PLOS Computational Biology

2005 - 2022

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Volume 7, issue 12, 2011

Chemotaxis when Bacteria Remember: Drift versus Diffusion pp. 1-8

Sakuntala Chatterjee, Rava Azeredo da Silveira and Yariv Kafri

Joint Ancestry and Association Testing in Admixed Individuals pp. 1-8

Daniel Shriner, Adebowale Adeyemo and Charles N Rotimi

Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons pp. 1-25

Dejan Pecevski, Lars Buesing and Wolfgang Maass

Increased Vulnerability of Human Ventricle to Re-entrant Excitation in hERG-linked Variant 1 Short QT Syndrome pp. 1-16

Ismail Adeniran, Mark J McPate, Harry J Witchel, Jules C Hancox and Henggui Zhang

Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry pp. 1-11

Pranesh Padmanabhan and Narendra M Dixit

Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model pp. 1-11

Edward B Baskerville, Andy P Dobson, Trevor Bedford, Stefano Allesina, T Michael Anderson and Mercedes Pascual

Radial and Spiral Stream Formation in Proteus mirabilis Colonies pp. 1-11

Chuan Xue, Elena O Budrene and Hans G Othmer

Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps) pp. 1-13

Zhichao Liu, Qiang Shi, Don Ding, Reagan Kelly, Hong Fang and Weida Tong

Balanced Synaptic Input Shapes the Correlation between Neural Spike Trains pp. 1-14

Ashok Litwin-Kumar, Anne-Marie M Oswald, Nathaniel N Urban and Brent Doiron

Computational Mass Spectrometry–Based Proteomics pp. 1-7

Lukas Käll and Olga Vitek

Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes pp. 1-10

Amin R Mazloom, Ruth Dannenfelser, Neil R Clark, Arsen V Grigoryan, Kathryn M Linder, Timothy J Cardozo, Julia C Bond, Aislyn D W Boran, Ravi Iyengar, Anna Malovannaya, Rainer B Lanz and Avi Ma'ayan

Genetic Co-Occurrence Network across Sequenced Microbes pp. 1-9

Pan-Jun Kim and Nathan D Price

A Hierarchical Neuronal Model for Generation and Online Recognition of Birdsongs pp. 1-18

Izzet B Yildiz and Stefan J Kiebel

BeadArray Expression Analysis Using Bioconductor pp. 1-6

Matthew E Ritchie, Mark J Dunning, Mike L Smith, Wei Shi and Andy G Lynch

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field pp. 1-6

Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu and Mark Gerstein

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers pp. 1-15

Andrew T Kwon, Alice Yi Chou, David J Arenillas and Wyeth W Wasserman

Volume 7, issue 11, 2011

How Landscape Heterogeneity Frames Optimal Diffusivity in Searching Processes pp. 1-8

E P Raposo, F Bartumeus, M G E da Luz, P J Ribeiro-Neto, T A Souza and G M Viswanathan

Optimizing Experimental Design for Comparing Models of Brain Function pp. 1-18

Jean Daunizeau, Kerstin Preuschoff, Karl Friston and Klaas Stephan

The What and Where of Adding Channel Noise to the Hodgkin-Huxley Equations pp. 1-9

Joshua H Goldwyn and Eric Shea-Brown

Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits pp. 1-9

Rutger Hermsen, David W Erickson and Terence Hwa

Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study pp. 1-9

Zhuo Song, Yang Cao and David C Samuels

Trade-Offs and Constraints in Allosteric Sensing pp. 1-13

Bruno MC Martins and Peter S Swain

Representational Switching by Dynamical Reorganization of Attractor Structure in a Network Model of the Prefrontal Cortex pp. 1-17

Yuichi Katori, Kazuhiro Sakamoto, Naohiro Saito, Jun Tanji, Hajime Mushiake and Kazuyuki Aihara

High Degree of Heterogeneity in Alzheimer's Disease Progression Patterns pp. 1-6

Natalia L Komarova and Craig J Thalhauser

A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules pp. 1-11

Alexandra Jilkine, Sigurd B Angenent, Lani F Wu and Steven J Altschuler

Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons pp. 1-22

Lars Buesing, Johannes Bill, Bernhard Nessler and Wolfgang Maass

Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy pp. 1-14

Seyed Yahya Anvar, Allan Tucker, Veronica Vinciotti, Andrea Venema, Gert-Jan B van Ommen, Silvere M van der Maarel, Vered Raz and Peter A C ‘t Hoen

Volume 7, issue 10, 2011

Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis pp. 1-15

Anna Divoli, Eneida A Mendonça, James A Evans and Andrey Rzhetsky

Brain Rhythms Reveal a Hierarchical Network Organization pp. 1-15

G Karl Steinke and Roberto F Galán

Ten Simple Rules for Getting Involved in Your Scientific Community pp. 1-3

Magali Michaut

Ten Simple Rules for Developing a Short Bioinformatics Training Course pp. 1-3

Allegra Via, Javier De Las Rivas, Teresa K Attwood, David Landsman, Michelle D Brazas, Jack A M Leunissen, Anna Tramontano and Maria Victoria Schneider

