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| Non-coding RNA
Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004 Jan 23;116(2):281-97. Review
Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics. 2006 Jul 15;22(14):e90-8.
Eddy SR. Computational genomics of noncoding RNA genes. Cell. 2002 Apr 19;109(2):137-40. Review
Eddy SR. Noncoding RNA genes. Curr Opin Genet Dev. 1999 Dec;9(6):695-9. Review
Hertel J, Stadler PF. Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics. 2006 Jul 15;22(14):e197-202. Uses RNAz genome screen.
Huttenhofer A, Schattner P, Polacek N. Non-coding RNAs: hope or hype? Trends Genet. 2005 May;21(5):289-97.
Lai EC, Tomancak P, Williams RW, Rubin GM. Computational identification of Drosophila microRNA genes. Genome Biol. 2003;4(7):R42. Epub 2003 Jun 30.
Moulton V. Tracking down noncoding RNAs. Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2269-70. Epub 2005 Feb 9.
Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006 Apr;2(4):e33. Epub 2006 Apr 21. Evofold.
Rivas E, Eddy SR. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics. 2001;2:8. Epub 2001 Oct 10. QRNA.
Rivas E, Eddy SR. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics. 2000 Jul;16(7):583-605.
Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9. Epub 2005 Jan 21. RNAz.
Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol. 2005 Nov;23(11):1383-90.
RNA
Doudna JA. Structural genomics of RNA. Nat Struct Biol. 2000 Nov;7 Suppl:954-6.
Dowell RD, Eddy SR. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics. 2004 Jun 4;5:71.
Gardner PP, Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics. 2004 Sep 30;5:140.
Hofacker IL, Stadler PF, Stocsits RR. Conserved RNA secondary structures in viral genomes: a survey. Bioinformatics. 2004 Jul 10;20(10):1495-9.
Hofacker IL, Priwitzer B, Stadler PF. Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics. 2004 Jan 22;20(2):186-90.
Holmes I. Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics. 2005 Mar 24;6:73. Stemloc
Leontis NB et al. The RNA Ontology Consortium: an open invitation to the RNA community. RNA. 2006 Apr;12(4):533-41. Epub 2006 Feb 16.
Mandal M, Breaker RR. Gene regulation by riboswitches. Nat Rev Mol Cell Biol. 2004 Jun;5(6):451-63. Review
Vicens Q, Westhof E. RNA as a drug target: the case of aminoglycosides. Chembiochem. 2003 Oct 6;4(10):1018-23. Review
Protein coding gene
Guigo R, Wiehe T. Gene prediction accuracy in large DNA sequences. Frontiers in Computational Genomics. Functional Genomics Series, Vol 3. Caister Academic Press, 2003, p. 1-33.
Munch K, Krogh A. Automatic generation of gene finders for eukaryotic species. BMC Bioinformatics. 2006 May 21;7:263. Agene.
Pedersen JS, Hein J. Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics. 2003 Jan 22;19(2):219-27. Evogene.
Siepel A, Haussler D. Computational identification of evolutionarily conserved exons. RECOMB 2004: Proceedings of the Eighth Annual International Conference on Computational Molecular Biology,2004 pg:177 -186. ExoniPhy.
Siepel A, Haussler D. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol. 2004;11(2-3):413-28.
Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 2004 Apr;5(4):276-87. Review
Zhang MQ. Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet. 2002 Sep;3(9):698-709. Review
Sequence Analysis
Bray N, Pachter L. MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 2004 Apr;14(4):693-9.
Chatterji S, Pachter L. Reference based annotation with GeneMapper. Genome Biol. 2006;7(4):R29. Epub 2006 Apr 5.
Sys Bio
Aron, Uri. Intro to Sys Bio Circuits. CRC Press.
Kahlem P, Birney E. Dry work in a wet world: computation in systems biology. Mol Syst Biol. 2006;2:40. Epub 2006 Jul 4.
Wilkinson, Darren. Stochastic Modelling in Systems Biology. CRC Press.
Syn Bio
Arkin AP, Fletcher DA. Fast, cheap and somewhat in control. Genome Biol. 2006;7(8):114. Opinion
Breaker RR. Natural and engineered nucleic acids as tools to explore biology. Nature. 2004 Dec 16;432(7019):838-45.
Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. Nat Biotechnol. 2006 May;24(5):545-54.
Khosla C, Keasling JD. Metabolic engineering for drug discovery and development. Nat Rev Drug Discov. 2003 Dec;2(12):1019-25. Review
Voigt CA. Genetic parts to program bacteria. Curr Opin Biotechnol. 2006 Oct;17(5):548-57. Epub 2006 Sep 15. Review
iGem Competition: http://parts2.mit.edu/wiki/index.php/Main_Page
CS/Machine Learning
K. Lari and S. J. Young. The estimation of stochastic context-free
grammars using the inside–outside algorithm. Computer Speech and
Language, 4:35–56, 1990.
Ng AY and Jordan MI. "On Discriminative vs. Generative classifiers: A comparison of logistic regression and naive Bayes." Advances in Neural Information Processing Systems, 2001.
Primers
Eddy, Sean. What is a hidden Markov model?
Eddy, Sean. What is Bayesian statistics?
Eddy, Sean. What is dynamic programming?
Eddy, Sean. How do RNA folding algorithms work?
Eddy, Sean. Where did the BLOSUM62 alignment score matrix come from?
-- YuriBendana - 19 May 2006 |
