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ana's library [460 articles]

最近录入 ana's ordered by to_read.
  • Locus control regions: coming of age at a decade plus.
    Trends Genet, Vol. 15, No. 10. (October 1999), pp. 403-408.
    by Q Li, S Harju, KR Peterson
  • ROCR: visualizing classifier performance in R
    Bioinformatics, Vol. 21, No. 20. (15 October 2005), pp. 3940-3941.
    by Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer
  • Residue packing in proteins: Uniform distribution on a coarse-grained scale
    Journal of Chemical Physics, Vol. 116, No. 5. (February 2002), pp. 2269-1176.
    by Z Bagci, RL Jernigan, Bahar
  • Molecular mechanism of domain swapping in proteins: an analysis of slower motions.
    Biophys J, Vol. 86, No. 6. (June 2004), pp. 3846-3854.
    by S Kundu, RL Jernigan
  • On the interactions of charged side chains with the alpha-helix backbone.
    Biophys Chem, Vol. 31, No. 1-2. (August 1988), pp. 29-34.
  • An analysis of side chain interactions and pair correlations within antiparallel beta-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs.
    Proteins, Vol. 22, No. 2. (June 1995), pp. 119-131.
    by MA Wouters, PM Curmi
  • The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model
    EMBO Reports, Vol. 5, No. 3. (March 2004), pp. 280-284.
    by Vera van Noort, Berend Snel, Martijn Huynen
  • Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.
    J Mol Biol, Vol. 345, No. 5. (4 February 2005), pp. 1281-1294.
    by O Keskin, B Ma, R Nussinov
  • The Relationship Between Domain Duplication and Recombination
    Journal of Molecular Biology, Vol. 346, No. 1. (11 February 2005), pp. 355-365.
    by Christine Vogel, Sarah A Teichmann, Jose Pereira-Leal
  • The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein-Protein Complexes with an Application to Protein-Protein Docking
    Journal of Molecular Biology, Vol. 347, No. 5. (15 April 2005), pp. 1077-1101.
    by Graham R Smith, Michael Sternberg, Paul A Bates
  • Conservation of Orientation and Sequence in Protein Domain-Domain Interactions
    Journal of Molecular Biology, Vol. 345, No. 5., pp. 1265-1279.
    by Stephen J Littler, Simon J Hubbard
  • A phylogenomic approach to microbial evolution.
    Nucleic Acids Res, Vol. 29, No. 2. (15 January 2001), pp. 545-552.
  • FSSA: a novel method for identifying functional signatures from structural alignments.
    Bioinformatics (28 April 2005)
    by Kai Wang, Ram Samudrala
  • Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics.
    BMC Bioinformatics, Vol. 5, No. 1. (26 July 2004)
    by A Cherkasov, SJ Ho Sui, RC Brunham, SJ Jones
  • notes Global optimization of clusters, crystals, and biomolecules.
    Science, Vol. 285, No. 5432. (27 August 1999), pp. 1368-1372.
    by DJ Wales, HA Scheraga
  • 3DCoffee: combining protein sequences and structures within multiple sequence alignments.
    J Mol Biol, Vol. 340, No. 2. (2 July 2004), pp. 385-395.
  • A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types.
    Mol Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350.
  • Common aging pathways in worms, flies, mice and humans
    J Exp Biol, Vol. 210, No. 9. (1 May 2007), pp. 1607-1612.
    by Stuart K Kim
    posted to no-tag by ana on 2007-11-20 01:58:51 as **
  • MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216.
    by Saurabh Sinha, Xin He
  • Profile-based string kernels for remote homology detection and motif extraction.
    J Bioinform Comput Biol, Vol. 3, No. 3. (June 2005), pp. 527-550.
    by R Kuang, E Ie, K Wang, K Wang, M Siddiqi, Y Freund, C Leslie
  • Activity of a C. elegans GATA transcription factor, ELT-1, expressed in yeast.
    J Mol Biol, Vol. 253, No. 5. (10 November 1995), pp. 665-676.
    by YH Shim, JJ Bonner, T Blumenthal
  • The evolutionary duplication and probable demise of an endodermal GATA factor in Caenorhabditis elegans.
    Genetics, Vol. 165, No. 2. (October 2003), pp. 575-588.
  • Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds
    BMC Bioinformatics, Vol. 6, No. 1. (2005)
    by Rainer Breitling, Patrick Armengaud, Anna Amtmann
  • Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.
    Proc Natl Acad Sci U S A (31 July 2006)
    by Celine Moorman, Ling V V Sun, Junbai Wang, Elzo de Wit, Wendy Talhout, Lucas D D Ward, Frauke Greil, Xiang-Jun J Lu, Kevin P P White, Harmen J J Bussemaker, Bas van Steensel
  • Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes.
    Brief Bioinform (12 July 2007)
    by Nikolay A A Kolchanov, Tatyana I I Merkulova, Elena V V Ignatieva, Elena A A Ananko, Dmitry Yu Y Oshchepkov, Viktor G G Levitsky, Gennady V V Vasiliev, Nataly V V Klimova, Vasily M M Merkulov, T Charles C Hodgman
  • The Evolution of Transcriptional Regulation in Eukaryotes
    Mol Biol Evol, Vol. 20, No. 9. (1 September 2003), pp. 1377-1419.
    by Gregory A Wray, Matthew W Hahn, Ehab Abouheif, James P Balhoff, Margaret Pizer, Matthew V Rockman, Laura A Romano
  • Orchestrated response: a symphony of transcription factors for gene control.
    Genes Dev, Vol. 14, No. 20. (15 October 2000), pp. 2551-2569.
    by B Lemon, R Tjian
  • FoxA1 binding to the MMTV LTR modulates chromatin structure and transcription.
