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What is Bioinformatics?

What is BI2010

Bioinformatics generally applies computer science to solve biological problems. However, the field is interdisciplinary and constantly developing, so it is difficult to answer this question in one sentence.
Here are 2010-2011 articles on Bioinformatics. Earlier Archives are available.

Introductory links

General References

  • Searls DB.
    The roots of bioinformatics.
    PLoS Comput Biol. 2010 Jun 24;6(6):e1000809 PubMed abstract

  • Doolittle RF.
    The roots of bioinformatics in protein evolution.
    PLoS Comput Biol. 2010 Jul 29;6(7):e1000875. PubMed abstract

  • Hogeweg P.
    The roots of bioinformatics in theoretical biology.
    PLoS Comput Biol. 2011 Mar;7(3):e1002021. PubMed abstract

  • Attwood TK, Gisel A, Eriksson N-E, Bongcam-Rudloff, E.
    Concepts, historical milestones and the central place of bioinformatics in modern biology: a European perspective.
    In Bioinformatics - Trends and Methodologies, M.A.Mahdavi Ed., Intech Online Publishers, November 2011
    Intech Online Chapter

Selected Topics

  • Thorn CF, Klein TE, Altman RB.
    Pharmacogenomics and bioinformatics: PharmGKB.
    Pharmacogenomics. 2010 Apr;11(4):501-5. PubMed abstract

  • Tan TW, Tong JC, Khan AM, de Silva M, Lim KS, Ranganathan S.
    Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi).
    BMC Genomics. 2010 Dec 2;11 Suppl 4:S27. PubMed abstract

  • Afshari CA, Hamadeh HK, Bushel PR.
    The Evolution of Bioinformatics in Toxicology: Advancing Toxicogenomics.
    Toxicol Sci. 2010 Dec 22. PubMed abstract

  • Bertini I and Gavallaro G.
    Bioinformatics in bioinorganic chemistry
    Metallomics, 2010, DOI: 10.1039/b912156k PubMed abstract

  • Fu WJ, Stromberg AJ, Viele K, Carroll RJ, Wu G.
    Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology.
    J Nutr Biochem. 2010 Mar 15. PubMed abstract

  • Mochida K, Shinozaki K.
    Genomics and bioinformatics resources for crop improvement.
    Plant Cell Physiol. 2010 Mar 5. PubMed abstract

  • Menschaert G, Vandekerckhove TT, Baggerman G, Schoofs L, Luyten W, Van Criekinge W.
    Peptidomics coming of age: a review of contributions from a bioinformatics angle.
    J Proteome Res. 2010 May 7;9(5):2051-61. PubMed abstract

  • Giacomelli L, Covani U.
    Bioinformatics and data mining studies in oral genomics and proteomics: new trends and challenges.
    Open Dent J. 2010 Jul 16;4:67-71. PubMed abstract

  • Jacob RJ.
    Bioinformatics for LC-MS/MS-based proteomics.
    Methods Mol Biol. 2010;658:61-91. PubMed abstract

  • Demmer RT, Pavlidis P, Papapanou PN. (2010)
    Bioinformatics techniques in microarray research: applied microarray data analysis using R and SAS software.
    Methods Mol Biol. 2010;666:395-417. PubMed abstract

  • Loewe RP, Nelson PJ.
    Microarray bioinformatics.
    Methods Mol Biol. 2011;671:295-320. PubMed abstract

  • Chen C, Huang H, Wu CH.
    Protein bioinformatics databases and resources.
    Methods Mol Biol. 2011;694:3-24. PubMed abstract

  • Shankar R.
    The Bioinformatics of Next Generation Sequencing: A Meeting Report.
    J Mol Cell Biol. 2010 Sep 7. PubMed abstract

  • Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ.
    Translational bioinformatics in the cloud: an affordable alternative.
    Genome Med. 2010 Aug 6;2(8):51. PubMed abstract

  • Fuellen G, Adjaye J, de Grey A, Lepperdinger G, de Magalhães JP, Sühnel J, Wipat A.
    Bioinformatics in aging research: a workshop report.
    Rejuvenation Res. 2010 Dec;13(6):763-7. PubMed abstract

  • Che D, Liu Q, Rasheed K, Tao X.
    Decision tree and ensemble learning algorithms with their applications in bioinformatics.
    Adv Exp Med Biol. 2011;696:191-9. PubMed abstract

  • Buchan NS, Rajpal DK, Webster Y, Alatorre C, Gudivada RC, Zheng C, Sanseau P, Koehler J.
    The role of translational bioinformatics in drug discovery.
    Drug Discov Today. 2011 Mar 21. PubMed abstract

  • Teong Han C, Kwee Hong JT, Akma F, Shamsir MS.
    birgHPC: Creating Instant Computing Clusters for Bioinformatics and Molecular Dynamics.
    Bioinformatics. 2011 Mar 12. PubMed abstract

  • Barga R, Howe B, Beck D, Bowers S, Dobyns W, Haynes W, Higdon R, Howard C, Roth C, Stewart E, Welch D, Kolker E.
    Bioinformatics and data-intensive scientific discovery in the beginning of the 21st century.
    OMICS. 2011 Apr;15(4):199-201. PubMed abstract

  • Foster JM, Martens L.
    Bioinformatics challenges in the proteomic analysis of human plasma.
    Methods Mol Biol. 2011;728:333-47. PubMed abstract

  • Anagnostopoulos AK, Tsiliki G, Spyrou G, Tsangaris GT.
    Bioinformatics approaches in the discovery and understanding of reproduction-related biomarkers.
    Expert Rev Proteomics. 2011 Apr;8(2):187-95. PubMed abstract

  • Lindblom A, Robinson PN.
    Bioinformatics for human genetics: promises and challenges.
    Hum Mutat. 2011 May;32(5):495-500. doi: 10.1002/humu.21468. PubMed abstract

  • Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L.
    Translational bioinformatics: linking knowledge across biological and clinical realms.
    J Am Med Inform Assoc. 2011 May 10. PubMed abstract

  • Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB.
    Bioinformatics Challenges for Personalized Medicine.
    Bioinformatics. 2011 May 19. PubMed abstract

  • Martens L.
    Bioinformatics challenges in mass spectrometry-driven proteomics.
    Methods Mol Biol. 2011;753:359-71. PubMed abstract

  • Pavlopoulou A, Michalopoulos I.
    State-of-the-art bioinformatics protein structure prediction tools (Review).
    Int J Mol Med. 2011 May 23. doi: 10.3892/ijmm.2011.705. PubMed abstract

  • Altman RB, Miller KS.
    2010 Translational bioinformatics year in review.
    J Am Med Inform Assoc. 2011 Jul 1;18(4):358-66. PubMed abstract

  • Sirota M, Butte AJ.
    The role of bioinformatics in studying rheumatic and autoimmune disorders.
    Nat Rev Rheumatol. 2011 Jun 21. doi: 10.1038/nrrheum.2011.87. PubMed abstract

  • Khatri P, Sarwal MM, Butte AJ.
    Applications of Translational Bioinformatics in Transplantation.
    Clin Pharmacol Ther. 2011 Jun 29. doi: 10.1038/clpt.2011.120. PubMed abstract

  • Hemphill JC, Andrews P, De Georgia M
    Multimodal monitoring and neurocritical care bioinformatics.
    Nat Rev Neurol. 2011 Jul 12. doi: 10.1038/nrneurol.2011.101. PubMed abstract

  • Kawano S, Ono H, Takagi T, Bono H.
    Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV.
    Brief Bioinform. 2011 Jul 29. PubMed abstract

  • Atkin AL.
    Yeast bioinformatics and strain engineering resources.
    Methods Mol Biol. 2011;765:173-87. PubMed abstract

  • Bassel GW, Holdsworth MJ, Provart NJ.
    Seed bioinformatics.
    Methods Mol Biol. 2011;773:403-19. PubMed abstract

  • Blekherman G, Laubenbacher R, Cortes DF, Mendes P, Torti FM, Akman S, Torti SV, Shulaev V.
    Bioinformatics tools for cancer metabolomics.
    Metabolomics. 2011 Sep;7(3):329-343. Epub 2011 Jan 12. PubMed abstract

  • Martinez M.
    Plant protein-coding gene families: emerging bioinformatics approaches.
    Trends Plant Sci. 2011 Oct;16(10):558-67 PubMed abstract

  • Romano P, Giugno R, Pulvirenti A.
    Tools and collaborative environments for bioinformatics research.
    Brief Bioinform. 2011 Oct 7. PubMed abstract

  • Ahn S.
    Introduction to bioinformatics: sequencing technology.
    Asia Pac Allergy. 2011 Jul;1(2):93-7. PubMed abstract

  • Nugent T, Jones DT.
    Membrane protein structural bioinformatics.
    J Struct Biol. 2011 Oct 31. PubMed abstract

  • Milanowska K, Rother K, Bujnicki JM.
    Databases and bioinformatics tools for the study of DNA repair.
    Mol Biol Int. 2011;2011:475718. PubMed abstract

  • Mochida K, Shinozaki K.
    Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions.
    Plant Cell Physiol. 2011 Dec;52(12):2017-2038. PubMed abstract

  • Lee HC, Lai K, Lorenc MT, Imelfort M, Duran C, Edwards D.
    Bioinformatics tools and databases for analysis of next-generation sequence data.
    Brief Funct Genomics. 2011 Dec 19. PubMed abstract

  • Mushegian A.
    Grand challenges in bioinformatics and computational biology.
    Front Genet. 2011;2:60. Epub 2011 Sep 15. PubMed abstract

Links and references provided by Lynda Ellis

 

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