PLoS Computational Biology, Volume 4

Volume 4, Number 1, January 2008

Message from ISCB

• 
  K. Bretonnel Cohen, Lawrence Hunter:
  Getting Started in Text Mining.

Education

• 
  Dirk Holste, Uwe Ohler:
  Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events.

Research Articles

• 
  Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson:
  A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells.
• 
  Guo-Cheng Yuan, Jun S. Liu:
  Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion.
• 
  Xinli Liu, Yechun Xu, Honglin Li, Xicheng Wang, Hualiang Jiang, Francisco J. Barrantes:
  Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor.
• 
  Richard A. Notebaart, Bas Teusink, Roland J. Siezen, Balázs Papp:
  Co-Regulation of Metabolic Genes Is Better Explained by Flux Coupling Than by Network Distance.
• 
  Nicolas Pinto, David D. Cox, James J. DiCarlo:
  Why is Real-World Visual Object Recognition Hard?
• 
  Malin C. Andersen, Pär G. Engström, Stuart Lithwick, David J. Arenillas, Per Eriksson, Boris Lenhard, Wyeth W. Wasserman, Jacob Odeberg:
  In Silico Detection of Sequence Variations Modifying Transcriptional Regulation.
• 
  Christina M. Weaver, Susan L. Wearne:
  Neuronal Firing Sensitivity to Morphologic and Active Membrane Parameters.
• 
  Huiquan Wang, Craig J. Benham:
  Superhelical Destabilization in Regulatory Regions of Stress Response Genes.
• 
  Chikara Furusawa, Kunihiko Kaneko:
  A Generic Mechanism for Adaptive Growth Rate Regulation.
• 
  Daniela Raijman, Ron Shamir, Amos Tanay:
  Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites.
• 
  Matthew Menke, Bonnie Berger, Lenore Cowen:
  Matt: Local Flexibility Aids Protein Multiple Structure Alignment.
• 
  Clinton H. Hansen, Robert G. Endres, Ned S. Wingreen:
  Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation.
• 
  Chuan-Yun Li, Xizeng Mao, Liping Wei:
  Genes and (Common) Pathways Underlying Drug Addiction.
• 
  Gil Hornung, Naama Barkai:
  Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback.

Correspondence

• 
  Will Fischer, H. X. Liao, Barton F. Haynes, Norman L. Letvin, Bette T. Korber:
  Coping with Viral Diversity in HIV Vaccine Design: A Response to Nickle et al.
• 
  David C. Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei L. Kosakovsky Pond, James I. Mullins:
  Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al.

Volume 4, Number 2, February 2008

Message from ISCB

• 
  Ganesh A. Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman, Stuart C. Sealfon:
  Getting Started in Biological Pathway Construction and Analysis.

Education

• 
  Michal J. Okoniewski, Crispin J. Miller:
  Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor.

Review

• 
  Leo C. McHugh, Jonathan W. Arthur:
  Computational Methods for Protein Identification from Mass Spectrometry Data.

Research Articles

• 
  Julius B. Lucks, David R. Nelson, Grzegorz R. Kudla, Joshua B. Plotkin:
  Genome Landscapes and Bacteriophage Codon Usage.
• 
  Nobuhiko Tokuriki, Francois Stricher, Luis Serrano, Dan S. Tawfik:
  How Protein Stability and New Functions Trade Off.
• 
  Lihua Zou, Sira Sriswasdi, Brian C. Ross, Patrycja Vasilyev Missiuro, Jun S. Liu, Hui Ge:
  Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis.
• 
  Antti Saarinen, Marja-Leena Linne, Olli Yli-Harja:
  Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability.
• 
  Derek A. Ruths, Melissa Muller, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram:
  The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks.
• 
  Ivan Coluzza, Alfonso De Simone, Franca Fraternali, Daan Frenkel:
  Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes.
• 
  Adrian W. R. Serohijos, Tamás Hegedüs, John R. Riordan, Nikolay V. Dokholyan:
  Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding.
• 
  Héctor Marlosti Montiel Molina, César Millán-Pacheco, Nina Pastor, Gabriel del Rio:
  Computer-Based Screening of Functional Conformers of Proteins.
• 
  Naomi Habib, Tommy Kaplan, Hanah Margalit, Nir Friedman:
  A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval.
• 
  Tae J. Lee, Guang Yao, Joseph Nevins, Lingchong You:
  Sensing and Integration of Erk and PI3K Signals by Myc.
• 
  Navin Elango, Seong-Ho Kim, Eric Vigoda, Soojin V. Yi:
  Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation.
• 
  Jennifer Listgarten, Zabrina L. Brumme, Carl Myers Kadie, Gao Xiaojiang, Bruce D. Walker, Mary Carrington, Philip J. R. Goulder, David Heckerman:
  Statistical Resolution of Ambiguous HLA Typing Data.
• 
  Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, Josh Dubnau:
  Identification of Synaptic Targets of Drosophila Pumilio.
• 
  Anna Dvorkin, Yoav Benjamini, Ilan Golani:
  Mouse Cognition-Related Behavior in the Open-Field: Emergence of Places of Attraction.
• 
  Zhaoping Li, Jingling Li:
  Filling-In and Suppression of Visual Perception from Context: A Bayesian Account of Perceptual Biases by Contextual Influences.
• 
  Dennis Kostka, Rainer Spang:
  Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures.
• 
  Vesa P. Hytönen, Viola Vogel:
  How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism.
• 
  Elena J. Edelman, Justin Guinney, Jen-Tsan A. Chi, Phillip G. Febbo, Sayan Mukherjee:
  Modeling Cancer Progression via Pathway Dependencies.
• 
  Avner Wallach, Danny Eytan, Shimon Marom, Ron Meir:
  Selective Adaptation in Networks of Heterogeneous Populations: Model, Simulation, and Experiment.
• 
  Joshua F. Apgar, Jared E. Toettcher, Drew Endy, Forest M. White, Bruce Tidor:
  Stimulus Design for Model Selection and Validation in Cell Signaling.
• 
  Fred H. Hamker, Marc Zirnsak, Dirk Calow, Markus Lappe:
  The Peri-Saccadic Perception of Objects and Space.
• 
  Sean Carver, Eatai Roth, Noah J. Cowan, Eric S. Fortune:
  Synaptic Plasticity Can Produce and Enhance Direction Selectivity.
• 
  Eric R. Paquet, Guillaume Rey, Felix Naef:
  Modeling an Evolutionary Conserved Circadian Cis-Element.
• 
  Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, James Andrew McCammon, Steven M. Sine:
  Control of Cation Permeation through the Nicotinic Receptor Channel.
• 
  Douglas L. Theobald, Deborah S. Wuttke:
  Accurate Structural Correlations from Maximum Likelihood Superpositions.
• 
  Arend Hintze, Christoph Adami:
  Evolution of Complex Modular Biological Networks.
• 
  Daniel Segura, Radhakrishnan Mahadevan, Katy Juarez, Derek R. Lovley:
  Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens.
• 
  Peter Dayan, Quentin J. M. Huys:
  Serotonin, Inhibition, and Negative Mood.
• 
  Rafi Haddad, Liran Carmel, Noam Sobel, David Harel:
  Predicting the Receptive Range of Olfactory Receptors.

