Prof. Kei-Hoi Cheung

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Yale University
School of Medicine
Yale Center for Medical Informatics
Associate ProfessorAppointed: 2006
Professional Headshot of Kei-Hoi Cheung

Mailing Address

300 George Street
Suite 501
New Haven, Connecticut 06511
United States

Contact Information

Phone: (203) 737-5783
Fax: (203) 737-5708
kei.cheung@yale.edu

Qualifications

Ph.D., University of Connecticut, Computer Science and Engineering, 1998.
M.S., University of Connecticut, Computer Science and Engineering, 1990.
B.S., Southern Connecticut State University, Computer Science, 1987.

Expertise and Research Interests

My research expertise and interest are in the interoperation of bioinformatics databases and tools (e.g., gene/protein expression databases and tools).

Memberships

American Medical Informatics Association
Institute of Electrical and Electronics Engineers
International Society for Computational Biology
International Who's and Who's
Phi Kappa Phi
Sigma Xi, The Scientific Research Society
Society of Chinese Bioscientists in America

Publications

  • Cheung KH, Lim E, Samwald M, Chen H, Marenco L, Holford ME, Morse TM, Mutalik P, Shepherd GM, Miller PL (Jul 2009) Approaches to neuroscience data integration., Briefings in bioinformatics, 10 (4), 345-53 Abstract
  • Cheung KH, Prud'hommeaux E, Wang Y, Stephens S (Mar 2009) Semantic Web for Health Care and Life Sciences: a review of the state of the art., Briefings in bioinformatics, 10 (2), 111-3 Abstract
  • Zhang Z, Cheung KH, Townsend JP (Jan 2009) Bringing Web 2.0 to bioinformatics., Briefings in bioinformatics, 10 (1), 1-10 Abstract
  • Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB (Jan 2009) Pseudofam: the pseudogene families database., Nucleic acids research, 37 (Database issue), D738-43 Abstract
  • Holford ME, Rajeevan H, Zhao H, Kidd KK, Cheung KH (2009) Semantic web-based integration of cancer pathways and allele frequency data., Cancer informatics, 8, 19-30 Abstract
  • Samwald M, Lim E, Masiar P, Marenco L, Chen H, Morse T, Mutalik P, Shepherd G, Miller P, Cheung KH (2009) Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research., Studies in health technology and informatics, 150, 317-21 Abstract
  • Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A (2009) A journey to Semantic Web query federation in the life sciences., BMC bioinformatics, 10 Suppl 10, S10 Abstract
  • Cheung KH, Yip KY, Townsend JP, Scotch M (Oct 2008) HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0., Journal of biomedical informatics, 41 (5), 694-705 Abstract
  • Cheung KH, Kashyap V, Luciano JS, Chen H, Wang Y, Stephens S (Oct 2008) Semantic mashup of biomedical data., Journal of biomedical informatics, 41 (5), 683-6 Abstract
  • Bjornson RD, Carriero NJ, Colangelo C, Shifman M, Cheung KH, Miller PL, Williams K (Jan 2008) X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers., Journal of proteome research, 7 (1), 293-9 Abstract
  • Boulos MN, Scotch M, Cheung KH, Burden D (2008) Web GIS in practice VI: a demo playlist of geo-mashups for public health neogeographers., International journal of health geographics, 7, 38 Abstract
  • Scotch M, Yip KY, Cheung KH (2008) Development of grid-like applications for public health using Web 2.0 mashup techniques., Journal of the American Medical Informatics Association : JAMIA, 15 (6), 783-6 Abstract
  • Smith A, Cheung K, Krauthammer M, Schultz M, Gerstein M (Nov 2007) Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics., Bioinformatics (Oxford, England), 23 (22), 3073-9 Abstract
  • Shifman MA, Li Y, Colangelo CM, Stone KL, Wu TL, Cheung KH, Miller PL, Williams KR (Oct 2007) YPED: a web-accessible database system for protein expression analysis., Journal of proteome research, 6 (10), 4019-24 Abstract
  • Crasto CJ, Marenco LN, Liu N, Morse TM, Cheung KH, Lai PC, Bahl G, Masiar P, Lam HY, Lim E, Chen H, Nadkarni P, Migliore M, Miller PL, Shepherd GM (May 2007) SenseLab: new developments in disseminating neuroscience information., Briefings in bioinformatics, 8 (3), 150-62 Abstract
  • Smith AK, Cheung KH, Yip KY, Schultz M, Gerstein MK (2007) LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics., BMC bioinformatics, 8 Suppl 3, S5 Abstract
  • Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH (2007) Advancing translational research with the Semantic Web., BMC bioinformatics, 8 Suppl 3, S2 Abstract
  • Lam HY, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung KH (2007) AlzPharm: integration of neurodegeneration data using RDF., BMC bioinformatics, 8 Suppl 3, S4 Abstract
