PLoS Computational Biology, Volume 6

Volume 6, Number 1, January 2010

Messages from ISCB

• 
  Kimmen Sjölander:
  Getting Started in Structural Phylogenomics.
• 
  Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider:
  Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009.

Perspective

• 
  Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider:
  Live Coverage of Scientific Conferences Using Web Technologies.

Research Articles

• 
  Mark M. Schira, Christopher W. Tyler, Branka Spehar, Michael Breakspear:
  Modeling Magnification and Anisotropy in the Primate Foveal Confluence.
• 
  Jaebum Kim, Ryan Cunningham, Brian James, Stefan Wyder, Joshua D. Gibson, Oliver Niehuis, Evgeny M. Zdobnov, Hugh M. Robertson, Gene E. Robinson, John H. Werren, Saurabh Sinha:
  Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances.
• 
  Ingo Bojak, David T. J. Liley:
  Axonal Velocity Distributions in Neural Field Equations.
• 
  Shakti Gupta, Mano Ram Maurya, Shankar Subramaniam:
  Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells.
• 
  Dennis L. Chao, M. Elizabeth Halloran, Valerie J. Obenchain, Ira M. Longini Jr.:
  FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model.
• 
  Lufang Zhou, Miguel Antonio Aon, Tabish Almas, Sonia Cortassa, Raimond L. Winslow, Brian O'Rourke:
  A Reaction-Diffusion Model of ROS-Induced ROS Release in a Mitochondrial Network.
• 
  Pei-Chi Yang, Junko Kurokawa, Tetsushi Furukawa, Colleen E. Clancy:
  Acute Effects of Sex Steroid Hormones on Susceptibility to Cardiac Arrhythmias: A Simulation Study.
• 
  Stefan Pinkert, Jörg Schultz, Jörg Reichardt:
  Protein Interaction Networks - More Than Mere Modules.
• 
  Richard A. Neher, Thomas Leitner:
  Recombination Rate and Selection Strength in HIV Intra-patient Evolution.
• 
  Volker Egelhofer, Ida Schomburg, Dietmar Schomburg:
  Automatic Assignment of EC Numbers.
• 
  Yossi Ben Zion, Gur Yaari, Nadav M. Shnerb:
  Optimizing Metapopulation Sustainability through a Checkerboard Strategy.
• 
  Aroop Sircar, Jeffrey J. Gray:
  SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models.
• 
  Isabella Daidone, Hannes Neuweiler, Sören Doose, Markus Sauer, Jeremy C. Smith:
  Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains.
• 
  Ronald Van den Berg, Jos B. T. M. Roerdink, Frans W. Cornelissen:
  A Neurophysiologically Plausible Population Code Model for Feature Integration Explains Visual Crowding.
• 
  Sharat J. Vayttaden, Jacqueline Friedman, Tuan M. Tran, Thomas C. Rich, Carmen W. Dessauer, Richard B. Clark:
  Quantitative Modeling of GRK-Mediated β2AR Regulation.
• 
  Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, James Andrew McCammon:
  A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology.
• 
  Wee Siong Goh, Yuriy L. Orlov, Jingmei Li, Neil D. Clarke:
  Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local.
• 
  Nicolas Tabareau, Jean-Jacques E. Slotine, Quang-Cuong Pham:
  How Synchronization Protects from Noise.
• 
  Anna Dvorkin, Henry Szechtman, Ilan Golani:
  Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration.
• 
  Rod K. Nibbe, Mehmet Koyutürk, Mark R. Chance:
  An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer.
• 
  Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi, Roded Sharan:
  Associating Genes and Protein Complexes with Disease via Network Propagation.
• 
  Wei Zhang, Jun Zhu, Eric E. Schadt, Jun S. Liu:
  A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules.
• 
  Daniel Seeliger, Bert L. de Groot:
  Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations.
• 
  Tal Peleg, Nir Yosef, Eytan Ruppin, Roded Sharan:
  Network-Free Inference of Knockout Effects in Yeast.
• 
  Marc Röttig, Christian Rausch, Oliver Kohlbacher:
  Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families.
• 
  Christiaan Klijn, Jan Bot, David J. Adams, Marcel J. T. Reinders, Lodewyk F. A. Wessels, Jos Jonkers:
  Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach.
• 
  Jason N. Bazil, Gregery T. Buzzard, Ann E. Rundell:
  Modeling Mitochondrial Bioenergetics with Integrated Volume Dynamics.
• 
  Lukas Burger, Erik van Nimwegen:
  Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments.

Volume 6, Number 2, February 2010

Editorials

• 
  Nelson N. Gichora, Segun A. Fatumo, Mtakai V. Ngara, Noura Chelbat, Kavisha Ramdayal, Kenneth B. Opap, Geoffrey H. Siwo, Marion O. Adebiyi, Amina El Gonnouni, Denis Zofou, Amal A. M. Maurady, Ezekiel F. Adebiyi, Etienne Pierre de Villiers, Daniel K. Masiga, Jeffrey W. Bizzaro, Prashanth Suravajhala, Sheila C. Ommeh, Winston Hide:
  Ten Simple Rules for Organizing a Virtual Conference - Anywhere.
• 
  Rosemary Dickin, Cecy Marden, Catherine Nancarrow, Philip E. Bourne:
  A Review of 2009 for PLoS Computational Biology.

Education

• 
  Florian Markowetz:
  How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens.

Perspective

• 
  Philip E. Bourne, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, Roland L. Dunbrack Jr., Andreas Prlic, Greg B. Quinn, Peter W. Rose, Raship Shah, Wendy Tao, Brian D. Weitzner, Benjamin T. Yukich:
  Will Widgets and Semantic Tagging Change Computational Biology?

Review

• 
  John C. Wooley, Adam Godzik, Iddo Friedberg:
  A Primer on Metagenomics.

Research Articles

• 
  Ju Han, Hang Chang, Orsi Giricz, Genee Y. Lee, Frederick L. Baehner, Joe W. Gray, Mina J. Bissell, Paraic A. Kenny, Bahram Parvin:
  Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture.
• 
  Liqi Han, Jim Hanan, Peter M. Gresshoff:
  Computational Complementation: A Modelling Approach to Study Signalling Mechanisms during Legume Autoregulation of Nodulation.
• 
  Antony B. Holmes, Sara Kalvala, David E. Whitworth:
  Spatial Simulations of Myxobacterial Development.
• 
  Murat Cirit, Matej Krajcovic, Colin K. Choi, Erik S. Welf, Alan F. Horwitz, Jason M. Haugh:
  Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells.
• 
  Neema L. Salimi, Bosco K. Ho, David A. Agard:
  Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease.
• 
  Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan, Eytan Ruppin:
  Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species.
• 
  Myungsook Kim, Ted Huang, Ted Abel, Kim T. Blackwell:
  Temporal Sensitivity of Protein Kinase A Activation in Late-Phase Long Term Potentiation.
• 
  Rahul C. Deo, Luke Hunter, Gregory D. Lewis, Guillaume Pare, Ramachandran S. Vasan, Daniel Chasman, Thomas J. Wang, Robert E. Gerszten, Frederick P. Roth:
  Interpreting Metabolomic Profiles using Unbiased Pathway Models.
• 
  Sashi Marella, Bard Ermentrout:
  Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks.
• 
  Kalpana Dokka, Robert V. Kenyon, Emily A. Keshner, Konrad P. Körding:
  Self versus Environment Motion in Postural Control.
• 
  Jonathan Tang, C. Anthony Hunt:
  Identifying the Rules of Engagement Enabling Leukocyte Rolling, Activation, and Adhesion.
• 
  Florence Thuderoz, Maria-Ana Simonet, Olivier Hansen, Nicolas Pasqual, Aurélie Dariz, Thierry-Pascal Baum, Vivien Hierle, Jacques Demongeot, Patrice-Noël Marche, Evelyne Jouvin-Marche:
  Numerical Modelling Of The V-J Combinations Of The T Cell Receptor TRA/TRD Locus.
• 
  Patrick G. T. Walker, Simon Cauchemez, Raphaëlle Métras, Do Huu Dung, Dirk Pfeiffer, Azra C. Ghani:
  A Bayesian Approach to Quantifying the Effects of Mass Poultry Vaccination upon the Spatial and Temporal Dynamics of H5N1 in Northern Vietnam.
• 
  Takashi Nakano, Tomokazu Doi, Junichiro Yoshimoto, Kenji Doya:
  A Kinetic Model of Dopamine- and Calcium-Dependent Striatal Synaptic Plasticity.
• 
  Jun Zhu, Yanqing Chen, Amy S. Leonardson, Kai Wang, John R. Lamb, Valur Emilsson, Eric E. Schadt:
  Characterizing Dynamic Changes in the Human Blood Transcriptional Network.
• 
  Sara Ballouz, Andrew R. Francis, Ruiting Lan, Mark M. Tanaka:
  Conditions for the Evolution of Gene Clusters in Bacterial Genomes.
• 
  Ester Vilaprinyó, Rui Alves, Albert Sorribas:
  Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes.
• 
  Shirley Pepke, Tamara Kinzer-Ursem, Stefan Mihalas, Mary B. Kennedy:
  A Dynamic Model of Interactions of Ca²⁺, Calmodulin, and Catalytic Subunits of Ca²⁺/Calmodulin-Dependent Protein Kinase II.
• 
  J. Christian J. Ray, Oleg A. Igoshin:
  Adaptable Functionality of Transcriptional Feedback in Bacterial Two-Component Systems.
• 
  Patrick Garrigan, Charles P. Ratliff, Jennifer M. Klein, Peter Sterling, David H. Brainard, Vijay Balasubramanian:
  Design of a Trichromatic Cone Array.
• 
  Ivan Junier, Olivier C. Martin, François Képès:
  Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization.
• 
  Silpa Suthram, Joel Dudley, Annie P. Chiang, Rong Chen, Trevor Hastie, Atul J. Butte:
  Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets.
• 
  Jinghui Luo, Jean-Didier Maréchal, Sebastian Wärmländer, Astrid Gräslund, Alex Perálvarez-Marín:
  In Silico Analysis of the Apolipoprotein E and the Amyloid β Peptide Interaction: Misfolding Induced by Frustration of the Salt Bridge Network.
• 
  Wanjun Gu, Tong Zhou, Claus O. Wilke:
  A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes.
• 
  Sohyoung Kim, Mirit I. Aladjem, Geoffrey B. McFadden, Kurt W. Kohn:
  Predicted Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage.
• 
  Vitaly V. Ganusov, José A. M. Borghans, Rob J. De Boer:
  Explicit Kinetic Heterogeneity: Mathematical Models for Interpretation of Deuterium Labeling of Heterogeneous Cell Populations.
• 
  Fred P. Davis, Andrej Sali:
  The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures.
• 
  Tong Yang, Zheng Wang, Fang Wu, Jingwei Tan, Yijun Shen, Erguang Li, Jingzhi Dai, Ronghai Shen, Gang Li, Jinsong Wu, Luochun Wang, Haibo Wang, Yanjun Liu:
  A Variant of TNFR2-Fc Fusion Protein Exhibits Improved Efficacy in Treating Experimental Rheumatoid Arthritis.