Correspondence

• 
  Morgan C. Giddings:
  On the Process of Becoming a Great Scientist.

Volume 4, Number 3, March 2008

Editorial

• 
  Philip E. Bourne, J. Lynn Fink, Mark Gerstein:
  Open Access: Taking Full Advantage of the Content.

Perspective

• 
  Edgardo Moreno, Bruno Lomonte, José María Gutiérrez:
  Computational Biology in Costa Rica: The Role of a Small Country in the Global Context of Bioinformatics.

Research Articles

• 
  Bin Kang, Yuan-Yuan Li, Xiao Chang, Lei Liu, Yi-Xue Li:
  Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation.
• 
  David Basanta, Mark A. Miodownik, Buzz Baum:
  The Evolution of Robust Development and Homeostasis in Artificial Organisms.
• 
  Lars V. Schäfer, Gerrit Groenhof, Martial Boggio-Pasqua, Michael A. Robb, Helmut Grubmüller:
  Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595.
• 
  Isaac Shemer, Björn Brinne, Jesper Tegnér, Sten Grillner:
  Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus.
• 
  Zenas C. Chao, Douglas J. Bakkum, Steve M. Potter:
  Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior.
• 
  Ugo Ala, Rosario Michael Piro, Elena Grassi, Christian Damasco, Lorenzo Silengo, Martin Oti, Paolo Provero, Ferdinando Di Cunto:
  Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis.
• 
  Jason Ernst, Qasim K. Beg, Krin A. Kay, Gábor Balázsi, Zoltán N. Oltvai, Ziv Bar-Joseph:
  A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli.
• 
  Carson C. Chow, Kevin D. Hall:
  The Dynamics of Human Body Weight Change.
• 
  Alex Roxin, Anders Ledberg:
  Neurobiological Models of Two-Choice Decision Making Can Be Reduced to a One-Dimensional Nonlinear Diffusion Equation.
• 
  Sichun Yang, Benoît Roux:
  Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms.
• 
  Yasser Roudi, Alessandro Treves:
  Representing Where along with What Information in a Model of a Cortical Patch.
• 
  Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich:
  Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics.
• 
  Yossi Yovel, Matthias O. Franz, Peter Stilz, Hans-Ulrich Schnitzler:
  Plant Classification from Bat-Like Echolocation Signals.
• 
  Thomas Manke, Helge G. Roider, Martin Vingron:
  Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions.
• 
  Alejandra C. Ventura, Jacques-A. Sepulchre, Sofía D. Merajver:
  A Hidden Feedback in Signaling Cascades Is Revealed.
• 
  William Ritchie, Samuel Granjeaud, Denis Puthier, Daniel Gautheret:
  Entropy Measures Quantify Global Splicing Disorders in Cancer.
• 
  Yonatan Loewenstein:
  Robustness of Learning That Is Based on Covariance-Driven Synaptic Plasticity.
• 
  Hédi Hegyi, Peter Tompa:
  Intrinsically Disordered Proteins Display No Preference for Chaperone Binding In Vivo.
• 
  Feng-Jie Sun, Gustavo Caetano-Anollés:
  Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses.
• 
  Siu Kang, Katsunori Kitano, Tomoki Fukai:
  Structure of Spontaneous UP and DOWN Transitions Self-Organizing in a Cortical Network Model.
• 
  Q. Tri Ho, Pieter Verboven, Bert E. Verlinden, Jeroen Lammertyn, Stefan Vandewalle, Bart M. Nicolaï:
  A Continuum Model for Metabolic Gas Exchange in Pear Fruit.
• 
  Ilya Nemenman, Geoffrey D. Lewen, William Bialek, Robert R. de Ruyter van Steveninck:
  Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution.

