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A Brief History of Bioinformatics Told by Data Visualization

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Advances in Bioinformatics and Computational Biology (BSB 2020)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 12558))

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Abstract

Bioinformatics is an interdisciplinary research field that aims to analyze biological data through computational approaches. In the last years, the evolution of technological resources has provided a tidal wave of biological data. Consequently, an unprecedented amount of studies using bioinformatics approaches have been released, increasing peer-reviewed published papers. Here, we tell a brief history of bioinformatics based on literature data analysis and visualization. We collected abstracts and other metadata from papers published from 1998 to 2019 in four leading bioinformatics journals: (i) Oxford Bioinformatics; (ii) BMC Bioinformatics; (iii) Briefings in Bioinformatics; and (iv) PLoS Computational Biology. Our results show an increase in publication number and international collaborations. We also observed an increase in publications by Chinese authors. Latin America continues to have a low percentage of global scientific bioinformatics production. However, Brazil excels in this region, being responsible for almost half of Latin America papers published. Our results also point out the recent trend of using Python as the programming language for bioinformatics applications, followed by Perl, Java, and R. We hope these data visualizations can provide insights to understand the recent changes and evolution in the bioinformatics field. The developed interactive visualizations are available at http://bioinfo.dcc.ufmg.br/history/.

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References

  1. Akalin, P.K.: Introduction to bioinformatics. Mol. Nutr. Food Res. 50, 610–619 (2006)

    Article  CAS  Google Scholar 

  2. Hagen, J.B.: The origins of bioinformatics. Nat. Rev. Genet. 1, 231–236 (2000)

    Article  CAS  Google Scholar 

  3. Moore, S., Spackman, D.H., Stein, W.H.: Automatic recording apparatus for use in the chromatography of amino acids, pp. 1107–1115 (1958)

    Google Scholar 

  4. Dayhoff, M.O.: Atlas of protein sequence and structure. National Biomedical Research Foundation (1972)

    Google Scholar 

  5. Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Molecular Biol. 48, 443–453 (1970)

    Article  CAS  Google Scholar 

  6. Levinthal, C.: Molecular model-building by computer. Sci. Am. 214, 42–52 (1966)

    Article  CAS  Google Scholar 

  7. Felsenstein, J.: Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376 (1981)

    Article  CAS  Google Scholar 

  8. Stephen, F., Altschu, P., Warren, G., Webb, M., Eugene, W., Myers, David, J.L.: Basic Local Alignment Search Tool (1990)

    Google Scholar 

  9. Sanger, F., Nicklen, S., Coulson, A.R.: DNA sequencing with chain-terminating inhibitors. Proc. National Acad. Sci. 74, 5463–5467 (1977)

    Article  CAS  Google Scholar 

  10. Staden, R.: A strategy of DNA sequencing employing computer programs. Nucleic Acids Res. 6, 2601–2610 (1979)

    Article  CAS  Google Scholar 

  11. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., et al.: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512 (1995)

    Article  CAS  Google Scholar 

  12. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., et al.: The genome sequence of drosophila melanogaster. Science 287, 2185–2195 (2000)

    Article  Google Scholar 

  13. Mariano, D.C.B., Pereira, F.L., Aguiar, E.L., Oliveira, L.C., Benevides, L., Guimarães, L.C., et al.: SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology. BMC Bioinform. 17(Suppl 18), 456 (2016)

    Article  Google Scholar 

  14. It’s sink or swim as a tidal wave of data approaches. Nature, 399, 517 (1999)

    Google Scholar 

  15. Gauthier, J., Vincent, A.T., Charette, S.J., Derome, N.: A brief history of bioinformatics. Brief. Bioinform. 20, 1981–1996 (2019)

    Article  Google Scholar 

  16. Hogeweg, P.: The Roots of Bioinformatics in Theoretical Biology. PLoS Comput. Biol. 7, e1002021 (2011)

    Article  CAS  Google Scholar 

  17. Canese, K., Weis, S.: PubMed: The Bibliographic Database. National Center for Biotechnology Information (US) (2013). https://www.ncbi.nlm.nih.gov/books/NBK153385/. Accessed 14 Sep 2020

  18. NCBI Resource Coordinators: Database resources of the national center for biotechnology information. Nucleic Acids Res. 46, D8–D13 (2018)

    Article  Google Scholar 

  19. Monastersky, R., Noorden, R.V.: 150 years of nature: a data graphic charts our evolution. Nature 575, 22–23 (2019)

    Article  CAS  Google Scholar 

  20. Carey, V.J., Gentry, J., Whalen, E., Gentleman, R.: Network structures and algorithms in Bioconductor. Bioinformatics 21, 135–136 (2005)