Volume 6, Number 3, March 2010

Message from ISCB

• 
  Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B. Gerstein:
  Getting Started in Gene Orthology and Functional Analysis.

Research Articles

• 
  Bernie J. Daigle Jr., Alicia Deng, Tracey McLaughlin, Samuel W. Cushman, Margaret C. Cam, Gerald Reaven, Philip S. Tsao, Russ B. Altman:
  Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance.
• 
  Carlos Espinosa-Soto, Andreas Wagner:
  Specialization Can Drive the Evolution of Modularity.
• 
  Max von Kleist, Stephan Menz, Wilhelm Huisinga:
  Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV.
• 
  Thomas A. House, Matt J. Keeling:
  The Impact of Contact Tracing in Clustered Populations.
• 
  James O. Wrabl, Vincent J. Hilser:
  Investigating Homology between Proteins using Energetic Profiles.
• 
  Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov:
  Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction.
• 
  Chuan-Yun Li, Yong Zhang, Zhanbo Wang, Yan Zhang, Chunmei Cao, Ping-Wu Zhang, Shu-Juan Lu, Xiao-Mo Li, Quan Yu, Xiaofeng Zheng, Quan Du, George R. Uhl, Qing-Rong Liu, Liping Wei:
  A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions.
• 
  Samuel Bernard, Branka Cajavec Bernard, Francis Lévi, Hanspeter Herzel:
  Tumor Growth Rate Determines the Timing of Optimal Chronomodulated Treatment Schedules.
• 
  Carsten Magnus, Roland R. Regoes:
  Estimating the Stoichiometry of HIV Neutralization.
• 
  Timothy Nugent, David T. Jones:
  Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm.
• 
  Tjibbe Donker, Jacco Wallinga, Hajo Grundmann:
  Patient Referral Patterns and the Spread of Hospital-Acquired Infections through National Health Care Networks.
• 
  Carey D. Nadell, Kevin R. Foster, João B. Xavier:
  Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation.
• 
  Nikita Vladimirov, Dirk Lebiedz, Victor Sourjik:
  Predicted Auxiliary Navigation Mechanism of Peritrichously Flagellated Chemotactic Bacteria.
• 
  Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt:
  Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function.
• 
  Sergi Bermúdez i Badia, Ulysses Bernardet, Paul F. M. J. Verschure:
  Non-Linear Neuronal Responses as an Emergent Property of Afferent Networks: A Case Study of the Locust Lobula Giant Movement Detector.
• 
  Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro:
  Effects of Transcriptional Pausing on Gene Expression Dynamics.
• 
  Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin:
  Detailed Simulations of Cell Biology with Smoldyn 2.1.
• 
  Christina Vasalou, Michael A. Henson:
  A Multiscale Model to Investigate Circadian Rhythmicity of Pacemaker Neurons in the Suprachiasmatic Nucleus.
• 
  Jun Cai, Dan Xie, Zhewen Fan, Hiram Chipperfield, John Marden, Wing H. Wong, Sheng Zhong:
  Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells.
• 
  Michael Sherback, Francisco J. Valero Cuevas, Raffaello D'Andrea:
  Slower Visuomotor Corrections with Unchanged Latency are Consistent with Optimal Adaptation to Increased Endogenous Noise in the Elderly.
• 
  Will D. Penny, Klaas E. Stephan, Jean Daunizeau, Maria J. Rosa, Karl J. Friston, Thomas M. Schofield, Alexander P. Leff:
  Comparing Families of Dynamic Causal Models.
• 
  Muyoung Heo, Eugene I. Shakhnovich:
  Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response.
• 
  Julian M. L. Budd, Krisztina Kovács, Alex S. Ferecskó, Péter Buzás, Ulf T. Eysel, Zoltán F. Kisvárday:
  Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation.
• 
  Chun Wu, Michael T. Bowers, Joan-Emma Shea:
  Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ_9-40 Peptide: A Comparison to Agitated Fibrils.
• 
  Sean R. McGuffee, Adrian H. Elcock:
  Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm.
• 
  Christelle Reynès, Hélène Host, Anne-Claude Camproux, Guillaume Laconde, Florence Leroux, Anne Mazars, Benoit Deprez, Robin Fahraeus, Bruno O. Villoutreix, Olivier Sperandio:
  Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods.
• 
  Gabriele Lillacci, Mustafa Khammash:
  Parameter Estimation and Model Selection in Computational Biology.
• 
  Peter W. Battaglia, Massimiliano Di Luca, Marc O. Ernst, Paul R. Schrater, Tonja Machulla, Daniel J. Kersten:
  Within- and Cross-Modal Distance Information Disambiguate Visual Size-Change Perception.
• 
  Yuanfang Guan, Maitreya J. Dunham, Amy A. Caudy, Olga G. Troyanskaya:
  Systematic Planning of Genome-Scale Experiments in Poorly Studied Species.
• 
  Carl Song, Hilary Phenix, Vida Abedi, Matthew Scott, Brian P. Ingalls, Mads Kærn, Theodore J. Perkins:
  Estimating the Stochastic Bifurcation Structure of Cellular Networks.
• 
  Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Yu. Zinovyev:
  Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement.

Volume 6, Number 4, April 2010

Perspective

• 
  Ruchira S. Datta, Matthew W. Lux, Philip E. Bourne:
  PLoS Computational Biology Conference Postcards from PSB 2010.

