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Ed Refs 2010

This page collects literature related to bioinformatics education and training. Here are 2009-2011 articles.

    • Obom KM, Cummings PJ.
      Comparison of Online and Onsite Bioinformatics Instruction for a Fully Online Bioinformatics Master's Program.
      J Microbiol Biol Educ. 2009 Dec 17;8(1):22-7. PubMed abstract

    • Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter MC, De Las Rivas J, Phillip Judge D, van der Gool W, Brooksbank C.
      Bioinformatics training: a review of challenges, actions and support requirements.
      Brief Bioinform. 2010 Jun 18. PubMed abstract

    • Wright VA, Vaughan BW, Laurent T, Lopez R, Brooksbank C, Schneider MV.
      Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.
      Brief Bioinform. 2010 Jul 2. PubMed abstract

    • Yamashita G, Miller H, Goddard A, Norton C.
      A model for Bioinformatics training: the marine biological laboratory.
      Brief Bioinform. 2010 Jul 25. PubMed abstract

    • Cummings MP, Temple GG.
      Broader incorporation of bioinformatics in education: opportunities and challenges.
      Brief Bioinform. 2010 Aug 26. PubMed abstract

    • Buttigieg PL.
      Perspectives on presentation and pedagogy in aid of bioinformatics education.
      Brief Bioinform. 2010 Aug 19. PubMed abstract

    • Kulkarni-Kale U, Sawant S, Chavan V.
      Bioinformatics education in India.
      Brief Bioinform. 2010 Aug 12. PubMed abstract

    • Jungck JR, Donovan SS, Weisstein AE, Khiripet N, Everse SJ.
      Bioinformatics education dissemination with an evolutionary problem solving perspective.
      Brief Bioinform. 2010 Nov;11(6):570-81. PubMed abstract

    • Rother K, Rother M, Pleus A, Upmeier zu Belzen A.
      Multi-stage learning aids applied to hands-on software training.
      Brief Bioinform. 2010 Nov;11(6):582-6. PubMed abstract

    • Ditty JL, Kvaal CA, Goodner B, Freyermuth SK, Bailey C, Britton RA, Gordon SG, Heinhorst S, Reed K, Xu Z, Sanders-Lorenz ER, Axen S, Kim E, Johns M, Scott K, Kerfeld CA.
      Incorporating genomics and bioinformatics across the life sciences curriculum.
      PLoS Biol. 2010 Aug 10;8(8):e1000448. PubMed abstract

    • Brazas MD, Yamada JT, Ouellette BF.
      Providing web servers and training in Bioinformatics: 2010 update on the Bioinformatics Links Directory.
      Nucleic Acids Res. 2010 Jul;38(Web Server issue):W3-6. PubMed abstract

    • Sanderson K.
      Bioinformatics: Curation generation.
      Nature. 2011 Feb 10;470(7333):295-6. PubMed abstract

    • Kerfeld CA, Scott KM.
      Using BLAST to teach "E-value-tionary" concepts.
      PLoS Biol. 2011 Feb 1;9(2):e1001014. PubMed abstract

    • Fuselier L, Bougary A, Malott M.
      From trace evidence to bioinformatics: Putting bryophytes into molecular biology education.
      Biochem Mol Biol Educ. 2011 Jan;39(1):38-46. doi: 10.1002/bmb.20458 PubMed abstract

    • Zhang X.
      Exploring cystic fibrosis using bioinformatics tools: A module designed for the freshman biology course.
      Biochem Mol Biol Educ. 2011 Jan;39(1):17-20. doi: 10.1002/bmb.20460. PubMed abstract

    • Locatis C, Berner ES, Hammack G, Smith S, Maisiak R, Ackerman M.
      Communication and proximity effects on outcomes attributable to sense of presence in distance bioinformatics education.
      BMC Med Educ. 2011 Mar 14;11(1):10. PubMed abstract

    • Pennisi E.
      Paleogenetics. Computer Kid Makes Good
      Science. 2010 May 7;328(5979):683. PubMed abstract

    • Taneri B.
      Is there Room for Ethics within Bioinformatics Education?
      J Comput Biol. 2011 Jul;18(7):907-16. 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

    • Lewitter F, Bourne PE.
      Teaching bioinformatics at the secondary school level.
      PLoS Comput Biol. 2011 Oct;7(10):e1002242. PubMed abstract

