Bibliography
Stephen F. Altschul, Warren Gish, Webb Miller, Eugene W. Myers, David J. Lipman: Basic Local Alignment Search Tool. Journal of Molecular Biology 215 (3): 403–410 (1990). https://doi.org/10.1016/S0022-2836(05)80360-2
Timothy L. Bailey and Charles Elkan: Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology 28–36. AAAI Press, Menlo Park, California (1994).
Douglas R. Cavener: Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates. Nucleic Acids Research 15 (4): 1353–1361 (1987). https://doi.org/10.1093/nar/15.4.1353
Chakraborty, A., Bandyopadhyay, S. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm. Sci Rep 3, 1746 (2013). https://doi.org/10.1038/srep01746
Brad Chapman and Jeff Chang: Biopython: Python tools for computational biology. ACM SIGBIO Newsletter 20 (2): 15–19 (August 2000).
Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczyński, Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25 (11), 1422–1423 (2009). https://doi.org/10.1093/bioinformatics/btp163
Peter J. A. Cock, Christopher J. Fields, Naohisa Goto, Michael L. Heuer, Peter M. Rice: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 38 (6): 1767–1771 (2010). https://doi.org/10.1093/nar/gkp1137
Athel Cornish-Bowden: Nomenclature for incompletely specified bases in nucleic acid sequences: Recommendations 1984. Nucleic Acids Research 13 (9): 3021–3030 (1985). https://doi.org/10.1093/nar/13.9.3021
Aaron E. Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna: Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Research 14 (7): 1394–1403 (2004). https://doi.org/10.1101/gr.2289704
M.O. Dayhoff, R.M. Schwartz, and B.C. Orcutt: A Model of Evolutionary Change in Proteins. Atlas of Protein Sequence and Structure, Volume 5, Supplement 3, 1978: 345–352. The National Biomedical Research Foundation, 1979.
Michiel J. L. de Hoon, Seiya Imoto, John Nolan, Satoru Miyano: Open source clustering software. Bioinformatics 20 (9): 1453–1454 (2004). https://doi.org/10.1093/bioinformatics/bth078
Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison: Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, UK (1998).
Michiel B. Eisen, Paul T. Spellman, Patrick O. Brown, David Botstein: Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences USA 95 (25): 14863–14868 (1998). https://doi.org/10.1073/pnas.95.25.14863
Nick Goldman and Ziheng Yang: A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11 (5) 725–736 (1994). https://doi.org/10.1093/oxfordjournals.molbev.a040153
Gene H. Golub, Christian Reinsch: Singular value decomposition and least squares solutions. In Handbook for Automatic Computation, 2, (Linear Algebra) (J. H. Wilkinson and C. Reinsch, eds), 134–151. New York: Springer-Verlag (1971).
Gene H. Golub, Charles F. Van Loan: Matrix computations, 2nd edition (1989).
Thomas Hamelryck and Bernard Manderick: PDB parser and structure class implemented in Python. Bioinformatics 19 (17): 2308–2310 (2003) https://doi.org/10.1093/bioinformatics/btg299
Thomas Hamelryck: Efficient identification of side-chain patterns using a multidimensional index tree. Proteins 51 (1): 96–108 (2003). https://doi.org/10.1002/prot.10338
Thomas Hamelryck: An amino acid has two sides; A new 2D measure provides a different view of solvent exposure. Proteins 59 (1): 29–48 (2005). https://doi.org/10.1002/prot.20379
Steven Henikoff, Jorja G. Henikoff: Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences USA 89 (2): 10915–10919 (1992). https://doi.org/10.1073/pnas.89.22.10915
Yukako Hihara, Ayako Kamei, Minoru Kanehisa, Aaron Kaplan and Masahiko Ikeuchi: DNA microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell 13 (4): 793–806 (2001). https://doi.org/10.1105/tpc.13.4.793
Richard Hughey, Anders Krogh: Hidden Markov models for sequence analysis: extension and analysis of the basic method. Computer Applications in the Biosciences: CABIOS 12 (2): 95–107 (1996). https://doi.org/10.1093/bioinformatics/12.2.95
Florian Jupe, Leighton Pritchard, Graham J. Etherington, Katrin MacKenzie, Peter JA Cock, Frank Wright, Sanjeev Kumar Sharma, Dan Bolser, Glenn J Bryan, Jonathan DG Jones, Ingo Hein: Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics 13: 75 (2012). https://doi.org/10.1186/1471-2164-13-75
Voratas Kachitvichyanukul, Bruce W. Schmeiser: Binomial Random Variate Generation. Communications of the ACM 31 (2): 216–222 (1988). https://doi.org/10.1145/42372.42381
W. James Kent: BLAT – The BLAST-Like Alignment Tool. Genome Research 12: 656–664 (2002). https://doi.org/10.1101/gr.229202
Teuvo Kohonen: Self-organizing maps, 2nd Edition. Berlin; New York: Springer-Verlag (1997).
Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjölander, David Haussler: Hidden Markov Models in computational biology: Applications to protein modeling. Journal of Molecular Biology 235 (5): 1501–1531 (1994). https://doi.org/10.1006/jmbi.1994.1104
Pierre L’Ecuyer: Efficient and Portable Combined Random Number Generators. Communications of the ACM 31 (6): 742–749,774 (1988). https://doi.org/10.1145/62959.62969
Wen-Hsiung Li, Chung-I Wu, Chi-Cheng Luo: A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Molecular Biology and Evolution 2 (2): 150–174 (1985). https://doi.org/10.1093/oxfordjournals.molbev.a040343
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin: The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 (16): 2078–2079 (2009). https://doi.org/10.1093/bioinformatics/btp352
David R. Maddison, David L. Swofford, Wayne P. Maddison: Nexus: An Extensible File Format for Systematic Information. Systematic Biology 46 (4): 590–621 (1997). https://doi.org/10.1093/sysbio/46.4.590
Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin: PALSSE: A program to delineate linear secondary structural elements from protein structures. BMC Bioinformatics 6: 202 (2005). https://doi.org/10.1186/1471-2105-6-202.
V. Matys, E. Fricke, R. Geffers, E. Gößling, M. Haubrock, R. Hehl, K. Hornischer, D. Karas, A.E. Kel, O.V. Kel-Margoulis, D.U. Kloos, S. Land, B. Lewicki-Potapov, H. Michael, R. Münch, I. Reuter, S. Rotert, H. Saxel, M. Scheer, S. Thiele, E. Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Research 31 (1): 374–378 (2003). https://doi.org/10.1093/nar/gkg108
Masatoshi Nei and Takashi Gojobori: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3 (5): 418–426 (1986). https://doi.org/10.1093/oxfordjournals.molbev.a040410
William R. Pearson, David J. Lipman: Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences USA 85 (8): 2444–2448 (1988). https://doi.org/10.1073/pnas.85.8.2444
Leighton Pritchard, Jennifer A. White, Paul R.J. Birch, Ian K. Toth: GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 22 (5): 616–617 (2006). https://doi.org/10.1093/bioinformatics/btk021
Caroline Proux, Douwe van Sinderen, Juan Suarez, Pilar Garcia, Victor Ladero, Gerald F. Fitzgerald, Frank Desiere, Harald Brüssow: The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-Like Siphoviridae in lactic acid bacteria. Journal of Bacteriology 184 (21): 6026–6036 (2002). https://doi.org/10.1128/JB.184.21.6026-6036.2002
Peter Rice, Ian Longden, Alan Bleasby: EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16 (6): 276–277 (2000). https://doi.org/10.1016/S0168-9525(00)02024-2
Alok Saldanha: Java Treeview—extensible visualization of microarray data. Bioinformatics 20 (17): 3246–3248 (2004). https://doi.org/10.1093/bioinformatics/bth349
Thomas D. Schneider, Gary D. Stormo, Larry Gold: Information content of binding sites on nucleotide sequences. Journal of Molecular Biology 188 (3): 415–431 (1986). https://doi.org/10.1016/0022-2836(86)90165-8
Adrian Schneider, Gina M. Cannarozzi, and Gaston H. Gonnet: Empirical codon substitution matrix. BMC Bioinformatics 6: 134 (2005). https://doi.org/10.1186/1471-2105-6-134
Robin Sibson: SLINK: An optimally efficient algorithm for the single-link cluster method. The Computer Journal 16 (1): 30–34 (1973). https://doi.org/10.1093/comjnl/16.1.30
Guy St C. Slater, Ewan Birney: Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31 (2005). https://doi.org/10.1186/1471-2105-6-31
George W. Snedecor, William G. Cochran: Statistical methods. Ames, Iowa: Iowa State University Press (1989).
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding: HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20: 473 (2019). https://doi.org/10.1186/s12859-019-3019-7
Eric Talevich, Brandon M. Invergo, Peter J.A. Cock, Brad A. Chapman: Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 13: 209 (2012). https://doi.org/10.1186/1471-2105-13-209
Pablo Tamayo, Donna Slonim, Jill Mesirov, Qing Zhu, Sutisak Kitareewan, Ethan Dmitrovsky, Eric S. Lander, Todd R. Golub: Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proceedings of the National Academy of Sciences USA 96 (6): 2907–2912 (1999). https://doi.org/10.1073/pnas.96.6.2907
Ian K. Toth, Leighton Pritchard, Paul R. J. Birch: Comparative genomics reveals what makes an enterobacterial plant pathogen. Annual Review of Phytopathology 44: 305–336 (2006). https://doi.org/10.1146/annurev.phyto.44.070505.143444
Géraldine A. van der Auwera, Jaroslaw E. Król, Haruo Suzuki, Brian Foster, Rob van Houdt, Celeste J. Brown, Max Mergeay, Eva M. Top: Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. Antonie van Leeuwenhoek 96 (2): 193–204 (2009). https://doi.org/10.1007/s10482-009-9316-9
Michael S. Waterman, Mark Eggert: A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. Journal of Molecular Biology 197 (4): 723–728 (1987). https://doi.org/10.1016/0022-2836(87)90478-5
Ziheng Yang and Rasmus Nielsen: Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution 17 (1): 32–43 (2000). https://doi.org/10.1093/oxfordjournals.molbev.a026236
Ka Yee Yeung, Walter L. Ruzzo: Principal Component Analysis for clustering gene expression data. Bioinformatics 17 (9): 763–774 (2001). https://doi.org/10.1093/bioinformatics/17.9.763