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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 - 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. Yin Y, Withers TR, Wang X, Yu HD. Evidence for Sigma Factor Competition in the Regulation of Alginate Production by Pseudomonas aeruginosa. PLoS One. 2013; 8(8):e72329.
          View in: PubMed
        2. 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
        3. Chen BJ, Chapuy B, Ouyang J, Sun HH, Roemer MG, Xu ML, Yu H, Fletcher CD, Freeman GJ, Shipp MA, Rodig SJ. PD-L1 Expression Is Characteristic of a Subset of Aggressive B-cell Lymphomas and Virus-Associated Malignancies. Clin Cancer Res. 2013 Jul 1; 19(13):3462-73.
          View in: PubMed
        4. 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
        5. Cerny J, Yu H, Miron PM. Novel FGFR3 rearrangement t(4;22)(p16;q11.2) in a patient with chronic lymphocytic leukemia/small lymphocytic lymphoma. Ann Hematol. 2013 Apr 13.
          View in: PubMed
        6. 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
        7. 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
        8. 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
        9. Agarwal S, Yu H, Kohane I. BioNØT: a searchable database of biomedical negated sentences. BMC Bioinformatics. 2011; 12:420.
          View in: PubMed
        10. 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
        11. 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
        12. 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
        13. 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
        14. Kim D, Ramesh BP, Yu H. Automatic figure classification in bioscience literature. J Biomed Inform. 2011 Oct; 44(5):848-58.
          View in: PubMed
        15. Agarwal S, Yu H. Figure summarizer browser extensions for PubMed Central. Bioinformatics. 2011 Jun 15; 27(12):1723-4.
          View in: PubMed
        16. 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
        17. 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
        18. Kim D, Yu H. Figure text extraction in biomedical literature. PLoS One. 2011; 6(1):e15338.
          View in: PubMed
        19. Ramesh BP, Yu H. Identifying discourse connectives in biomedical text. AMIA Annu Symp Proc. 2010; 2010:657-61.
          View in: PubMed
        20. 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
        21. 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
        22. 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
        23. 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
        24. 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
        25. 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
        26. 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
        27. 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
        28. Kim D, Yu H. Hierarchical image classification in the bioscience literature. AMIA Annu Symp Proc. 2009; 2009:327-31.
          View in: PubMed
        29. 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
        30. 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
        31. 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
        32. Yu H, Cao YG. Automatically extracting information needs from Ad Hoc clinical questions. AMIA Annu Symp Proc. 2008; 96-100.
          View in: PubMed
        33. 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
        34. 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
        35. 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
        36. Yu H, Lee M. Accessing bioscience images from abstract sentences. Bioinformatics. 2006 Jul 15; 22(14):e547-56.
          View in: PubMed
        37. 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
        38. 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
        39. 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
        40. 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
        41. 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
        42. Yu H, Agichtein E. Extracting synonymous gene and protein terms from biological literature. Bioinformatics. 2003; 19 Suppl 1:i340-9.
          View in: PubMed
        43. 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
        44. 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
        45. 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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