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Bioinformatic approaches to functionally characterise RNAs


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Bioinformatic approaches to functionally characterise RNAs

  1. 1. Research programBioinformatic approaches to functionally characterise RNAs Paul Gardner June 2, 2011 Paul Gardner Bioinformatic approaches to functionally characterise RNAs
  2. 2. Research programThe data deluge and bioinformatics There is a deluge of data being generated by new techniques in sequencing and structure determination Bioinformatic analysis is the only way to analyse and annotate this level of data, now driving a lot of biological discoveries The growth of Genbank The growth of UniProt The growth of PDB Number of structures (thousands) Number of nucleotides (billions) 300 Number of proteins (millions) 12 60 250 10 50 200 8 40 150 6 30 100 4 20 50 2 10 0 0 0 1985 1995 2005 1998 2002 2006 2010 1980 1990 2000 2010 Year Year Year Paul Gardner Bioinformatic approaches to functionally characterise RNAs
  3. 3. Research programBioinformatics is important Table 1: The most cited articles for each OECD country. Citations Country Reference 32399 de Thompson et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment... NAR 30616 us Altschul et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. NAR 20099 ch Towbin et al. (1979) Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets... PNAS 18479 fr Thompson et al. (1997) The CLUSTAL X windows interface... NAR 17011 uk Bland & Altman (1986) Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 16451 jp Iijima (1991) Helical microtubules of graphitic carbon. Nature 9773 at Kresse & Furthm¨ller (1996) Efficient iterative schemes for ab initio total-energy calculations... Physical Review B u 8593 ie, il Lander et al. (2001) Initial sequencing and analysis of the human genome. Nature 8113 no Pedersen (1994) Randomised trial of cholesterol lowering in 4444 patients with coronary heart disease... Lancet 7976 pt Perdew et al. (1992) Atoms, molecules, solids, and surfaces: Applications of the generalized... Physical Review B 7202 it Berendsen et al. (1984) Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics 6972 be Murshudov et al. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D. 6902 se Huelsenbeck & Ronquist (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 1 5850 pl Cornell et al. (1995) A second generation force field for the simulation of proteins, nucleic acids... J Am Chem Soc 4681 fi Simons & Ikonen (1997) Functional rafts in cell membranes. Nature 4588 au, es Perlmutter et al. (1999) Measurements of Ω and Λ from 42 high-redshift Supernovae. Astrophysical Journal 3950 dk Nielsen et al. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of... Protein Eng. 3805 nz Ihaka & Gentleman (1996) R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics 3351 kr, mx Eidelman et al. (2004) Review of particle physics Physics Letters... 3244 si Wilk et al. (2001) High-κ gate dielectrics: Current status and materials properties considerations. Journal of Applied Physics 2953 gr Polymeropoulos et al. (1997) Mutation in the α-synuclein gene identified in families with Parkinson’s disease. Science 2881 sk Miertus et al. (1981) Electrostatic interaction of a solute with a continuum... Chemical Physics 2393 hu Morice et al. (2002) A randomized comparison of a sirolimus-eluting stent... New England Journal of Medicine 1977 is Sever et al. (2003) Prevention of coronary and stroke events with atorvastatin... Lancet 1790 ca Sedlak & Lindsay (1968) Estimation of total, protein-bound, and nonprotein sulfhydryl groups... Analytical Biochemistry 1366 tr ¨ u Ozg¨r et al. (2005) A comprehensive review of ZnO materials and devices. Journal of Applied Physics 291 lu James et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature *This data was collected from Scopus in April 2011. NB. The US data is the union of multiple searches. Paul Gardner Bioinformatic approaches to functionally characterise RNAs
  4. 4. Research program“All science is either physics or stamp collecting” – ErnestRutherford Paul Gardner Bioinformatic approaches to functionally characterise RNAs
  5. 5. Research programStamp collectors Paul Gardner Bioinformatic approaches to functionally characterise RNAs