  • Christopher J.O. Baker, Kei-Hoi Cheung (2007) Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, Springer and Verlag, ISBN=0387484361
  • Yip KY, Qi P, Schultz M, Cheung DW, Cheung KH (2006) SemBiosphere: a semantic web approach to recommending microarray clustering services., Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 188-99 Abstract
  • Lam HY, Marenco L, Shepherd GM, Miller PL, Cheung KH (2006) Using web ontology language to integrate heterogeneous databases in the neurosciences., AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, 464-8 Abstract
  • Cheung KH, Yip KY, Smith A, Deknikker R, Masiar A, Gerstein M (Jun 2005) YeastHub: a semantic web use case for integrating data in the life sciences domain., Bioinformatics (Oxford, England), 21 Suppl 1, i85-96 Abstract
  • Rajeevan H, Cheung KH, Gadagkar R, Stein S, Soundararajan U, Kidd JR, Pakstis AJ, Miller PL, Kidd KK (2005) ALFRED: An Allele Frequency Database for Microevolutionary Studies., Evolutionary bioinformatics online, 1, 1-10 Abstract
  • Shifman MA, Sun K, Colangelo CM, Cheung KH, Miller P, Williams K (2005) YPED: a proteomics database for protein expression analysis., AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, 1111 Abstract
  • Kumar A, Seringhaus M, Biery MC, Sarnovsky RJ, Umansky L, Piccirillo S, Heidtman M, Cheung KH, Dobry CJ, Gerstein MB, Craig NL, Snyder M (Oct 2004) Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon., Genome research, 14 (10A), 1975-86 Abstract
  • Yip KY, Cheung DW, Ng MK, Cheung KH (Oct 2004) Identifying projected clusters from gene expression profiles., Journal of biomedical informatics, 37 (5), 345-57 Abstract
  • Osier MV, Zhao H, Cheung KH (Sep 2004) Handling multiple testing while interpreting microarrays with the Gene Ontology Database., BMC bioinformatics, 5, 124 Abstract
  • de Knikker R, Guo Y, Li JL, Kwan AK, Yip KY, Cheung DW, Cheung KH (Mar 2004) A web services choreography scenario for interoperating bioinformatics applications., BMC bioinformatics, 5, 25 Abstract
  • Cheung KH, de Knikker R, Guo Y, Zhong G, Hager J, Yip KY, Kwan AK, Li P, Cheung DW (2004) Biosphere: the interoperation of web services in microarray cluster analysis., Applied bioinformatics, 3 (4), 253-6 Abstract
  • Cheung KH, Hager J, Nelson K, White K, Li Y, Snyder M, Williams K, Miller P (2003) A dynamic approach to mapping coordinates between microplates and microarrays, Journal of Biomedical Informatics, 35, 306-12
  • Rajeevan H, Osier MV, Cheung KH, Deng H, Druskin L, Heinzen R, Kidd JR, Stein S, Pakstis AJ, Tosches NP, Yeh CC, Miller PL, Kidd KK (January 2003) ALFRED: The ALelle FREquency Database. Update, Nucleic Acids Research, 31 (1), 270-1
  • Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK (September 2002) ALFRED: An allele frequency database for anthropology, American Journal of Physical Anthropology, 119 (1), 77-83 Abstract
  • Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, Cheung KH, Miller P, Gerstein M, Roeder GS, Snyder M (March 2002) Subcellular localization of the yeast proteome, Genes and Development, 16 (6), 707-19 Abstract
  • Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M (January 2002) An integrated approach for finding overlooked genes in yeast, Nature Biotechnology, 20 (1), 58-63 Abstract
  • Kumar A, Cheung KH, Tosches N, Masiar P, Liu Y, Miller P, Snyder M (January 2002) The TRIPLES database: A community resource for yeast molecular biology, Nucleic Acids Research, 30 (1), 73-5
  • Cheung KH, White K, Hager J, Gerstein M, Reinke V, Nelson K, Masiar P, Srivastava R, Li Y, Li J, Zhao H, Li J, Allison DB, Snyder M, Miller P, Williams K (2002) YMD: A microarray database for large-scale gene expression analysis, Proceedings/Amia ... Annual Symposium. AMIA Symposium, 140-4 pages
  • Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK (Jan 2001) ALFRED: An allele frequency database for diverse populations and DNA polymorphisms--an update, Nucleic Acids Research, 29 (1), 317-9
  • Cheung KH, Liu Y, Kumar K, Snyder M, Gerstein M, Miller P (2001) An XML application for genomic data interoperation, IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE), 97-103 pages
  • Cheung KH, Deshpande AM, Tosches N, Nath S, Agrawal A, Miller P, Kumar A, Snyder M (2001) A metadata framework for interoperating heterogeneous genome data using XML, Proceedings/Amia ... Annual Symposium. AMIA Symposium, 110-4 pages
  • Miller PL, Brandt C, Cheung K, Mattie M, Nadkarni P, Shiffman RN (2000) The Yale Center for Medical Informatics: Clinical, neuro- and genomic informatics, M.d. Computing: Computers in Medical Practice, 17 (4), 29-32