    Article  CAS  Google Scholar 

  21. Chen, H., Lau, M.C., Wong, M.T., Newell, E.W., Poidinger, M., Chen, J.: Cytofkit: a bioconductor package for an integrated mass cytometry data analysis pipeline. PLoS Comput. Biol. 12, e1005112 (2016)

    Article  Google Scholar 

  22. Fournier, F., Joly Beauparlant, C., Paradis, R., Droit, A.: rTANDEM, an R/Bioconductor package for MS/MS protein identification. Bioinformatics 30, 2233–2234 (2014)

    Article  CAS  Google Scholar 

  23. Gådin, J.R., van’t Hooft, F.M., Eriksson, P., Folkersen, L.: AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing. BMC Bioinform. 16, 194 (2015)

    Google Scholar 

  24. Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., et al.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004)

    Article  Google Scholar 

  25. Talevich, E., Invergo, B.M., Cock, P.J., Chapman, B.A.: Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinform. 13, 209 (2012)

    Google Scholar 

  26. Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., et al.: Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422–1423 (2009)

    Article  CAS  Google Scholar 

  27. Sun, X., Hu, B.: Mathematical modeling and computational prediction of cancer drug resistance. Brief. Bioinform. 19, 1382–1399 (2018)

    Article  CAS  Google Scholar 

  28. Sethi, A., Tian, J., Derdeyn, C.A., Korber, B., Gnanakaran, S.: A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein. PLoS Comput. Biol. 9, e1003046 (2013)

    Article  CAS  Google Scholar 

  29. Costa, L.S.C., Mariano, D.C.B., Rocha, R.E.O., Kraml, J., da Silveira, C.H., Liedl, K.R., et al.: Molecular dynamics gives new insights into the glucose tolerance and inhibition mechanisms on β-glucosidases. Molecules 24, 3215 (2019)

    Article  CAS  Google Scholar 

  30. Lima, L.H.F., de Fernandez-Quintéro, M., Rocha, R.E.O., Mariano, D.C.B., Melo-Minardi, R.C., de Liedl, K.R.: Conformational flexibility correlates with glucose tolerance for point mutations in β-glucosidases – a computational study. J. Biomolecular Structure Dyn. 1–20 (2020)

    Google Scholar 

  31. Russell, P.H., Johnson, R.L., Ananthan, S., Harnke, B., Carlson, N.E.: A large-scale analysis of bioinformatics code on GitHub. PLoS ONE 13, e0205898 (2018)

    Article  Google Scholar 

  32. Ekmekci, B., McAnany, C.E., Mura, C.: An Introduction to Programming for Bioscientists: A Python-Based Primer. PLoS Comput. Biol. 12, e1004867 (2016)

    Article  Google Scholar 

  33. Mariano, D., Martins, P., Helene Santos, L., de Melo- Minardi, R.C.: Introducing Programming Skills for Life Science Students. Biochemistry and Molecular Biology Education (2019). https://doi.org/10.1002/bmb.21230

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Acknowledgments

The authors thank the funding agencies: CAPES, FAPEMIG, and CNPq. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001. Project grant number 51/2013 - 23038.004007/2014-82.

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Authors and Affiliations

  1. LBS - Laboratory of Bioinformatics and Systems, Department of Computer Science, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil

    Diego Mariano, Lucianna H. Santos & Raquel C. de Melo-Minardi

  2. LLP - Laboratory of Programming Languages, Department of Computer Science, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil

    Mívian Ferreira & Bruno L. Sousa

Authors
  1. Diego Mariano
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  2. Mívian Ferreira
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  3. Bruno L. Sousa
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  4. Lucianna H. Santos
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  5. Raquel C. de Melo-Minardi
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Corresponding author

Correspondence to Diego Mariano .

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Editors and Affiliations

  1. University of São Paulo, São Paulo, Brazil

    João C. Setubal

  2. Instituto Federal de Goiás, Formosa, Goiás, Brazil

    Waldeyr Mendes Silva

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Mariano, D., Ferreira, M., Sousa, B.L., Santos, L.H., de Melo-Minardi, R.C. (2020). A Brief History of Bioinformatics Told by Data Visualization. In: Setubal, J.C., Silva, W.M. (eds) Advances in Bioinformatics and Computational Biology. BSB 2020. Lecture Notes in Computer Science(), vol 12558. Springer, Cham. https://doi.org/10.1007/978-3-030-65775-8_22

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  • DOI: https://doi.org/10.1007/978-3-030-65775-8_22

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-65774-1

  • Online ISBN: 978-3-030-65775-8

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