Bioinformatics and Management Science: Some Common Tools and Techniques
Published Online:1 Apr 2004https://doi.org/10.1287/opre.1030.0095
References
- Basic local alignment search tool. J. Molecular Biol. (1990) 215:403–410Crossref, Google Scholar
- Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. (1997) 25:3389–3402Crossref, Google Scholar
- Stochastic roadmap simulation: An efficient representation and algorithm for analyzing molecular motion. (2002) (Washington, DC)12–21RECOMB2002Crossref, Google Scholar
- Bioinformatics: The Machine Learning Approach (2001) 2nd ed.(MIT Press, Cambridge, MA) Google Scholar
- Microarrays and Gene Expression (2001) (Cambridge University Press, Cambridge, U.K.) Google Scholar
- Hidden Markov models of biological primary sequence information. Proc. National Acad. Sci. USA (1994) 91:1059–1063Crossref, Google Scholar
- The Pfam protein families database. Nucleic Acids Res. (2002) 30(1):276–280Crossref, Google Scholar
- Some multi-step methods for use in molecular dynamics calculations. J. Comput. Phys. (1976) 20:130–139Crossref, Google Scholar
- The protein data bank. Nucleic Acids Res. (2000) 28:235–242Crossref, Google Scholar
- Predicting function: From genes to genomes and back. J. Molecular Biol. (1998) 283:707–725Crossref, Google Scholar
- CASP and CAFASP experiments and their findings. Methods Biochem. Anal. (2003) 44:501–507Google Scholar
- Computational Modeling of Genetic and Biochemical Networks (2001) (MIT Press, Cambridge, MA) Google Scholar
- AVID: A global alignment program. Genome Res. (2003) 13(1):97–102Crossref, Google Scholar
- Exploring the new world of the genome with DNA microarrays. Nature Genetics (1999) 21:33–37Crossref, Google Scholar
- LAGAN and multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. (2003a) 13(4):721–731Crossref, Google Scholar
- Glocal alignment: Finding rearrangements during alignment. Bioinformatics (2003b) 19:54i–62i(Special Issue on the Proceedings of the ISMB 2003)Crossref, Google Scholar
- Statistics of sequence-structure threading. Current Opinion in Structural Biol. (1995) 5:236–244Crossref, Google Scholar
- Prediction of complete gene structures in human genomic DNA. J. Molecular Biol. (1997) 268:78–94Crossref, Google Scholar
- Protein misfolding and prion diseases. J. Molecular Biol. (1999) 293:313–320Crossref, Google Scholar
- A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure (1978) 5(Supplement 3(National Biomedical Research Foundation, Washington, D.C.) 345–352Google Scholar
- Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. (2002) 30:2478–2483Crossref, Google Scholar
- Random walks on trees and matchings. Electronic J. Probab. (2002) 7:1–17Crossref, Google Scholar
- Robustness and dynamics in biological networks. The First International Conf. Systems Biology (2000) New York(Japan Science and Technology Corporation, MIT Press)Google Scholar
- Comparison of discrimination methods for the classification of tumors using gene expression data. J. Amer. Statist. Association (2002) 97:77–87Crossref, Google Scholar
- Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (1998) (Cambridge University Press, Cambridge, U.K.) Crossref, Google Scholar
- Profile hidden Markov models. Bioinformatics (1998) 14:755–763Crossref, Google Scholar
- Non-coding RNA genes and the modern RNA world. Nature Rev. Genetics (2001) 2:919–929Crossref, Google Scholar
- Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol. (1995) 2:9–23Crossref, Google Scholar
- Bootstrap confidence levels for phylogenetic trees. Proc. National Acad. Sci. (1996) 93:13429–13434Crossref, Google Scholar
- , Platnick N. I., Funk V. A. The logical basis of phylogenetic analysis. Advances in Cladistics (1983) 2(Columbia University Press, New York) 7–36Google Scholar
- Contranslational protein folding. J. Biol. Chemistry (1997) 272(52):32715–32718Crossref, Google Scholar
- Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Molecular Evol. (1981) 17(6):368–376Crossref, Google Scholar
- PHYLIP(Phylogeny Inference Package), version 3.6. (2004) (Department of Genetics, University of Washington, Seattle, WA) . http://evolution.genetics.washington.edu/phylip.htmlGoogle Scholar
- CAFASP-1: Critical assessment of fully automated structure prediction methods. Proteins (1999) 3:209–217Crossref, Google Scholar
- Construction of phylogenetic trees. Science (1967) 155:279–284Crossref, Google Scholar
- The Steiner problem in phylogeny is NP-complete. Adv. Appl. Math. (1982) 3:43–49Crossref, Google Scholar
- Using Bayesian networks to analyze expression data. J. Comput. Biol. (2000) 7:601–620Crossref, Google Scholar