Teaching Bioinformatics at the Secondary School Level pp. 1-2

Fran Lewitter and Philip E Bourne

Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models pp. 1-9

Jeffrey D Fitzgerald, Ryan J Rowekamp, Lawrence C Sincich and Tatyana O Sharpee

Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer pp. 1-10

Anup Dewanji, Jihyoun Jeon, Rafael Meza and E Georg Luebeck

Coupled Information Diffusion–Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs pp. 1-10

François Rebaudo and Olivier Dangles

The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers pp. 1-10

Sean A Rands

A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation pp. 1-32

Susan D Hester, Julio M Belmonte, J Scott Gens, Sherry G Clendenon and James A Glazier

Representation of Dynamical Stimuli in Populations of Threshold Neurons pp. 1-19

Tatjana Tchumatchenko and Fred Wolf

NHE Inhibition Does Not Improve Na+ or Ca2+ Overload During Reperfusion: Using Modeling to Illuminate the Mechanisms Underlying a Therapeutic Failure pp. 1-19

Byron N Roberts and David J Christini

A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization pp. 1-14

Neil Dalchau, Andrew Phillips, Leonard D Goldstein, Mark Howarth, Luca Cardelli, Stephen Emmott, Tim Elliott and Joern M Werner

Coexistence of Lateral and Co-Tuned Inhibitory Configurations in Cortical Networks pp. 1-14

Robert B Levy and Alex D Reyes

Barriers to Diffusion in Dendrites and Estimation of Calcium Spread Following Synaptic Inputs pp. 1-14

Armin Biess, Eduard Korkotian and David Holcman

Automatic Morphological Subtyping Reveals New Roles of Caspases in Mitochondrial Dynamics pp. 1-14

Jyh-Ying Peng, Chung-Chih Lin, Yen-Jen Chen, Lung-Sen Kao, Young-Chau Liu, Chung-Chien Chou, Yi-Hung Huang, Fang-Rong Chang, Yang-Chang Wu, Yuh-Show Tsai and Chun-Nan Hsu

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity pp. 1-14

Hyun Joo, Archana G Chavan, Ryan Day, Kristin P Lennox, Paul Sukhanov, David B Dahl, Marina Vannucci and Jerry Tsai

Grid Cells, Place Cells, and Geodesic Generalization for Spatial Reinforcement Learning pp. 1-14

Nicholas J Gustafson and Nathaniel D Daw

Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release pp. 1-14

Heidi Koldsø, Pernille Noer, Julie Grouleff, Henriette Elisabeth Autzen, Steffen Sinning and Birgit Schiøtt

Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation pp. 1-7

César Augusto F de Oliveira, Barry J Grant, Michelle Zhou and J Andrew McCammon

A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms pp. 1-7

Suzanne Renick Gallagher, William Coon, Kristin Donley, Abby Scott and Debra S Goldberg

Using Structure to Explore the Sequence Alignment Space of Remote Homologs pp. 1-11

Andrew Kuziemko, Barry Honig and Donald Petrey

Accelerated Profile HMM Searches pp. 1-16

Sean R Eddy

The Dynamics of Supply and Demand in mRNA Translation pp. 1-16

Chris A Brackley, M Carmen Romano and Marco Thiel

Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability pp. 1-16

Kirsten H ten Tusscher and Paulien Hogeweg

Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks pp. 1-16

Mark Hallen, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West and Lingchong You

Receptive Field Inference with Localized Priors pp. 1-16

Mijung Park and Jonathan W Pillow

Metabolic Regulation in Progression to Autoimmune Diabetes pp. 1-16

Marko Sysi-Aho, Andrey Ermolov, Peddinti V Gopalacharyulu, Abhishek Tripathi, Tuulikki Seppänen-Laakso, Johanna Maukonen, Ismo Mattila, Suvi T Ruohonen, Laura Vähätalo, Laxman Yetukuri, Taina Härkönen, Erno Lindfors, Janne Nikkilä, Jorma Ilonen, Olli Simell, Maria Saarela, Mikael Knip, Samuel Kaski, Eriika Savontaus and Matej Orešič

Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex pp. 1-13

Anurag Sethi, Byron Goldstein and S Gnanakaran

A Neurodynamic Account of Spontaneous Behaviour pp. 1-13

Jun Namikawa, Ryunosuke Nishimoto and Jun Tani

Integrated Information Increases with Fitness in the Evolution of Animats pp. 1-13

Jeffrey A Edlund, Nicolas Chaumont, Arend Hintze, Christof Koch, Giulio Tononi and Christoph Adami

Formation of Regulatory Modules by Local Sequence Duplication pp. 1-12

Armita Nourmohammad and Michael Lässig

Estimating the Relevance of World Disturbances to Explain Savings, Interference and Long-Term Motor Adaptation Effects pp. 1-12

Max Berniker and Konrad P Kording

Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response pp. 1-12

Yaakov Maman, Ran Nir-Paz and Yoram Louzoun

Three People Can Synchronize as Coupled Oscillators during Sports Activities pp. 1-8

