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Hong Yu PhD

TitleAdjunct Professor
InstitutionUniversity of Massachusetts Medical School
DepartmentMedicine
AddressUniversity of Massachusetts Medical School
55 Lake Avenue North, AC7-059
Worcester MA 01655
Phone508-856-3474
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentMedicine
    DivisionCardiovascular Medicine

    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


    Collapse Biography 
    Collapse education and training
    Huazhong University of Science and Technology, Wuhan, , ChinaBSBiomedical Engineering
    Beijing Normal University, Haidian, , ChinaMSPhysiology
    Columbia University, New York, NY, United StatesMABiomedical Informatics
    Columbia University, New York, NY, United StatesMPHILPhysiology & Molecular Biophys
    Columbia University, New York, NY, United StatesPHDBiomedical Informatics

    Collapse Overview 
    Collapse overview

    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.




    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Kaymaz Y, Oduor CI, Yu H, Otieno JA, Ong'echa JM, Moormann AM, Bailey JA. Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-Specific Differences. Mol Cancer Res. 2017 05; 15(5):563-576. PMID: 28465297.
      View in: PubMed
    2. Chen J, Yu H. Unsupervised Ensemble Ranking of Terms in Electronic Health Record Notes Based on Their Importance to Patients. J Biomed Inform. 2017 Mar 03. PMID: 28267590.
      View in: PubMed
    3. Zheng J, Yu H. Readability Formulas and User Perceptions of Electronic Health Records Difficulty: A Corpus Study. J Med Internet Res. 2017 Mar 02; 19(3):e59. PMID: 28254738.
      View in: PubMed
    4. Bai S, Chen H, Zhu L, Liu W, Yu HD, Wang X, Yin Y. Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota. PLoS One. 2017; 12(2):e0171576. PMID: 28170428.
      View in: PubMed
    5. Chen J, Zheng J, Yu H. Finding Important Terms for Patients in Their Electronic Health Records: A Learning-to-Rank Approach Using Expert Annotations. JMIR Med Inform. 2016 Nov 30; 4(4):e40. PMID: 27903489.
      View in: PubMed
    6. Jagannatha AN, Yu H. Structured prediction models for RNN based sequence labeling in clinical text. Proc Conf Empir Methods Nat Lang Process. 2016 Nov; 2016:856-865. PMID: 28004040.
      View in: PubMed
    7. Lalor JP, Wu H, Yu H. Building an Evaluation Scale using Item Response Theory. Proc Conf Empir Methods Nat Lang Process. 2016 Nov; 2016:648-657. PMID: 28004039.
      View in: PubMed
    8. Xing W, Dresser K, Zhang R, Evens AM, Yu H, Woda BA, Chen BJ. PD-L1 expression in EBV-negative diffuse large B-cell lymphoma: clinicopathologic features and prognostic implications. Oncotarget. 2016 Sep 13; 7(37):59976-59986. PMID: 27527850.
      View in: PubMed
    9. Li R, Withers RT, Dai J, Ruan J, Li W, Dai Y, An W, Yu D, Wei H, Xia M, Tian C, Yu HD, Qiu D. Truncated type IV pilin PilA(108) activates the intramembrane protease AlgW to cleave MucA and PilA(108) itself in vitro. Arch Microbiol. 2016 Nov; 198(9):885-92. PMID: 27270273.
      View in: PubMed
    10. Liu Q, Tomaszewicz K, Hutchinson L, Hornick JL, Woda B, Yu H. Somatic mutations in histiocytic sarcoma identified by next generation sequencing. Virchows Arch. 2016 Aug; 469(2):233-41. PMID: 27259537.
      View in: PubMed
    11. Jagannatha AN, Yu H. Bidirectional RNN for Medical Event Detection in Electronic Health Records. Proc Conf. 2016 Jun; 2016:473-482. PMID: 27885364.
      View in: PubMed
    12. Long TE, Keding LC, Lewis DD, Anstead MI, Withers TR, Yu HD. Anionic fluoroquinolones as antibacterials against biofilm-producing Pseudomonas aeruginosa. Bioorg Med Chem Lett. 2016 Feb 15; 26(4):1305-9. PMID: 26826023; PMCID: PMC4753842 [Available on 02/15/17].
    13. Yu H, Pinkus JL, Pinkus GS. a-Hemoglobin-stabilizing Protein: An Effective Marker for Erythroid Precursors in Bone Marrow Biopsy Specimens. Appl Immunohistochem Mol Morphol. 2016 Jan; 24(1):51-6. PMID: 25611244.
      View in: PubMed
    14. Fang M, Pak ML, Chamberlain L, Xing W, Yu H, Green MR. The CREB Coactivator CRTC2 Is a Lymphoma Tumor Suppressor that Preserves Genome Integrity through Transcription of DNA Mismatch Repair Genes. Cell Rep. 2015 Jun 9; 11(9):1350-7. PMID: 26004186.