    Exp Cell Res, Vol. 304, No. 2. (1 April 2005), pp. 593-603.
    by PH Holmqvist, S Belikov, KS Zaret, O Wrange
    posted to new by ana on 2007-07-02 23:36:40 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Comparative genomics of nematodes.
    Trends Genet, Vol. 21, No. 10. (October 2005), pp. 573-581.
    by M Mitreva, ML Blaxter, DM Bird, JP McCarter
  • A global analysis of Caenorhabditis elegans operons
    Nature, Vol. 417, No. 6891. (20 June 2002), pp. 851-854.
    by Thomas Blumenthal, Donald Evans, Christopher D Link, Alessandro Guffanti, Daniel Lawson, Jean Thierry-Mieg, Danielle Thierry-Mieg, Wei L Chiu, Kyle Duke, Moni Kiraly, Stuart K Kim
    posted to new by ana on 2007-06-12 23:44:04 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Genome organization: Teamed up for transcription
    Nature, Vol. 417, No. 6891. (20 June 2002), pp. 797-798.
    by Christian von Mering, Peer Bork
    posted to new by ana on 2007-06-12 23:41:46 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Transcription factors: structural families and principles of DNA recognition.
    Annu Rev Biochem, Vol. 61 (1992), pp. 1053-1095.
    by CO Pabo, RT Sauer
  • Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5.
    Nature, Vol. 364, No. 6436. (29 July 1993), pp. 412-420.
    by KL Clark, ED Halay, E Lai, SK Burley
    posted to new by ana on 2007-06-08 02:55:14 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • The fork head domain: a novel DNA binding motif of eukaryotic transcription factors?
    Cell, Vol. 63, No. 3. (2 November 1990), pp. 455-456.
    by D Weigel, H Jäckle
  • An evolutionary framework for the study of developmental evolution in a set of nematodes related to Caenorhabditis elegans.
    Mol Phylogenet Evol, Vol. 8, No. 2. (October 1997), pp. 249-259.
    by JG Baldwin, LM Frisse, JT Vida, CD Eddleman, WK Thomas
  • A molecular evolutionary framework for the phylum Nematoda
    Nature, Vol. 392, No. 6671. (5 March 1998), pp. 71-75.
    by Mark L Blaxter, Paul De Ley, James R Garey, Leo X Liu, Patsy Scheldeman, Andy Vierstraete, Jacques R Vanfleteren, Laura Y Mackey, Mark Dorris, Linda M Frisse, JT Vida, Kelley W Thomas
    posted to new by ana on 2007-06-06 01:16:45 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Caenorhabditis elegans is a nematode.
    Science, Vol. 282, No. 5396. (11 December 1998), pp. 2041-2046.
    by M Blaxter
  • DAF-16 target genes that control C. elegans life-span and metabolism.
    Science, Vol. 300, No. 5619. (25 April 2003), pp. 644-647.
    by SS Lee, S Kennedy, AC Tolonen, G Ruvkun
  • Transcriptional outputs of the Caenorhabditis elegans forkhead protein DAF-16
    Aging Cell, Vol. 2, No. 2. (2003), pp. 111-121.
    by Joshua Mcelwee, Kerry Bubb, James H Thomas
  • SMK-1, an Essential Regulator of DAF-16-Mediated Longevity
    Cell, Vol. 124, No. 5. (10 March 2006), pp. 1039-1053.
    by Suzanne Wolff, Hui Ma, Denise Burch, Gustavo A Maciel, Tony Hunter, Andrew Dillin
    posted to new by ana on 2007-06-05 00:16:05 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Protein families and TRIBES in genome sequence space.
    Nucleic Acids Res, Vol. 31, No. 15. (1 August 2003), pp. 4632-4638.
    by AJ Enright, V Kunin, CA Ouzounis
  • Protein structure and evolutionary history determine sequence space topology.
    Genome Res, Vol. 15, No. 3. (March 2005), pp. 385-392.
  • Understanding nature's catalytic toolkit.
    Trends Biochem Sci (5 October 2005)
    by Alex Gutteridge, Janet M M Thornton
  • Flavin-dependent enzymes
    (1998), pp. 84-100.
    by BA Palfey, V Massey
    edited by M Sinnot
  • To be or not to be an oxidase: challenging the oxygen reactivity of flavoenzymes
    Trends in Biochemical Sciences, Vol. 31, No. 5. (May 2006), pp. 276-283.
    by Andrea Mattevi
  • The three-dimensional structure of flavodoxin reductase from Escherichia coli at 1.7 a resolution
    Journal of Molecular Biology, Vol. 268, No. 1. (25 April 1997), pp. 147-157.
    by Margareta Ingelman, Vera Bianchi, Hans Eklund
  • Microarray Analysis
    PLoS Biology, Vol. 1, No. 1. (1 October 2003), e15.
    by Greg Gibson
  • New avenues in protein function prediction.
    Protein Sci, Vol. 15, No. 6. (June 2006), pp. 1527-1529.
  • The molecular structure of Rv2074, a probable pyridoxine 5′-phosphate oxidase from Mycobacterium tuberculosis, at 1.6 Å resolution
    Acta Crystallographica Section F: Structural Biology and Crystallization Communications, Vol. 62, No. 8. (August 2006), pp. 735-742.
    by Biswal, , Au, , Cherney, , Garen, , James,
  • The crystal structure of CREG, a secreted glycoprotein involved in cellular growth and differentiation.
    Proc Natl Acad Sci U S A, Vol. 102, No. 51. (20 December 2005), pp. 18326-18331.
    by M Sacher, A Di Bacco, VV Lunin, Z Ye, J Wagner, G Gill, M Cygler
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