Volume 4, Number 4, April 2008

Education

• 
  Manuel João Costa, Eduardo Galembeck, Guilherme A. Marson, Bayardo B. Torres:
  A Quick Guide for Computer-Assisted Instruction in Computational Biology and Bioinformatics.

Perspective

• 
  Liping Wei, Jun Yu:
  Bioinformatics in China: A Personal Perspective.

Review

• 
  Yoram Vodovotz, Márie Csete, John Bartels, Steven Chang, Gary An:
  Translational Systems Biology of Inflammation.

Research Articles

• 
  Greg J. Stephens, Bethany Johnson-Kerner, William Bialek, William S. Ryu:
  Dimensionality and Dynamics in the Behavior of C. elegans.
• 
  Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael:
  Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer.
• 
  Lubomir Kostal, Petr Lánský, Jean-Pierre Rospars:
  Efficient Olfactory Coding in the Pheromone Receptor Neuron of a Moth.
• 
  Raoul Huys, Breanna E. Studenka, Nicole L. Rheaume, Howard N. Zelaznik, Viktor K. Jirsa:
  Distinct Timing Mechanisms Produce Discrete and Continuous Movements.
• 
  Alexej Abyzov, Alper Uzun, Phyllis R. Strauss, Valentin A. Ilyin:
  An AP Endonuclease 1-DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces.
• 
  Jian Qiu, William Stafford Noble:
  Predicting Co-Complexed Protein Pairs from Heterogeneous Data.
• 
  Jon Bohlin, Eystein Skjerve, David Ussery:
  Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes.
• 
  Luca A. Finelli, Seth Haney, Maxim Bazhenov, Mark Stopfer, Terrence J. Sejnowski:
  Synaptic Learning Rules and Sparse Coding in a Model Sensory System.
• 
  Sourav Bandyopadhyay, Ryan M. Kelley, Nevan J. Krogan, Trey Ideker:
  Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data.
• 
  Michael F. Lin, Ameya N. Deoras, Matthew D. Rasmussen, Manolis Kellis:
  Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes.
• 
  María Fabiana Laguna, Steffen Bohn, Eduardo A. Jagla:
  The Role of Elastic Stresses on Leaf Venation Morphogenesis.
• 
  Alexandr P. Kornev, Susan S. Taylor, Lynn F. Ten Eyck:
  A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains.
• 
  Mark W. J. van Passel, Pradeep Reddy Marri, Howard Ochman:
  The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli.
• 
  Adrian Gustavo Turjanski, J. Silvio Gutkind, Robert B. Best, Gerhard Hummer:
  Binding-Induced Folding of a Natively Unstructured Transcription Factor.
• 
  Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette, Björn Peters:
  A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach.
• 
  Franziska Matthäus, Carlos Salazar, Oliver Ebenhöh:
  Biosynthetic Potentials of Metabolites and Their Hierarchical Organization.
• 
  Bruno B. Averbeck, Moonsang Seo:
  The Statistical Neuroanatomy of Frontal Networks in the Macaque.
• 
  Ignacio E. Sánchez, Pedro Beltrão, Francois Stricher, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Frederic Rousseau, Luis Serrano:
  Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm.

Volume 4, Number 5, May 2008

Editorial

• 
  Edgardo Moreno, José María Gutiérrez:
  Ten Simple Rules for Aspiring Scientists in a Low-Income Country.

Education

• 
  Kiyoko F. Aoki-Kinoshita:
  An Introduction to Bioinformatics for Glycomics Research.

Review

• 
  Erik De Schutter:
  Why Are Computational Neuroscience and Systems Biology So Separate?

Research Articles

• 
  Sean R. Eddy:
  A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation.
• 
  Shuixia Guo, Jianhua Wu, Mingzhou Ding, Jianfeng Feng:
  Uncovering Interactions in the Frequency Domain.
• 
  Suhita Nadkarni, Peter Jung, Herbert Levine:
  Astrocytes Optimize the Synaptic Transmission of Information.
• 
  Katrin Hübner, Thomas Schwager, Karl Winkler, Jens-Georg Reich, Hermann-Georg Holzhütter:
  Computational Lipidology: Predicting Lipoprotein Density Profiles in Human Blood Plasma.
• 
  Lies Baeten, Joke Reumers, Vicente Tur, François Stricher, Tom Lenaerts, Luis Serrano, Frederic Rousseau, Joost Schymkowitz:
  Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments.
• 
  Richard A. Goldstein, Orkun S. Soyer:
  Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics.
• 
  John Porrill, Paul Dean:
  Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing.
• 
  Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin:
  Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks.
• 
  Nan Song, Jacob M. Joseph, George B. Davis, Dannie Durand:
  Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins.
• 
  Diego U. Ferreiro, Aleksandra M. Walczak, Elizabeth A. Komives, Peter G. Wolynes:
  The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures.
• 
  Yasuko Sugase-Miyamoto, Zheng Liu, Matthew C. Wiener, Lance M. Optican, Barry J. Richmond:
  Short-Term Memory Trace in Rapidly Adapting Synapses of Inferior Temporal Cortex.
• 
  Bobbie-Jo M. Webb-Robertson, Lee Ann McCue, Charles E. Lawrence:
  Measuring Global Credibility with Application to Local Sequence Alignment.
• 
  Scott A. Becker, Bernhard O. Palsson:
  Context-Specific Metabolic Networks Are Consistent with Experiments.
• 
  Adam Wasserstrom, Dan Frumkin, Rivka Adar, Shalev Itzkovitz, Tomer Stern, Shai Kaplan, Gabi Shefer, Irena Shur, Lior Zangi, Yitzhak Reizel, Alon Harmelin, Yuval Dor, Nava Dekel, Yair Reisner, Dafna Benayahu, Eldad Tzahor, Eran Segal, Ehud Shapiro:
  Estimating Cell Depth from Somatic Mutations.
• 
  Sean M. Cory, Theodore J. Perkins:
  Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation.
• 
  Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe, Timothy L. Bailey:
  Discovering Sequence Motifs with Arbitrary Insertions and Deletions.
• 
  Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel:
  Viral Population Estimation Using Pyrosequencing.
• 
  Arbel D. Tadmor, Tsvi Tlusty:
  A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number.
• 
  Mikhail I. Rabinovich, Ramón Huerta, Pablo Varona, Valentin S. Afraimovich:
  Transient Cognitive Dynamics, Metastability, and Decision Making.
• 
  Tatyana K. Korendyaseva, Denis N. Kuvatov, Vladimir A. Volkov, Michael V. Martinov, Victor M. Vitvitsky, Ruma Banerjee, Fazoil I. Ataullakhanov:
  An Allosteric Mechanism for Switching between Parallel Tracks in Mammalian Sulfur Metabolism.

