• Lesk, A. (2008). Introdução à Bioinformática. Tradução da 2a edição. Editora Artmed, Porto Alegre, Brasil.

• Moreira, L.M. (2015). Ciências Genômicas: Fundamentos e Aplicações. Sociedade Brasileira de Genética, Ribeirão Preto, Brasil.

• Verli, H. (2014). Bioinformática: da Biologia à Flexibilidade Moleculares. 1a edição, Porto Alegre, Brasil. Este livro está disponível para download gratuitamente.

• Agostino, M. (2012). Practical Bioinformatics. Garland Science, 1st edition, USA.

• Alberts, B.; Johnson, A,; Lewis, J.; Morgan, D.; Raff, M.; Roberts, K. & Walter, P. (2014). Molecular Biology of the Cell. 6th edition. Garland Science, USA.

• Baxevanis, A.D. & Ouellette, B.F.F. (2005). Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. 3rd edition. John Wiley & Sons, Inc., New York, USA. 

• Brown, S.M. (2013). Next-Generation DNA Sequencing Informatics. Cold Spring Harbor Laboratory Press, 1st edition, USA.

• Brown, T.A. (2006). Genomes 3. Garland Science, 3rd edition, USA.

• Compeau, P. & Pevzner, P. (2015). Bioinformatics Algorithms: An Active Learning Approach. 2nd edition. Vol 1. Active Learning Publishers, USA.

• Compeau, P. & Pevzner, P. (2015). Bioinformatics Algorithms: An Active Learning Approach. 2nd edition. Vol 2. Active Learning Publishers, USA.

• Dougherty, E.R. & Bittner, M.L. (2011). Epistemology of the Cell: A Systems Perspective on Biological Knowledge. IEEE Press Series on Biomedical Engineering, 1st Edition, Wiley-IEEE Press, USA.

• Dougherty, E.R.; Shmulevich, I.; Chen, J. & Wang, Z.J. (2005). Genomic Signal Processing and Statistics. Eurasip Book Series on Signal Processing and Communications, Hindawi Publishing Corporation.

• Lesk, A.M. (2012). Introduction to Genomics. Oxford University Press, 2nd edition, USA.

• Lesk, A.M. (2014). Introduction to Bioinformatics. Oxford University Press, 4th edition, USA.

• Mount, D.W. (2004). Bioinformatics: Sequence and Genome Analysis. 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, USA.

• Pevzner, P. & Shamir, R. (2011). Bioinformatics for Biologists. Cambridge University Press, 1st edition, UK.

• Setubal, J.C. & Meidanis, J. (1997). Introduction to Computational Molecular Biology. 1st edition. PWS Publishing, USA.

• Shmulevich, I. & Dougherty, R.D. (2009). Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks. SIAM-Society for Industrial and Applied Mathematics.

• Barrera, J., Cesar Jr., R.M., Martins Jr., D.C., Vêncio, R.Z.N., Merino, E.F., Yamamoto, M.M., Leonardi, F.G., Pereira, C.A.B. & Portillo , H.A. (2006). Constructing Probabilistic Genetic Networks of Plasmodium falciparum from Dynamical Expression Signals of the Intraerythrocytic Development Cycle. In: Patrick McConnell, Simon M. Lin & Patrick Hurban (eds.) - Methods of Microarray Data Analysis V. Springer, pp 11-26.

• Durham, A.; Setubal, J.C. & Barrera, J. (2015). Interdisciplinaridade em ação na pesquisa e pós-graduação em bioinformática. In Arlindo Philippi Jr & Valdir Fernandes (Eds.). Práticas da Interdisciplinaridade No Ensino e Pesquisa. 1a Edição. Editora Manole, pp. 619-642.

• Altschul S, Gish W, Miller W, Myers E, Lipman D. (1990). Basic local alignment search tool. J Mol Biol. 215(3): 403–410.

• Altschul S, Madden T, Schäffer A, Zhang J, Zhang Z, Miller W, Lipman D. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389–3402.

• Dalton L, Ballarin V & Brun M. (2009). Clustering algorithms: on learning, validation, performance, and applications to genomics. Current Genomics 10(6): 430-545.

• Datta, A., Pal, R., and Dougherty, E. R. (2006). Intervention in Probabilistic Gene Regulatory Networks. Current Bioinformatics 1(2): 167-184.

• Dougherty, E.R. (2001). Small sample issues for microarray-based classification. Comp
  Funct Genomics 2(1): 28-34.

• Dougherty, E.R., Barrera, J., Brun, M., Kim, S., Cesar, R.M., Chen, Y., Bittner, M. & Trent, J.M.
  (2002). Inference from clustering with application to gene-expression microarrays. J Comput Biol 9(1): 105-126.

• Dougherty, E.R. , and Datta, A. (2005). Genomic Signal Processing: Diagnosis and Therapy. IEEE Signal Processing Magazine 22(1): 107-112.

• Dougherty, E.R., Datta, A. & Sima, C.(2005). Research Issues in Genomic Signal Processing. IEEE Signal Processing Magazine 22(6): 46-68.

• Dougherty, E.R., Pal, R., Qian, X., Bittner, M. L., and Datta, A. (2010). Stationary and Structural Control in Gene Regulatory Networks: Basic Concepts. International Journal of Systems Science 41(1): 5-16.

• Dougherty, E.R., Sima, C., Hua, J., Hanczar, B. & Braga-Neto, U.M. (2010). Performance of Error Estimators for Classification. Current Bioinformatics 5 (1): 53-67.

• Dougherty, E.R. (2012). Genomic Signal Processing. IEEE Signal Processing Magazine 2 (3): 124-129.

• Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44(D1):D286-93.

• Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics. 30(9):1236-1240.

• Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M.(2016). KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44(D1):D457-62.

• Kim, S., Dougherty, E.R., Barrera, J., Chen, Y., Bittner, M.L. & Trent, J.M. (2002). Strong feature
  sets from small samples. J Comput Biol (1):127-146.

• Lopes, F.M., Martins, D.C., Barrera, J. & Cesar Jr, R.M. (2014). A feature selection technique for inference of graphs from their known topological properties: Revealing scale-free gene regulatory networks. Information Sciences 272: 1–15.

• Miller JR, Koren S, Sutton G. (2010). Assembly algorithms for next-generation sequencing data. Genomics 95(6): 315-327.

• Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB. (2011). The real cost of sequencing: higher than you think! Genome Biol. 12(8):125.

• Silva, P. J. S., Hashimoto, R. F., Kim, S., Barrera, J., Brandao, L. O., Suh, E., and Dougherty, E. R. (2005). Feature Selection Algorithms to Find Strong Genes. Pattern Recognition Letters 26(10): 1444-1453.

• Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. (2009). ABySS: a parallel assembler for short read sequence data. Genome Res 19(6):1117-1123.

• Stransky B, Barrera J, Ohno-Machado L & De Souza SJ. (2007). Modeling cancer: integration of "omics" information in dynamic systems. J Bioinform Comput Biol. 5(4):977-986.

• Trepode NW, Armelin HA, Bittner M, Barrera J, Gubitoso MD &Hashimoto RF. (2007). A
  robust structural PGN model for control of cell-cycle progression stabilized by negative feedback. EURASIP J Bioinform Syst Biol 2007:73109-73120.

• Zerbino DR, Birney E.(2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821-829.

Também sugerimos consultar os seguintes sites que têm livros gratuitos em formato eletrônico e tutoriais:

• NCBI Bookshelf
• SlideShare