Research Articles

• 
  Dirk Helbing, Attila Szolnoki, Matjaz Perc, György Szabó:
  Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions.
• 
  Erika Cerasti, Alessandro Treves:
  How Informative Are Spatial CA3 Representations Established by the Dentate Gyrus?
• 
  Akihiko Nakajima, Takako Isshiki, Kunihiko Kaneko, Shuji Ishihara:
  Robustness under Functional Constraint: The Genetic Network for Temporal Expression in Drosophila Neurogenesis.
• 
  Xuejing Li, Casandra Panea, Chris H. Wiggins, Valerie Reinke, Christina S. Leslie:
  Learning "graph-mer" Motifs that Predict Gene Expression Trajectories in Development.
• 
  Jussi Aittoniemi, Heidi de Wet, Frances M. Ashcroft, Mark S. P. Sansom:
  Asymmetric Switching in a Homodimeric ABC Transporter: A Simulation Study.
• 
  Daniel Ting, Guoli Wang, Maxim V. Shapovalov, Rajib Mitra, Michael I. Jordan, Roland L. Dunbrack Jr.:
  Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model.
• 
  Liming Wang, Jack Xin, Qing Nie:
  A Critical Quantity for Noise Attenuation in Feedback Systems.
• 
  Ariel Zylberberg, Diego Fernández Slezak, Pieter R. Roelfsema, Stanislas Dehaene, Mariano Sigman:
  The Brain's Router: A Cortical Network Model of Serial Processing in the Primate Brain.
• 
  Timothy E. Schlub, Redmond P. Smyth, Andrew J. Grimm, Johnson Mak, Miles P. Davenport:
  Accurately Measuring Recombination between Closely Related HIV-1 Genomes.
• 
  Elena Phoka, Hermann Cuntz, Arnd Roth, Michael Häusser:
  A New Approach for Determining Phase Response Curves Reveals that Purkinje Cells Can Act as Perfect Integrators.
• 
  Vinal V. Lakhani, Feng Ding, Nikolay V. Dokholyan:
  Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences.
• 
  Kenzie D. MacIsaac, Kinyui A. Lo, William Gordon, Shmulik Motola, Tali Mazor, Ernest Fraenkel:
  A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression.
• 
  Lucy J. Colwell, Michael P. Brenner, Katharina Ribbeck:
  Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex.
• 
  Danielle S. Bassett, Daniel Greenfield, Andreas Meyer-Lindenberg, Daniel R. Weinberger, Simon W. Moore, Edward T. Bullmore:
  Efficient Physical Embedding of Topologically Complex Information Processing Networks in Brains and Computer Circuits.
• 
  Julien Lefèvre, Jean-François Mangin:
  A Reaction-Diffusion Model of Human Brain Development.
• 
  Narcis Fernandez-Fuentes, Joseph M. Dybas, András Fiser:
  Structural Characteristics of Novel Protein Folds.
• 
  Dagmar Sternad, Se-Woong Park, Hermann Müller, Neville Hogan:
  Coordinate Dependence of Variability Analysis.
• 
  Jayne Y. Hehir-Kwa, Nienke Wieskamp, Caleb Webber, Rolph Pfundt, Han G. Brunner, Christian Gilissen, Bert B. A. de Vries, Chris P. Ponting, Joris A. Veltman:
  Accurate Distinction of Pathogenic from Benign CNVs in Mental Retardation.
• 
  Hugo Zeberg, Clas Blomberg, Peter Århem:
  Ion Channel Density Regulates Switches between Regular and Fast Spiking in Soma but Not in Axons.
• 
  Jenny C. A. Read:
  Vertical Binocular Disparity is Encoded Implicitly within a Model Neuronal Population Tuned to Horizontal Disparity and Orientation.
• 
  John Wambaugh, Imran Shah:
  Simulating Microdosimetry in a Virtual Hepatic Lobule.
• 
  Cristina Savin, Prashant Joshi, Jochen Triesch:
  Independent Component Analysis in Spiking Neurons.
• 
  Giovanni Russo, Mario di Bernardo, Eduardo D. Sontag:
  Global Entrainment of Transcriptional Systems to Periodic Inputs.
• 
  Rafi Haddad, Abebe Medhanie, Yehudah Roth, David Harel, Noam Sobel:
  Predicting Odor Pleasantness with an Electronic Nose.
• 
  M. Rowan Brown, Huw D. Summers, Paul Rees, Paul J. Smith, Sally C. Chappell, Rachel J. Errington:
  Flow-Based Cytometric Analysis of Cell Cycle via Simulated Cell Populations.
• 
  Manikandan Narayanan, Adrian Vetta, Eric E. Schadt, Jun Zhu:
  Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets.
• 
  Jan Nikolaj Dybowski, Dominik Heider, Daniel Hoffmann:
  Prediction of Co-Receptor Usage of HIV-1 from Genotype.
• 
  Sridhar Ranganathan, Patrick F. Suthers, Costas D. Maranas:
  OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions.
• 
  Bambang S. Adiwijaya, Eva Herrmann, Brian Hare, Tara L. Kieffer, Chao Lin, Ann D. Kwong, Varun Garg, John C. R. Randle, Christoph Sarrazin, Stefan Zeuzem, Paul R. Caron:
  A Multi-Variant, Viral Dynamic Model of Genotype 1 HCV to Assess the in vivo Evolution of Protease-Inhibitor Resistant Variants.
• 
  Lili Jiang, Qi Ouyang, Yuhai Tu:
  Quantitative Modeling of Escherichia coli Chemotactic Motion in Environments Varying in Space and Time.
• 
  Marcel Salathé, James H. Jones:
  Dynamics and Control of Diseases in Networks with Community Structure.
• 
  Enrico Petretto, Leonardo Bottolo, Sarah R. Langley, Matthias Heinig, Chris McDermott-Roe, Rizwan Sarwar, Michal Pravenec, Norbert Hübner, Timothy J. Aitman, Stuart A. Cook, Sylvia Richardson:
  New Insights into the Genetic Control of Gene Expression using a Bayesian Multi-tissue Approach.
• 
  Enrique Marcos, Ramon Crehuet, Ivet Bahar:
  On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm.
• 
  Peter W. Gething, Anand P. Patil, Simon I. Hay:
  Quantifying Aggregated Uncertainty in Plasmodium falciparum Malaria Prevalence and Populations at Risk via Efficient Space-Time Geostatistical Joint Simulation.
• 
  William J. Riehl, Paul L. Krapivsky, Sidney Redner, Daniel Segrè:
  Signatures of Arithmetic Simplicity in Metabolic Network Architecture.
• 
  Luis Mier-y-Teran-Romero, Mary Silber, Vassily Hatzimanikatis:
  The Origins of Time-Delay in Template Biopolymerization Processes.
• 
  Petras J. Kundrotas, Ilya A. Vakser:
  Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling.
• 
  Mark Campanelli, Tomás Gedeon:
  Somitogenesis Clock-Wave Initiation Requires Differential Decay and Multiple Binding Sites for Clock Protein.
• 
  Aleksej Zelezniak, Tune H. Pers, Simão Soares, Mary Elizabeth Patti, Kiran Raosaheb Patil:
  Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes.
• 
  Younghee Lee, Xinan Yang, Yong Huang, Hanli Fan, Qingbei Zhang, Youngfei Wu, Jianrong Li, Rifat Hasina, Chao Cheng, Mark W. Lingen, Mark B. Gerstein, Ralph R. Weichselbaum, H. Rosie Xing, Yves A. Lussier:
  Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis.
• 
  Daniel Bölinger, Joanna I. Sulkowska, Hsiao-Ping Hsu, Leonid A. Mirny, Mehran Kardar, José N. Onuchic, Peter Virnau:
  A Stevedore's Protein Knot.
• 
  Vaughn S. Cooper, Samuel H. Vohr, Sarah C. Wrocklage, Philip J. Hatcher:
  Why Genes Evolve Faster on Secondary Chromosomes in Bacteria.
• 
  Eric Samorodnitsky, B. Franklin Pugh:
  Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data.

Volume 6, Number 5, May 2010

Education Articles

• 
  Curtis Huttenhower, Oliver Hofmann:
  A Quick Guide to Large-Scale Genomic Data Mining.
• 
  Mark Reimers:
  Making Informed Choices about Microarray Data Analysis.

Perspective

• 
  Philip E. Bourne:
  What Do I Want from the Publisher of the Future?

Research Articles

• 
  Nitin Bhardwaj, Matthew B. Carson, Alexej Abyzov, Koon-Kiu Yan, Hui Lu, Mark B. Gerstein:
  Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets.
• 
  James A. Eddy, Leroy E. Hood, Nathan D. Price, Donald Geman:
  Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC).
• 
  Timothy C. Reluga:
  Game Theory of Social Distancing in Response to an Epidemic.
• 
  Henry C. Tuckwell, Jürgen Jost:
  Weak Noise in Neurons May Powerfully Inhibit the Generation of Repetitive Spiking but Not Its Propagation.
• 
  Diana Clausznitzer, Olga Oleksiuk, Linda Løvdok, Victor Sourjik, Robert G. Endres:
  Chemotactic Response and Adaptation Dynamics in Escherichia coli.
• 
  Karine Audouze, Agnieszka Sierakowska Juncker, Francisco S. Roque, Konrad Krysiak-Baltyn, Nils Weinhold, Olivier Taboureau, Thomas Skøt Jensen, Søren Brunak:
  Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks.
• 
  Amelie Stein, Patrick Aloy:
  Novel Peptide-Mediated Interactions Derived from High-Resolution 3-Dimensional Structures.
• 
  Alexander R. Statnikov, Constantin F. Aliferis:
  Analysis and Computational Dissection of Molecular Signature Multiplicity.
• 
  Sepp Kollmorgen, Nora Nortmann, Sylvia Schröder, Peter König:
  Influence of Low-Level Stimulus Features, Task Dependent Factors, and Spatial Biases on Overt Visual Attention.
• 
  Fidel Santamaría, Jossina Gonzalez, George J. Augustine, Sridhar Raghavachari:
  Quantifying the Effects of Elastic Collisions and Non-Covalent Binding on Glutamate Receptor Trafficking in the Post-Synaptic Density.
• 
  Ronald A. J. van Elburg, Arjen van Ooyen:
  Impact of Dendritic Size and Dendritic Topology on Burst Firing in Pyramidal Cells.
• 
  Simon DeDeo, David C. Krakauer, Jessica C. Flack:
  Inductive Game Theory and the Dynamics of Animal Conflict.
• 
  Anneke Brümmer, Carlos Salazar, Vittoria Zinzalla, Lilia Alberghina, Thomas Höfer:
  Mathematical Modelling of DNA Replication Reveals a Trade-off between Coherence of Origin Activation and Robustness against Rereplication.
• 
  Maxim N. Artyomov, Alexander Meissner, Arup K. Chakraborty:
  A Model for Genetic and Epigenetic Regulatory Networks Identifies Rare Pathways for Transcription Factor Induced Pluripotency.
• 
  Raul Mendez, Miriam Fritsche, Markus Porto, Ugo Bastolla:
  Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations.
• 
  Malcolm A. MacIver, Neelesh A. Patankar, Anup A. Shirgaonkar:
  Energy-Information Trade-Offs between Movement and Sensing.
• 
  Oliver Stegle, Leopold Parts, Richard Durbin, John M. Winn:
  A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies.
• 
  Jatin Narula, Aileen M. Smith, Berthold Göttgens, Oleg A. Igoshin:
  Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate.
• 
  Jochen S. Hub, Marcus B. Kubitzki, Bert L. de Groot:
  Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation.
• 
  Roberto Marchese, Rita Grandori, Paolo Carloni, Simone Raugei:
  On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions.
• 
  Ghanim Ullah, Steven J. Schiff:
  Assimilating Seizure Dynamics.
• 
  Markus Riester, Camille Stephan-Otto Attolini, Robert J. Downey, Samuel Singer, Franziska Michor:
  A Differentiation-Based Phylogeny of Cancer Subtypes.
• 
  Mohammad Fallahi-Sichani, Matthew A. Schaller, Denise E. Kirschner, Steven L. Kunkel, Jennifer J. Linderman:
  Identification of Key Processes that Control Tumor Necrosis Factor Availability in a Tuberculosis Granuloma.

