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Content
November 2006, Volume 2, Issue 11
- 1-8 Humans Can Adopt Optimal Discounting Strategy under Real-Time Constraints
by N Schweighofer & K Shishida & C E Han & Y Okamoto & S C Tanaka & S Yamawaki & K Doya - 1-10 Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle
by Jin Wang & Bo Huang & Xuefeng Xia & Zhirong Sun - 1-12 Optimal Noise Filtering in the Chemotactic Response of Escherichia coli
by Burton W Andrews & Tau-Mu Yi & Pablo A Iglesias - 1-12 Meta-Analysis of Differentiating Mouse Embryonic Stem Cell Gene Expression Kinetics Reveals Early Change of a Small Gene Set
by Clive H Glover & Michael Marin & Connie J Eaves & Cheryl D Helgason & James M Piret & Jennifer Bryan - 1-14 Computational Inference of Neural Information Flow Networks
by V Anne Smith & Jing Yu & Tom V Smulders & Alexander J Hartemink & Erich D Jarvis
October 2006, Volume 2, Issue 10
- 1-8 Cooperation Prevails When Individuals Adjust Their Social Ties
by Francisco C Santos & Jorge M Pacheco & Tom Lenaerts - 1-17 Simulating Properties of In Vitro Epithelial Cell Morphogenesis
by Mark R Grant & Keith E Mostov & Thea D Tlsty & C Anthony Hunt
September 2006, Volume 2, Issue 9
- 1-2 Ten Simple Rules for Reviewers
by Philip E Bourne & Alon Korngreen - 1-4 Scientific Software Development Is Not an Oxymoron
by Susan M Baxter & Steven W Day & Jacquelyn S Fetrow & Stephanie J Reisinger - 1-12 Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors
by Xiaolin Cheng & Hailong Wang & Barry Grant & Steven M Sine & J Andrew McCammon - 1-13 Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability
by Stefan Legewie & Nils Blüthgen & Hanspeter Herzel - 1-13 Sampling Realistic Protein Conformations Using Local Structural Bias
by Thomas Hamelryck & John T Kent & Anders Krogh - 1-14 Imitating Manual Curation of Text-Mined Facts in Biomedicine
by Raul Rodriguez-Esteban & Ivan Iossifov & Andrey Rzhetsky - 1-14 Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation
by Manuel Barrio & Kevin Burrage & André Leier & Tianhai Tian - 1-16 Transient Calcium and Dopamine Increase PKA Activity and DARPP-32 Phosphorylation
by Maria Lindskog & MyungSook Kim & Martin A Wikström & Kim T Blackwell & Jeanette Hellgren Kotaleski
August 2006, Volume 2, Issue 8
- 1-2 One Year of PLoS Computational Biology
by Philip E Bourne - 1-7 Transient Resetting: A Novel Mechanism for Synchrony and Its Biological Examples
by Chunguang Li & Luonan Chen & Kazuyuki Aihara - 1-7 Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families
by Guohui Ding & Jiuhong Kang & Qi Liu & Tieliu Shi & Gang Pei & Yixue Li - 1-8 The Ion Channel Inverse Problem: Neuroinformatics Meets Biophysics
by Robert C Cannon & Giampaolo D'Alessandro - 1-11 High Epitope Expression Levels Increase Competition between T Cells
by Almut Scherer & Marcel Salathé & Sebastian Bonhoeffer
July 2006, Volume 2, Issue 7
- 1-1 On the Estimation of Intron Evolution
by Miklós Csűrös - 1-2 Authors' Reply
by Hung D Nguyen & Maki Yoshihama & Naoya Kenmochi - 1-8 Toward a Census of Bacteria in Soil
by Patrick D Schloss & Jo Handelsman - 1-11 Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition
by Jin Wang & Qiang Lu & H Peter Lu - 1-11 Nonoptimal Component Placement, but Short Processing Paths, due to Long-Distance Projections in Neural Systems
by Marcus Kaiser & Claus C Hilgetag - 1-11 Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles
by Markus J Herrgård & Stephen S Fong & Bernhard Ø Palsson - 1-11 Complex Parameter Landscape for a Complex Neuron Model
by Pablo Achard & Erik De Schutter - 1-15 Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method
by Martin Meier-Schellersheim & Xuehua Xu & Bastian Angermann & Eric J Kunkel & Tian Jin & Ronald N Germain - 1-17 Wiggle—Predicting Functionally Flexible Regions from Primary Sequence
by Jenny Gu & Michael Gribskov & Philip E Bourne - 1-18 Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome
by Adrian H Elcock
June 2006, Volume 2, Issue 6
- 1-8 Assessing the Accuracy of Ancestral Protein Reconstruction Methods
by Paul D Williams & David D Pollock & Benjamin P Blackburne & Richard A Goldstein - 1-9 Parametric Alignment of Drosophila Genomes
by Colin N Dewey & Peter M Huggins & Kevin Woods & Bernd Sturmfels & Lior Pachter - 1-10 On Modeling HIV and T Cells In Vivo: Assessing Causal Estimators in Vaccine Trials
by W David Wick & Peter B Gilbert & Steven G Self - 1-10 How Does Cross-Reactive Stimulation Affect the Longevity of CD8+ T Cell Memory?
