston M, Cohen A. Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension. J Biomed Discov Collab. 2009; 4:1.
          View in: PubMed
        38. Yu H, Cao YG. Automatically extracting information needs from Ad Hoc clinical questions. AMIA Annu Symp Proc. 2008; 96-100.
          View in: PubMed
        39. Poschet JF, Timmins GS, Taylor-Cousar JL, Ornatowski W, Fazio J, Perkett E, Wilson KR, Yu HD, de Jonge HR, Deretic V. Pharmacological modulation of cGMP levels by phosphodiesterase 5 inhibitors as a therapeutic strategy for treatment of respiratory pathology in cystic fibrosis. Am J Physiol Lung Cell Mol Physiol. 2007 Sep; 293(3):L712-9.
          View in: PubMed
        40. Yu H, Lee M, Kaufman D, Ely J, Osheroff JA, Hripcsak G, Cimino J. Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians. J Biomed Inform. 2007 Jun; 40(3):236-51.
          View in: PubMed
        41. Yu H, Kaufman D. A cognitive evaluation of four online search engines for answering definitional questions posed by physicians. Pac Symp Biocomput. 2007; 328-39.
          View in: PubMed
        42. Tulipano PK, 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 Jun; 40(3):270-81.
          View in: PubMed
        43. Yu H, Lee M. Accessing bioscience images from abstract sentences. Bioinformatics. 2006 Jul 15; 22(14):e547-56.
          View in: PubMed
        44. Yu H, Kim W, Hatzivassiloglou V, Wilbur WJ. Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. J Biomed Inform. 2007 Apr; 40(2):150-9.
          View in: PubMed
        45. Lee M, Wang W, Yu H. Exploring supervised and unsupervised methods to detect topics in biomedical text. BMC Bioinformatics. 2006; 7:140.
          View in: PubMed
        46. Yu H. Towards answering biological questions with experimental evidence: automatically identifying text that summarize image content in full-text articles. AMIA Annu Symp Proc. 2006; 834-8.
          View in: PubMed
        47. Lee M, Cimino J, Zhu HR, Sable C, Shanker V, Ely J, Yu H. Beyond information retrieval--medical question answering. AMIA Annu Symp Proc. 2006; 469-73.
          View in: PubMed
        48. Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboué PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform. 2004 Feb; 37(1):43-53.
          View in: PubMed
        49. Yu H, Agichtein E. Extracting synonymous gene and protein terms from biological literature. Bioinformatics. 2003; 19 Suppl 1:i340-9.
          View in: PubMed
        50. Yu H, Hatzivassiloglou V, Rzhetsky A, Wilbur WJ. Automatically identifying gene/protein terms in MEDLINE abstracts. J Biomed Inform. 2002 Oct-Dec; 35(5-6):322-30.
          View in: PubMed
        51. Yu H, Hripcsak G, Friedman C. Mapping abbreviations to full forms in biomedical articles. J Am Med Inform Assoc. 2002 May-Jun; 9(3):262-72.
          View in: PubMed
        52. Yu H, Hatzivassiloglou V, Friedman C, Rzhetsky A, Wilbur WJ. Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. Proc AMIA Symp. 2002; 919-23.
          View in: PubMed
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