Volume 4, Number 6, June 2008

Editorials

• 
  Manuel Corpas, Nils Gehlenborg, Sarath Chandra Janga, Philip E. Bourne:
  Ten Simple Rules for Organizing a Scientific Meeting.
• 
  Barbara Bryant:
  How To Advance Open International Scientific Exchange.

Message from ISCB

• 
  Michal Linial, Jill P. Mesirov, B. J. Morrison McKay, Burkhard Rost:
  ISMB 2008 Toronto.

Research Articles

• 
  Jason W. Locasale, Arup K. Chakraborty:
  Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins.
• 
  Kaustubh Supekar, Vinod Menon, Daniel L. Rubin, Mark A. Musen, Michael D. Greicius:
  Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease.
• 
  Peter S. Kim, Peter P. Lee, Doron Levy:
  Dynamics and Potential Impact of the Immune Response to Chronic Myelogenous Leukemia.
• 
  Gunnar Cedersund, Jacob Roll, Erik Ulfhielm, Anna Danielsson, Henrik Tidefelt, Peter Strålfors:
  Model-Based Hypothesis Testing of Key Mechanisms in Initial Phase of Insulin Signaling.
• 
  Upinder S. Bhalla:
  How To Record a Million Synaptic Weights in a Hippocampal Slice.
• 
  David Balduzzi, Giulio Tononi:
  Integrated Information in Discrete Dynamical Systems: Motivation and Theoretical Framework.
• 
  Joseph Schlecht, Matthew E. Kaplan, Kobus Barnard, Tatiana Karafet, Michael F. Hammer, Nirav C. Merchant:
  Machine-Learning Approaches for Classifying Haplogroup from Y Chromosome STR Data.
• 
  Duncan E. Donohue, Giorgio A. Ascoli:
  A Comparative Computer Simulation of Dendritic Morphology.
• 
  Pradipta Ray, Suyash Shringarpure, Mladen Kolar, Eric P. Xing:
  CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing.

Volume 4, Number 7, July 2008

Message from ISCB

• 
  Clare Sansom, B. J. Morrison McKay:
  ISCB Honors David Haussler and Aviv Regev.

Perspectives

• 
  Wannipha Tongsima, Sissades Tongsima, Prasit Palittapongarnpim:
  Outlook on Thailand's Genomics and Computational Biology Research and Development.
• 
  Stella Veretnik, J. Lynn Fink, Philip E. Bourne:
  Computational Biology Resources Lack Persistence and Usability.

Review

• 
  Karthik Devarajan:
  Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology.