  • Cheung KH, Kumar A, Snyder M, Miller P (May 2000) An integrated web interface for large-scale characterization of sequence data, Functional & Integrative Genomics, 1 (1), 70-5 Abstract
  • Kumar A, Cheung KH, Ross-Macdonald P, Coelho PS, Miller P, Snyder M (Jan 2000) TRIPLES: A database of gene function in Saccharomyces cerevisiae, Nucleic Acids Research, 28 (1), 81-4
  • Cheung KH, Osier MV, Kidd JR, Pakstis AJ, Miller PL, Kidd KK (Jan 2000) ALFRED: an allele frequency database for diverse populations and DNA polymorphisms, Nucleic Acids Research, 28 (1), 361-3 Abstract
  • Cheung KH, Shin DG (2000) A graph-based meta-data framework for interoperation between genome databases, IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE) 2000, 109-17 pages
  • Cheung KH, Miller P, Sherman A, Weston S, Stratmann E, Schultz M, Snyder M, Kumar A (2000) Graphically-enabled integration of bioinformatics tools allowing parallel execution, Proceedings/Amia ... Annual Symposium. AMIA Symposium, 141-5 pages
  • Cheung KH, Miller PL, Kidd JR, Kidd KK, Osier MV, Pakstis AJ (2000) ALFRED: A Web-accessible allele frequency database, Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing, 639-50 pages
  • Ross-Macdonald P, Coelho PS, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung KH, Sheehan A, Symoniatis D, Umansky L, Heidtman M, Nelson FK, Iwasaki H, Hager K, Gerstein M, Miller P, Roeder GS, Snyder M (November 1999) Large-scale analysis of the yeast genome by transposon tagging and gene disruption, Nature, 402 (6760), 413-8 Abstract
  • Cheung KH, Nadkarni PM, Shin DG (1998) A metadata approach to query interoperation between molecular biology databases, Bioinformatics (Oxford, England), 14 (6), 486-97
  • Cheung KH, Shin DG (1998) A simple model capable of expressing metadata for database interoperability, Proc. of the ISCA 13th International Conference, 182-5 pages
  • Cheung KH, Nadkarni P, Miller P, Shin DG (1998) Automatic query mapping among genomic databases: A pilot exploration, Proceedings/Amia ... Annual Symposium. AMIA Symposium, 942-6 pages
  • Cheung KH, Nadkarni P, Silverstein S, Kidd JR, Pakstis AJ, Miller P, Kidd KK (August 1996) PhenoDB: An integrated client/server database for linkage and population genetics, Computers and Biomedical Research, an International Journal, 29 (4), 327-37
  • Nadkarni P, Cheung KH, Castiglione C, Miller P, Kidd K (Summer 1996) DNA workbench: A database package to manage regional physical mapping, Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 3 (2), 319-29
  • Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Kidd JR, Cheung K, Bonne-Tamir B, Santachiara-Benerecetti AS, Moral P, Krings M (March 1996) Global patterns of linkage disequilibrium at the CD4 locus and modern human origins, Science, 271 (5254), 1380-7 Abstract
  • Nadkarni PM, Cheung KH (December 1995) SQLGEN: A framework for rapid client-server database application development, Computers and Biomedical Research, an International Journal, 28 (6), 479-99
  • Miller PL, Nadkarni PM, Kidd KK, Cheung K, Ward DC, Banks A, Bray-Ward P, Cupelli L, Herdman V, Marondel I, et al (1995) Internet-based support for bioscience research: A collaborative genome center for human chromosome 12, Journal of the American Medical Informatics Association : Jamia, 2 (6), 351-64
  • Sittig DF, Cheung KH, Berman L (December 1992) Fuzzy classification of hemodynamic trends and artifacts: Experiments with the heart rate, International Journal of Clinical Monitoring and Computing, 9 (4), 251-7
  • Sittig DF, Cheung KH (1992) A parallel implementation of a multi-state Kalman filtering algorithm to detect ECG arrhythmias, International Journal of Clinical Monitoring and Computing, 9 (1), 13-22 Abstract
  • Paton JA, Belanger A, Cheung KH, Grajek S, Branch KA, Ikeda N, Sette L, Miller PL, Fryer RK (1992) Online bibliographic information: integration into an emerging IAIMS environment, Proceedings/the ... Annual Symposium On Computer Application [sic] in Medical Care. Symposium On Computer Applications in Medical Care, 605-9 pages
  • Cheung KH, Fox MD (1989) Three-dimensional craniofacial reconstruction with electronic optical contouring, Proc. of Engineering in Medicine and Biology, 1655-6
  • Cheung KH, Fox MD (December 1988) Isoreflectance contours for medical imaging, IEEE Transactions On Biomedical Engineering, 35 (12), 1059-63 Abstract
  • Cheung KH, Shin DG, A framework designed to represent both data and metadata to enhance database interoperability, Proc.of the 3rd Biennial World Conf. On Integrated Design and Process Technology, 184-91 pages

Profile Details

Last Updated: 10/20/2009

COS Expertise ID #1034073
Reference this profile directly: http://myprofile.cos.com/keihoicheung