Volume 6, Number 6, June 2010

Message from ISCB

• 
  B. J. Morrison McKay, Clare Sansom:
  2010 ISCB Overton Prize Awarded to Steven E. Brenner.

Education

• 
  Javier De Las Rivas, Celia Fontanillo:
  Protein-Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks.

Perspective

• 
  David B. Searls:
  The Roots of Bioinformatics.

Research Articles

• 
  Grigoriy E. Pinchuk, Eric A. Hill, Oleg V. Geydebrekht, Jessica De Ingeniis, Xiaolin Zhang, Andrei Osterman, James H. Scott, Samantha B. Reed, Margaret F. Romine, Allan E. Konopka, Alexander S. Beliaev, Jim K. Fredrickson, Jennifer L. Reed:
  Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation.
• 
  Nicholas J. P. Wiebe, Irmtraud M. Meyer:
  Transat - A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures.
• 
  Carolina Vizcaíno, Daniel Restrepo-Montoya, Diana Rodríguez, Luis F. Niño, Marisol Ocampo, Magnolia Vanegas, María T. Reguero, Nora L. Martínez, Manuel-Elkin Patarroyo, Manuel A. Patarroyo:
  Computational Prediction and Experimental Assessment of Secreted/Surface Proteins from Mycobacterium tuberculosis H37Rv.
• 
  Yan Gai, Brent Doiron, John Rinzel:
  Slope-Based Stochastic Resonance: How Noise Enables Phasic Neurons to Encode Slow Signals.
• 
  Andrew J. K. Phillips, Peter A. Robinson, David Jacob Kedziora, Romesh G. Abeysuriya:
  Mammalian Sleep Dynamics: How Diverse Features Arise from a Common Physiological Framework.
• 
  Ronald D. Hills Jr., Lanyuan Lu, Gregory A. Voth:
  Multiscale Coarse-Graining of the Protein Energy Landscape.
• 
  Yishai Shimoni, Marc Y. Fink, Soon-gang Choi, Stuart C. Sealfon:
  Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows.
• 
  Peter M. Kasson, Erik Lindahl, Vijay S. Pande:
  Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails.
• 
  Juliane Liepe, Michele Mishto, Kathrin Textoris-Taube, Katharina Janek, Christin Keller, Petra Henklein, Peter Michael Kloetzel, Alexey Zaikin:
  The 20S Proteasome Splicing Activity Discovered by SpliceMet.
• 
  Yuichi Togashi, Toshio Yanagida, Alexander S. Mikhailov:
  Nonlinearity of Mechanochemical Motions in Motor Proteins.
• 
  Padraig Gleeson, Sharon M. Crook, Robert C. Cannon, Michael L. Hines, Guy O. Billings, Matteo Farinella, Thomas M. Morse, Andrew P. Davison, Subhasis Ray, Upinder S. Bhalla, Simon R. Barnes, Yoana D. Dimitrova, Angus Silver:
  NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail.
• 
  Timothy R. Lezon, Ivet Bahar:
  Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology.
• 
  Sumeet Agarwal, Charlotte M. Deane, Mason A. Porter, Nick S. Jones:
  Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks.
• 
  Robert Karoly, Nora Lenkey, Andras O. Juhasz, E. Sylvester Vizi, Arpad Mike:
  Fast- or Slow-inactivated State Preference of Na⁺ Channel Inhibitors: A Simulation and Experimental Study.
• 
  Pontus Melke, Patrik Sahlin, Andre Levchenko, Henrik Jönsson:
  A Cell-Based Model for Quorum Sensing in Heterogeneous Bacterial Colonies.
• 
  Andres Kriete, William J. Bosl, Glenn Booker:
  Rule-Based Cell Systems Model of Aging using Feedback Loop Motifs Mediated by Stress Responses.
• 
  Juliette Martin:
  Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way.
• 
  Anton Zilman, Stefano Di Talia, Tijana Jovanovic-Talisman, Brian T. Chait, Michael P. Rout, Marcelo O. Magnasco:
  Enhancement of Transport Selectivity through Nano-Channels by Non-Specific Competition.
• 
  Sergey Gavrilets:
  Rapid Transition towards the Division of Labor via Evolution of Developmental Plasticity.
• 
  Robert Schulz, Attilio Vittorio Vargiu, Francesca Collu, Ulrich Kleinekathöfer, Paolo Ruggerone:
  Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations.
• 
  Jorge Sepulcre, Hesheng Liu, Tanveer Talukdar, Iñigo Martincorena, B. T. Thomas Yeo, Randy L. Buckner:
  The Organization of Local and Distant Functional Connectivity in the Human Brain.
• 
  Semen O. Yesylevskyy, Lars V. Schäfer, Durba Sengupta, Siewert J. Marrink:
  Polarizable Water Model for the Coarse-Grained MARTINI Force Field.
• 
  Eamon B. O'Dea, Thomas E. Keller, Claus O. Wilke:
  Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations?
• 
  Valentina Baldazzi, Delphine Ropers, Yves Markowicz, Daniel Kahn, Johannes Geiselmann, Hidde de Jong:
  The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes.
• 
  Rutger Hermsen, Bas Ursem, Pieter Rein ten Wolde:
  Combinatorial Gene Regulation Using Auto-Regulation.
• 
  Waleed A. Farahat, Hugh M. Herr:
  Optimal Workloop Energetics of Muscle-Actuated Systems: An Impedance Matching View.
• 
  Joseph Peter Torella, Remy Chait, Roy Kishony:
  Optimal Drug Synergy in Antimicrobial Treatments.
• 
  Sandra J. Kuhlman, Jiangteng Lu, Matthew S. Lazarus, Z. Josh Huang:
  Maturation of GABAergic Inhibition Promotes Strengthening of Temporally Coherent Inputs among Convergent Pathways.
• 
  Kyle Ellrott, Lukasz Jaroszewski, Weizhong Li, John C. Wooley, Adam Godzik:
  Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families.
• 
  Orland R. Gonzalez, Tanja Oberwinkler, Locedie Mansueto, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt:
  Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis.
• 
  Jingshan Zhang, Eugene I. Shakhnovich:
  Optimality of Mutation and Selection in Germinal Centers.
• 
  Rebecca Strawn, Milan Melichercik, Michael Green, Thomas Stockner, Jannette Carey, Rüdiger Ettrich:
  Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues.
• 
  Sidhartha Goyal, Jie Yuan, Thomas Chen, Joshua D. Rabinowitz, Ned S. Wingreen:
  Achieving Optimal Growth through Product Feedback Inhibition in Metabolism.
• 
  Mikael Lundqvist, Albert Compte, Anders Lansner:
  Bistable, Irregular Firing and Population Oscillations in a Modular Attractor Memory Network.

Volume 6, Number 7, July 2010

Perspective

• 
  Russell F. Doolittle:
  The Roots of Bioinformatics in Protein Evolution.