Research Articles

• 
  Dmitry A. Dmitriev, Roman A. Rakitov:
  Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels.
• 
  Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert:
  Predicting and Validating Protein Interactions Using Network Structure.
• 
  Guy A. Hoelzer, Rich Drewes, Jeffrey Meier, René Doursat:
  Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences.
• 
  Shaoying Lu, Mingxing Ouyang, Jihye Seong, Jin Zhang, Shu Chien, Yingxiao Wang:
  The Spatiotemporal Pattern of Src Activation at Lipid Rafts Revealed by Diffusion-Corrected FRET Imaging.
• 
  Todd E. Hudson, Laurence T. Maloney, Michael S. Landy:
  Optimal Compensation for Temporal Uncertainty in Movement Planning.
• 
  Teunis J. P. van Dam, Berend Snel:
  Protein Complex Evolution Does Not Involve Extensive Network Rewiring.
• 
  Tammy M. K. Cheng, Yu-En Lu, Michele Vendruscolo, Pietro Liò, Tom L. Blundell:
  Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms.
• 
  Christian L. Althaus, Rob J. De Boer:
  Dynamics of Immune Escape during HIV/SIV Infection.
• 
  Matthew C. Cowperthwaite, Evan P. Economo, William R. Harcombe, Eric L. Miller, Lauren Ancel Meyers:
  The Ascent of the Abundant: How Mutational Networks Constrain Evolution.
• 
  Adam A. Smith, Aaron L. Vollrath, Christopher A. Bradfield, Mark Craven:
  Similarity Queries for Temporal Toxicogenomic Expression Profiles.
• 
  Sungho Hong, Brian Nils Lundstrom, Adrienne L. Fairhall:
  Intrinsic Gain Modulation and Adaptive Neural Coding.
• 
  Naren Ramakrishnan, Upinder S. Bhalla:
  Memory Switches in Chemical Reaction Space.
• 
  Enrico Rossoni, Jianfeng Feng, Brunello Tirozzi, David Brown, Gareth Leng, Françoise Moos:
  Emergent Synchronous Bursting of Oxytocin Neuronal Network.
• 
  Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder:
  Unraveling Protein Networks with Power Graph Analysis.
• 
  Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen:
  The Generation of Promoter-Mediated Transcriptional Noise in Bacteria.
• 
  Denise G. Teotico, Monica L. Frazier, Feng Ding, Nikolay V. Dokholyan, Brenda R. S. Temple, Matthew R. Redinbo:
  Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions.
• 
  Anton Crombach, Paulien Hogeweg:
  Evolution of Evolvability in Gene Regulatory Networks.
• 
  Joseph Ivanic, Anders Wallqvist, Jaques Reifman:
  Probing the Extent of Randomness in Protein Interaction Networks.
• 
  Leehod Baruch, Shalev Itzkovitz, Michal Golan-Mashiach, Ehud Shapiro, Eran Segal:
  Using Expression Profiles of Caenorhabditis elegans Neurons To Identify Genes That Mediate Synaptic Connectivity.
• 
  Ivan V. Surovtsev, Jeffrey J. Morgan, Paul A. Lindahl:
  Kinetic Modeling of the Assembly, Dynamic Steady State, and Contraction of the FtsZ Ring in Prokaryotic Cytokinesis.
• 
  Neda Bagheri, Jörg Stelling, Francis J. Doyle III:
  Circadian Phase Resetting via Single and Multiple Control Targets.
• 
  Nils Weinhold, Oliver Sander, Francisco S. Domingues, Thomas Lengauer, Ingolf Sommer:
  Local Function Conservation in Sequence and Structure Space.
• 
  Anthony Randal McIntosh, Natasa Kovacevic, Roxane J. Itier:
  Increased Brain Signal Variability Accompanies Lower Behavioral Variability in Development.
• 
  Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund:
  Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan.

Volume 4, Number 8, August 2008

Editorial

• 
  Karl J. Friston:
  Mean-Fields and Neural Masses.

Message from ISCB

• 
  Steven H. Kleinstein:
  Getting Started in Computational Immunology.

Perspective

• 
  Mark A. Ragan, Tim Littlejohn, Bruce Ross:
  Genome-Scale Computational Biology and Bioinformatics in Australia.

Review

• 
  Gustavo Deco, Viktor K. Jirsa, Peter A. Robinson, Michael Breakspear, Karl J. Friston:
  The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields.

Research Articles

• 
  Rahul Siddharthan:
  PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling.
• 
  Tyler McMillen, T. Williams, P. Holmes:
  Nonlinear Muscles, Passive Viscoelasticity and Body Taper Conspire To Create Neuromechanical Phase Lags in Anguilliform Swimmers.
• 
  Michael Capalbo, Eric Postma, Rainer Goebel:
  Combining Structural Connectivity and Response Latencies to Model the Structure of the Visual System.
• 
  Albert Kern, C. Heid, Willi-Hans Steeb, Norbert Stoop, Ruedi Stoop:
  Biophysical Parameters Modification Could Overcome Essential Hearing Gaps.
• 
  Sangjo Han, Dongsup Kim:
  Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways.
• 
  Turkan Haliloglu, Nir Ben-Tal:
  Cooperative Transition between Open and Closed Conformations in Potassium Channels.
• 
  Ronald C. Taylor, George K. Acquaah-Mensah, Mudita Singhal, Deepti Malhotra, Shyam Biswal:
  Network Inference Algorithms Elucidate Nrf2 Regulation of Mouse Lung Oxidative Stress.
• 
  Yu Tanouchi, Dennis Tu, Jungsang Kim, Lingchong You:
  Noise Reduction by Diffusional Dissipation in a Minimal Quorum Sensing Motif.
• 
  Cheol E. Han, Michael A. Arbib, Nicolas Schweighofer:
  Stroke Rehabilitation Reaches a Threshold.
• 
  Shobhit Gupta, Jonathan H. Dennis, Robert E. Thurman, Robert E. Kingston, John A. Stamatoyannopoulos, William Stafford Noble:
  Predicting Human Nucleosome Occupancy from Primary Sequence.
• 
  James V. Stone, Peter E. Jupp:
  Falling towards Forgetfulness: Synaptic Decay Prevents Spontaneous Recovery of Memory.
• 
  Philip G. McQueen, F. Ellis McKenzie:
  Host Control of Malaria Infections: Constraints on Immune and Erythropoeitic Response Kinetics.
• 
  Miler T. Lee, Junhyong Kim:
  Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs.
• 
  Angelo Rosa, Ralf Everaers:
  Structure and Dynamics of Interphase Chromosomes.
• 
  Eilon Sharon, Shai Lubliner, Eran Segal:
  A Feature-Based Approach to Modeling Protein-DNA Interactions.
• 
  Austin Huang, Collin M. Stultz:
  The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau.
• 
  Zhengdong D. Zhang, Joel S. Rozowsky, Michael Snyder, Joseph T. Chang, Mark Gerstein:
  Modeling ChIP Sequencing In Silico with Applications.
• 
  Steve Horvath, Jun Dong:
  Geometric Interpretation of Gene Coexpression Network Analysis.
• 
  Sorin Tanase-Nicola, Pieter Rein ten Wolde:
  Regulatory Control and the Costs and Benefits of Biochemical Noise.
• 
  Marco Cecchini, A. Houdusse, Martin Karplus:
  Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements.
• 
  Marc Turcotte, Wei Tang, Elliott M. Ross:
  Coordinate Regulation of G Protein Signaling via Dynamic Interactions of Receptor and GAP.
• 
  Jana L. Gevertz, Salvatore Torquato:
  A Novel Three-Phase Model of Brain Tissue Microstructure.
• 
  Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote:
  Efficient Algorithms for Probing the RNA Mutation Landscape.
• 
  Giancarlo La Camera, Barry J. Richmond:
  Modeling the Violation of Reward Maximization and Invariance in Reinforcement Schedules.
• 
  Alessandro Ambrosi, Claudia Cattoglio, Clelia Di Serio:
  Retroviral Integration Process in the Human Genome: Is It Really Non-Random? A New Statistical Approach.
• 
  V. V. Krishnan, Edmond Y. Lau, Justin Yamada, Daniel P. Denning, Samir S. Patel, Michael E. Colvin, Michael F. Rexach:
  Intramolecular Cohesion of Coils Mediated by Phenylalanine-Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin.
• 
  Shula Shazman, Yael Mandel-Gutfreund:
  Classifying RNA-Binding Proteins Based on Electrostatic Properties.
• 
  Michael Sammeth, Sylvain Foissac, Roderic Guigó:
  A General Definition and Nomenclature for Alternative Splicing Events.
• 
  Mark V. Albert, Adam Schnabel, David J. Field:
  Innate Visual Learning through Spontaneous Activity Patterns.
• 
  Jihua Hao, Adrian W. R. Serohijos, Gail Newton, Gina Tassone, Zuncai Wang, Dennis C. Sgroi, Nikolay V. Dokholyan, James P. Basilion:
  Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers.
• 
  Dominique Martinez, Noelia Montejo:
  A Model of Stimulus-Specific Neural Assemblies in the Insect Antennal Lobe.
• 
  Elena Zotenko, Julián Mestre, Dianne P. O'Leary, Teresa M. Przytycka:
  Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality.
• 
  Lorenzo Farina, Alberto De Santis, Samanta Salvucci, Giorgio Morelli, Ida Ruberti:
  Embedding mRNA Stability in Correlation Analysis of Time-Series Gene Expression Data.
• 
  Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt:
  Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies.