by Vitaly V Ganusov & Sergei S Pilyugin & Rafi Ahmed & Rustom Antia - 1-11 A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules
by Bjoern Peters & Huynh-Hoa Bui & Sune Frankild & Morten Nielsen & Claus Lundegaard & Emrah Kostem & Derek Basch & Kasper Lamberth & Mikkel Harndahl & Ward Fleri & Stephen S Wilson & John Sidney & Ole Lund & Soren Buus & Alessandro Sette - 1-12 Noise-Induced Min Phenotypes in E. coli
by David Fange & Johan Elf
May 2006, Volume 2, Issue 5
- 1-8 Statistics of Knots, Geometry of Conformations, and Evolution of Proteins
by Rhonald C Lua & Alexander Y Grosberg - 1-10 Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays
by Rameen Beroukhim & Ming Lin & Yuhyun Park & Ke Hao & Xiaojun Zhao & Levi A Garraway & Edward A Fox & Ephraim P Hochberg & Ingo K Mellinghoff & Matthias D Hofer & Aurelien Descazeaud & Mark A Rubin & Matthew Meyerson & Wing Hung Wong & William R Sellers & Cheng Li - 1-10 Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach
by Christian L Barrett & Bernhard O Palsson - 1-12 Reverse Engineering the Gap Gene Network of Drosophila melanogaster
by Theodore J Perkins & Johannes Jaeger & John Reinitz & Leon Glass - 1-14 Transcription Factor Map Alignment of Promoter Regions
by Enrique Blanco & Xavier Messeguer & Temple F Smith & Roderic Guigó
April 2006, Volume 2, Issue 4
- 1-2 The Signal in the Genomes
by David Sankoff - 1-10 Practical Strategies for Discovering Regulatory DNA Sequence Motifs
by Kenzie D MacIsaac & Ernest Fraenkel - 1-13 Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation
by Eli S Groban & Arjun Narayanan & Matthew P Jacobson - 1-13 Codon Usage Domains over Bacterial Chromosomes
by Marc Bailly-Bechet & Antoine Danchin & Mudassar Iqbal & Matteo Marsili & Massimo Vergassola
March 2006, Volume 2, Issue 3
- 1-2 Authors' Reply
by Eliot C Bush & Bruce T Lahn - 1-8 The Emergence of Up and Down States in Cortical Networks
by David Holcman & Misha Tsodyks - 1-10 Circadian Clocks Are Resounding in Peripheral Tissues
by Andrey A Ptitsyn & Sanjin Zvonic & Steven A Conrad & L Keith Scott & Randall L Mynatt & Jeffrey M Gimble - 1-14 Role of Mechanical Factors in the Morphology of the Primate Cerebral Cortex
by Claus C Hilgetag & Helen Barbas
February 2006, Volume 2, Issue 2
- 1-1 Ismb 2006
by Goran Neshich & Philip E Bourne & Søren Brunak - 1-2 Ten Simple Rules for Getting Grants
by Philip E Bourne & Leo M Chalupa - 1-9 Seriation in Paleontological Data Using Markov Chain Monte Carlo Methods
by Kai Puolamäki & Mikael Fortelius & Heikki Mannila - 1-12 The Fragile Breakage versus Random Breakage Models of Chromosome Evolution
by Qian Peng & Pavel A Pevzner & Glenn Tesler
December 2005, Volume 1, Issue 7
- 1-3 Time to Organize the Bioinformatics Resourceome
by Nicola Cannata & Emanuela Merelli & Russ B Altman - 1-8 New Maximum Likelihood Estimators for Eukaryotic Intron Evolution
by Hung D Nguyen & Maki Yoshihama & Naoya Kenmochi - 1-23 PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
by Rahul Siddharthan & Eric D Siggia & Erik van Nimwegen
November 2005, Volume 1, Issue 6
- 1-2 Bioinformatics Education—Perspectives and Challenges
by Shoba Ranganathan - 1-7 Quantitative Analysis of Genetic and Neuronal Multi-Perturbation Experiments
by Alon Kaufman & Alon Keinan & Isaac Meilijson & Martin Kupiec & Eytan Ruppin - 1-10 A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes
by Daniel H Haft & Jeremy Selengut & Emmanuel F Mongodin & Karen E Nelson - 1-11 Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis
by Thomas LaFramboise & Barbara A Weir & Xiaojun Zhao & Rameen Beroukhim & Cheng Li & David Harrington & William R Sellers & Matthew Meyerson - 1-13 Use of Artificial Genomes in Assessing Methods for Atypical Gene Detection
by Rajeev K Azad & Jeffrey G Lawrence
October 2005, Volume 1, Issue 5
- 1-1 Protein Molecular Function Prediction by Bayesian Phylogenomics
by Barbara E Engelhardt & Michael I Jordan & Kathryn E Muratore & Steven E Brenner - 1-2 Ten Simple Rules for Getting Published
by Philip E Bourne - 1-6 The ISCB: Growing and Evolving in Step with Science
by Michael Gribskov - 1-13 Genomic Variability within an Organism Exposes Its Cell Lineage Tree
by Dan Frumkin & Adam Wasserstrom & Shai Kaplan & Uriel Feige & Ehud Shapiro
September 2005, Volume 1, Issue 4
- 1-1 Modeling the Amplification Dynamics of Human Alu Retrotransposons
by Dale J Hedges & Richard Cordaux & Jinchuan Xing & David J Witherspoon & Alan R Rogers & Lynn B Jorde & Mark A Batzer - 1-1 Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family
by Carsten Rautengarten & Dirk Steinhauser & Dirk Büssis & Annick Stintzi & Andreas Schaller & Joachim Kopka & Thomas Altmann - 1-1 A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation
by Daniel A Beard - 1-1 Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4–5 in Splicing
by Yuanyuan Xiao & Yee H Yang & Todd A Burckin & Lily Shiue & Grant A Hartzog & Mark R Segal
August 2005, Volume 1, Issue 3
- 1-1 Evidence of a Double-Lid Movement in Pseudomonas aeruginosa Lipase: Insights from Molecular Dynamics Simulations
by Subbulakshmi Latha Cherukuvada & Aswin Sai Narain Seshasayee & Krishnan Raghunathan & Sharmila Anishetty & Gautam Pennathur
July 2005, Volume 1, Issue 2
- 1-1 Recognition of Unknown Conserved Alternatively Spliced Exons
by Uwe Ohler & Noam Shomron & Christopher B Burge - 1-1 Molecular Switches at the Synapse Emerge from Receptor and Kinase Traffic
by Arnold Hayer & Upinder S Bhalla
June 2005, Volume 1, Issue 1
- 1-1 PLoS Computational Biology: A New Community Journal
by Philip E Bourne & Steven E Brenner & Michael B Eisen - 1-1 Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a β-Hairpin
by Laxmi Parida & Ruhong Zhou - 1-1 An Open Forum for Computational Biology
by Michael Gribskov