Dr. Adriano Barbosa, Ph.D - Suggested Literature

On-line Workshops: Suggested Literature

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, 3^rd 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.

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.

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.

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.

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.

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.

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.

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.

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