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    Journal: PLoS Computational Biology

    Volume 1, Issue 7

    0 -- 0Jie Song, Qikai Xu, Rolf Olsen, William F. Loomis, Gad Shaulsky, Adam Kuspa, Richard Sucgang. Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage
    0 -- 0Nicola Cannata, Emanuela Merelli, Russ B. Altman. Time to Organize the Bioinformatics Resourceome
    0 -- 0Quan Wen, Dmitri B. Chklovskii. Segregation of the Brain into Gray and White Matter: A Design Minimizing Conduction Delays
    0 -- 0Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen. PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
    0 -- 0Ala Trusina, Kim Sneppen, Ian B. Dodd, Keith E. Shearwin, J. Barry Egan. Functional Alignment of Regulatory Networks: A Study of Temperate Phages
    0 -- 0Eliot C. Bush, Bruce T. Lahn. Selective Constraint on Noncoding Regions of Hominid Genomes
    0 -- 0Hung D. Nguyen, Maki Yoshihama, Naoya Kenmochi. New Maximum Likelihood Estimators for Eukaryotic Intron Evolution
    0 -- 0Phillip W. Lord, Robert Stevens, James A. Butler, Robin McEntire. The Eighth Annual Bio-Ontologies Meeting
    0 -- 0Markus Ringnér, Morten Krogh. Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast
    0 -- 0Chang S. Chan, Olivier Elemento, Saeed Tavazoie. Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation
    0 -- 0Fredj Tekaia, Edouard Yeramian. Genome Trees from Conservation Profiles
    0 -- 0Eivind Almaas, Zoltán N. Oltvai, Albert-László Barabási. The Activity Reaction Core and Plasticity of Metabolic Networks

    Volume 1, Issue 6

    0 -- 0Michelle S. Scott, Sara J. Calafell, David Y. Thomas, Michael T. Hallett. Refining Protein Subcellular Localization
    0 -- 0Deqiang Zhang, James Andrew McCammon. The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis
    0 -- 0Michael F. Huerta, Gregory K. Farber, Elizabeth L. Wilder, Dushanka V. Kleinman, Patricia A. Grady, David A. Schwartz, Lawrence A. Tabak. NIH Roadmap Interdisciplinary Research Initiatives
    0 -- 0J. J. Bull, Lauren Ancel Meyers, Michael Lachmann. Quasispecies Made Simple
    0 -- 0Daniel H. Haft, Jeremy D. Selengut, Emmanuel F. Mongodin, Karen E. Nelson. A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes
    0 -- 0Rajeev K. Azad, Jeffrey G. Lawrence. Use of Artificial Genomes in Assessing Methods for Atypical Gene Detection
    0 -- 0Dan Frumkin, Adam Wasserstrom, Shai Kaplan, Uriel Feige, Ehud Y. Shapiro. Genomic Variability within an Organism Exposes Its Cell Lineage Tree
    0 -- 0Shoba Ranganathan. Bioinformatics Education - Perspectives and Challenges
    0 -- 0Thomas LaFramboise, Barbara A. Weir, Xiaojun Zhao, Rameen Beroukhim, Cheng Li, David Harrington, William R. Sellers, Matthew Meyerson. Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis
    0 -- 0Peter Sperisen, Christoph D. Schmid, Philipp Bucher, Olav Zilian. Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense
    0 -- 0Alon Kaufman, Alon Keinan, Isaac Meilijson, Martin Kupiec, Eytan Ruppin. Quantitative Analysis of Genetic and Neuronal Multi-Perturbation Experiments

    Volume 1, Issue 5

    0 -- 0Barbara E. Engelhardt, Michael I. Jordan, Kathryn E. Muratore, Steven E. Brenner. Protein Molecular Function Prediction by Bayesian Phylogenomics
    0 -- 0Stefan Legewie, Nils Blüthgen, Reinhold Schäfer, Hanspeter Herzel. Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction
    0 -- 0Eric D. Scheeff, Philip E. Bourne. Structural Evolution of the Protein Kinase-Like Superfamily
    0 -- 0Jinghui Zhang, David A. Wheeler, Imtiaz Yakub, Sharon Wei, Raman Sood, William Rowe, Paul P. Liu, Richard A. Gibbs, Kenneth H. Buetow. SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection
    0 -- 0Dmitry A. Rodionov, Inna Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand. Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks
    0 -- 0Michael Gribskov. The ISCB: Growing and Evolving in Step with Science
    0 -- 0Karthik Raman 0002, Preethi Rajagopalan, Nagasuma Chandra. Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs
    0 -- 0Philip E. Bourne. Ten Simple Rules for Getting Published

    Volume 1, Issue 4

    0 -- 0Dale J. Hedges, Richard Cordaux, Jinchuan Xing, David J. Witherspoon, Alan R. Rogers, Lynn B. Jorde, Mark A. Batzer. Alu Retrotransposons
    0 -- 0Daniel A. Beard. A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation
    0 -- 0Ruiqiang Li, Jia Ye, Songgang Li, Jing Wang 0003, Yujun Han, Chen Ye, Jian Wang, Huanming Yang, Jun Yu, Gane Ka-Shu Wong, Jun Wang 0004. ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
    0 -- 0James P. Carson, Tao Ju, Hui-Chen Lu, Christina Thaller, Mei Xu, Sarah L. Pallas, Michael C. Crair, Joe D. Warren, Wah Chiu, Gregor Eichele. A Digital Atlas to Characterize the Mouse Brain Transcriptome
    0 -- 0Igor N. Berezovsky, William W. Chen, Paul J. Choi, Eugene I. Shakhnovich. Entropic Stabilization of Proteins and Its Proteomic Consequences
    0 -- 0Yuanyuan Xiao, Yee Hwa Yang, Todd A. Burckin, Lily Shiue, Grant A. Hartzog, Mark R. Segal. Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing
    0 -- 0Andrew B. Goryachev, Da-Jun Toh, Keng Boon Wee, Travis Lee, Hai-Bao Zhang, Lian-Hui Zhang. Agrobacterium Population: A Stochastic Model
    0 -- 0Carsten Rautengarten, Dirk Steinhauser, Dirk Büssis, Annick Stintzi, Andreas Schaller, Joachim Kopka, Thomas Altmann. Arabidopsis thaliana Subtilase Gene Family

    Volume 1, Issue 3

    0 -- 0Lei Xie, Philip E. Bourne. Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models
    0 -- 0Lauren Ancel Meyers, Fredric D. Ancel, Michael Lachmann. Evolution of Genetic Potential
    0 -- 0Philip E. Bourne. Will a Biological Database Be Different from a Biological Journal?
    0 -- 0Pedro Beltrão, Luis Serrano. Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions
    0 -- 0Boris E. Shakhnovich. Correction: Improving the Precision of the Structure-Function Relationship by Considering Phylogenetic Context
    0 -- 0Qinghu Ren, Ian T. Paulsen. Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes
    0 -- 0Sagar D. Khare, Feng Ding, Kenneth N. Gwanmesia, Nikolay V. Dokholyan. Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases
    0 -- 0Subbulakshmi Latha Cherukuvada, Aswin Sai Narain Seshasayee, Krishnan Raghunathan, Sharmila Anishetty, Pennathur Gautam. Pseudomonas aeruginosa Lipase: Insights from Molecular Dynamics Simulations
    0 -- 0B. J. Morrison McKay. ISMB 2005 Conference Report
    0 -- 0Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano. Bacillus subtilis and Related Species

    Volume 1, Issue 2

    0 -- 0Hadi Quesneville, Casey M. Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, Michael Ashburner, Dominique Anxolabéhère. Combined Evidence Annotation of Transposable Elements in Genome Sequences
    0 -- 0Marian Groenenboom, Athanasius F. M. Marée, Paulien Hogeweg. The RNA Silencing Pathway: The Bits and Pieces That Matter
    0 -- 0Kevin Chen, Lior Pachter. Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
    0 -- 0Andrew M. Bisits, Roger Smith, Sam Mesiano, George Yeo, Kenneth Kwek, David MacIntyre, Eng C. Chan. Inflammatory Aetiology of Human Myometrial Activation Tested Using Directed Graphs
    0 -- 0Uwe Ohler, Noam Shomron, Christopher B. Burge. Recognition of Unknown Conserved Alternatively Spliced Exons
    0 -- 0Mercedes Pascual. Computational Ecology: From the Complex to the Simple and Back
    0 -- 0Adriana Migliaro, Angel A. Caputi, Ruben Budelli. Theoretical Analysis of Pre-Receptor Image Conditioning in Weakly Electric Fish
    0 -- 0Arnold Hayer, Upinder S. Bhalla. Molecular Switches at the Synapse Emerge from Receptor and Kinase Traffic

    Volume 1, Issue 1

    0 -- 0Johan Elf, Måns Ehrenberg. What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation?
    0 -- 0David H. Ardell, Leif A. Kirsebom. E. coli
    0 -- 0Bagrat R. Amirikian. A Phenomenological Theory of Spatially Structured Local Synaptic Connectivity
    0 -- 0Dominic Grün, Yi-Lu Wang, David Langenberger, Kristin C. Gunsalus, Nikolaus Rajewsky. Drosophila Species and Comparison to Mammalian Targets
    0 -- 0Daniel Barker, Mark Pagel. Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes
    0 -- 0Philip E. Bourne, Steven E. Brenner, Michael B. Eisen. PLoS Computational Biology: A New Community Journal
    0 -- 0Laxmi Parida, Ruhong Zhou. β-Hairpin
    0 -- 0Tommy Kaplan, Nir Friedman, Hanah Margalit. Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
    0 -- 0Prashanth Ak, Craig J. Benham. Susceptibility to Superhelically Driven DNA Duplex Destabilization: A Highly Conserved Property of Yeast Replication Origins
    0 -- 0Michael Gribskov. An Open Forum for Computational Biology
    0 -- 0Parantu K. Shah, Lars Juhl Jensen, Stéphanie Boué, Peer Bork. Extraction of Transcript Diversity from Scientific Literature
    0 -- 0Olaf Sporns, Giulio Tononi, Rolf Kötter. The Human Connectome: A Structural Description of the Human Brain
    0 -- 0Sean R. Eddy. "Antedisciplinary" Science
    0 -- 0Boris E. Shakhnovich. Improving the Precision of the Structure-Function Relationship by Considering Phylogenetic Context
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