Research Articles

• 
  Jamie I. MacPherson, Jonathan E. Dickerson, John W. Pinney, David L. Robertson:
  Patterns of HIV-1 Protein Interaction Identify Perturbed Host-Cellular Subsystems.
• 
  Raffaello Potestio, Cristian Micheletti, Henri Orland:
  Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops.
• 
  Marlena Siwiak, Piotr Zielenkiewicz:
  A Comprehensive, Quantitative, and Genome-Wide Model of Translation.
• 
  Yonghua Wang, Yan Li, Zhi Ma, Wei Yang, Chunzhi Ai:
  Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis.
• 
  Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber:
  More Than 1, 001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology.
• 
  Steven Phillips, William H. Wilson:
  Categorial Compositionality: A Category Theory Explanation for the Systematicity of Human Cognition.
• 
  Deusdedit Lineu Spavieri Jr., Hubert Eichner, Alexander Borst:
  Coding Efficiency of Fly Motion Processing Is Set by Firing Rate, Not Firing Precision.
• 
  John A. Capra, Katrin Paeschke, Mona Singh, Virginia A. Zakian:
  G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae.
• 
  Oscar Harari, Sun-Yang Park, Henry Huang, Eduardo A. Groisman, Igor Zwir:
  Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria.
• 
  Stephen F. Altschul, John C. Wootton, Elena Zaslavsky, Yi-Kuo Yu:
  The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment.
• 
  Omar Awile, Anita Krisko, Ivo F. Sbalzarini, Bojan Zagrovic:
  Intrinsically Disordered Regions May Lower the Hydration Free Energy in Proteins: A Case Study of Nudix Hydrolase in the Bacterium Deinococcus radiodurans.
• 
  Terrence M. Dobrowsky, Brian R. Daniels, Robert F. Siliciano, Sean X. Sun, Denis Wirtz:
  Organization of Cellular Receptors into a Nanoscale Junction during HIV-1 Adhesion.
• 
  Jonathan B. Dingwell, Joby John, Joseph P. Cusumano:
  Do Humans Optimally Exploit Redundancy to Control Step Variability in Walking?
• 
  Arne J. Nagengast, Daniel A. Braun, Daniel M. Wolpert:
  Risk-Sensitive Optimal Feedback Control Accounts for Sensorimotor Behavior under Uncertainty.
• 
  Sergio Bordel, Rasmus Agren, Jens Nielsen:
  Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes.
• 
  Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble:
  Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens.
• 
  Volkan Sevim, Xinwei Gong, Joshua E. S. Socolar:
  Reliability of Transcriptional Cycles and the Yeast Cell-Cycle Oscillator.
• 
  Patrick D. Schloss:
  The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies.
• 
  Turkan Haliloglu, Ahmet Gül, Burak Erman:
  Predicting Important Residues and Interaction Pathways in Proteins Using Gaussian Network Model: Binding and Stability of HLA Proteins.
• 
  Marc Benayoun, Jack D. Cowan, Wim van Drongelen, Edward W. J. Wallace:
  Avalanches in a Stochastic Model of Spiking Neurons.
• 
  Chrysa Pantzartzi, Elena Drosopoulou, Minas Yiangou, Ignat Drozdov, Sophia Tsoka, Christos A. Ouzounis, Zacharias G. Scouras:
  Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, a Sessile Marine Invertebrate Species.
• 
  Tiago Paixão, Ricardo B. R. Azevedo:
  Redundancy and the Evolution of Cis-Regulatory Element Multiplicity.
• 
  James R. Wagner, Bing Ge, Dmitry Pokholok, Kevin L. Gunderson, Tomi Pastinen, Mathieu Blanchette:
  Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human.
• 
  Jonathan Platkiewicz, Romain Brette:
  A Threshold Equation for Action Potential Initiation.
• 
  Tetsuya Shiraishi, Shinako Matsuyama, Hiroaki Kitano:
  Large-Scale Analysis of Network Bistability for Human Cancers.
• 
  Philippe Andrey, Kiên Kiêu, Clémence Kress, Gaëtan Lehmann, Leïla Tirichine, Zichuan Liu, Eric Biot, Pierre-Gaël Adenot, Cathy Hue-Beauvais, Nicole Houba-Hérin, Véronique Duranthon, Eve Devinoy, Nathalie Beaujean, Valérie Gaudin, Yves Maurin, Pascale Debey:
  Statistical Analysis of 3D Images Detects Regular Spatial Distributions of Centromeres and Chromocenters in Animal and Plant Nuclei.
• 
  Hilal Kazan, Debashish Ray, Esther T. Chan, Timothy R. Hughes, Quaid Morris:
  RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins.
• 
  Hao Dong, Sanbo Qin, Huan-Xiang Zhou:
  Effects of Macromolecular Crowding on Protein Conformational Changes.
• 
  Michael C. Prentiss, David J. Wales, Peter G. Wolynes:
  The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein.
• 
  Carsten Marr, Fabian J. Theis, Larry S. Liebovitch, Marc-Thorsten Hütt:
  Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli.
• 
  Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg, Ulf Leser:
  A Comprehensive Benchmark of Kernel Methods to Extract Protein-Protein Interactions from Literature.
• 
  Amber E. Hudson, Astrid A. Prinz:
  Conductance Ratios and Cellular Identity.
• 
  Daniel Bush, Andrew Philippides, Phil Husbands, Michael O'Shea:
  Dual Coding with STDP in a Spiking Recurrent Neural Network Model of the Hippocampus.
• 
  Biswa Sengupta, Martin Stemmler, Simon B. Laughlin, Jeremy E. Niven:
  Action Potential Energy Efficiency Varies Among Neuron Types in Vertebrates and Invertebrates.
• 
  David E. Larson, Ruth I. Johnson, Maciej Swat, Julia B. Cordero, James A. Glazier, Ross L. Cagan:
  Computer Simulation of Cellular Patterning Within the Drosophila Pupal Eye.
• 
  Augix Guohua Xu, Liu He, Zhongshan Li, Ying Xu, Mingfeng Li, Xing Fu, Zheng Yan, Yuan Yuan, Corinna Menzel, Na Li, Mehmet Somel, Hao Hu, Wei Chen, Svante Pääbo, Philipp Khaitovich:
  Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq.

Volume 6, Number 8, August 2010

Education

• 
  Cameron Mura, Colin M. McCrimmon, Jason Vertrees, Michael R. Sawaya:
  An Introduction to Biomolecular Graphics.

Research Articles

• 
  Carlos J. Melián, David Alonso, Diego P. Vázquez, James Regetz, Stefano Allesina:
  Frequency-Dependent Selection Predicts Patterns of Radiations and Biodiversity.
• 
  Katarzyna A. Rejniak, Shizhen E. Wang, Nicole S. Bryce, Hang Chang, Bahram Parvin, Jerome Jourquin, Lourdes Estrada, Joe W. Gray, Carlos L. Arteaga, Alissa M. Weaver, Vito Quaranta, Alexander R. A. Anderson:
  Linking Changes in Epithelial Morphogenesis to Cancer Mutations Using Computational Modeling.
• 
  Roger D. Kouyos, Shari N. Gordon, Silvija I. Staprans, Guido Silvestri, Roland R. Regoes:
  Similar Impact of CD8+ T Cell Responses on Early Virus Dynamics during SIV Infections of Rhesus Macaques and Sooty Mangabeys.
• 
  Chen Hou, Stefan Gheorghiu, Virginia H. Huxley, Peter Pfeifer:
  Reverse Engineering of Oxygen Transport in the Lung: Adaptation to Changing Demands and Resources through Space-Filling Networks.
• 
  Saher Afshan Shaikh, Emad Tajkhorshid:
  Modeling and Dynamics of the Inward-Facing State of a Na⁺/Cl^- Dependent Neurotransmitter Transporter Homologue.
• 
  Orkun S. Soyer, Thomas Pfeiffer:
  Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks.
• 
  Thomas C. Whisenant, David T. Ho, Ryan W. Benz, Jeffrey S. Rogers, Robyn M. Kaake, Elizabeth A. Gordon, Lan Huang, Pierre Baldi, Lee Bardwell:
  Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors.
• 
  Mati Goldberg, Maurizio De Pittà, Vladislav Volman, Hugues Berry, Eshel Ben-Jacob:
  Nonlinear Gap Junctions Enable Long-Distance Propagation of Pulsating Calcium Waves in Astrocyte Networks.
• 
  Jingjing Li, Yu Liu, TaeHyung Kim, Renqiang Min, Zhaolei Zhang:
  Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility.
• 
  Jonathan E. Kohn, Pavel V. Afonine, Jory Z. Ruscio, Paul D. Adams, Teresa Head-Gordon:
  Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles.
• 
  Melda Tozluoglu, Ezgi Karaca, Ruth Nussinov, Türkan Haliloglu:
  A Mechanistic View of the Role of E3 in Sumoylation.
• 
  Botond Szatmáry, Eugene M. Izhikevich:
  Spike-Timing Theory of Working Memory.
• 
  Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B. Gravenor, Spencer V. Muse, Sergei L. Kosakovsky Pond:
  CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences.
• 
  M. Ahsanul Islam, Elizabeth A. Edwards, Radhakrishnan Mahadevan:
  Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model.
• 
  Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schönhuth, Gary P. Schroth, David I. K. Martin, Lior Pachter:
  MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations.
• 
  Kakajan Komurov, Michael A. White, Prahlad T. Ram:
  Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data.
• 
  Jonathan Saragosti, Vincent Calvez, Nikolaos Bournaveas, Axel Buguin, Pascal Silberzan, Benoit Perthame:
  Mathematical Description of Bacterial Traveling Pulses.
• 
  Wolfram Möbius, Ulrich Gerland:
  Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites.
• 
  Gary C. Sing, Maurice A. Smith:
  Reduction in Learning Rates Associated with Anterograde Interference Results from Interactions between Different Timescales in Motor Adaptation.
• 
  Robert Legenstein, Niko Wilbert, Laurenz Wiskott:
  Reinforcement Learning on Slow Features of High-Dimensional Input Streams.
• 
  Sven Van Segbroeck, Francisco C. Santos, Jorge M. Pacheco:
  Adaptive Contact Networks Change Effective Disease Infectiousness and Dynamics.
• 
  Marcus J. Tindall, Steven L. Porter, Philip K. Maini, Judith P. Armitage:
  Modeling Chemotaxis Reveals the Role of Reversed Phosphotransfer and a Bi-Functional Kinase-Phosphatase.
• 
  Ingo R. Titze, Tobias Riede:
  A Cervid Vocal Fold Model Suggests Greater Glottal Efficiency in Calling at High Frequencies.
• 
  Michael J. Schachter, Nicholas Oesch, Robert G. Smith, W. Rowland Taylor:
  Dendritic Spikes Amplify the Synaptic Signal to Enhance Detection of Motion in a Simulation of the Direction-Selective Ganglion Cell.
• 
  Peter J. M. Van Haastert:
  A Model for a Correlated Random Walk Based on the Ordered Extension of Pseudopodia.
• 
  David J. Huggins, Grahame J. McKenzie, Daniel D. Robinson, Ana J. Narváez, Bryn Hardwick, Meredith Roberts-Thomson, Ashok R. Venkitaraman, Guy H. Grant, Mike C. Payne:
  Computational Analysis of Phosphopeptide Binding to the Polo-Box Domain of the Mitotic Kinase PLK1 Using Molecular Dynamics Simulation.
• 
  Brian Y. Chen, Barry Honig:
  VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity.
• 
  Aiping Wu, Yousong Peng, Xiangjun Du, Yuelong Shu, Taijiao Jiang:
  Correlation of Influenza Virus Excess Mortality with Antigenic Variation: Application to Rapid Estimation of Influenza Mortality Burden.
• 
  Sharon Aviran, Priya S. Shah, David V. Schaffer, Adam P. Arkin:
  Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles.
• 
  Jana Selent, Ferran Sanz, Manuel Pastor, Gianni De Fabritiis:
  Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors.
• 
  Robert C. Cannon, Cian O'Donnell, Matthew F. Nolan:
  Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes.
• 
  Aziz Mithani, Gail M. Preston, Jotun Hein:
  A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny.
• 
  Sandro Romani, Misha Tsodyks:
  Continuous Attractors with Morphed/Correlated Maps.
• 
  Alexander Skupin, Helmut Kettenmann, Martin Falcke:
  Calcium Signals Driven by Single Channel Noise.
• 
  David R. Wozny, Ulrik R. Beierholm, Ladan Shams:
  Probability Matching as a Computational Strategy Used in Perception.
• 
  Gabriel Piedrafita, Francisco Montero, Federico Morán, María Luz Cárdenas, Athel Cornish-Bowden:
  A Simple Self-Maintaining Metabolic System: Robustness, Autocatalysis, Bistability.
• 
  Masaki E. Tsuda, Masakado Kawata:
  Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints.
• 
  Yael Artzy-Randrup, Lewi Stone:
  Connectivity, Cycles, and Persistence Thresholds in Metapopulation Networks.
• 
  Hermann Cuntz, Friedrich Forstner, Alexander Borst, Michael Häusser:
  One Rule to Grow Them All: A General Theory of Neuronal Branching and Its Practical Application.
• 
  Yongping Pan, Ruth Nussinov:
  Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization.

