What is Bioinformatics?

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developing, so it is difficult to answer this question in one sentence. 2013,  2012 and 2010-2011 articles have been archived. Earlier Archives are available.

Introductory links

General References

Selected Topics

  • Dolled-Filhart MP, Lee M Jr, Ou-Yang CW, Haraksingh RR, Lin JC.
    Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing.
    ScientificWorldJournal. 2013;2013:730210. PubMed abstract

  • Carrico J, Sabat A, Friedrich A, Ramirez M; on behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM).
    Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution.
    Euro Surveill. 2013 Jan 24;18(4). PubMed abstract

  • Rossi S, Calin GA.
    Bioinformatics, Non-coding RNAs and Its Possible Application in Personalized Medicine.
    Adv Exp Med Biol. 2013;774:21-37. PubMed abstract

  • Góngora-Castillo E, Buell CR.
    Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence.
    Nat Prod Rep. 2013 Apr;30(4):490-500. PubMed abstract

  • Hong H, Zhang W, Shen J, Su Z, Ning B, Han T, Perkins R, Shi L, Tong W.
    Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine.
    Sci China Life Sci. 2013 Feb;56(2):110-8. PubMed abstract

  • Caccia D, Dugo M, Callari M, Ongarzone I.
    Bioinformatics tools for secretome analysis.
    Biochim Biophys Acta. 2013 Feb 5. pii: S1570-9639(13)00050-2. PubMed abstract

  • Gromiha MM, Ou YY.
    Bioinformatics approaches for functional annotation of membrane proteins.
    Brief Bioinform. 2013 Mar 23. PubMed abstract

  • Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Deinhardt K, Darie CC.
    Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches.
    Cell Mol Life Sci. 2013 Apr 12. PubMed abstract

  • Tsongalis GJ, Chao E, Hagenkord JM, Hambuch T, Moore JH.
    Bioinformatics: What the Clinical Laboratorian Needs to Know and Prepare For.
    Clin Chem. 2013 May 30. PubMed abstract

  • Li MW, Qi X, Ni M, Lam HM.
    Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research.
    Int J Mol Sci. 2013 May 29;14(6):11444-83. PubMed abstract

  • Moriconi F, Beard MR, Yuen LK.
    Bioinformatics methods for the analysis of hepatitis viruses.
    Antivir Ther. 2013;18(3 Pt B):531-9. PubMed abstract

  • Hassanien AE, Al-Shammari ET, Ghali NI.
    Computational intelligence techniques in bioinformatics.
    Comput Biol Chem. 2013 Jul 10;47C:37-47. PubMed abstract

  • Kouskoumvekaki I, Shublaq N, Brunak S.
    Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics.
    Brief Bioinform. 2013 Aug 1. PubMed abstract

  • Sun P, Ju H, Liu Z, Ning Q, Zhang J, Zhao X, Huang Y, Ma Z, Li Y.
    Bioinformatics resources and tools for conformational B-cell epitope prediction.
    Comput Math Methods Med. 2013;2013:943636. PubMed abstract

  • Sankar S, Nayanar SK, Balasubramanian S.
    Current trends in cancer vaccines - a bioinformatics perspective.
    Asian Pac J Cancer Prev. 2013;14(7):4041-7. PubMed abstract

  • Overby CL, Tarczy-Hornoch P.
    Personalized medicine: challenges and opportunities for translational bioinformatics.
    Per Med. 2013 Jul 1;10(5):453-462. PubMed abstract

  • Misra N, Panda PK, Parida BK.
    Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy.
    OMICS. 2013 Sep 17. PubMed abstract

  • Gu P, Chen H.
    Modern bioinformatics meets traditional Chinese medicine.
    Brief Bioinform. 2013 Sep 24. PubMed abstract

  • Choong YS, Tye GJ, Lim TS.
    Minireview: Applied Structural Bioinformatics in Proteomics.
    Protein J. 2013 Oct 6. PubMed abstract

  • Bencharit S, Border MB, Edelmann A, Byrd WC.
    Update in research and methods in proteomics and bioinformatics.
    Expert Rev Proteomics. 2013 Oct;10(5):413-415. PubMed abstract

  • Zhou S, Liao R, Guan J.
    When cloud computing meets bioinformatics: a review.
    J Bioinform Comput Biol. 2013 Oct;11(5):1330002. PubMed abstract

  • Naulaerts S, Meysman P, Bittremieux W, Vu TN, Vanden Berghe W, Goethals B, Laukens K.
    A primer to frequent itemset mining for bioinformatics.
    Brief Bioinform. 2013 Oct 26. PubMed abstract

  • Lopes RD, Resende NM, Honorio-França AC, França EL.
    Application of Bioinformatics in Chronobiology Research.
    ScientificWorldJournal. 2013 Sep 25;2013:153839. PubMed abstract

  • Huang X, Bruce B, Buchan A, Congdon CB, Cramer CL, Jennings SF, Jiang H, Li Z, McClure G, McMullen R, Moore JH, Nanduri B, Peckham J, Perkins A, Polson SW, Rekepalli B, Salem S, Specker J, Wunsch D, Xiong D, Zhang S, Zhao Z.
    No-boundary thinking in bioinformatics research.
    BioData Min. 2013 Nov 6;6(1):19. PubMed abstract

  • Suwa M.
    Bioinformatics Tools for Predicting GPCR Gene Functions.
    Adv Exp Med Biol. 2014;796:205-24. PubMed abstract

  • Allmer J.
    Computational and Bioinformatics Methods for MicroRNA Gene Prediction.
    Methods Mol Biol. 2014;1107:157-75. PubMed abstract

  • Mardis ER.
    Coming to grips with bioinformatics.
    Pathology. 2014 Feb;46 Suppl 1:S25. PubMed abstract

  • Ning L, Liu G, Li G, Hou Y, Tong Y, He J.
    Current Challenges in the Bioinformatics of Single Cell Genomics.
    Front Oncol. 2014 Jan 27;4:7. PubMed abstract

  • Marz M, Beerenwinkel N, Drosten C, Fricke M, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Töpfer A.
    Challenges in RNA Virus Bioinformatics.
    Bioinformatics. 2014 Mar 3. PubMed abstract

  • Chang CC, Tey BT, Song J, Ramanan RN.
    Towards more accurate prediction of protein folding rates: a review of the existing web-based bioinformatics approaches.
    Brief Bioinform. 2014 Mar 11. PubMed abstract

  • Ryu SY.
    Bioinformatics tools to identify and quantify proteins using mass spectrometry data.
    Adv Protein Chem Struct Biol. 2014;94:1-17. PubMed abstract

  • Jung S, Main D.
    Genomics and bioinformatics resources for translational science in Rosaceae.
    Plant Biotechnol Rep. 2014;8:49-64. PubMed abstract

  • Gorodkin J, Hofacker IL, Ruzzo WL.
    Concepts and introduction to RNA bioinformatics.
    Methods Mol Biol. 2014;1097:1-31. PubMed abstract

  • Tafer H.
    Bioinformatics of siRNA Design.
    Methods Mol Biol. 2014;1097:477-90. PubMed abstract

  • Tang H, Mayampurath A, Yu CY, Mechref Y.
    Bioinformatics protocols in glycomics and glycoproteomics.
    Curr Protoc Protein Sci. 2014 Apr 1;76:2.15.1-7. PubMed abstract

  • Acosta-Martin AE, Lane L.
    Combining bioinformatics and MS-based proteomics: clinical implications.
    Expert Rev Proteomics. 2014 Apr 10. PubMed abstract

  • Guffanti A, Simchovitz A, Soreq H.
    Emerging bioinformatics approaches for analysis of NGS-derived coding and non-coding RNAs in neurodegenerative diseases.
    Front Cell Neurosci. 2014 Mar 27;8:89. PubMed abstract

  • Li S, Kang L, Zhao XM.
    A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics.
    Biomed Res Int. 2014;2014:362738. Epub 2014 Mar 6. PubMed abstract

  • Backofen R, Amman F, Costa F, Findeiß S, Richter AS, Stadler PF.
    Bioinformatics of prokaryotic RNAs.
    RNA Biol. 2014 Apr 2;11(5). PubMed abstract

  • Vaudel M, Barsnes H, Martens L, Berven FS.
    Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community.
    Methods Mol Biol. 2014;1156:239-48. PubMed abstract

  • Greene CS, Tan J, Ung M, Moore JH, Cheng C.
    Big Data Bioinformatics.
    J Cell Physiol. 2014 May 6. PubMed abstract

  • Arora PK, Bae H.
    Integration of bioinformatics to biodegradation.
    Biol Proced Online. 2014 Apr 27;16:8. PubMed abstract

  • Willet CE, Wade CM.
    From the Phenotype to the Genotype via Bioinformatics.
    Methods Mol Biol. 2014;1168:1-16. PubMed abstract

  • Allcock RJ.
    Production and analytic bioinformatics for next-generation DNA sequencing.
    Methods Mol Biol. 2014;1168:17-29. PubMed abstract

  • De R, Bush WS, Moore JH.
    Bioinformatics Challenges in Genome-Wide Association Studies (GWAS).
    Methods Mol Biol. 2014;1168:63-81. PubMed abstract

  • Doyle MA, Li J, Doig K, Fellowes A, Wong SQ.
    Studying cancer genomics through next-generation DNA sequencing and bioinformatics.
    Methods Mol Biol. 2014;1168:83-98 PubMed abstract

  • Passetti F, Jorge NA, Durham A.
    Using Bioinformatics Tools to Study the Role of microRNA in Cancer.
    Methods Mol Biol. 2014;1168:99-116. PubMed abstract

  • Alawieh A, Sabra Z, Nokkari A, El-Assaad A, Mondello S, Zaraket F, Fadlallah B, Kobeissy FH.
    Bioinformatics approach to understanding interacting pathways in neuropsychiatric disorders.
    Methods Mol Biol. 2014;1168:157-72. PubMed abstract

  • Sintchenko V, Roper MP.
    Pathogen genome bioinformatics.
    Methods Mol Biol. 2014;1168:173-93. PubMed abstract

  • Petrey D, Honig B.
    Structural bioinformatics of the interactome.
    Annu Rev Biophys. 2014 May 6;43:193-210. PubMed abstract

  • Lagunin AA, Goel RK, Gawande DY, Pahwa P, Gloriozova TA, Dmitriev AV, Ivanov SM, Rudik AV, Konova VI, Pogodin PV, Druzhilovsky DS, Poroikov VV.
    Chemo- and bioinformatics resources for in silico drug discovery from medicinal plants beyond their traditional use: a critical review.
    Nat Prod Rep. 2014 Jul 22. PubMed abstract

  • Sudha G, Nussinov R, Srinivasan N.
    An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles.
    Prog Biophys Mol Biol. 2014 Jul 29. pii: S0079-6107(14)00066-2. PubMed abstract

  • Vincent AT, Charette SJ.
    Freedom in bioinformatics.
    Front Genet. 2014 Jul 31;5:259. PubMed abstract

  • Yan Q.
    Translational bioinformatics approaches for systems and dynamical medicine.
    Methods Mol Biol. 2014;1175:19-34. PubMed abstract

  • Smith DR.
    Buying in to bioinformatics: an introduction to commercial sequence analysis software.
    Brief Bioinform. 2014 Sep 1 PubMed abstract

  • Dalpé G, Joly Y.
    Opportunities and challenges provided by cloud repositories for bioinformatics-enabled drug discovery.
    Drug Dev Res. 2014 Sep;75(6):393-401. PubMed abstract

  • Van Neste L, Van Criekinge W.
    We are all individuals… bioinformatics in the personalized medicine era.
    Cell Oncol (Dordr). 2014 Sep 10. PubMed abstract

Links and references provided by Lynda Ellis