Células procarióticas e eucarióticas (Fabiano Pais)

Nelson, D.L. and Cox, M.M. 2004. Lehninger Principles of Biochemistry. Sarvier, 4th Ed. New York and Basingstoke.

Tortora, G.J., Funke, B.R. and Case, C.L. 2005. Microbiologia. Artmed Editora, 8 Ed. Porto Alegre, RS.

Watson, J.D., Baker, T.A., Bell, S.P., Gann, A., Levine, M. and Losick, R. 2006. Artmed Editora, 5 Ed. Porto Alegre, RS.

 

Conceitos básicos de genética: herança mendeliana, dominância, recessividade e codominância, herança multifatorial, haplótipos, equilíbrio de Hardy & Weinberg (Fabiano Pais)

Dodé, C. et al. Loss-of-function mutations in FGFR1 cause autosomal dominant Kallmann syndrome. Nature. 2003; 33: 1-3. PMID: 12627230.

Griffiths, A.J., Miller, J.H., Suzuki, D.T., Lewontin, R.C. e Gelbart, W.M. 2002. Introdução a Genética. Editora Guanabara Koogan, 7 Ed. Rio de Janeiro, RJ.

Watson, J.D., Baker, T.A., Bell, S.P., Gann, A., Levine, M. e Losick, R. 2006. Biologia Molecular do Gene. Artmed Editora, 5 Ed. Porto Alegre, RS.

 

Estrutura do DNA, replicação, transcrição e tradução (Fabiano Pais)

Nelson, D.L. and Cox, M.M. 2004. Lehninger Principles of Biochemistry. Sarvier, 4th Ed. New York and Basingstoke.

Watson, J.D., Baker, T.A., Bell, S.P., Gann, A., Levine, M. and Losick, R. 2006. Artmed Editora, 5 Ed. Porto Alegre, RS.

Wilkins MHF, Stokes AR & Wilson, HR. 1953 Molecular Structure of Deoxypentose Nucleic Acids. Nature. 1953; 171: 738-740. PMID:

 

Métodos em Biologia Molecular: Clonagem, PCR, seqüenciamento SANGER, microarranjos, SAGE (Fabiano Pais)

Nelson, D.L. and Cox, M.M. 2004. Lehninger Principles of Biochemistry. Sarvier, 4th Ed. New York and Basingstoke

Graves PR and Haystead TAJ. Molecular Biologist's Guide to Proteomics. Microbiology and Molecular Biology Reviews. 2002; 66: 39-63.

  

Alinhamento de sequências / matrizes de substituição (Roney Coimbra)

Gusfield, D. 1999. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, The Press Syndicate of the University of Cambridge, New York, NY.

Mount, D.W. 2004. Bioinformatics - Sequence and Genome Analysis, 2nd ed, Cold Spring Harbour Laboratory Press, Cold Spring Harbour, NY.

Coimbra RS, Artiguenave F, Jacques LS, Oliveira GC. MSTS – Molecular Serotyping Tool: a program for computer-assisted molecular identification of Escherichia coli and Shigella O-antigens. J. Clin. Microbiol. 2010; Mar 3 [Epub ahead of print]. PMID: 20200287.

 

Métodos para sequenciamento de nova geração (Flávio Araújo)

Suplemento da revista Nature Methods. Next generation sequencing data analysis. Novembro 2009, volume 6 No. 11s, S1-S32.

 

Alinhamentos múltiplos / predição de genes (Roney Coimbra)

 Gusfield, D. 1999. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, The Press Syndicate of the University of Cambridge, New York, NY.

Mount, D.W. 2004. Bioinformatics - Sequence and Genome Analysis, 2nd ed, Cold Spring Harbour Laboratory Press, Cold Spring Harbour, NY.

Gascuel O, Steel M. Neighbor-Joining Revealed. Mol. Biol. Evol. 2006; 23: 1997-2000. PMID: 16877499.

Lassmann T, Sonnhammer E. Quality assessment of multiple alignment programs. FEBS Letters. 2002; 529: 126-130. PMID: 12354624.

Höhl M, Kurtz S, Ohlebusch E. Efficient multiple genome alignment. Bioinformatics. 2002; 18 Suppl 1: S312-20. PMID: 12169561.

Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A; NISC Comparative Sequencing Program, Green ED, Hardison RC, Miller. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 2003; 31: 3518-24. PMID: 12824357.

Bray N, Pachter L. MAVID multiple alignment server. Nucleic Acids Res. 2003; 31: 3525-6. PMID: 12824358.

 

Estrutura e função de proteínas (Laila Nahum)

Caetano-Anollés G, Wang M, Caetano-Anollés D, Mittenthal JE. The origin, evolution and structure of the protein world. Biochem J. 2009; 417: 621-37. PMID: 19133840.

