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Bielefeld University Center of Biotechnoloy Institute of Bioinformatics BiBiServ
A collection of
research papers
for further
self-studies.
 
Research Papers
  • Altschul, S.F. and Gish, W. and Miller, W. and Myers, E.W. and Lipman, D.J.:
    Basic local alignment search tool
    J Mol Biol 1990: 215 (3) , 403-10
  • Bairoch, A.:
    The ENZYME database in 2000.
    Nucleic Acids Res 2000: 28 (1) , 304-305
  • Benson, D. A. and Karsch-Mizrachi, I. and Lipman, D.J. and Ostell, J. and Wheeler, D.L.:
    GenBank
    Nucleic Acids Res 2007: 35 (Database issue) , D21-D25
  • Berman, H. and Henrick, K. and Nakamura, H. and Markley, J.L.:
    The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
    Nucleic Acids Res 2007: 35 (Database issue) , D301-D303
  • Crosby, M.A. and Goodman, J.L. and Strelets, V.B. and Zhang, P. and Gelbart, W.M. and FlyBase Consortium:
    FlyBase: genomes by the dozen
    Nucleic Acids Res 2007: 35 (Database issue) , D486-D491
  • Evers, D. and Giegerich, R.:
    RNA movies: visualizing RNA secondary structure spaces
    Bioinformatics 1999: 15 (1) , 32-37
  • Havgaard, J.H. and Torarinsson, E. and Gorodkin, J.:
    Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.
    PLoS Comput Biol 2007: 3 (10) , 1896-1908
  • Höchsmann,M. and Töller, T. and Giegerich, R. and Kurtz, S.:
    Local Similarity in RNA Secondary Structures
    Proceedings of the IEEE Computational Systems Bioinformatics Conference (CSB 2003) 2003: , 159-168
  • Höchsmann, M. and Voss, B. and Giegerich, R.:
    Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 2004: 1 (1) , 53-62
  • Hofacker, I.L.:
    RNA Consensus Structure Prediction With RNAalifold.
    Methods Mol Biol 2007: 395 , 527-544
  • Hubbard,T.J.P. et al.:
    Ensembl 2007.
    Nucleic Acids Res 2007: 35 (Database issue) , D610-D617
  • Hoogland, C. and Mostaguir, K. and Sanchez, J.-C. and Hochstrasser, D.F. and Appel, R.D.:
    SWISS-2DPAGE, ten years later.
    Proteomics 2004: 4 (8) , 2352-2356
  • Junier, T. and Pagni, M.:
    Dotlet: diagonal plots in a web browser.
    Bioinformatics 2000: 16 (2) , 178-179
  • Kaiser, A. and Krüger, J. and Evers, D.J.:
    RNA Movies 2: sequential animation of RNA secondary structures.
    Nucleic Acids Res 2007: 35 (Web Server issue) , W330-W334
  • Kapranov, P. et al.:
    RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription.
    Science 2007:
  • Kent, W.J. and Sugnet, C.W.and Furey, T.S.and Roskin, K.M. and Pringle, T.H. and Zahler, A. M. and Haussler, D.:
    The Human Genome Browser at UCSC.
    Genome Res 2002: 12(6) , 996-1006
  • Krüger, J. and Sczyrba, A. and Kurtz, S. and Giegerich, R.:
    e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences
    Nucl. Acids. Res. 2004: 32 (suppl2) , W301-304
  • Kulikova, T.et al.:
    EMBL Nucleotide Sequence Database in 2006.
    Nucleic Acids Res 2007: 35 (Database issue) , D16-D20
  • Morgenstern, B.:
    DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
    Bioinformatics 1999: 15 (3) , 211-218
  • Morgenstern, B.:
    DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
    Bioinformatics 1999: 15 (3) , 211-218
  • Morgenstern, B.:
    DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
    Bioinformatics 1999: 15 (3) , 211-218
  • Pearson, W.R. and Lipman, D.J.:
    Improved tools for biological sequence comparison.
    Proc Natl Acad Sci U S A 1988: 85 (8) , 2444-2448
  • Phan, I.Q.H. and Pilbout, S.F. and Fleischmann, W. and Bairoch, A.:
    NEWT, a new taxonomy portal
    Nucleic Acids Res 2003: 31 (13) , 3822-3823
  • Rice, P. and Longden, I. and Bleasby, A.:
    EMBOSS: the European Molecular Biology Open Software Suite.
    Trends Genet 2000: 16 (6) , 276-277
  • Steffen, P. and Voss, B. and Rehmsmeier, M. and Reeder, J. and Giegerich, R.:
    RNAshapes: an integrated RNA analysis package based on abstract shapes.
    Bioinformatics 2006: 22 (4) , 500-503
  • Stoye, J. and Moulton, V. and Dress, A.W.:
    DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment
    Comput. Appl. Biosci. 1997: 13 (6) , 625-626
  • Thompson, J.D.and Higgins, D.G. and Gibson, T.J.:
    CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    Nucleic Acids Res 1994: 22 (22) , 4673-80
  • Thompson, J.D. and Plewniak, F. and Poch, O.:
    BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
    Bioinformatics 1999: 15 (1) , 87-88
  • UniProt Consortium:
    The Universal Protein Resource (UniProt)
    Nucleic Acids Res 2007: 35 (Database issue) , D193-D197
  • Wheeler, D.L.et al.:
    Database resources of the National Center for Biotechnology Information
    Nucleic Acids Res 2007: 35 (Database issue) , D5-12
  • Mulder, N.J. et al.:
    InterPro: An integrated documentation resource for protein families, domains and functional sites
    Brief Bioinform 2002: 3 (3) , 225-235
  • Mulder, N.J. et al.:
    New developments in the InterPro database
    Nucleic Acids Res 2007: 35 (Database issue) , D224-D228
A collection
of textbooks
for further
self-studies.
  
Textbooks
  • Aluru, S.:
    Handbook of Computational Molecular Biology.
    Chapman and Hall/CRC 2006.
  • Baxevanis, A.D. and Ouelette, B.F.F.:
    Bioinformatics - A practical Guide to the Analysis of Genes and Proteins.
    Wiley-Interscience 2005, 3rd edition.
  • Campbell, A.M. and Heyer, L.J.:
    Discovering Genomics, Proteomics and Bioinformatics.
    CSHL Press, Benjamin Cummings, Pearson Education 2003.
  • Durbin, R. and Eddy, S. and Krogh, A. andMitchison, G.:
    Biological sequence analysis.
    Cambridge Univerity Press 1998.
  • Gusfield, D.:
    Algorithms on strings, trees, ans sequences.
    Cambridge Univerity Press 1997.
  • Krane, D.E. and Marieb, E.N. and Raymer, M.L.:
    Fundamental Concepts of Bioinformatics.
    Addison Wesley 2002.
  • Mount, D.W.:
    Bioinformatics. Sequence and Genome Analysis.
    CSHL Press 2004, 2nd edition.
  • Setubal, J. and Meidanis, J.:
    Introduction to Computational Molecular Biology.
    PWS Publishing Company 1997.
A collection
of links
regarding WebServices
  
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