- The Last Recreations (1997) (Copernicus-Springer Verlag, New York) Crossref, Google Scholar
- Stochastic relaxation, Gibbs distribution and the Bayesian restoration of images. IEEE Trans. Pattern Anal. Machine Intelligence (1984) 6:721–741Crossref, Google Scholar
- Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization. J. Comput. Chem. (1987) 9:327–355Google Scholar
- SPA, (S)ankoff (P)arsimony (A)nalysis, version 1.1. (1995) . Computer program distributed by J. M. Carpenter, Department of Entomology, American Museum of Natural History, New YorkGoogle Scholar
- Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science (1999) 286:531–537Crossref, Google Scholar
- An improved algorithm for matching biological sequences. J. Molecular Biol. (1982) 162:705–708Crossref, Google Scholar
- The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery. J. Molecular Evol. (1998) 47(5):508–516Crossref, Google Scholar
- Morphologie der Organismen: Allgemeine Grundzuge der organischen FormenWissenschaft, mechanisch begrundet durch die von Charles Darwin reformirte Descendenz-Theorie (1866) (Georg Riemer, Berlin, Germany) Crossref, Google Scholar
- Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals. STOC (1995) (Las Vegas, NV)178–189Crossref, Google Scholar
- Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Molecular Biol. (1998) 281:827–842Crossref, Google Scholar
- Amino acid substitution matrices from protein blocks. Proc. National Acad. Sci. USA (1992) 89:10915–10919Crossref, Google Scholar
- Bootstrapping phylogenetic trees: Theory and methods. Statist. Sci. (2003) 18(2):241–255Crossref, Google Scholar
- The River (1999) (Little, Brown, Boston, MA) Google Scholar
- Mr. Bayes. Bayesian inference of phylogeny. (2002) . http://morphbank.ebc.uu.se/mrbayes/links.phpGoogle Scholar
- , Munro H. N. Evolution of protein molecules. Mammalian Protein Metabolism (1969) (Academic Press, New York) 21–132Crossref, Google Scholar
- Methods for assessing the statistical significance of molecular sequences features by using general scoring schemes. Proc. National Acad. Sci. USA (1990) 87(6):2264–2268Crossref, Google Scholar
- A simulated annealing algorithm for finding consensus sequences. Bioinformatics (2002) 18:1494–1499Crossref, Google Scholar
- BLAT—The BLAST-like alignment tool. Genome Res. (2002) 12(4):656–664Crossref, Google Scholar
- Optimization by simulated annealing. Science (1983) 220:671–680Crossref, Google Scholar
- Integrating genomic homology into gene structure prediction. Bioinformatics (2001) 17:S140–S148Crossref, Google Scholar
- Hidden Markov models in computational biology. J. Molecular Biol. (1994) 235:1501–1531Crossref, Google Scholar
- Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science (1993) 262:208–214Crossref, Google Scholar
- Protein folding by restrained energy minimization and molecular dynamics. J. Molecular Biol. (1983a) 170:723–764Crossref, Google Scholar
- Molecular dynamics of native protein: Computer simulation of the trajectories. J. Molecular Biol. (1983b) 168:595–620Crossref, Google Scholar
- Refinement of protein confirmations using a macromolecular energy minimization procedure. J. Molecular Biol. (1969) 46:269–279Crossref, Google Scholar
- Computer simulation of protein folding. Nature (1975) 253:694–698Crossref, Google Scholar
- Phylogenetic tree construction using MCMC. J. Amer. Statist. Association (2000) 95:493–503Crossref, Google Scholar
- Molecular Evolution (1997) (Sinauer Associates, Boston, MA) Google Scholar
- A tool for multiple sequence alignment. Proc. National Acad. Sci. (1989) 86:4412–4415Crossref, Google Scholar
- Multiple alignment using simulated annealing: Branch point definition in human mRNA splicing. Nucleic Acids Res. (1992) 20:2511–2516Crossref, Google Scholar
- Mitotic misregulation and human aging. Science (2000) 287:1241–1248Crossref, Google Scholar
- PatternHunter: Faster and more sensitive homology search. Bioinformatics (2002) 18:440–445Crossref, Google Scholar
- Alignment between two multiple alignments. Combinatorial Pattern Matching: 14th Annual Symposium, CPM 2003 (2003) June 25–27Morelia, Michoacán, MexicoLecture Notes in Computer Science 2676. Springer-Verlag Heidelberg, Germany.Crossref, Google Scholar
- MacClade Vol. 4: Analysis of Phylogeny and Character Evolution (2000) (Sinauer Associates, Sunderland, MA) Google Scholar
- Circuit simulation of genetic networks. Science (1995) 269:650–656Crossref, Google Scholar
- Simulated annealing. J. Chem. Phys. (1953) 21:1087–1092Crossref, Google Scholar