Chothia C, Gough J. Genomic and structural aspects of protein evolution. Biochem J. 2009; 419: 15-28. PMID: 19272021.

Dessailly BH, Reid AJ, Yeats C, Lees JG, Cuff A, Orengo CA. The evolution of protein functions and networks: a family-centric approach. Biochem Soc Trans. 2009; 37: 745-50. PMID: 19614587.

Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003; 31: 3784-8. PMID: 12824418.

Gerlt JA, Babbitt PC. Can sequence determine function? Genome Biol. 2000; 1: REVIEWS0005. PMID: 11178260.

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009; 37: D211-5. PMID: 18940856.

Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ. PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2010; 38: D308-17. PMID: 19858099.

Lehninger Principles of Biochemistry, 5th edition (http://bcs.whfreeman.com/lehninger5e/)

Biochemistry in 3D (Lehninger Principles of Biochemistry) (http://bcs.whfreeman.com/lehninger5e/content/cat_030/)

Interactive Concepts of Biochemistry (http://www.wiley.com/legacy/college/boyer/0470003790/index.htm)

 

Medidas de similaridade e de distância / Métodos de agrupamento e de classificação / Avaliação de agrupamentos (Roney Coimbra)

Mount, D.W. 2004. Bioinformatics - Sequence and Genome Analysis, 2nd ed, Cold Spring Harbour Laboratory Press, Cold Spring Harbour, NY.

Larrañaga P et al.. 2006. Machine Learning in Bioinformatics. Brief. Bioinform., 7: 82-112. PMID: 16761367.

Han L et al.. 2006. Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity. Proteomics, 6: 4023-37. PMID: 16791826

Golub TR et al.. 1999. Molecular Classification of Cancer: Class Discovery and Class PRediction by Gene Expression Monitoring. Science, 286: 531-537.

 

Análise filogenética (Laila Nahum)

Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

Gabaldón T, Huynen MA. Prediction of protein function and pathways in the genome era. Cell Mol Life Sci. 2004; 61: 930-44. PMID: 15095013.

Galperin MY, Koonin EV. Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol. 2000; 18: 609-13. PMID: 10835597

Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. Metagenomic analysis of the human distal gut microbiome. Science. 2006; 312(5778): 1355-9. PMID: 16741115.

Guindon S, Lethiec F, Duroux P, Gascuel O. PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 2005; 33: W557-9. PMID: 15980534.

Hedges SB, Dudley J, Kumar S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics. 2006; 22: 2971-2. PMID: 17021158.

Hillis DM, Huelsenbeck JP, Cunningham CW. Application and accuracy of molecular phylogenies. Science. 1994; 264(5159): 671-7. PMID: 8171318.

Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T. PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res. 2008; 36: D491-6. PMID: 17962297.

Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003; 19: 1572-4. PMID: 12912839

Kensche PR, van Noort V, Dutilh BE, Huynen MA. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface. 2008; 5: 151-70. PMID: 17535793.

Maddison, DR, Schulz, K, Maddin, WP. The Tree of Life Web Project. Zootaxa 2007. 1668: 19–40.

Nahum LA, Goswami S, Serres MH. Protein families reflect the metabolic diversity of organisms and provide support for functional prediction. Physiol Genomics. 2009; 38: 250-60. PMID: 19491149.

Nahum, L.A. and Pereira, S.L. Phylogenomics, Protein Family Evolution, and the Tree of Life: An Integrated Approach between Molecular Evolution and Computational Intelligence. In: Smolinski TG, Milanova MG, Hassanien A-E (eds), Studies in Computational Intelligence (SCI) 2008 122, 259–279. Springer-Verlag Berlin Heidelberg.

Nahum, L.A. Evolução dos Genomas. In: Biologia Molecular e Evolução. S.R. Matioli editor. 1st edition. Holos Editora, Ribeirão Preto, SP.

Rambaut, A. 2007. Tree Figure Drawing Tool, Version 1.2. Institute of Evolutionary Biology, University of Edinburgh.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997; 25: 4876-82. PMID: 9396791.

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004; 304(5667): 66-74. PMID: 15001713.