Volume 4, Number 9, September 2008

Education Articles

• 
  Xosé M. Fernández-Suárez, Ewan Birney:
  Advanced Genomic Data Mining.
• 
  Raja Mazumder, Sona Vasudevan:
  Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function.

Review

• 
  Phineus R. Markwick, Therese E. Malliavin, Michael Nilges:
  Structural Biology by NMR: Structure, Dynamics, and Interactions.

Research Articles

• 
  Yuanfang Guan, Chad L. Myers, Rong Lu, Ihor Lemischka, Carol J. Bult, Olga G. Troyanskaya:
  A Genomewide Functional Network for the Laboratory Mouse.
• 
  Kai Wang, Jeremy A. Horst, Gong Cheng, David C. Nickle, Ram Samudrala:
  Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information.
• 
  Klaus Wimmer, K. Jannis Hildebrandt, R. Matthias Hennig, Klaus Obermayer:
  Adaptation and Selective Information Transmission in the Cricket Auditory Neuron AN2.
• 
  Francisco J. P. Lopes, Fernando M. C. Vieira, David M. Holloway, Paulo Mascarello Bisch, Alexander V. Spirov:
  Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo.
• 
  Patrick Flaherty, Mala L. Radhakrishnan, Tuan Dinh, Robert A. Rebres, Tamara I. Roach, Michael I. Jordan, Adam P. Arkin:
  A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction.
• 
  Steven L. Salzberg, Daniel D. Sommer, Daniela Puiu, Vincent T. Lee:
  Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads.
• 
  Jeff Clune, Dusan Misevic, Charles Ofria, Richard E. Lenski, Santiago F. Elena, Rafael Sanjuán:
  Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes.
• 
  Shrihari Sonavane, Pinak Chakrabarti:
  Cavities and Atomic Packing in Protein Structures and Interfaces.
• 
  Mark Müller-Linow, Claus C. Hilgetag, Marc-Thorsten Hütt:
  Organization of Excitable Dynamics in Hierarchical Biological Networks.
• 
  Roeland Merks, Erica D. Perryn, Abbas Shirinifard, James A. Glazier:
  Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth.
• 
  Elena Rivas, Sean R. Eddy:
  Probabilistic Phylogenetic Inference with Insertions and Deletions.
• 
  Wallace F. Marshall:
  Modeling Recursive RNA Interference.
• 
  Van M. Savage, Eric J. Deeds, Walter Fontana:
  Sizing Up Allometric Scaling Theory.
• 
  Robert Riley, Matteo Pellegrini, David S. Eisenberg:
  Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis.
• 
  Ji-Ping Wang, Yvonne Fondufe-Mittendorf, Liqun Xi, Guei-Feng Tsai, Eran Segal, Jonathan Widom:
  Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae.
• 
  Neema Jamshidi, Bernhard Ø. Palsson:
  Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks.
• 
  John P. Archer, John W. Pinney, Jun Fan, Etienne Simon-Loriere, Eric J. Arts, Matteo Negroni, David L. Robertson:
  Identifying the Important HIV-1 Recombination Breakpoints.
• 
  Mark A. Kramer, Anita K. Roopun, Lucy M. Carracedo, Roger D. Traub, Miles A. Whittington, Nancy Kopell:
  Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex.
• 
  R. Sathyapriya, M. S. Vijayabaskar, Saraswathi Vishveshwara:
  Insights into Protein-DNA Interactions through Structure Network Analysis.