Volume 6, Number 9, September 2010

Editorial

• 
  Darren W. Logan, Massimo Sandal, Paul P. Gardner, Magnus Manske, Alex Bateman:
  Ten Simple Rules for Editing Wikipedia.

Research Articles

• 
  Benjamin Torben-Nielsen, Klaus M. Stiefel:
  Wide-Field Motion Integration in Fly VS Cells: Insights from an Inverse Approach.
• 
  Martin R. Miller, Lars Råberg, Andrew F. Read, Nicholas J. Savill:
  Quantitative Analysis of Immune Response and Erythropoiesis during Rodent Malarial Infection.
• 
  Ruben J. Kubiak, Nimalan Arinaminpathy, Angela R. McLean:
  Insights into the Evolution and Emergence of a Novel Infectious Disease.
• 
  Manash S. Chatterjee, William S. Denney, Huiyan Jing, Scott L. Diamond:
  Systems Biology of Coagulation Initiation: Kinetics of Thrombin Generation in Resting and Activated Human Blood.
• 
  Nathan W. Gouwens, Hugo Zeberg, Kunichika Tsumoto, Takashi Tateno, Kazuyuki Aihara, Hugh P. C. Robinson:
  Synchronization of Firing in Cortical Fast-Spiking Interneurons at Gamma Frequencies: A Phase-Resetting Analysis.
• 
  Ron Skupsky, John C. Burnett, Jonathan E. Foley, David V. Schaffer, Adam P. Arkin:
  HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency.
• 
  João D. Ferreira, Francisco M. Couto:
  Semantic Similarity for Automatic Classification of Chemical Compounds.
• 
  Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson:
  Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model.
• 
  Ly Le, Eric H. Lee, David J. Hardy, Thanh N. Truong, Klaus Schulten:
  Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases.
• 
  Rong Chen, Tara K. Sigdel, Li Li, Neeraja Kambham, Joel Dudley, Szu-chuan Hsieh, R. Bryan Klassen, Amery Chen, Tuyen Caohuu, Alexander A. Morgan, Hannah A. Valantine, Kiran K. Khush, Minnie M. Sarwal, Atul J. Butte:
  Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions.
• 
  Raoul Frijters, Marianne van Vugt, Ruben Smeets, René C. van Schaik, Jacob de Vlieg, Wynand Alkema:
  Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases.
• 
  Matthew Y. Tang, Carole J. Proctor, John Woulfe, Douglas A. Gray:
  Experimental and Computational Analysis of Polyglutamine-Mediated Cytotoxicity.
• 
  Juan A. G. Ranea, Ian Morilla, Jonathan G. Lees, Adam James Reid, Corin Yeats, Andrew B. Clegg, Francisca Sánchez-Jiménez, Christine A. Orengo:
  Finding the "Dark Matter" in Human and Yeast Protein Network Prediction and Modelling.
• 
  Sergei V. Krivov:
  Is Protein Folding Sub-Diffusive?
• 
  Andreas Kowarsch, Angelika Fuchs, Dmitrij Frishman, Philipp Pagel:
  Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions.
• 
  Ying Liu, Lila M. Gierasch, Ivet Bahar:
  Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs.
• 
  Thomas S. Rask, Daniel A. Hansen, Thor G. Theander, Anders Gorm Pedersen, Thomas Lavstsen:
  Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes - Divide and Conquer.
• 
  Andres Buehlmann, Gustavo Deco:
  Optimal Information Transfer in the Cortex through Synchronization.
• 
  Xin He, Md. Abul Hassan Samee, Charles Blatti, Saurabh Sinha:
  Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression.
• 
  Clare E. Giacomantonio, Geoffrey J. Goodhill:
  A Boolean Model of the Gene Regulatory Network Underlying Mammalian Cortical Area Development.
• 
  Ulrik R. Beierholm, Peter Dayan:
  Pavlovian-Instrumental Interaction in 'Observing Behavior'.
• 
  Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble, Christina S. Leslie:
  High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions.
• 
  Valentin Markounikau, Christian Igel, Amiram Grinvald, Dirk Jancke:
  A Dynamic Neural Field Model of Mesoscopic Cortical Activity Captured with Voltage-Sensitive Dye Imaging.
• 
  Suryani Lukman, Barry J. Grant, Alemayehu A. Gorfe, Guy H. Grant, James Andrew McCammon:
  The Distinct Conformational Dynamics of K-Ras and H-Ras A59G.
• 
  Sundar Srinivasan, Brandon J. Ausk, Jitendra Prasad, Dewayne Threet, Steven D. Bain, Thomas S. Richardson, Ted S. Gross:
  Rescuing Loading Induced Bone Formation at Senescence.
• 
  Murat Iskar, Monica Campillos, Michael Kuhn, Lars Juhl Jensen, Vera van Noort, Peer Bork:
  Drug-Induced Regulation of Target Expression.
• 
  Neeraj J. Agrawal, Jonathan Nukpezah, Ravi Radhakrishnan:
  Minimal Mesoscale Model for Protein-Mediated Vesiculation in Clathrin-Dependent Endocytosis.
• 
  Se-Bum Paik, Donald A. Glaser:
  Synaptic Plasticity Controls Sensory Responses through Frequency-Dependent Gamma Oscillation Resonance.
• 
  Gaurav Pandey, Bin Zhang, Aaron N. Chang, Chad L. Myers, Jun Zhu, Vipin Kumar, Eric E. Schadt:
  An Integrative Multi-Network and Multi-Classifier Approach to Predict Genetic Interactions.
• 
  Moritz Helias, Moritz Deger, Stefan Rotter, Markus Diesmann:
  Instantaneous Non-Linear Processing by Pulse-Coupled Threshold Units.
• 
  Sheng Zhang, Miguel P. Eckstein:
  Evolution and Optimality of Similar Neural Mechanisms for Perception and Action during Search.
• 
  Karina Laneri, Anindya Bhadra, Edward L. Ionides, Menno J. Bouma, Ramesh C. Dhiman, Rajpal S. Yadav, Mercedes Pascual:
  Forcing Versus Feedback: Epidemic Malaria and Monsoon Rains in Northwest India.
• 
  Ludovic Cottret, Paulo Vieira Milreu, Vicente Acuña, Alberto Marchetti-Spaccamela, Leen Stougie, Hubert Charles, Marie-France Sagot:
  Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata.
• 
  Rob J. De Boer, Ruy M. Ribeiro, Alan S. Perelson:
  Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues.
• 
  Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, Denis Thieffry:
  Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling.
• 
  Amrita X. Sarkar, Eric A. Sobie:
  Regression Analysis for Constraining Free Parameters in Electrophysiological Models of Cardiac Cells.
• 
  Liesbet Geris, Anita A. C. Reed, Jos Vander Sloten, A. Hamish R. W. Simpson, Hans Van Oosterwyck:
  Occurrence and Treatment of Bone Atrophic Non-Unions Investigated by an Integrative Approach.
• 
  Cédric Sueur, Jean-Louis Deneubourg, Odile Petit, Iain D. Couzin:
  Differences in Nutrient Requirements Imply a Non-Linear Emergence of Leaders in Animal Groups.
• 
  Joseph E. Lucas, Hsiu-Ni Kung, Jen-Tsan A. Chi:
  Latent Factor Analysis to Discover Pathway-Associated Putative Segmental Aneuploidies in Human Cancers.

