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Database and informatics methods

Early Evolution of Ionotropic GABA Receptors and Selective Regimes Acting on the Mammalian-Specific Theta and Epsilon Subunits

Christopher J. Martyniuk, Stéphane Aris-Brosou, Guy Drouin, Joel Cahn, Vance L. Trudeau

published 19 Sep 2007

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Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations

Sunhwan Jo, Taehoon Kim, Wonpil Im

published 12 Sep 2007

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Structural and Functional Analyses of Five Conserved Positively Charged Residues in the L1 and N-Terminal DNA Binding Motifs of Archaeal RadA Protein

Li-Tzu Chen, Tzu-Ping Ko, Yu-Wei Chang, Kuei-An Lin, Andrew H.-J. Wang, Ting-Fang Wang

published 12 Sep 2007

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Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site

Yuval Tabach, Ran Brosh, Yossi Buganim, Anat Reiner, Or Zuk, Assif Yitzhaky, Mark Koudritsky, Varda Rotter, Eytan Domany

published 29 Aug 2007

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Contribution of Exogenous Genetic Elements to the Group A Streptococcus Metagenome

Stephen B. Beres, James M. Musser

published 29 Aug 2007

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NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence

Morten Nielsen, Claus Lundegaard, Thomas Blicher, Kasper Lamberth, Mikkel Harndahl, Sune Justesen, Gustav Røder, Bjoern Peters, Alessandro Sette, Ole Lund, Søren Buus

published 29 Aug 2007

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Simple Sequence Repeats Provide a Substrate for Phenotypic Variation in the Neurospora crassa Circadian Clock

Todd P. Michael, Sohyun Park, Tae-Sung Kim, Jim Booth, Amanda Byer, Qi Sun, Joanne Chory, Kwangwon Lee

published 29 Aug 2007

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Phylogenomics Reshuffles the Eukaryotic Supergroups

Fabien Burki, Kamran Shalchian-Tabrizi, Marianne Minge, Åsmund Skjæveland, Sergey I. Nikolaev, Kjetill S. Jakobsen, Jan Pawlowski

published 29 Aug 2007

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A Dimer of the Toll-Like Receptor 4 Cytoplasmic Domain Provides a Specific Scaffold for the Recruitment of Signalling Adaptor Proteins

Ricardo Núñez Miguel, Joyce Wong, Julian F. Westoll, Heather J. Brooks, Luke A. J. O'Neill, Nicholas J. Gay, Clare E. Bryant, Tom P. Monie

published 29 Aug 2007

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Expressed Sequence Tags as a Tool for Phylogenetic Analysis of Placental Mammal Evolution

Morgan Kullberg, Björn Hallström, Ulfur Arnason, Axel Janke

published 22 Aug 2007

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Yersinia pestis Evolution on a Small Timescale: Comparison of Whole Genome Sequences from North America

Raymond K. Auerbach, Apichai Tuanyok, William S. Probert, Leo Kenefic, Amy J. Vogler, David C. Bruce, Christine Munk, Thomas S. Brettin, Mark Eppinger, Jacques Ravel, David M. Wagner, Paul Keim

published 22 Aug 2007

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The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists

Sven Heinicke, Michael S. Livstone, Charles Lu, Rose Oughtred, Fan Kang, Samuel V. Angiuoli, Owen White, David Botstein, Kara Dolinski

published 22 Aug 2007

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Selection against Spurious Promoter Motifs Correlates with Translational Efficiency across Bacteria

Jeffrey L. Froula, M. Pilar Francino

published 15 Aug 2007

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