Volume 4, Number 10, October 2008

Education Articles

• 
  Marco Punta, Yanay Ofran:
  The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function.
• 
  Asa Ben-Hur, Cheng Soon Ong, Sören Sonnenburg, Bernhard Schölkopf, Gunnar Rätsch:
  Support Vector Machines and Kernels for Computational Biology.

Review

• 
  Duncan Hull, Steve Pettifer, Douglas B. Kell:
  Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web.

Research Articles

• 
  Carina Curto, Vladimir Itskov:
  Cell Groups Reveal Structure of Stimulus Space.
• 
  Szymon Stoma, Mikael Lucas, Jérôme Chopard, Marianne Schaedel, Jan Traas, Christophe Godin:
  Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development.
• 
  David M. Santucci, Sridhar Raghavachari:
  The Effects of NR2 Subunit-Dependent NMDA Receptor Kinetics on Synaptic Transmission and CaMKII Activation.
• 
  Jacek Puchalka, Matthew A. Oberhardt, Miguel Godinho, Agata Bielecka, Daniela Regenhardt, Kenneth N. Timmis, Jason A. Papin, Vítor A. P. Martins dos Santos:
  Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology.
• 
  Bastien Berret, Christian Darlot, Frédéric Jean, Thierry Pozzo, Charalambos Papaxanthis, Jean-Paul Gauthier:
  The Inactivation Principle: Mathematical Solutions Minimizing the Absolute Work and Biological Implications for the Planning of Arm Movements.
• 
  Pascal Durrens, Macha Nikolski, David James Sherman:
  Fusion and Fission of Genes Define a Metric between Fungal Genomes.
• 
  Elhanan Borenstein, David C. Krakauer:
  An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution.
• 
  Eric Banks, Elena Nabieva, Bernard Chazelle, Mona Singh:
  Organization of Physical Interactomes as Uncovered by Network Schemas.
• 
  Elodie Monsellier, Matteo Ramazzotti, Niccolò Taddei, Fabrizio Chiti:
  Aggregation Propensity of the Human Proteome.
• 
  Gary Chung Hon, Bing Ren, Wei Wang:
  ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome.
• 
  Robert Legenstein, Dejan Pecevski, Wolfgang Maass:
  A Learning Theory for Reward-Modulated Spike-Timing-Dependent Plasticity with Application to Biofeedback.
• 
  Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda:
  Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes.
• 
  Piers J. Ingram, Michael P. H. Stumpf, Jaroslav Stark:
  Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data.
• 
  Jun Yan, Haifang Wang, Yuting Liu, Chunxuan Shao:
  Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm.
• 
  Alexei Vazquez, Marcio A. de Menezes, Albert-László Barabási, Zoltán N. Oltvai:
  Impact of Limited Solvent Capacity on Metabolic Rate, Enzyme Activities, and Metabolite Concentrations of S. cerevisiae Glycolysis.
• 
  Anandamohan Ghosh, Y. Rho, Anthony Randal McIntosh, Rolf Kötter, Viktor K. Jirsa:
  Noise during Rest Enables the Exploration of the Brain's Dynamic Repertoire.
• 
  Marcelo Behar, Nan Hao, Henrik G. Dohlman, Timothy C. Elston:
  Dose-to-Duration Encoding and Signaling beyond Saturation in Intracellular Signaling Networks.
• 
  Steven A. Prescott, Yves De Koninck, Terrence J. Sejnowski:
  Biophysical Basis for Three Distinct Dynamical Mechanisms of Action Potential Initiation.
• 
  Sungsam Gong, Tom L. Blundell:
  Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures.
• 
  Ran Elkon, Reuven Agami:
  Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs.

Volume 4, Number 11, November 2008

Education

• 
  Joern Toedling, Wolfgang Huber:
  Analyzing ChIP-chip Data Using Bioconductor.

Review

• 
  Marcel E. Dinger, Ken C. Pang, Tim R. Mercer, John S. Mattick:
  Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities.