Volume 6, Number 10, October 2010

Obituary

• 
  Klaas Enno Stephan, Anthony Randal McIntosh, Claus C. Hilgetag:
  In Memoriam: Rolf Kötter (1961-2010).

Research Articles

• 
  Timo Vuorela, Andrea Catte, Perttu S. Niemelä, Anette Hall, Marja T. Hyvönen, Siewert J. Marrink, Mikko Karttunen, Ilpo Vattulainen:
  Role of Lipids in Spheroidal High Density Lipoproteins.
• 
  Ian H. Spicknall, James S. Koopman, Mark Nicas, Josep M. Pujol, Sheng Li, Joseph N. S. Eisenberg:
  Informing Optimal Environmental Influenza Interventions: How the Host, Agent, and Environment Alter Dominant Routes of Transmission.
• 
  Dipak Barua, Joonhoon Kim, Jennifer L. Reed:
  An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models.
• 
  Bing Zhao, Changjiang Zhang, Kimberly Forsten-Williams, Jun Zhang, Michael Fannon:
  Endothelial Cell Capture of Heparin-Binding Growth Factors under Flow.
• 
  Yuhui Cheng, Zeyun Yu, Masahiko Hoshijima, Michael J. Holst, Andrew D. McCulloch, James Andrew McCammon, Anushka Michailova:
  Numerical Analysis of Ca²⁺ Signaling in Rat Ventricular Myocytes with Realistic Transverse-Axial Tubular Geometry and Inhibited Sarcoplasmic Reticulum.
• 
  Susanne Menden-Deuer:
  Inherent High Correlation of Individual Motility Enhances Population Dispersal in a Heterotrophic, Planktonic Protist.
• 
  Michael Mäs, Andreas Flache, Dirk Helbing:
  Individualization as Driving Force of Clustering Phenomena in Humans.
• 
  Benjamin I. Rapoport:
  Metabolic Factors Limiting Performance in Marathon Runners.
• 
  Del Lucent, Christopher D. Snow, Colin Echeverría Aitken, Vijay S. Pande:
  Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel.
• 
  Misha Koshelev, Terry Lohrenz, Marina Vannucci, P. Read Montague:
  Biosensor Approach to Psychopathology Classification.
• 
  Donald R. Cantrell, Jianhua Cang, John B. Troy, Xiaorong Liu:
  Non-Centered Spike-Triggered Covariance Analysis Reveals Neurotrophin-3 as a Developmental Regulator of Receptive Field Properties of ON-OFF Retinal Ganglion Cells.
• 
  Gaurav Bhatia, Vikas Bansal, Olivier Harismendy, Nicholas J. Schork, Eric J. Topol, Kelly A. Frazer, Vineet Bafna:
  A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes.
• 
  Kenneth L. Ho, Heather A. Harrington:
  Bistability in Apoptosis by Receptor Clustering.
• 
  Michail Yu. Lobanov, Eugenia Furletova, Natalya S. Bogatyreva, Mikhail A. Roytberg, Oxana V. Galzitskaya:
  Library of Disordered Patterns in 3D Protein Structures.
• 
  Brenda R. S. Temple, Corbin D. Jones, Alan M. Jones:
  Evolution of a Signaling Nexus Constrained by Protein Interfaces and Conformational States.
• 
  Dimitris Iliopoulos, Arend Hintze, Christoph Adami:
  Critical Dynamics in the Evolution of Stochastic Strategies for the Iterated Prisoner's Dilemma.
• 
  Zhipeng Cai, Tong Zhang, Xiu-Feng Wan:
  A Computational Framework for Influenza Antigenic Cartography.
• 
  Fátima Al-Shahrour, Pablo Minguez, Tomàs Marquès-Bonet, Elodie Gazave, Arcadi Navarro, Joaquín Dopazo:
  Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes.
• 
  S. Gnanakaran, Marcus G. Daniels, Tanmoy Bhattacharya, Alan S. Lapedes, Anurag Sethi, Ming Li, Haili Tang, Kelli Greene, Hongmei Gao, Barton F. Haynes, Myron S. Cohen, George M. Shaw, Michael S. Seaman, Amit Kumar, Feng Gao, David C. Montefiori, Bette T. Korber:
  Genetic Signatures in the Envelope Glycoproteins of HIV-1 that Associate with Broadly Neutralizing Antibodies.

Volume 6, Number 11, November 2010

Education

• 
  Lior Shamir, John D. Delaney, Nikita Orlov, D. Mark Eckley, Ilya G. Goldberg:
  Pattern Recognition Software and Techniques for Biological Image Analysis.

Perspective

• 
  Guilhem Chalancon, Mickey Kosloff, Hatice U. Osmanbeyoglu, Saras Saraswathi:
  PLoS Computational Biology Conference Postcards from ISMB 2010.

Research Articles

• 
  Federico Andrea Santoni, Oliver Hartley, Jeremy Luban:
  Deciphering the Code for Retroviral Integration Target Site Selection.
• 
  Christopher Y. Park, David C. Hess, Curtis Huttenhower, Olga G. Troyanskaya:
  Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components.
• 
  Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit:
  A New Method to Reconstruct Recombination Events at a Genomic Scale.
• 
  Mark D. Humphries, Ric Wood, Kevin N. Gurney:
  Reconstructing the Three-Dimensional GABAergic Microcircuit of the Striatum.
• 
  Naveen K. Vaidya, Libin Rong, Vincent C. Marconi, Daniel R. Kuritzkes, Steven G. Deeks, Alan S. Perelson:
  Treatment-Mediated Alterations in HIV Fitness Preserve CD4⁺ T Cell Counts but Have Minimal Effects on Viral Load.
• 
  André Corvelo, Martina Hallegger, Christopher W. J. Smith, Eduardo Eyras:
  Genome-Wide Association between Branch Point Properties and Alternative Splicing.
• 
  Aalt D. J. van Dijk, Giuseppa Morabito, Martijn Fiers, Roeland C. H. J. van Ham, Gerco C. Angenent, Richard G. H. Immink:
  Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction.
• 
  Christel Kamp:
  Untangling the Interplay between Epidemic Spread and Transmission Network Dynamics.
• 
  Chun Wu, Joan-Emma Shea:
  On the Origins of the Weak Folding Cooperativity of a Designed ββα Ultrafast Protein FSD-1.
• 
  Martin Lages, Suzanne Heron:
  On the Inverse Problem of Binocular 3D Motion Perception.
• 
  Marc Gueroult, Daniel Picot, Joséphine Abi-Ghanem, Brigitte Hartmann, Marc Baaden:
  How Cations Can Assist DNase I in DNA Binding and Hydrolysis.
• 
  Thomas R. Burkard, Uwe Rix, Florian P. Breitwieser, Giulio Superti-Furga, Jacques Colinge:
  A Computational Approach to Analyze the Mechanism of Action of the Kinase Inhibitor Bafetinib.
• 
  Niels Klitgord, Daniel Segrè:
  Environments that Induce Synthetic Microbial Ecosystems.
• 
  Joseph Chan, Antony Holmes, Raul Rabadan:
  Network Analysis of Global Influenza Spread.
• 
  Zhijun Yao, Yuanchao Zhang, Lei Lin, Yuan Zhou, Cunlu Xu, Tianzi Jiang:
  Abnormal Cortical Networks in Mild Cognitive Impairment and Alzheimer's Disease.
• 
  Amy L. Bauer, William S. Hlavacek, Pat J. Unkefer, Fangping Mu:
  Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites.
• 
  Suhita Nadkarni, Thomas M. Bartol, Terrence J. Sejnowski, Herbert Levine:
  Modelling Vesicular Release at Hippocampal Synapses.
• 
  Sandra H. Dandach, Mustafa Khammash:
  Analysis of Stochastic Strategies in Bacterial Competence: A Master Equation Approach.
• 
  Saeed Saberi, Eldon Emberly:
  Chromosome Driven Spatial Patterning of Proteins in Bacteria.
• 
  Yoshihisa Kubota, M. Neal Waxham:
  Lobe Specific Ca²⁺-Calmodulin Nano-Domain in Neuronal Spines: A Single Molecule Level Analysis.
• 
  Sebastian M. Waszak, Yehudit Hasin, Thomas Zichner, Tsviya Olender, Ifat Keydar, Miriam Khen, Adrian M. Stütz, Andreas Schlattl, Doron Lancet, Jan O. Korbel:
  Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity.
• 
  Francisco M. Camas, Eric J. Alm, Juan F. Poyatos:
  Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family.
• 
  Quentin Thommen, Benjamin Pfeuty, Pierre-Emmanuel Morant, Florence Corellou, François-Yves Bouget, Marc Lefranc:
  Robustness of Circadian Clocks to Daylight Fluctuations: Hints from the Picoeucaryote Ostreococcus tauri.
• 
  Yuanfang Guan, Cheryl L. Ackert-Bicknell, Braden Kell, Olga G. Troyanskaya, Matthew A. Hibbs:
  Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations.
• 
  Allen Cheung, Robert Vickerstaff:
  Finding the Way with a Noisy Brain.
• 
  Dan F. M. Goodman, Romain Brette:
  Spike-Timing-Based Computation in Sound Localization.
• 
  M. Qaiser Fatmi, Chia-en A. Chang:
  The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase.
• 
  Michael Milford, Janet Wiles, Gordon F. Wyeth:
  Solving Navigational Uncertainty Using Grid Cells on Robots.
• 
  Elisabet Ortiz-Tudela, Antonio Martinez-Nicolas, Manuel Campos, María Ángeles Rol, Juan Antonio Madrid:
  A New Integrated Variable Based on Thermometry, Actimetry and Body Position (TAP) to Evaluate Circadian System Status in Humans.
• 
  Theresa M. Yuraszeck, Pierre Neveu, Maria Rodriguez-Fernandez, Anne S. Robinson, Kenneth S. Kosik, Francis J. Doyle III:
  Vulnerabilities in the Tau Network and the Role of Ultrasensitive Points in Tau Pathophysiology.
• 
  Pilar Cossio, Antonio Trovato, Fabio Pietrucci, Flavio Seno, Amos Maritan, Alessandro Laio:
  Exploring the Universe of Protein Structures beyond the Protein Data Bank.
• 
  Baktash Babadi, L. F. Abbott:
  Intrinsic Stability of Temporally Shifted Spike-Timing Dependent Plasticity.
• 
  Alison L. Hill, David G. Rand, Martin A. Nowak, Nicholas A. Christakis:
  Infectious Disease Modeling of Social Contagion in Networks.
• 
  Vladislav Volman, Herbert Levine, Terrence J. Sejnowski:
  Shunting Inhibition Controls the Gain Modulation Mediated by Asynchronous Neurotransmitter Release in Early Development.
• 
  Julien F. Ollivier, Vahid Shahrezaei, Peter S. Swain:
  Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks.
• 
  Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne:
  The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications.
• 
  Genadiy Vasserman, Maoz Shamir, Avi Ben Simon, Ronen Segev:
  Coding "What" and "When" in the Archer Fish Retina.
• 
  Cristina Marino Buslje, Elin Teppa, Tomás Di Domenico, José María Delfino, Morten Nielsen:
  Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification.
• 
  Matthieu Wyart, David Botstein, Ned S. Wingreen:
  Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data.
• 
  Matthew L. Kutys, John Fricks, William O. Hancock:
  Monte Carlo Analysis of Neck Linker Extension in Kinesin Molecular Motors.
• 
  Ulrich D. Kadolsky, Becca Asquith:
  Quantifying the Impact of Human Immunodeficiency Virus-1 Escape From Cytotoxic T-Lymphocytes.
• 
  Todd E. Hudson, Hadley Tassinari, Michael S. Landy:
  Compensation for Changing Motor Uncertainty.

