Skip to main content
SpringerLink
Log in

Translational Bioinformatics

  • Chapter
  • First Online:
Biomedical Informatics

Abstract

After reading this chapter, you should know the answers to these questions:

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 74.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    http://www.amia.org/applications-informatics/translational-bioinformatics (Accessed 30/11/2012).

  2. 2.

    http://aspe.hhs.gov/admnsimp/pl104191.htm (Accessed 30/11/2012).

  3. 3.

    http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?cfrpart=11 (Accessed 30/11/2012).

  4. 4.

    http://dictionary.reference.com/browse/genome (Accessed 30/11/2012).

  5. 5.

    AMIA is the American Medical Informatics Association, Bethesda, MD: http://www.amia.org

  6. 6.

    http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-06-002.html (Accessed 30/11/2012).

  7. 7.

    http://wiki.hl7.org/index.php?title=CG (Accessed 12/3/2012).

  8. 8.

    http://www.geneontology.org/GO.tools.shtml#alphabet (Accessed 12/3/2012).

  9. 9.

    http://humanparalogy.gs.washington.edu/structuralvariation/general/intro.html (Accessed 12/3/2012).

  10. 10.

    http://grants.nih.gov/grants/guide/notice-files/NOT-OD-07-088.html (Accessed 12/6/2012).

  11. 11.

    http://www.wellcome.ac.uk/ (Accessed 12/6/2012).

  12. 12.

    http://grants.nih.gov/grants/guide/notice-files/NOT-OD-07-088.html (Accessed 12/6/2012).

  13. 13.

    http://cancergenome.nih.gov/ (Accessed 12/6/2012).

  14. 14.

    https://www.wtccc.org.uk/index.shtml (Accessed 12/6/2012).

  15. 15.

    http://www.personalgenomes.org/ (Accessed 12/6/2012).

  16. 16.

    http://www.snpedia.com/index.php/SNPedia (Accessed 12/6/2012).

  17. 17.

    https://github.com/xwu/trait-o-matic/wiki (Accessed 12/19/2012).

  18. 18.

    http://www.jsonline.com/news/milwaukee/120091754.html (Accessed 12/21/12).

  19. 19.

    http://spittoon.23andme.com/2008/12/17/turning-research-participants-into-research-partners/ (Accessed 12/6/2012).

  20. 20.

    http://www.decode.com/research/ (Accessed 12/6/2012).

  21. 21.

    http://www.genomeweb.com/dxpgx/will-other-states-follow-ny-calif-taking-dtc-genetic-testing-firms (Accessed 12/6/2012).

  22. 22.

    https://www.23andme.com/health/BRCA-Cancer/ (Accessed 12/19/12).

References

  • Alecu, I., Bousquet, C., Mougin, F., & Jaulent, M. C. (2006). Mapping of the WHO-ART terminology on Snomed CT to improve grouping of related adverse drug reactions. Studies in Health Technology and Informatics, 124, 833–838.

    PubMed  Google Scholar 

  • Altman, R. B. (2007). PharmGKB: A logical home for knowledge relating genotype to drug response phenotype. Nature Genetics, 39, 426.

    PubMed  CAS  Google Scholar 

  • Altshuler, D. M., Durbin, R. M., & Genomes Project Consortium. (2010a). A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073.

    PubMed  Google Scholar 

  • Altshuler, D. M., Gibbs, R. A., Peltonen, L., et al. (2010b). Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52–58.

    PubMed  CAS  Google Scholar 

  • Angrist, M. (2010). Here is a human being: At the dawn of personal genomics. New York: Harper.

    Google Scholar 

  • Aronson, A.R. (2001). Effective mapping of biomedical text to the UMLS metathesaurus: the MetaMap program. Proceedings of AMIA Symposium, 17–21.

    Google Scholar 

  • Aronson, A. R., & Lang, F. M. (2010). An overview of MetaMap: Historical perspective and recent advances. Journal of the American Medical Informatics Association: JAMIA, 17, 229–236.

    PubMed  Google Scholar 

  • Aronson, A.R., Mork, J.G., Neveol, V., Shooshan, S.E., & Demner-Fushman, D. (2008). Methodology for creating UMLS content views appropriate for biomedical natural language processing. AMIA Annual Symposium Proceedings, 21–25.

    Google Scholar 

  • Ashburner, M., Ball, C. A., Blake, J. A., et al. (2000). Gene ontology: Tool for the unification of biology. The gene ontology consortium. Nature Genetics, 25, 25–29.