Research Articles

• 
  Adam B. Barrett, Mark C. W. van Rossum:
  Optimal Learning Rules for Discrete Synapses.
• 
  Wan Kyu Kim, Edward M. Marcotte:
  Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence.
• 
  Jonathan M. Guberman, Allison Fay, Jonathan Dworkin, Ned S. Wingreen, Zemer Gitai:
  PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution.
• 
  Cédric Chauve, Eric Tannier:
  A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes.
• 
  Raúl Guantes, Juan F. Poyatos:
  Multistable Decision Switches for Flexible Control of Epigenetic Differentiation.
• 
  Shubhada R. Hegde, Palanisamy Manimaran, Shekhar C. Mande:
  Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data.
• 
  Jonathan M. Carlson, Zabrina L. Brumme, Christine M. Rousseau, Chanson J. Brumme, Philippa Matthews, Carl Myers Kadie, James I. Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J. R. Goulder, David Heckerman:
  Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag.
• 
  Andreea Munteanu, Ricard V. Solé:
  Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition.
• 
  Goded Shahaf, Danny Eytan, Asaf Gal, Einat Kermany, Vladimir Lyakhov, Christoph Zrenner, Shimon Marom:
  Order-Based Representation in Random Networks of Cortical Neurons.
• 
  Nicolas Maubourguet, Annick Lesne, Jean-Pierre Changeux, Uwe Maskos, Philippe Faure:
  Behavioral Sequence Analysis Reveals a Novel Role for ß2* Nicotinic Receptors in Exploration.
• 
  Carlos J. Camacho, Yasuhiro Katsumata, Dana P. Ascherman:
  Structural and Thermodynamic Approach to Peptide Immunogenicity.
• 
  Stefan J. Kiebel, Jean Daunizeau, Karl J. Friston:
  A Hierarchy of Time-Scales and the Brain.
• 
  Roxana A. Stefanescu, Viktor K. Jirsa:
  A Low Dimensional Description of Globally Coupled Heterogeneous Neural Networks of Excitatory and Inhibitory Neurons.
• 
  Martin C. Stumpe, Helmut Grubmüller:
  Polar or Apolar - The Role of Polarity for Urea-Induced Protein Denaturation.
• 
  Stefan Auer, Filip Meersman, Christopher M. Dobson, Michele Vendruscolo:
  A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates.
• 
  Yuki Tsukada, Kazuhiro Aoki, Takeshi Nakamura, Yuichi Sakumura, Michiyuki Matsuda, Shin Ishii:
  Quantification of Local Morphodynamics and Local GTPase Activity by Edge Evolution Tracking.
• 
  Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, Christina S. Leslie:
  A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast.
• 
  Merav Parter, Nadav Kashtan, Uri Alon:
  Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments.
• 
  Karl J. Friston:
  Hierarchical Models in the Brain.
• 
  Murad Banaji, Alfred Mallet, Clare E. Elwell, Peter Nicholls, Chris E. Cooper:
  A Model of Brain Circulation and Metabolism: NIRS Signal Changes during Physiological Challenges.
• 
  Sheila M. Reynolds, Lukas Käll, Michael Riffle, Jeff A. Bilmes, William Stafford Noble:
  Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks.
• 
  Osnat Penn, Adi Stern, Nimrod D. Rubinstein, Julien Dutheil, Eran Bacharach, Nicolas Galtier, Tal Pupko:
  Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes.
• 
  Yair Field, Noam Kaplan, Yvonne Fondufe-Mittendorf, Irene K. Moore, Eilon Sharon, Yaniv Lubling, Jonathan Widom, Eran Segal:
  Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals.
• 
  Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee:
  Inferring Pathway Activity toward Precise Disease Classification.
• 
  Mark Yandell, Barry Moore, Fidel Salas, Chris Mungall, Andrew MacBride, Charles White, Martin G. Reese:
  Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins.
• 
  Yuichi Yamashita, Jun Tani:
  Emergence of Functional Hierarchy in a Multiple Timescale Neural Network Model: A Humanoid Robot Experiment.

Volume 4, Number 12, December 2008

Perspective

• 
  Philip E. Bourne, J. Lynn Fink:
  I Am Not a Scientist, I Am a Number.

Research Articles

• 
  Antonio Scialdone, Mario Nicodemi:
  Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation.
• 
  Nora C. Toussaint, Pierre Dönnes, Oliver Kohlbacher:
  A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-Based Vaccines.
• 
  Claudia Clopath, Lorric Ziegler, Eleni Vasilaki, Lars Büsing, Wulfram Gerstner:
  Tag-Trigger-Consolidation: A Model of Early and Late Long-Term-Potentiation and Depression.
• 
  Diego Calzolari, Stefania Bruschi, Laurence Coquin, Jennifer Schofield, Jacob D. Feala, John C. Reed, Andrew D. McCulloch, Giovanni Paternostro:
  Search Algorithms as a Framework for the Optimization of Drug Combinations.
• 
  Niamh C. Nowlan, Patrick J. Prendergast, Paula Murphy:
  Identification of Mechanosensitive Genes during Embryonic Bone Formation.
• 
  Hermann Cuntz, Friedrich Forstner, Jürgen Haag, Alexander Borst:
  The Morphological Identity of Insect Dendrites.
• 
  Feng Liu, Xiao-Jing Wang:
  A Common Cortical Circuit Mechanism for Perceptual Categorical Discrimination and Veridical Judgment.
• 
  Wako Yoshida, Raymond J. Dolan, Karl J. Friston:
  Game Theory of Mind.
• 
  Sanne Abeln, Daan Frenkel:
  Disordered Flanks Prevent Peptide Aggregation.
• 
  Nikita Vladimirov, Linda Løvdok, Dirk Lebiedz, Victor Sourjik:
  Dependence of Bacterial Chemotaxis on Gradient Shape and Adaptation Rate.
• 
  Ágnes Tóth-Petróczy, Christopher J. Oldfield, István Simon, Yuichiro Takagi, A. Keith Dunker, Vladimir N. Uversky, Mónika Fuxreiter:
  Malleable Machines in Transcription Regulation: The Mediator Complex.
• 
  Christina Kiel, Dorothee Aydin, Luis Serrano:
  Association Rate Constants of Ras-Effector Interactions Are Evolutionarily Conserved.
• 
  Alberto Mazzoni, Stefano Panzeri, Nikos K. Logothetis, Nicolas Brunel:
  Encoding of Naturalistic Stimuli by Local Field Potential Spectra in Networks of Excitatory and Inhibitory Neurons.
• 
  Ha Youn Lee, Alan S. Perelson, Su-Chan Park, Thomas Leitner:
  Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression.
• 
  Takashi Nishikawa, Natali Gulbahce, Adilson E. Motter:
  Spontaneous Reaction Silencing in Metabolic Optimization.
• 
  Da-Wei Li, Sandipan Mohanty, Anders Irbäck, Shuanghong Huo:
  Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment.