On-line Workshops: Suggested Literature

DNA & RNA databases

  • Genomes. 2nd edition. Brown TA. 2002. Chapter 1: The Human Genome.

  • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition. Chapter 4: Genomic Databases (Tyra G. Wolfsberg).

  • Bioinformatics and Functional Genomics, 3rd Edition. Chapter 2: Access to sequence data and related information.

  • Mizrachi I. GeneBank. 2013 Nov 12. In: The NCBI Handbook [Internet]. 2nd edition. Bethesda (MD): National Center for Biotechnology Information (US);

  • O'Leary NA, Wright MW, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45.

  • Yates AD, Achuthan P, et al. Ensembl 2020. Nucleic Acids Res. 2020 Jan 8;48(D1):D682-D688.

  • Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8. doi: 10.1093/nar/gkm952. Epub 2007 Nov 8. PMID: 17991681; PMCID: PMC2238936.


DNA & RNA analysis

  • Pevsner, J (2015) Bioinformatics and Functional Genomics, 3rd Edition. Chapter 9: Analysis of next-generation sequence data.

  • Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387-402. doi: 10.1146/annurev.genom.9.081307.164359. PMID: 18576944.

  • Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 2016 Nov 25;17(1):239.

  • Genomics England. The 100,000 Genomes Project. Available at: https://www.genomicsengland.co.uk

  • Pevsner, J (2015) Bioinformatics and Functional Genomics, 3rd Edition. Chapter 10: Bioinformatic Approaches to Ribonucleic Acid (RNA). Chapter 11: Gene Expression: Microarray and RNA-seq Data Analysis.

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. doi: 10.1038/nmeth.1226. Epub 2008 May 30. PMID: 18516045.


Differential Gene Expression Analysis

  • Barrett T. Gene Expression Omnibus (GEO). 2013 May 19. In: The NCBI Handbook [Internet]. 2nd edition. Bethesda (MD): National Center for Biotechnology Information (US); 2013-. Bookshelf URL: https://www.ncbi.nlm.nih.gov/books/

  • Davis S, Meltzer P (2007). “GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.” Bioinformatics, 14, 1846–1847.

  • Athar A, Füllgrabe A, et al. ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 2019 Jan 8;47(D1):D711-D715. doi: 10.1093/nar/gky964. PMID: 30357387; PMCID: PMC6323929.

  • Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W (2009). “Importing ArrayExpress datasets into R/Bioconductor.” Bioinformatics, 25(16), 2092–4.


Protein sequence analysis

  • Pevsner, J (2015) Bioinformatics and Functional Genomics, 3rd Edition. Chapter 12: Protein Analysis and Proteomics.

  • Pundir S, Magrane M, Martin MJ, O'Donovan C; UniProt Consortium. Searching and Navigating UniProt Databases. Curr Protoc Bioinformatics. 2015;50:1.

  • Finn RD, Bateman A, Clements J, et al. Pfam: the protein families database. Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30.

  • Hulo N, Bairoch A, et al. The PROSITE database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D227-30.

  • Lu S, Wang J, Chitsaz F, et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2020 Jan 8;48(D1):D265-D268.

  • Goodsell DS, Zardecki C, et al. RCSB Protein Data Bank: Enabling biomedical research and drug discovery. Protein Sci. 2020 Jan;29(1):52-65.


Sequences alignment

  • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition. Chapter 11: Assessing Pairwise Sequence Similarity: BLAST and FASTA (Andreas D. Baxevanis).

  • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition. Chapter 12: Creation and Analysis of Protein Multiple Sequence Alignments (Geoffrey J. Barton).

  • Pevsner, J (2015) Bioinformatics and Functional Genomics, 3rd Edition. Chapter 3: Pairwise Sequence Alignmen1. Chapter 4: Basic Local Alignment Search Tool (BLAST). Chapter: 6 Multiple Sequence Alignment.

  • Pearson WR. Selecting the Right Similarity-Scoring Matrix. Curr Protoc Bioinformatics. 2013;43:3.5.1-3.5.9.

  • Trivedi R, Nagarajaram HA. Substitution scoring matrices for proteins - An overview. Protein Sci. 2020 Sep 21.

  • EMBOSS Needle - Pairwise Sequence Alignment. Available at: https://www.ebi.ac.uk/services.

  • Clustal Omega - Multiple Sequence Alignment. Available at: https://www.ebi.ac.uk/services.

  • EMBOSS Water - Pairwise Sequence Alignment. Available at: https://www.ebi.ac.uk/services.


Phylogenetics Analysis

  • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition. Chapter 14: Phylogenetic Analysis (Fiona S. L. Brinkman).

  • Pevsner, J (2015) Bioinformatics and Functional Genomics, 3rd Edition. Chapter 7: Molecular Phylogeny and Evolution.

  • Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008;9(4):299-306.

  • Rosenberg MS, Kumar S. Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Mol Biol Evol. 2001 Sep;18(9):1823-7.

  • Nei M., S. Kumar, 2000. Molecular evolution and phylogenetics Oxford University Press, Oxford, England.


Protein-Protein Interactions

  • Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, Castagnoli L, Cesareni G. MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 2012 Jan;40(Database issue):D857-61.

  • Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613.

  • Sergeeva AP, Katsamba PS, Cosmanescu F, et al. DIP/Dpr interactions and the evolutionary design of specificity in protein families. Nat Commun. 2020;11(1):2125.

  • Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stümpflen V, Mewes HW, Ruepp A, Frishman D. The MIPS mammalian protein-protein interaction database. Bioinformatics. 2005 Mar;21(6):832-4.


Structural Bioinformatics

  • Pevsner, J (2015) Bioinformatics and Functional Genomics, 3rd Edition. Chapter 13: Protein Structure.

  • Gruber A, Durham AM, Huynh C, et al., editors. Bethesda (MD): National Center for Biotechnology Information (US); 2008. Chapter A06.

  • wwPDB consortium. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res. 2019 Jan 8;47(D1):D520-D528.

  • Bioinformatics tools for protein structure analysis @ EMBL-EBI. Available at: https://www.ebi.ac.uk/Tools/structure/

  • MODELLER - A Program for Protein Structure Modeling - Release 9.25, r11894. Available at: https://salilab.org/modeller/9.25/manual/

  • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition. Chapter 9: Protein Structure Prediction and Analysis (David Wishart).

  • Bienert S, Waterhouse A, de Beer TA, Tauriello G, Studer G, Bordoli L, Schwede T. The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Res. 2017 Jan 4;45(D1):D313-D319.

  • O'Donoghue SI, Sabir KS, Kalemanov M, Stolte C, Wellmann B, Ho V, Roos M, Perdigão N, Buske FA, Heinrich J, Rost B, Schafferhans A. Aquaria: simplifying discovery and insight from protein structures. Nat Methods. 2015 Feb;12(2):98-9.