A general overview of resources for bioinformatics. The content is intended for students in the sciences and provides both introductory and some advanced resources.
Reviews in bioinformatics can cover many topics including instrumentation for next generation sequencing, data repositories, web servers, data visualization and software. The reviews listed below cover most of these topics.
Shendure, J., Balasubramanian, S., Church, G. et al. DNA sequencing at 40: past, present and future. Nature 550, 345–353 (2017). https://doi.org/10.1038/nature24286
Schurch NJ, Schofield P, Gierliński M, et al. How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? [published correction appears in RNA. 2016 Oct;22(10 ):1641]. RNA. 2016;22(6):839-851. doi:10.1261/rna.053959.115
Library construction for next-generation sequencing: Overviews and challenges
Steven R. Head, H. Kiyomi Komori, Sarah A. LaMere, Thomas Whisenant, Filip Van Nieuwerburgh, Daniel R. Salomon, and Phillip Ordoukhanian
BioTechniques 2014 56:2, 61-77
Zhou, X. and Rokas, A. (2014), Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Mol Ecol, 23: 1679-1700. https://doi.org/10.1111/mec.12680
Costa-Silva J, Domingues D, Lopes FM (2017) RNA-Seq differential expression analysis: An extended review and a software tool. PLOS ONE 12(12): e0190152. https://doi.org/10.1371/journal.pone.0190152
Conesa, A., Madrigal, P., Tarazona, S. et al. A survey of best practices for RNA-seq data analysis. Genome Biol 17, 13 (2016). https://doi.org/10.1186/s13059-016-0881-8
Seán I. O'Donoghue, Benedetta Frida Baldi, Susan J. Clark, Aaron E. Darling, James M. Hogan, Sandeep Kaur, Lena Maier-Hein, Davis J. McCarthy, William J. Moore, Esther Stenau, Jason R. Swedlow, Jenny Vuong, James B. Procter
Annual Review of Biomedical Data Science 2018 1:1, 275-304
Mangan, M.E., Williams, J.M., Kuhn, R.M. and Lathe, W.C., III (2014), The UCSC Genome Browser: What Every Molecular Biologist Should Know. Current Protocols in Molecular Biology, 107: 19.9.1-19.9.36. https://doi.org/10.1002/0471142727.mb1909s107
Gaudet, P., Škunca, N., Hu, J.C., Dessimoz, C. (2017). Primer on the Gene Ontology. In: Dessimoz, C., Škunca, N. (eds) The Gene Ontology Handbook. Methods in Molecular Biology, vol 1446. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3743-1_3
The Gene Ontology Resource is important project that collects and curates gene function data. This short review covers important points to utilize this resource.
The Nucleic Acids Research journal publishes and annual issue on databases that are relevant to bioinformatics. This page lists over 1400 articles published in these issues.
The journal Nucleic Acids Research published issues dedicated to web servers relevant to bioinformatics. This page lists the articles published in those issues.