      View in: PubMed
    15. Bedayat A, Mirzabeigi M, Yu H, Hultman R, MacMaster S. Breast: Sezary Syndrome: A Unique Presentation. Breast J. 2015 Jul-Aug; 21(4):423-7. PMID: 25939954.
      View in: PubMed
    16. Zheng J, Yu H. Methods for Linking EHR Notes to Education Materials. AMIA Jt Summits Transl Sci Proc. 2015; 2015:209-15. PMID: 26306273.
      View in: PubMed
    17. Polepalli Ramesh B, Sethi RJ, Yu H. Figure-associated text summarization and evaluation. PLoS One. 2015; 10(2):e0115671. PMID: 25643357.
      View in: PubMed
    18. Li Y, Yu H. A robust data-driven approach for gene ontology annotation. Database (Oxford). 2014; 2014:bau113. PMID: 25425037.
      View in: PubMed
    19. Zheng J, Yarzebski J, Ramesh BP, Goldberg RJ, Yu H. Automatically Detecting Acute Myocardial Infarction Events from EHR Text: A Preliminary Study. AMIA Annu Symp Proc. 2014; 2014:1286-93. PMID: 25954440.
      View in: PubMed
    20. Zhang Q, Yu H. Computational approaches for predicting biomedical research collaborations. PLoS One. 2014; 9(11):e111795. PMID: 25375164.
      View in: PubMed
    21. Morgan EA, Pihan GA, Said JW, Yu H, Pinkus JL, Dorfman DM, Rodig SJ, Pinkus GS. Profile of CD103 expression in T-cell neoplasms: immunoreactivity is not restricted to enteropathy-associated T-cell lymphoma. Am J Surg Pathol. 2014 Nov; 38(11):1557-70. PMID: 25025448.
      View in: PubMed
    22. 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. PMID: 25157073.
      View in: PubMed
    23. 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. PMID: 24913916.
      View in: PubMed
    24. 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. PMID: 25068102.
      View in: PubMed
    25. Polepalli Ramesh B, Belknap SM, Li Z, Frid N, West DP, Yu H. Automatically Recognizing Medication and Adverse Event Information From Food and Drug Administration's Adverse Event Reporting System Narratives. JMIR Med Inform. 2014 Jun 27; 2(1):e10. PMID: 25600332.
      View in: PubMed
    26. 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. PMID: 24955327.
      View in: PubMed
    27. 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. PMID: 24705315.
      View in: PubMed
    28. Shi M, Xiao R, Woda BA, Yu H. Five important advances in hematopathology. Arch Pathol Lab Med. 2014 Mar; 138(3):410-9. PMID: 24576034.
      View in: PubMed
    29. 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. PMID: 23997986.
      View in: PubMed
    30. 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. PMID: 23856776.
      View in: PubMed
    31. 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. PMID: 23596118.
      View in: PubMed
    32. 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. PMID: 23151642.
      View in: PubMed
    33. 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. PMID: 23304328.
      View in: PubMed
    34. 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. PMID: 22815711.
      View in: PubMed
    35. 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. PMID: 22744958.
      View in: PubMed
    36. 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. PMID: 22429007.
      View in: PubMed
    37. Agarwal S, Yu H, Kohane I. BioNØT: a searchable database of biomedical negated sentences. BMC Bioinformatics. 2011 Oct 27; 12:420. PMID: 22032181.
      View in: PubMed
    38. 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. PMID: 22195154.
      View in: PubMed
    39. 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 Oct 03; 12 Suppl 8:S10. PMID: 22151701.
      View in: PubMed
    40. 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. PMID: 21856442.
      View in: PubMed
    41. 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. PMID: 21705457.
      View in: PubMed
    42. Kim D, Ramesh BP, Yu H. Automatic figure classification in bioscience literature. J Biomed Inform. 2011 Oct; 44(5):848-58. PMID: 21645638.
      View in: PubMed
    43. Agarwal S, Yu H. Figure summarizer browser extensions for PubMed Central. Bioinformatics. 2011 Jun 15; 27(12):1723-4. PMID: 21493658.
      View in: PubMed
    44. Zhang Q, Cao YG, Yu H. Parsing citations in biomedical articles using conditional random fields. Comput Biol Med. 2011 Apr; 41(4):190-4. PMID: 21419403.
      View in: PubMed
    45. 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. PMID: 21256977.
      View in: PubMed
    46. Kim D, Yu H. Figure text extraction in biomedical literature. PLoS One. 2011 Jan 13; 6(1):e15338. PMID: 21249186.
      View in: PubMed
    47. Ramesh BP, Yu H. Identifying discourse connectives in biomedical text. AMIA Annu Symp Proc. 2010 Nov 13; 2010:657-61. PMID: 21347060.
      View in: PubMed
    48. Agarwal S, Choubey L, Yu H. Automatically classifying the role of citations in biomedical articles. AMIA Annu Symp Proc. 2010 Nov 13; 2010:11-5. PMID: 21346931.
      View in: PubMed
    49. Agarwal S, Yu H. Biomedical negation scope detection with conditional random fields. J Am Med Inform Assoc. 2010 Nov-Dec; 17(6):696-701. PMID: 20962133.
      View in: PubMed
    50. Yu H, Liu F, Ramesh BP. Automatic figure ranking and user interfacing for intelligent figure search. PLoS One. 2010 Oct 07; 5(10):e12983. PMID: 20949102.
      View in: PubMed
    51. 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. PMID: 20819865.
      View in: PubMed
    52. 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. PMID: 20709188.
      View in: PubMed
    53. 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. PMID: 20670693.
      View in: PubMed
    54. 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. PMID: 20671317.
      View in: PubMed
    55. Agarwal S, Yu H. FigSum: automatically generating structured text summaries for figures in biomedical literature. AMIA Annu Symp Proc. 2009 Nov 14; 2009:6-10. PMID: 20351812.
      View in: PubMed
    56. Kim D, Yu H. Hierarchical image classification in the bioscience literature. AMIA Annu Symp Proc. 2009 Nov 14; 2009:327-31. PMID: 20351874.
      View in: PubMed
    57. 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. PMID: 21170175.
      View in: PubMed
    58. 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. PMID: 19783830.
      View in: PubMed
    59. 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. PMID: 19126221.
      View in: PubMed
    60. Yu H, Cao YG. Automatically extracting information needs from Ad Hoc clinical questions. AMIA Annu Symp Proc. 2008 Nov 06; 96-100. PMID: 18999100.
      View in: PubMed
    61. 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. PMID: 17586695.
      View in: PubMed
    62. 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. PMID: 17462961.
      View in: PubMed
    63. 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. PMID: 17990503.
      View in: PubMed
    64. 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. PMID: 17084109.
      View in: PubMed
    65. Yu H, Lee M. Accessing bioscience images from abstract sentences. Bioinformatics. 2006 Jul 15; 22(14):e547-56. PMID: 16873519.
      View in: PubMed
    66. 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. PMID: 16843731.
      View in: PubMed
    67. Lee M, Wang W, Yu H. Exploring supervised and unsupervised methods to detect topics in biomedical text. BMC Bioinformatics. 2006; 7:140. PMID: 16539745.
      View in: PubMed
    68. 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. PMID: 17238458.
      View in: PubMed
    69. 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. PMID: 17238385.
      View in: PubMed
    70. 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. PMID: 15016385.
      View in: PubMed
    71. Yu H, Agichtein E. Extracting synonymous gene and protein terms from biological literature. Bioinformatics. 2003; 19 Suppl 1:i340-9. PMID: 12855479.
      View in: PubMed
    72. 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. PMID: 12968781.
      View in: PubMed
    73. 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. PMID: 11971887.
      View in: PubMed
    74. 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. PMID: 12463959.
      View in: PubMed
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