- A connectionist model of development. J. Theoret. Biol. (1991) 152:429–453Crossref, Google Scholar
- Applications of simulated annealing to the multiple-minima problem in small peptides. J. Biomolecular Structure Dynam. (1991) 8:721–735Crossref, Google Scholar
- Dialign2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics (1999) 15:211–218Crossref, Google Scholar
- Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc. National Acad. Sci. USA (1994) 91:6515–6519Crossref, Google Scholar
- Stochastic pairwise alignments. Bioinformatics (2002) 18(2):S153–S160Crossref, Google Scholar
- Nature Double helix at 50. Nature (2003) 422:6934Google Scholar
- A general method applicable to the search for similarities in amino acid sequence of two proteins. J. Molecular Biol. (1970) 48:443–453Crossref, Google Scholar
- Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method. Biopolymers (1965) 3:155–184Crossref, Google Scholar
- T-Coffee: A novel method for multiple sequence alignments. J. Molecular Biol. (2000) 302:205–217Crossref, Google Scholar
- The complexity and accuracy of discrete state models of protein structure. J. Molecular Biol. (1995) 249(2):493–507Crossref, Google Scholar
- ProMod and Swiss-Model: Internet-based tools for automated comparative protein modeling. Biochem. Soc. Trans. (1996) 24:274–279Crossref, Google Scholar
- Computational Molecular Biology, an Algorithmic Approach (2000) (MIT Press, Cambridge, MA) Crossref, Google Scholar
- ModBase, a database of annotated comparative protein structure models. Nucleic Acids Res. (2002) 30:255–259Crossref, Google Scholar
- Proteins: Structure, Function, and GeneticsProteins (1997) 29(Supplement 1):1–230Google Scholar
- Conformation of polypeptides and proteins. Adv. Protein Chem. (1968) 23:283–438Crossref, Google Scholar
- Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Molecular Evol. (1996) 43:304–311Crossref, Google Scholar
- The protein folding problem. Sci. Amer. (1991) 264(1):54–63Crossref, Google Scholar
- The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biol. Evol. (1987) 4(4):406–425Google Scholar
- , Lipkowitz K. B., Boyd D. B. Optimization methods in computational chemistry. Reviews in Computational Chemistry (1992) III(VCH Publishers, New York) 1–71Crossref, Google Scholar
- Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks. Bioinformatics (2002) 18:261–274Crossref, Google Scholar
- Vier combinatorische Probleme. Z. Math. Phys. (1870) 15:361–376Google Scholar
- Science Bulding on the DNA revolution. Science (2003) 300:5617Google Scholar
- A mathematical theory of communication. Bell System Tech. J. (1948) 27:379–423623656Crossref, Google Scholar
- Identification of common molecular subsequences. J. Molecular Biol. (1981) 147:195–197Crossref, Google Scholar
- Powerful simulated annealing algorithm locates global minima of protein folding potentials from multiple starting conformations. J. Comput. Chem. (1992) 13:579–584Crossref, Google Scholar
- Enumerative Combinatorics (1996) I2nd ed.(Cambridge University Press, Cambridge, U.K.) Google Scholar
- PAUP. (2001) . Phylogenetic analysis using parsimony, V4.0. Sinauer Associates, Boston, MAGoogle Scholar
- 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) 22:4673–4680Crossref, Google Scholar
- New Biology for Engineers and Computer Scientists (2003) (Prentice Hall, Englewood Cliffs, NJ) Google Scholar
- Genetic algorithms for protein folding simulations. J. Molecular Biol. (1993) 231:75–81Crossref, Google Scholar
- The sequence of the human genome. Science (2001) 29:1304–1351Crossref, Google Scholar
- Fast phylogenetic methods for genome rearrangement evolution: An empirical study. Proc. 5th Pacific Sympos. Biocomput. (2002) Hawaii:524–535Google Scholar
- A structure for deoxyribose nucleic acid. Nature (1953) 171(April):737–738Crossref, Google Scholar
- Microanalysis of drosphila development during metamorphosis. Science (1999) 286:2179–2184Crossref, Google Scholar
- Verbeitung und Ursache der Parthenogenesis im Pflanzen und Tierreiche (1920) (Verlag Fischer, Jena, Germany) Crossref, Google Scholar
- Review: Chemoinformatics and drug discovery. Molecules (2002) 7:566–600Crossref, Google Scholar
- Protein threading using PROSPECT: Design and evaluation. Proteins: Structure, Function, Genetics (2000) 40:343–354Crossref, Google Scholar
- Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Molecular Biol. Evol. (1997) 14:717–724Crossref, Google Scholar
- Bayesian adaptive sequence alignment algorithms. Bioinformatics (1998) 14:25–39Crossref, Google Scholar