 

Bancos de dados relacionais (Francislon Silva)

Ramez E, Shamkrant N. 2010. Fundamentals of Database Systems. 6th Ed. Addison Wesley

 

miRNAs e silenciamento gênico (Sara Cuadros)

Visualizadores de genomas (AdhemarZerlotini )

Zertolini A, Heiges M, Wang H, Moraes RL, Dominitini AJ, Ruiz JC, Kissinger JC, Oliveira G. SchistoDB: a Schistosoma mansoni genome resource. Nucleic Acids Res. 2009; 37: D579-82. PMID: 18842636

Artemis (http://www.sanger.ac.uk/Software/Artemis)

Apollo (http://apollo.berkeleybop.org)

Argo Genome Browser (http://www.broadinstitute.org/annotation/argo)

NCBI Genome Workbench (http://www.ncbi.nlm.nih.gov/projects/gbench)

Integrated Genome Browser (http://igb.bioviz.org)

UGene (http://ugene.unipro.ru)

Sockeye (http://www.bcgsc.ca/project/bomge/sockeye)

SRI Pathway Tools (http://bioinformatics.ai.sri.com/ptools)

NCBI Sequence Viewer (http://www.ncbi.nlm.nih.gov/projects/sviewer)

UCSC Genome Browser (http://genome.ucsc.edu)

VEGA (http://vega.sanger.ac.uk)

GMOD - GBrowse (http://gmod.org/wiki/GBrowse)

GMOD - JBrowse (http://gmod.org/wiki/JBrowse)

UCSC Genome Browser (http://genome.ucsc.edu)

SRI Pathway Tools (http://bioinformatics.ai.sri.com/ptools)

 

Imunoinformática (predição de antígenos em células B e T) (Rômulo Moraes)

Abbas, A. K. et al. Cellular and molecular immunology. 6th. ed. Philadelphia: Saunders Elsevier, 2007.

Lund, O. Immunological bioinformatics. Cambridge, Mass.: MIT Press, 2005.

Rappuoli, R. Reverse vaccinology, a genome-based approach to vaccine development. Vaccine [S.I.], v. 19, n. 17-19, p. 2688-91, Mar 21 2001.

Kanoi, B. N.; Egwang, T. G. New concepts in vaccine development in malaria. Curr Opin Infect Dis [S.I.], v. 20, n. 3, p. 311-6, Jun 2007.

Pizza, M. et al. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science [S.I.], v. 287, n. 5459, p. 1816-20, Mar 10 2000.

von Heijne, G. The signal peptide. J Membr Biol [S.I.], v. 115, n. 3, p. 195-201, May 1990

Nakai, K. Protein sorting signals and prediction of subcellular localization. Adv Protein Chem [S.I.], v. 54, p. 277-344,  2000.

Nair, R.; Rost, B. Inferring sub-cellular localization through automated lexical analysis. Bioinformatics [S.I.], v. 18 Suppl 1, p. S78-86,  2002.

McManus, D. P.; Loukas, A. Current status of vaccines for schistosomiasis. Clin Microbiol Rev [S.I.], v. 21, n. 1, p. 225-42, Jan 2008.

Rammensee, H. et al. SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics [S.I.], v. 50, n. 3-4, p. 213-9, Nov 1999.

Nielsen, M.; LUND, O. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics [S.I.], v. 10, p. 296,  2009.

Lauemoller, S. L. et al. Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project.". Rev Immunogenet [S.I.], v. 2, n. 4, p. 477-91,  2000.

Sonnhammer, E. L. et al. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol [S.I.], v. 6, p. 175-82,  1998.

Emanuelsson, O. et al. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc [S.I.], v. 2, n. 4, p. 953-71,  2007.

Shatkay, H. et al. SherLoc: High-Accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data. Bioinformatics, v. 23(11) p. 1410-1417, 2007

Feldhan, M. et al. FRED--a framework for T-cell epitope detection. Bioinformatics [S.I.], v. 25, n. 20, p. 2758-9, Oct 15 2009.

 

Projeto de rede, serviços web e segurança do CEBio (Leandro Jacques)

Tanenbaum, Andrew S. Redes de Computadores. Editora Campus, 4ª edição, 2003, 948 pp..  ISBN: 853521185-3

 

Projeto físico e lógico da infraestrutura do CEBio (Anderson Dominitini)

Calculator Dell
http://solutions.dell.com/DellStarOnline/Launch.aspx/ESSA
http://www.clusterresources.com/products/torque-resource-manager.php

http://www.dell.com.br

IT Service Management Forum Brasil
http://www.itsmf.com.br

ISACA – Serving IT Governance Professionals
http://www.isaca.org

ITGI – IT Governance Institute
http://www.itgi.org

 

Modelagem molecular (Rosângela Hickson)

Trott, O. & Olson, A.J.. 2009. Software News and Update AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading. Journal of Computational Chemistry, 31: 455-461.

Seeliger, D. & de Groot, B. L.. 2010. Ligand docking and binding site analysis with PyMOL and Antodock/Vina. J. Comput. Aided Mol Des, 24: 417-422.

LigandScout - Gernard Wolber 

 

Genotipagem (Maria Raquel Carvalho)

Brookfield, J.F.Y.. Q&A: Promisse and pitfalls of genome-wide association studies. BMC Biology, 8: 41-45.