    PubMed  CAS  Google Scholar 

  • Ashley, E. A., Butte, A. J., Wheeler, M. T., et al. (2010). Clinical assessment incorporating a personal genome. The Lancet, 375, 1525–1535.

    CAS  Google Scholar 

  • Atkinson, A. J., Colburn, W. A., DeGruttola, V. G., et al. (2001). Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework*. Clinical Pharmacology and Therapeutics, 69, 89–95.

    Google Scholar 

  • Barabasi, A. L., Gulbahce, N., & Loscalzo, J. (2011). Network medicine: A network-based approach to human disease. Nature Reviews Genetics, 12, 56–68.

    PubMed  CAS  Google Scholar 

  • Becker, K. G., Barnes, K. C., Bright, T. J., & Wang, S. A. (2004). The genetic association database. Nature Genetics, 36, 431–432.

    PubMed  CAS  Google Scholar 

  • Bodenreider, O. (2004). The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Research, 32, D267–D270.

    PubMed  CAS  Google Scholar 

  • Bradley, W. G., Golding, S. G., Herold, C. J., et al. (2011, August 27–29). Globalization of P4 medicine: Predictive, personalized, preemptive, and participatory–summary of the proceedings of the Eighth International Symposium of the International Society for Strategic Studies in Radiology. Radiology, 258, 571–582.

    Google Scholar 

  • Brinkman, R. R., Courtot, M., Derom, D., et al. (2010). Modeling biomedical experimental processes with OBI. Journal of Biomedical Semantics, 1(Suppl 1), S7.

    PubMed  Google Scholar 

  • Brown, E. G., Wood, L., & Wood, S. (1999). The medical dictionary for regulatory activities (MedDRA). Drug Safety, 20, 109–117.

    PubMed  CAS  Google Scholar 

  • Bruls, T., & Weissenbach, J. (2011). The human metagenome: Our other genome? Human Molecular Genetics, 20(R2), R142–R148.

    PubMed  CAS  Google Scholar 

  • Butte, A. J. (2008a). Medicine. The ultimate model organism. Science, 320(5874), 325–327.

    PubMed  CAS  Google Scholar 

  • Butte, A. J. (2008b). Translational bioinformatics: Coming of age. Journal of the American Medical Informatics Association: JAMIA, 15, 709–714.

    PubMed  Google Scholar 

  • Butte, A. (2009). Bioinformatic and computational analysis for genomic medicine. In G. S. Ginsburg & H. F. Willard (Eds.), Essentials of genomic and personalized medicine. Burlington: Elsevier.

    Google Scholar 

  • Butte, A.J., & Chen, R. (2006). Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. AMIA Annual Symposium Proceedings, 106–110.

    Google Scholar 

  • Camon, E., Magrane, M., Barrell, D., et al. (2003). The gene ontology annotation (GOA) project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Research, 13, 662–672.

    PubMed  CAS  Google Scholar 

  • Campillos, M., Kuhn, M., Gavin, A. C., et al. (2008). Drug target identification using side-effect similarity. Science, 321, 263–266.

    PubMed  CAS  Google Scholar 

  • Cedar, H. (1988). DNA methylation and gene activity. Cell, 53, 3–4.

    PubMed  CAS  Google Scholar 

  • Chan, I. S., & Ginsburg, G. S. (2011). Personalized medicine: Progress and promise. Annual Review of Genomics and Human Genetics, 12, 217–244.

    PubMed  CAS  Google Scholar 

  • Chan, E. Y., Qian, W. J., Diamond, D. L., et al. (2007). Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: Dysregulated cell cycle progression and nuclear transport coincide with robust virus production. Journal of Virology, 81, 7571–7583.

    PubMed  CAS  Google Scholar 

  • Choi, M., Scholl, U. I., Ji, W., et al. (2009). Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Sciences of the United States of America, 106, 19096–19101.

    PubMed  CAS  Google Scholar 

  • Church, G., Heeney, C., Hawkins, N., et al. (2009). Public access to genome-wide data: Five views on balancing research with privacy and protection. PLoS Genetics, 5, e1000665.

    PubMed  Google Scholar 

  • Cirulli, E. T., & Goldstein, D. B. (2010). Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nature Reviews Genetics, 11, 415–425.

    PubMed  CAS  Google Scholar 

  • Cook-Deegan, R. (2012). Personal communication.

    Google Scholar 

  • Coulet, A., Shah, N. H., Garten, Y., et al. (2010). Using text to build semantic networks for pharmacogenomics. Journal of Biomedical Informatics, 43, 1009–1019.

    PubMed  CAS  Google Scholar 

  • Crick, F. (1970). Central dogma of molecular biology. Nature, 227, 561–563.

    PubMed  CAS  Google Scholar 

  • Davies, K. (2008). Keeping score of your sequence. BioIT World, 7, 16–21.

    Google Scholar 

  • Denny, J. C., Ritchie, M. D., Basford, M. A., et al. (2010). PheWAS: Demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics, 26, 1205–1210.

    PubMed  CAS  Google Scholar 

  • Dewey, F. E., Chen, R., Cordero, S. P., et al. (2011). Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genetics, 7, e1002280.

    PubMed  CAS  Google Scholar 

  • Donley, G., Hull, S. C., & Berkman, B. E. (2012). Prenatal whole genome sequencing. The Hastings Center Report, 42, 28–40.

    PubMed  Google Scholar 

  • Du, X., Callister, S. J., Manes, N. P., et al. (2008). A computational strategy to analyze label-free temporal bottom-up proteomics data. Journal of Proteome Research, 7, 2595–2604.

    PubMed  CAS  Google Scholar 

  • Dunham, I., Kundaje, A., Aldred, S. F., et al. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57–74.

    PubMed  CAS  Google Scholar 

  • Edgar, R., Domrachev, M., & Lash, A. E. (2002). Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Research, 30, 207–210.

    PubMed  CAS  Google Scholar 

  • Frueh, F. W., & Gurwitz, D. (2004). From pharmacogenetics to personalized medicine: A vital need for educating health professionals and the community. Pharmacogenomics, 5, 571–579.

    PubMed  Google Scholar 

  • Gamazon, E. R., Huang, R. S., Cox, N. J., & Dolan, M. E. (2010). Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Proceedings of the National Academy of Sciences of the United States of America, 107, 9287–9292.

    PubMed  CAS  Google Scholar 

  • Garten, Y., & Altman, R. B. (2009). Pharmspresso: A text mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics, 10(Suppl 2), S6.

    PubMed  Google Scholar 

  • Garten, Y., Coulet, A., & Altman, R. B. (2010). Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics, 11, 1467–1489.

    PubMed  Google Scholar 

  • Ge, D., Ruzzo, E. K., Shianna, K. V., et al. (2011). SVA: Software for annotating and visualizing sequenced human genomes. Bioinformatics, 27, 1998–2000.

    PubMed  CAS  Google Scholar 

  • Ghazvinian, A., Noy, N. F., & Musen, M. A. (2009). Creating mappings for ontologies in biomedicine: Simple methods work. AMIA Annual Symposium Proceedings, 2009, 198–202.

    PubMed  Google Scholar 

  • Ghazvinian, A., Noy, N. F., & Musen, M. A. (2011). How orthogonal are the OBO foundry ontologies? Journal of Biomedical Semantics, 2(Suppl 2), S2.

    PubMed  Google Scholar 

  • Ginsburg, G. S., & Willard, H. F. (2009). Genomic and personalized medicine: Foundations and applications. Translational Research, 154, 277–287.

    PubMed  Google Scholar 

  • Goetz, T. (2010). Sergey Brin’s search for a Parkinson’s cure. Wired, June 22

    Google Scholar 

  • Goh, K. I., Cusick, M. E., Valle, D., et al. (2007). The human disease network. Proceedings of the National Academy of Sciences of the United States of America, 104, 8685–8690.

    PubMed  CAS  Google Scholar 

  • Green, R. C., Roberts, J. S., Cupples, L. A., et al. (2009). Disclosure of APOE genotype for risk of Alzheimer’s disease. The New England Journal of Medicine, 361, 245–254.

    PubMed  CAS  Google Scholar 

  • Gregory, S. (2011). Personal communication.

    Google Scholar 

  • Hansen, N. T., Brunak, S., & Altman, R. B. (2009). Generating genome-scale candidate gene lists for pharmacogenomics. Clinical Pharmacology and Therapeutics, 86, 183–189.

    PubMed  CAS  Google Scholar 

  • Heikamp, K., & Bajorath, J. (2011). Large-scale similarity search profiling of ChEMBL compound data sets. Journal of Chemical Information and Modeling, 51, 1831–1839.

    PubMed  CAS  Google Scholar 

  • Hoffman, M. A. (2007). The genome-enabled electronic medical record. Journal of Biomedical Informatics, 40, 44–46.

    PubMed  CAS  Google Scholar 

  • Homerova, D., Sprusansky, O., Kutejova, E., & Kormanec, J. (2002). Some features of DNA-binding proteins involved in the regulation of the Streptomyces aureofaciens gap gene, encoding glyceraldehyde-3-phosphate dehydrogenase. Folia Microbiologica (Praha), 47, 311–317.

    CAS  Google Scholar 

  • Hood, L., & Friend, S. H. (2011). Predictive, personalized, preventive, participatory (P4) cancer medicine. Nature Reviews. Clinical Oncology, 8, 184–187.

    PubMed  Google Scholar 

  • Hsi-Yang Fritz, M., Leinonen, R., Cochrane, G., & Birney, E. (2011). Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Research, 21, 734–740.

    PubMed  Google Scholar 

  • Hudson, K. L., Holohan, M. K., & Collins, F. S. (2008). Keeping pace with the times–the Genetic Information Nondiscrimination Act of 2008. The New England Journal of Medicine, 358, 2661–2663.

    PubMed  CAS  Google Scholar 

  • Imai, K., Kricka, L. J., & Fortina, P. (2011). Concordance study of 3 direct-to-consumer genetic-testing services. Clinical Chemistry, 57(3), 518–521.

    PubMed  CAS  Google Scholar 

  • Irwin, J. J., & Shoichet, B. K. (2005). ZINC–a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45, 177–182.

    PubMed  CAS  Google Scholar 

  • Jonquet, C., Musen, M. A., & Shah, N. H. (2010). Building a biomedical ontology recommender web service. Journal of Biomedical Semantics, 1(Suppl 1), S1.

    PubMed  Google Scholar 

  • Jonquet, C., LePendu, P., Falconer, S., Coulet, A., Noy, N. F., Musen, M. A., & Shah, N. H. (2011). NCBO resource index: Ontology-based search and mining of biomedical resources. Journal of Web Semantics: Science, Services and Agents on the World Wide Web, 9(3), 316–324.

    Google Scholar 

  • Joshi-Tope, G., Gillespie, M., Vastrik, I., et al. (2005). Reactome: A knowledgebase of biological pathways. Nucleic Acids Research, 33, D428–D432.

    PubMed  CAS  Google Scholar 

  • Kang, M. J., Lee, C. G., Cho, S. J., et al. (2006). IFN-gamma-dependent DNA injury and/or apoptosis are critical in cigarette smoke-induced murine emphysema. Proceedings of the American Thoracic Society, 3, 517–518.

    PubMed  Google Scholar 

  • Keiser, M. J., Setola, V., Irwin, J. J., et al. (2009). Predicting new molecular targets for known drugs. Nature, 462, 175–181.

    PubMed  CAS  Google Scholar 

  • Khatri, P., & Draghici, S. (2005). Ontological analysis of gene expression data: Current tools, limitations, and open problems. Bioinformatics, 21, 3587–3595.

    PubMed  CAS  Google Scholar 

  • Kho, A. N., Pacheco, J. A., Peissig, P. L., et al. (2011). Electronic medical records for genetic research: Results of the eMERGE consortium. Science Translational Medicine, 3, 79re71.

    Google Scholar 

  • Kinnings, S. L., Liu, N., Buchmeier, N., et al. (2009). Drug discovery using chemical systems biology: Repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Computational Biology, 5, e1000423.

    PubMed  Google Scholar 

  • Knox, C., Law, V., Jewison, T., et al. (2011). DrugBank 3.0: A comprehensive resource for ‘omics’ research on drugs. Nucleic Acids Research, 39, D1035–D1041.

    PubMed  CAS  Google Scholar 

  • Kraus, V. B., Burnett, B., Coindreau, J., et al. (2011). Application of biomarkers in the development of drugs intended for the treatment of osteoarthritis. Osteoarthritis and Cartilage, 19, 515–542.

    PubMed  CAS  Google Scholar 

  • Kuhn, M., Campillos, M., Letunic, I., Jensen, L. J., & Bork, P. (2010). A side effect resource to capture phenotypic effects of drugs. Molecular Systems Biology, 6, 343.

    PubMed  Google Scholar 

  • Lamb, J. (2007). The connectivity map: A new tool for biomedical research. Nature Reviews Cancer, 7(1), 54–60.

    PubMed  CAS  Google Scholar 

  • Lamb, J., Crawford, E. D., Peck, D., et al. (2006). The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease. Science, 313, 1929–1935.

    PubMed  CAS  Google Scholar 

  • Lander, E. S., Linton, L. M., Birren, B., et al. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860–921.

    PubMed  CAS  Google Scholar 

  • Landrigan, P. J., Trasande, L., Thorpe, L. E., et al. (2006). The National Children’s Study: A 21-year prospective study of 100,000 American children. Pediatrics, 118, 2173–2186.

    PubMed  Google Scholar 

  • Lenfant, C. (2003). Shattuck lecture – clinical research to clinical practice – lost in translation? The New England Journal of Medicine, 349, 868–874.

    PubMed  Google Scholar 

  • Lependu, P., Musen, M. A., & Shah, N. H. (2011a). Enabling enrichment analysis with the human disease ontology. Journal of Biomedical Informatics, 44(Suppl 1), S31–S38.

    PubMed  Google Scholar 

  • LePendu, P., Racunas, S,A., Iyer, S., et al. (2011b). Annotation analysis for testing drug safety signals. The 14th Bio-Ontologies SIG meeting at ISMB 2011, Vienna, Austria.

    Google Scholar 

  • Lindhurst, M. J., Sapp, J. C., Teer, J. K., et al. (2011). A mosaic activating mutation in AKT1 associated with the Proteus syndrome. The New England Journal of Medicine, 365(7), 611–619.

    PubMed  CAS  Google Scholar 

  • Liu, T., Lin, Y., Wen, X., Jorissen, R. N., & Gilson, M. K. (2007). BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Research, 35, D198–D201.

    PubMed  CAS  Google Scholar 

  • Lunshof, J. E., Bobe, J., Aach, J., et al. (2010). Personal genomes in progress: From the human genome project to the personal genome project. Dialogues in Clinical Neuroscience, 12, 47–60.

    PubMed  Google Scholar 

  • Mailman, M. D., Feolo, M., Jin, Y., et al. (2007). The NCBI dbGaP database of genotypes and phenotypes. Nature Genetics, 39, 1181–1186.

    PubMed  CAS  Google Scholar 

  • Manolio, T. A., Collins, F. S., Cox, N. J., et al. (2009). Finding the missing heritability of complex diseases. Nature, 461, 747–753.

    PubMed  CAS  Google Scholar 

  • Meckley, L. M., & Neumann, P. J. (2010). Personalized medicine: Factors influencing reimbursement. Health Policy, 94, 91–100.

    PubMed  Google Scholar 

  • Miller, G. C., & Britt, H. (1995). A new drug classification for computer systems: The ATC extension code. International Journal of Bio-Medical Computing, 40, 121–124.

    PubMed  CAS  Google Scholar 

  • Mork, J. G., Bodenreider, O., Demner-Fushman, D., et al. (2010). Extracting Rx information from clinical narrative. Journal of the American Medical Informatics Association: JAMIA, 17, 536–539.

    PubMed  Google Scholar 

  • Mort, M., Evani, U. S., Krishnan, V. G., et al. (2010). In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Human Mutation, 31, 335–346.

    PubMed  Google Scholar 

  • Musen, M. A., Noy, N. F., Shah, N. H., et al. (2011). The national center for biomedical ontology. Journal of the American Medical Informatics Association: JAMIA, 18(4), 441–448.

    Google Scholar 

  • Ng, S. B., Buckingham, K. J., Lee, C., et al. (2010). Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics, 42, 30–35.

    PubMed  CAS  Google Scholar 

  • Nicolae, D. L., Gamazon, E., Zhang, W., et al. (2010). Trait-associated SNPs are more likely to be eQTLs: Annotation to enhance discovery from GWAS. PLoS Genetics, 6, e1000888.

    PubMed  Google Scholar 

  • Novack, D. H., Plumer, R., Smith, R. L., et al. (1979). Changes in physicians’ attitudes toward telling the cancer patient. JAMA: The Journal of the American Medical Association, 241, 897–900.

    CAS  Google Scholar 

  • Obeid, J., Gabriel, D., & Sanderson, I. (2010). A biomedical research permissions ontology: Cognitive and knowledge representation considerations. In Proceedings of the 2010 workshop on Governance of Technology, Information and Policies (pp. 9–13). Austin: ACM.

    Google Scholar 

  • Olson, S. (2007, July/August). Who’s your daddy? The Atlantic.

    Google Scholar 

  • Ormond, K. E., Wheeler, M. T., Hudgins, L., et al. (2010). Challenges in the clinical application of whole-genome sequencing. Lancet, 375, 1749–1751.

    PubMed  Google Scholar 

  • Overington, J. (2009). ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr. Journal of Computer-Aided Molecular Design, 23, 195–198.

    PubMed  Google Scholar 

  • Parrish, F., Do, N., Bouhaddou, O., & Warnekar, P. (2006). Implementation of RxNorm as a terminology mediation standard for exchanging pharmacy medication between federal agencies. AMIA Annual Symposium Proceedings, 1057.

    Google Scholar 

  • Pencina, M. J., D’Agostino, R. B., Sr., D’Agostino, R. B., Jr., & Vasan, R. S. (2008). Evaluating the added predictive ability of a new marker: From area under the ROC curve to reclassification and beyond. Statistics in Medicine, 27, 157–172; discussion 207–112.

    PubMed  Google Scholar 

  • Pollack, A. (2011, July 29). Ruling upholds gene patent in cancer test. The New York Times. New York City: The New York Times Company.

    Google Scholar 

  • Quake, S. (2011). Personal communication.

    Google Scholar 

  • Rhee, S. Y., Wood, V., Dolinski, K., & Draghici, S. (2008). Use and misuse of the gene ontology annotations. Nature Reviews Genetics, 9, 509–515.

    PubMed  CAS  Google Scholar 

  • Ritchie, M. D., Denny, J. C., Crawford, D. C., et al. (2010). Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. American Journal of Human Genetics, 86, 560–572.

    PubMed  CAS  Google Scholar 

  • Rocca-Serra, P., Brandizi, M., Maguire, E., et al. (2010). ISA software suite: Supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics, 26, 2354–2356.

    PubMed  CAS  Google Scholar 

  • Ross, D. T., Scherf, U., Eisen, M. B., et al. (2000). Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics, 24, 227–235.

    PubMed  CAS  Google Scholar 

  • Rusk, N. (2010). Expanding HapMap. Nature Methods, 7, 780–781.

    PubMed  CAS  Google Scholar 

  • Sarkar, I. N., Butte, A. J., Lussier, Y. A., et al. (2011a). Translational bioinformatics: Linking knowledge across biological and clinical realms. Journal of the American Medical Informatics Association: JAMIA, 18, 354–357.

    PubMed  Google Scholar 

  • Sarkar, U., Karter, A. J., Liu, J. Y., Adler, N. E., Nguyen, R., Lopez, A., et al. (2011b). Social disparities in internet patient portal use in diabetes: Evidence that the digital divide extends beyond access. Journal of the American Medical Informatics Association: JAMIA, 18(3), 318–321.

    PubMed  Google Scholar 

  • Saunders, C. J., Miller, N. A., Soden, S. E., et al. (2012). Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Science Translational Medicine, 4(154), 154ra135.

    PubMed  Google Scholar 

  • Schadt, E. E. (2012). The changing privacy landscape in the era of big data. Molecular Systems Biology, 8, 612.

    PubMed  Google Scholar 

  • Schaefer, C. F., Anthony, K., Krupa, S., et al. (2009). PID: The pathway interaction database. Nucleic Acids Research, 37, D674–D679.

    PubMed  CAS  Google Scholar 

  • Schwartz, D., & Collins, F. (2007). Medicine. Environmental biology and human disease. Science, 316, 695–696.

    PubMed  CAS  Google Scholar 

  • Seal, R. L., Gordon, S. M., Lush, M. J., et al. (2011). Genenames.org: The HGNC resources in 2011. Nucleic Acids Research, 39, D514–D519.

    PubMed  CAS  Google Scholar 

  • Shah, N. H., & Musen, M.A. (2008). UMLS-Query: a perl module for querying the UMLS. AMIA Annual Symposium Proceedings, 652–656.

    Google Scholar 

  • Shah, N. H., Rubin, D. L., Espinosa, I., et al. (2007). Annotation and query of tissue microarray data using the NCI thesaurus. BMC Bioinformatics, 8, 296.

    PubMed  Google Scholar 

  • Shah, N. H., Jonquet, C., Chiang, A. P., et al. (2009a). Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics, 10(Suppl 2), S1.

    PubMed  Google Scholar 

  • Shah, S. H., Crosslin, D.R., Nelson, S., et al. (2009b). Metabolomic profiles are associated with baseline insulin resistance and improvement in insulin resistance with weight loss in the WLM trial. Ciculation.

    Google Scholar 

  • Sherry, S. T., Ward, M. H., Kholodov, M., Baker, J., Phan, L., Smigielski, E. M., & Sirotkin, K. (2001). DbSNP: The NCBI database of genetic variation. Nucleic Acids Research, 29, 308–311.

    PubMed  CAS  Google Scholar 

  • Shortliffe, E. H., Califano, A., & Hunter, L. (2009). New JBI emphasis on translational bioinformatics. Journal of Biomedical Informatics, 42, 199–200.

    PubMed  Google Scholar 

  • Shuldiner, A. R., O’Connell, J. R., Bliden, K. P., et al. (2009). Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy. JAMA: The Journal of the American Medical Association, 302, 849–857.

    CAS  Google Scholar 

  • Singer, E. (2011). A family learns the secrets of its genomes. MIT Technology Review.

    Google Scholar 

  • Sirota, M., Dudley, J. T., Kim, J., et al. (2011). Discovery and preclinical validation of drug indications using compendia of public gene expression data. Science Translational Medicine, 3, 96ra77.

    PubMed  CAS  Google Scholar 

  • Sobradillo, P., Pozo, F., & Agusti, A. (2011). P4 medicine: The future around the corner. Archivos de Bronconeumología, 47, 35–40.

    PubMed  Google Scholar 

  • Spackman, K.A., Campbell, K.E., & Cote, R.A. (1997a). SNOMED RT: a reference terminology for health care. Proceedings of the AMIA Annual Fall Symposium, 640–644.

    Google Scholar 

  • Spackman, K. A., Campbell, K. E., et al. (1997b). SNOMED-RT: A reference terminology for health care. In D. R. Masys (Ed.), Proceedings, AMIA annual fall symposium (pp. 640–644). Philadelphia: Hanley and Belfus.

    Google Scholar 

  • Stein, L. D. (2010). The case for cloud computing in genome informatics. Genome Biology, 11, 207.

    PubMed  Google Scholar 

  • Stenson, P. D., Mort, M., Ball, E. V., et al. (2009). The human gene mutation database: 2008 update. Genome Medicine, 1, 13.

    PubMed  Google Scholar 

  • Steyerberg, E. W., Pencina, M. J., Lingsma, H. F., et al. (2011). Assessing the incremental value of diagnostic and prognostic markers: A review and illustration. European Journal of Clinical Investigation, 42(2), 216–228.

    PubMed  Google Scholar 

  • Subramanian, A., Tamayo, P., Mootha, V. K., et al. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America, 102, 15545–15550.

    PubMed  CAS  Google Scholar 

  • Sung, N. S., Crowley, W. F., Jr., Genel, M., et al. (2003). Central challenges facing the national clinical research enterprise. JAMA: The Journal of the American Medical Association, 289(10), 1278–1287.

    Google Scholar 

  • Tarczy-Hornoch, P., Markey, M. K., Smith, J. A., & Hiruki, T. (2007). Bio*medical informatics and genomic medicine: Research and training. Journal of Biomedical Informatics, 40, 1–4.

    Google Scholar 

  • Tatonetti, N. P., Fernald, G. H., & Altman, R. B. (2011a). A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. Journal of the American Medical Informatics Association: JAMIA, 19(1), 79–85.

    PubMed  Google Scholar 

  • Tatonetti, N. P., Denny, J. C., Murphy, S. N., et al. (2011b). Detecting drug interactions from adverse-event reports: Interaction between paroxetine and pravastatin increases blood glucose levels. Clinical Pharmacology and Therapeutics, 90, 133–142.

    PubMed  CAS  Google Scholar 

  • Taylor, C. F., Field, D., Sansone, S. A., Aerts, J., et al. (2008). Promoting coherent minimum reporting guidelines for biological and biomedical investigations: The MIBBI project. Nature Biotechnology, 26, 889–896.

    PubMed  CAS  Google Scholar 

  • Tenenbaum, J., James, A., & Paulyson-Nuñez, K. (2012). An altered treatment plan based on direct to consumer (DTC) genetic testing: Personalized medicine from the patient/pin-cushion perspective. Journal of Personalized Medicine, 2(4), 192–200.

    Google Scholar 

  • Thorisson, G. A., Smith, A. V., Krishnan, L., & Stein, L. D. (2005). The international HapMap project web site. Genome Research, 15, 1592–1593.

    PubMed  CAS  Google Scholar 

  • Trusheim, M. R., Berndt, E. R., & Douglas, F. L. (2007). Stratified medicine: Strategic and economic implications of combining drugs and clinical biomarkers. Nature Reviews Drug Discovery, 6, 287–293.

    PubMed  CAS  Google Scholar 

  • Venter, J. C., Adams, M. D., Myers, E. W., et al. (2001). The sequence of the human genome. Science, 291, 1304–1351.

    PubMed  CAS  Google Scholar 

  • Via, M., Gignoux, C., & Burchard, E. G. (2010). The 1000 genomes project: new opportunities for research and social challenges. Genome Medicine, 2, 3.

    PubMed  Google Scholar 

  • Wang, X., Hripcsak, G., Markatou, M., & Friedman, C. (2009a). Active computerized pharmacovigilance using natural language processing, statistics, and electronic health records: A feasibility study. Journal of the American Medical Informatics Association: JAMIA, 16(3), 328–337.

    PubMed  Google Scholar 

  • Wang, Y., Xiao, J., Suzek, T. O., et al. (2009b). PubChem: A public information system for analyzing bioactivities of small molecules. Nucleic Acids Research, 37, W623–W633.

    PubMed  CAS  Google Scholar 

  • Wang, Y., Bolton, E., Dracheva, S., Karapetyan, K., Shoemaker, B. A., Suzek, T. O., Wang, J., Xiao, J., Zhang, J., & Bryant, S. H. (2010). An overview of the PubChem BioAssay resource. Nucleic Acids Research, 38, D255–D266.

    PubMed  CAS  Google Scholar 

  • Waxman, A. B., Einarsson, O., Seres, T., et al. (1999). Targeted lung expression of interleukin-11 enhances murine tolerance of 100% oxygen and diminishes hyperoxia-induced DNA fragmentation. Chest, 116, 8S–9S.

    PubMed  CAS  Google Scholar 

  • Weston, A. D., & Hood, L. (2004). Systems biology, proteomics, and the future of health care: Toward predictive, preventative, and personalized medicine. Journal of Proteome Research, 3, 179–196.

    PubMed  CAS  Google Scholar 

  • Wishart, D. S. (2011). Advances in metabolite identification. Bioanalysis, 3, 1769–1782.

    PubMed  CAS  Google Scholar 

  • Worthey, E. A., Mayer, A. N., Syverson, G. D., et al. (2011). Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genetics in Medicine, 13(3), 255–262.

    PubMed  Google Scholar 

  • WTCCC. (2007). Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661–678.

    Google Scholar 

  • Yildirim, M. A., Goh, K. I., Cusick, M. E., et al. (2007). Drug-target network. Nature Biotechnology, 25, 1119–1126.

    PubMed  CAS  Google Scholar 

  • Zerhouni, E. A. (2006). Clinical research at a crossroads: The NIH roadmap. Journal of Investigative Medicine, 54, 171–173.

    PubMed  Google Scholar 

  • Zhu, J., Zhang, B., & Schadt, E. E. (2008). A systems biology approach to drug discovery. Advances in Genetics, 60, 603–635.

    PubMed  CAS  Google Scholar 

  • Zhu, Q., Ge, D., Maia, J. M., et al. (2011). A genome-wide comparison of the functional properties of rare and common genetic variants in humans. American Journal of Human Genetics, 88, 458–468.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Duke Translational Medicine Institute, Duke University, 2424 Erwin Rd, Durham, 27705, NC, USA

    Jessica D. Tenenbaum PhD

  2. Department of Medicine, Stanford University, 1265 Welch Road, X-229, Stanford, 94305, CA, USA

    Nigam H. Shah MBBS, PhD

  3. Departments of Bioengineering, Genetics and Medicine, Stanford University, Clark Center, 318 Campus Drive, S242, Stanford, 94305, CA, USA

    Russ B. Altman MD, PhD

Authors
  1. Jessica D. Tenenbaum PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nigam H. Shah MBBS, PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Russ B. Altman MD, PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jessica D. Tenenbaum PhD .

Editor information

Editors and Affiliations

  1. Departments of Biomedical Informatics at Columbia University and Arizona State University, New York, New York, USA

    Edward H. Shortliffe

  2. Bethesda, Maryland, USA

    James J. Cimino

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer-Verlag London

About this chapter

Cite this chapter

Tenenbaum, J.D., Shah, N.H., Altman, R.B. (2014). Translational Bioinformatics. In: Shortliffe, E., Cimino, J. (eds) Biomedical Informatics. Springer, London. https://doi.org/10.1007/978-1-4471-4474-8_25

Download citation

  • DOI: https://doi.org/10.1007/978-1-4471-4474-8_25

  • Published:

  • Publisher Name: Springer, London

  • Print ISBN: 978-1-4471-4473-1

  • Online ISBN: 978-1-4471-4474-8

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation