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Bioinformatics

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Biomedical Informatics

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Abstract

This chapter introduces bioinformatics and the impacts of data generated by advanced biotechnology applications. A brief introduction regarding the underlying biology of these technologies is described. The types of data being generated and how they are important clinically are introduced. An overview of notable methods that operate on those data types and their history is discussed. Finally, bioinformatic databases and resources are presented as well as modern approaches, leveraging the Internet, for making that data more useful, including the interoperability of data in large networked databases.

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Notes

  1. 1.

    7 https://www.nhlbiwgs.org/ (accessed December 1, 2018).

  2. 2.

    7 https://www.ncbi.nlm.nih.gov/clinvar/ (accessed November 1, 2018).

  3. 3.

    7 http://www.hgmd.org/ (accessed November 1, 2018).

  4. 4.

    7 http://www.pharmgkb.org/ (accessed November 1, 2018).

  5. 5.

    7 http://www.genome.gov/10002328 (accessed November 1, 2018).

  6. 6.

    7 http://www.personalgenomes.org/ (accessed November 1, 2018).

  7. 7.

    7 https://cser-consortium.org/ (accessed November 1, 2018).

  8. 8.

    If you are not familiar with the basic terminology of molecular biology and genetics, reference to an introductory textbook in the area would be helpful before you read the rest of this chapter.

  9. 9.

    7 <ExternalRef><RefSource>http://www.genome.gov/sequencingcosts/ (accessed November 1, 2018).

  10. 10.

    For more information see 7 http://www.rcsb.org/ (accessed November 1, 2018).

  11. 11.

    7 http://scop2.mrc-lmb.cam.ac.uk/ (accessed December 1, 2018).

  12. 12.

    7 http://en.wikipedia.org/wiki/DNA_sequencing (accessed November 1, 2018).

  13. 13.

    See 7 http://www.rcsb.org/ (accessed December 1, 2018).

  14. 14.

    7 http://www.ncbi.nlm.nih.gov/genbank/ (accessed December 1, 2018).

  15. 15.

    7 http://www.uniprot.org/ (accessed December 1, 2018).

  16. 16.

    7 http://www.ncbi.nlm.nih.gov/omim (accessed December 1, 2018).

  17. 17.

    7 http://www.ncbi.nlm.nih.gov/pubmed (accessed December 1, 2018).

  18. 18.

    7 https://pymol.org/ (accessed December 1, 2018).

  19. 19.

    7 http://www.cgl.ucsf.edu/chimera/ (accessed December 1, 2018).

  20. 20.

    7 http://predictioncenter.org/ (accessed December 1, 2018).

  21. 21.

    7 https://www.nature.com/articles/d41586-020-03348-4.

  22. 22.

    7 http://bioconductor.org/ (accessed December 1, 2018).

  23. 23.

    7 http://www.cs.waikato.ac.nz/ml/weka/ (accessed December 1, 2018).

  24. 24.

    7 http://en.wikipedia.org/wiki/Bonferroni_correction (accessed December 1, 2018).

  25. 25.

    7 https://www.ncbi.nlm.nih.gov/search/ (accessed December 7th, 2020).

  26. 26.

    7 http://bioconductor.org/ (accessed December 1, 2018).

  27. 27.

    7 http://www.ornl.gov/sci/techresources/Human_Genome/research/bermuda.shtml (accessed December 1, 2018).

  28. 28.

    7 http://edocket.access.gpo.gov/2009/E9-29322.htm (accessed December 1, 2018).

  29. 29.

    7 http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-032.html (accessed December 1, 2018).

  30. 30.

    7 https://fairsharing.org/ (accessed December 1, 2018).

  31. 31.

    7 https://datamed.org/ (accessed April 20, 2019).

  32. 32.

    7 http://www.open-bio.org/ (accessed December 1, 2018).

  33. 33.

    7 https://metadatacenter.org/ (accessed December 1, 2018).

  34. 34.

    7 http://genome.ucsc.edu/ (accessed December 1, 2018).

  35. 35.

    7 https://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/ (accessed December 15, 2018).

  36. 36.

    7 https://www.rcsb.org/ (accessed December 18, 2018).

  37. 37.

    7 http://scop2.mrc-lmb.cam.ac.uk/ (accessed December 15, 2018).

  38. 38.

    7 http://ecocyc.org/ (accessed December 15, 2018).

  39. 39.

    7 http://www.genome.jp/kegg/pathway.html (accessed December 1, 2018).

  40. 40.

    7 http://www.ncbi.nlm.nih.gov/omim/ (accessed December 1, 2018).

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Author information

Authors and Affiliations

  1. Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA

    Sean D. Mooney

  2. Department of Biostatistics & Bioinformatics, Duke University, Durham, NC, USA

    Jessica D. Tenenbaum

  3. Departments of Bioengineering, Genetics and Medicine, Stanford University, Stanford, CA, USA

    Russ B. Altman

Authors
  1. Sean D. Mooney
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  2. Jessica D. Tenenbaum
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  3. Russ B. Altman
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Corresponding author

Correspondence to Sean D. Mooney .

Editor information

Editors and Affiliations

  1. Biomedical Informatics, Columbia University, New York, NY, USA

    Edward H. Shortliffe

  2. Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA

    James J. Cimino

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Mooney, S.D., Tenenbaum, J.D., Altman, R.B. (2021). Bioinformatics. In: Shortliffe, E.H., Cimino, J.J. (eds) Biomedical Informatics. Springer, Cham. https://doi.org/10.1007/978-3-030-58721-5_9

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  • DOI: https://doi.org/10.1007/978-3-030-58721-5_9

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-58720-8

  • Online ISBN: 978-3-030-58721-5

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