    • Form D, Lewitter F.
      Ten simple rules for teaching bioinformatics at the high school level.
      PLoS Comput Biol. 2011 Oct;7(10):e1002243. PubMed abstract

    • Gallagher SR, Coon W, Donley K, Scott A, Goldberg DS.
      A first attempt to bring computational biology into advanced high school biology classrooms.
      PLoS Comput Biol. 2011 Oct;7(10):e1002244. PubMed abstract

    • Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JA, Tramontano A, Schneider MV.
      Ten simple rules for developing a short bioinformatics training course.
      PLoS Comput Biol. 2011 Oct;7(10):e1002245. PubMed abstract

    • Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C.
      Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
      Brief Bioinform. 2011 Nov 22. PubMed abstract

Maintained by Lynda Ellis and Kristian Rother


Education References

This page collects literature related to bioinformatics education and training. 2009-2011 articles have been archived.

Article Collections

  • PLOS Computational Biology Collection: Education
    Articles in this collection provide practical tutorials and background information on important computational methods used to investigate key biological questions as well as resources for training scientists at all stages of their careers.

  • PLOS Computational Biology Collection: Starting Early
    Articles in this collection are devoted to teaching bioinformatics in secondary schools.

  • PLOS Computational Biology Collection: Translational Bioinformatics
    'Translational Bioinformatics' is a collection of PLOS Computational Biology Education articles which reads as a "book" to be used as a reference or tutorial for a graduate level introductory course on the science of translational bioinformatics.

Individual Articles

  • Corpas M, Jimenez RC, Bongcam-Rudloff E, Budd A, Brazas MD, Fernandes PL, Gaeta B, van Gelder C, Korpelainen E, Lewitter F, McGrath A, MacLean D, Palagi PM, Rother K, Taylor J, Via A, Watson M, Schneider MV, Attwood TK.
    The GOBLET Training Portal: A Global Repository of Bioinformatics Training Materials, Courses and Trainers.
    Bioinformatics. 2014 Sep 4. PubMed abstract

  • Mihalas GI, Tudor A, Paralescu S, Andor M, Stoicu-Tivadar L.
    Teaching bioinformatics to engineers.
    Stud Health Technol Inform. 2014;205:828-32. PubMed abstract

  • Tastan Bishop O, Adebiyi EF, Alzohairy AM, Everett D, Ghedira K, Ghouila A, Kumuthini J, Mulder NJ, Panji S, Patterton HG.
    Bioinformatics Education-Perspectives and Challenges out of Africa.
    Brief Bioinform. 2014 Jul 2. PubMed abstract

  • Machanick P, Tastan Bishop O.
    How to establish a bioinformatics postgraduate degree programme--a case study from South Africa.
    Brief Bioinform. 2014 May 2. PubMed abstract

  • Toby I, Pope A.
    Bioinformatics tools available for K-12 students to engage in research.
    Aviat Space Environ Med. 2014 Apr;85(4):484-5. PubMed abstract

  • Brazas MD, Lewitter F, Schneider MV, van Gelder CW, Palagi PM.
    A quick guide to genomics and bioinformatics training for clinical and public audiences.
    PLoS Comput Biol. 2014 Apr 10;10(4):e1003510. PubMed abstract

  • Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV.
    Bioinformatics curriculum guidelines: toward a definition of core competencies.
    PLoS Comput Biol. 2014 Mar 6;10(3):e1003496. PubMed abstract

  • Ramdayal K, Stobbe MD, Mishra T, Michaut M.
    Building the Future of Bioinformatics through Student-Facilitated Conferencing.
    PLoS Comput Biol. 2014 Jan 30;10(1):e1003458. PubMed abstract

  • Marques I, Almeida P, Alves R, Dias MJ, Godinho A, Pereira-Leal JB.
    Bioinformatics projects supporting life-sciences learning in high schools.
    PLoS Comput Biol. 2014 Jan;10(1):e1003404. PubMed abstract

  • Shapiro C, Ayon C, Moberg-Parker J, Levis-Fitzgerald M, Sanders ER.
    Strategies for Using Peer-assisted Learning Effectively in an Undergraduate Bioinformatics Course.
    Biochem Mol Biol Educ. 2013 Jan;41(1):24-33. PubMed abstract