Volume 6, Number 12, December 2010

Research Articles

• 
  Ephraim Kenigsberg, Amir Bar, Eran Segal, Amos Tanay:
  Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast.
• 
  Andreja Jovic, Bryan Howell, Michelle Cote, Susan M. Wade, Khamir Mehta, Atsushi Miyawaki, Richard R. Neubig, Jennifer J. Linderman, Shuichi Takayama:
  Phase-Locked Signals Elucidate Circuit Architecture of an Oscillatory Pathway.
• 
  Ronit V. Oren, Colleen E. Clancy:
  Determinants of Heterogeneity, Excitation and Conduction in the Sinoatrial Node: A Model Study.
• 
  John P. Archer, Andrew Rambaut, Bruce E. Taillon, P. Richard Harrigan, Marilyn Lewis, David L. Robertson:
  The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time - An Ultra-Deep Approach.
• 
  Tilo Schwalger, Karin Fisch, Jan Benda, Benjamin Lindner:
  How Noisy Adaptation of Neurons Shapes Interspike Interval Histograms and Correlations.
• 
  Giovanni Caruso, Paolo Bisegna, Leonardo Lenoci, Daniele Andreucci, Vsevolod V. Gurevich, Heidi E. Hamm, Emmanuele DiBenedetto:
  Kinetics of Rhodopsin Deactivation and Its Role in Regulating Recovery and Reproducibility of Rod Photoresponse.
• 
  Marco Pedicini, Fredrik Barrenäs, Trevor Clancy, Filippo Castiglione, Eivind Hovig, Kartiek Kanduri, Daniele Santoni, Mikael Benson:
  Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation.
• 
  Jie Zhang, Kai Zhang, Jianfeng Feng, Michael Small:
  Rhythmic Dynamics and Synchronization via Dimensionality Reduction: Application to Human Gait.
• 
  Florian Markowetz, Klaas W. Mulder, Edoardo M. Airoldi, Ihor Lemischka, Olga G. Troyanskaya:
  Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells.
• 
  Marco Vilela, Jeffrey J. Morgan, Paul A. Lindahl:
  Mathematical Model of a Cell Size Checkpoint.
• 
  William H. Majoros, Uwe Ohler:
  Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs.
• 
  Eleftheria Kyriaki Pissadaki, Kyriaki Sidiropoulou, Martin Reczko, Panayiota Poirazi:
  Encoding of Spatio-Temporal Input Characteristics by a CA1 Pyramidal Neuron Model.
• 
  Richard E. Reeve, Belinda Blignaut, Jan J. Esterhuysen, Pamela Opperman, Louise Matthews, Elizabeth E. Fry, Tjaart A. P. de Beer, Jacques Theron, Elizabeth Rieder, Wilna Vosloo, Hester G. O'Neill, Daniel T. Haydon, Francois F. Maree:
  Sequence-Based Prediction for Vaccine Strain Selection and Identification of Antigenic Variability in Foot-and-Mouth Disease Virus.
• 
  Raamesh Deshpande, Shikha Sharma, Catherine M. Verfaillie, Wei-Shou Hu, Chad L. Myers:
  A Scalable Approach for Discovering Conserved Active Subnetworks across Species.
• 
  Robert J. Fieldhouse, Zachari Turgeon, Dawn White, A. Rod Merrill:
  Cholera- and Anthrax-Like Toxins Are among Several New ADP-Ribosyltransferases.
• 
  Maarten Chris Boerlijst, Willem Marijn van Ballegooijen:
  Spatial Pattern Switching Enables Cyclic Evolution in Spatial Epidemics.
• 
  Abhinav Singh, Nicholas A. Lesica:
  Incremental Mutual Information: A New Method for Characterizing the Strength and Dynamics of Connections in Neuronal Circuits.
• 
  Daniel E. Acuña, Paul R. Schrater:
  Structure Learning in Human Sequential Decision-Making.
• 
  Matthew D. Egbert, Xabier E. Barandiaran, Ezequiel A. Di Paolo:
  A Minimal Model of Metabolism-Based Chemotaxis.
• 
  Christian Tetzlaff, Samora Okujeni, Ulrich Egert, Florentin Wörgötter, Markus Butz:
  Self-Organized Criticality in Developing Neuronal Networks.
• 
  Benjamin A. Logsdon, Jason G. Mezey:
  Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations.
• 
  Faruck Morcos, Santanu Chatterjee, Christopher L. McClendon, Paul R. Brenner, Roberto López-Rendón, John Zintsmaster, Mária Ercsey-Ravasz, Christopher R. Sweet, Matthew P. Jacobson, Jeffrey W. Peng, Jesús A. Izaguirre:
  Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW.
• 
  C. David Williams, Michael Regnier, Thomas L. Daniel:
  Axial and Radial Forces of Cross-Bridges Depend on Lattice Spacing.
• 
  John C. Panetta, Alex Sparreboom, Ching-Hon Pui, Mary Relling, William E. Evans:
  Modeling Mechanisms of In Vivo Variability in Methotrexate Accumulation and Folate Pathway Inhibition in Acute Lymphoblastic Leukemia Cells.
• 
  Jing Su, Sarah A. Teichmann, Thomas A. Down:
  Assessing Computational Methods of Cis-Regulatory Module Prediction.
• 
  Fabrizio Iozzi, Francesco Trusiano, Matteo Chinazzi, Francesco C. Billari, Emilio Zagheni, Stefano Merler, Marco Ajelli, Emanuele Del Fava, Piero Manfredi:
  Little Italy: An Agent-Based Approach to the Estimation of Contact Patterns- Fitting Predicted Matrices to Serological Data.
• 
  Hang Zhang, Camille Morvan, Laurence T. Maloney:
  Gambling in the Visual Periphery: A Conjoint-Measurement Analysis of Human Ability to Judge Visual Uncertainty.
• 
  Najl V. Valeyev, Christian Hundhausen, Yoshinori Umezawa, Nikolai V. Kotov, Gareth Williams, Alex Clop, Crysanthi Ainali, Christos A. Ouzounis, Sophia Tsoka, Frank O. Nestle:
  A Systems Model for Immune Cell Interactions Unravels the Mechanism of Inflammation in Human Skin.
• 
  Eugene Davydov, David L. Goode, Marina Sirota, Gregory M. Cooper, Arend Sidow, Serafim Batzoglou:
  Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++.