  • Brazas MD, Ouellette BF.
    Navigating the changing learning landscape: Perspective from bioinformatics.ca.
    Brief Bioinform. 2013 Mar 20. PubMed abstract

  • Carvalho BS, Rustici G.
    The challenges of delivering bioinformatics training in the analysis of high-throughput data.
    Brief Bioinform. 2013 Mar 29. PubMed abstract

  • de Ridder D, de Ridder J, Reinders MJ.
    Pattern recognition in bioinformatics.
    Brief Bioinform. 2013 Apr 4. PubMed abstract

  • Abeln S, Molenaar D, Feenstra KA, Hoefsloot HC, Teusink B, Heringa J.
    Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds.
    Brief Bioinform. 2013 Apr 19. PubMed abstract

  • Korcsmaros T, Dunai ZA, Vellai T, Csermely P.
    Teaching the bioinformatics of signaling networks: an integrated approach to facilitate multi-disciplinary learning.
    Brief Bioinform. 2013 May 2. PubMed abstract

  • Machluf Y, Yarden A.
    Integrating bioinformatics into senior high school: design principles and implications.
    Brief Bioinform. 2013 May 10. PubMed abstract

  • Orozco A, Morera J, Jiménez S, Boza R.
    A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America.
    Brief Bioinform. 2013 May 30. PubMed abstract

  • Wood L, Gebhardt P.
    Bioinformatics goes to school-new avenues for teaching contemporary biology.
    PLoS Comput Biol. 2013 Jun;9(6):e1003089. PubMed abstract

  • Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK.
    Best practices in bioinformatics training for life scientists.
    Brief Bioinform. 2013 Jun 25. PubMed abstract

  • Jungck JR, Weisstein AE.
    Mathematics and evolutionary biology make bioinformatics education comprehensible.
    Brief Bioinform. 2013 Jul 2. May 6;14(1):107-9. PubMed abstract

  • Ng W.
    Teaching Microbial Identification with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and Bioinformatics Tools.
    J Microbiol Biol Educ. 2013 May 6;14(1):103-6. PubMed abstract

  • May BJ.
    Engaging students in a bioinformatics activity to introduce gene structure and function.
    J Microbiol Biol Educ. 2013 May 6;14(1):107-9. PubMed abstract

  • Barker D, Ferrier DE, Holland PW, Mitchell JB, Plaisier H, Ritchie MG, Smart SD.
    4273pi: Bioinformatics education on low cost ARM hardware.
    BMC Bioinformatics. 2013 Aug 12;14(1):243. PubMed abstract

  • Kovarik DN, Patterson DG, Cohen C, Sanders EA, Peterson KA, Porter SG, Chowning JT.
    Bioinformatics education in high school: implications for promoting science, technology, engineering, and mathematics careers.
    CBE Life Sci Educ. 2013 Fall;12(3):441-59. PubMed abstract

  • Campbell CE, Nehm RH.
    A critical analysis of assessment quality in genomics and bioinformatics education research.
    CBE Life Sci Educ. 2013 Fall;12(3):530-41. PubMed abstract

  • Luo J.
    Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course.
    Brief Bioinform. 2013 Sep 5. PubMed abstract

  • Reisdorph N, Stearman R, Kechris K, Phang TL, Reisdorph R, Prenni J, Erle DJ, Coldren C, Schey K, Nesvizhskii A, Geraci M.
    Hands-on Workshops as An Effective Means of Learning Advanced Technologies Including Genomics, Proteomics and Bioinformatics.
    Genomics Proteomics Bioinformatics. 2013 Dec 5. pii: S1672-0229(13)00120-4. PubMed abstract

  • Fernandes P, Jain P, Moita C.
    Training experimental biologists in bioinformatics.
    Adv Bioinformatics. 2012;2012:672749. PubMed abstract

  • Wightman B, Hark AT.
    Integration of bioinformatics into an undergraduate biology curriculum and the impact on development of mathematical skills.
    Biochem Mol Biol Educ. 2012 Sep;40(5):310-9. PubMed abstract

  • Bagga PS.
    Development of an undergraduate bioinformatics degree program at a liberal arts college.
    Yale J Biol Med. 2012 Sep;85(3):309-21. PubMed abstract

  • Auerbach RK.
    Thriving in multidisciplinary research: advice for new bioinformatics students.
    Yale J Biol Med. 2012 Sep;85(3):323-9. PubMed abstract

  • Searls DB.
    Ten Simple Rules for Online Learning.
    PLoS Comput Biol. 2012 Sep;8(9):e1002631. PubMed abstract

  • Searls DB.
    An Online Bioinformatics Curriculum.
    PLoS Comput Biol. 2012 Sep;8(9):e1002632. PubMed abstract

  • Klein JR, Gulsvig T.
    Using Bioinformatics to Develop and Test Hypotheses: E. coli-Specific Virulence Determinants.
    J Microbiol Biol Educ. 2012 Dec 3;13(2):161-9. PubMed abstract

Maintained by Lynda Ellis and Kristian Rother

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


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

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    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

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    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

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    Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community.
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    Big Data Bioinformatics.
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    From the Phenotype to the Genotype via Bioinformatics.
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    Production and analytic bioinformatics for next-generation DNA sequencing.
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    Bioinformatics Challenges in Genome-Wide Association Studies (GWAS).
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  • Doyle MA, Li J, Doig K, Fellowes A, Wong SQ.
    Studying cancer genomics through next-generation DNA sequencing and bioinformatics.
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  • Passetti F, Jorge NA, Durham A.
    Using Bioinformatics Tools to Study the Role of microRNA in Cancer.
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    Bioinformatics approach to understanding interacting pathways in neuropsychiatric disorders.
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    Pathogen genome bioinformatics.
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    An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles.
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    Opportunities and challenges provided by cloud repositories for bioinformatics-enabled drug discovery.
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    We are all individuals… bioinformatics in the personalized medicine era.
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Links and references provided by Lynda Ellis


Curriculum Guidelines for Colleges & Universities

- Curriculum Task Force
The Curriculum Task Force of the ISCB Education Committee seeks to define curricular guidelines for those who train and educate bioinformaticians. Rapid advances in the life sciences and in related information technologies necessitate the ongoing refinement of bioinformatics educational programs in order to maintain their relevance. As the discipline of bioinformatics and computational biology expands and matures, it is important to characterize the elements that contribute to the success of professionals in this field. These individuals work in a wide variety of settings, including bioinformatics core facilities, biological and medical research laboratories, software development organizations, pharmaceutical and instrument development companies, and institutions that provide education, service, and training.
- Curriculum Guidelines


The development and application of bioinformatics core competencies to improve bioinformatics training and education. (2018) Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan S, Pauley M, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L.

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee) (2016), Welch, L., Brooksbank, C., Schwartz, R. et al,

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies. PLoS Comput Biol 10(3): e1003496. doi:10.1371/journal.pcbi.1003496. Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, et al. (2014) 

The Genome Analysis Center News, March 12, 2014.

Defining Guidelines for Bioinformatics Curricula, GenomeWeb Bioinform, March 21, 2014.

A Report of the Curriculum Task Force of the ISCB Education Committee. PLoS Comput Biol 8(6): e1002570. doi:10.1371/journal.pcbi.1002570. Welch LR, Schwartz R, Lewitter F (2012) 

Education Committee Blog to Seek Input for a Bioinformatics Curriculum ( Draft version 1.27.12 )

- Programs

Online learning programs

Degree and certificate programs


ISCB Education Committee

The Education Committee promotes worldwide education and training in computational biology by providing guidance and support for educational resources and community activities.


ISCB is a founding member of the Global Organisation of Bioinformatics Learning, Education and Training (GOBLET, mygoblet.org), which aims to coordinate worldwide bioinformatics training activities. GOBLET was established to provide a global, sustainable support and networking structure for bioinformatics educators and trainees, to facilitate capacity development in bioinformatics in all countries, and to develop standards and guidelines for bioinformatics education and training. GOBLET and the ISCB Education committee are working on a number of joint projects.

The ISCB Education Committee and GOBLET joined together in 2014 to form the ISCB Education COSI. A major goal of this Community of Special Interest is to foster a collaborative community in which bioscientists can share bioinformatics education and training resources and experiences, and facilitate the development of education programs, courses, curricula, etc., and teaching tools and methods.

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