Keiko Yokoyama and Yuji Yamamoto

Volume 7, issue 9, 2011

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes pp. 1-9

Miklos Csuros, Igor B Rogozin and Eugene V Koonin

A Combined Experimental and Mathematical Approach for Molecular-based Optimization of Irinotecan Circadian Delivery pp. 1-12

Annabelle Ballesta, Sandrine Dulong, Chadi Abbara, Boris Cohen, Alper Okyar, Jean Clairambault and Francis Levi

An Integrated Disease/Pharmacokinetic/Pharmacodynamic Model Suggests Improved Interleukin-21 Regimens Validated Prospectively for Mouse Solid Cancers pp. 1-12

Moran Elishmereni, Yuri Kheifetz, Henrik Søndergaard, Rune Viig Overgaard and Zvia Agur

Time Scale Hierarchies in the Functional Organization of Complex Behaviors pp. 1-18

Dionysios Perdikis, Raoul Huys and Viktor K Jirsa

Signalling and the Evolution of Cooperative Foraging in Dynamic Environments pp. 1-10

Colin J Torney, Andrew Berdahl and Iain D Couzin

Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations pp. 1-14

Lipi Thukral, Isabella Daidone and Jeremy C Smith

A Model for the Origin and Properties of Flicker-Induced Geometric Phosphenes pp. 1-14

Michael Rule, Matthew Stoffregen and Bard Ermentrout

Filament Depolymerization Can Explain Chromosome Pulling during Bacterial Mitosis pp. 1-11

Edward J Banigan, Michael A Gelbart, Zemer Gitai, Ned S Wingreen and Andrea J Liu

Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network pp. 1-11

Jérémie Bourdon, Damien Eveillard and Anne Siegel

LsrR Quorum Sensing “Switch” Is Revealed by a Bottom-Up Approach pp. 1-11

Sara Hooshangi and William E Bentley

Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions pp. 1-11

Adi Shklarsh, Gil Ariel, Elad Schneidman and Eshel Ben-Jacob

Determinants of the Spatiotemporal Dynamics of the 2009 H1N1 Pandemic in Europe: Implications for Real-Time Modelling pp. 1-13

Stefano Merler, Marco Ajelli, Andrea Pugliese and Neil M Ferguson

Neuromotor Noise, Error Tolerance and Velocity-Dependent Costs in Skilled Performance pp. 1-15

Dagmar Sternad, Masaki O Abe, Xiaogang Hu and Hermann Müller

Network-Based Prediction and Analysis of HIV Dependency Factors pp. 1-15

T M Murali, Matthew D Dyer, David Badger, Brett M Tyler and Michael G Katze

Ten Simple Rules for Getting Help from Online Scientific Communities pp. 1-3

Giovanni M Dall'Olio, Jacopo Marino, Michael Schubert, Kevin L Keys, Melanie I Stefan, Colin S Gillespie, Pierre Poulain, Khader Shameer, Robert Sugar, Brandon M Invergo, Lars J Jensen, Jaume Bertranpetit and Hafid Laayouni

Volume 7, issue 8, 2011

Binding Free Energy Landscape of Domain-Peptide Interactions pp. 1-9

Iskra Staneva and Stefan Wallin

Evolutionary Accessibility of Mutational Pathways pp. 1-9

Jasper Franke, Alexander Klözer, J Arjan G M de Visser and Joachim Krug

Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series pp. 1-11

David A Rasmussen, Oliver Ratmann and Katia Koelle

Understanding Auditory Spectro-Temporal Receptive Fields and Their Changes with Input Statistics by Efficient Coding Principles pp. 1-16

Lingyun Zhao and Li Zhaoping

Biomedical Cloud Computing With Amazon Web Services pp. 1-6

Vincent A Fusaro, Prasad Patil, Erik Gafni, Dennis P Wall and Peter J Tonellato

Effective Stimuli for Constructing Reliable Neuron Models pp. 1-13

Shaul Druckmann, Thomas K Berger, Felix Schürmann, Sean Hill, Henry Markram and Idan Segev

A Neurocomputational Model of Stimulus-Specific Adaptation to Oddball and Markov Sequences pp. 1-15

Robert Mill, Martin Coath, Thomas Wennekers and Susan L Denham

Alterations in Brain Connectivity Underlying Beta Oscillations in Parkinsonism pp. 1-15

Rosalyn J Moran, Nicolas Mallet, Vladimir Litvak, Raymond J Dolan, Peter J Magill, Karl J Friston and Peter Brown

Statistical Inference for Multi-Pathogen Systems pp. 1-14

Sourya Shrestha, Aaron A King and Pejman Rohani

Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9 pp. 1-14

Vlad Cojocaru, Kia Balali-Mood, Mark S P Sansom and Rebecca C Wade

Podbat: A Novel Genomic Tool Reveals Swr1-Independent H2A.Z Incorporation at Gene Coding Sequences through Epigenetic Meta-Analysis pp. 1-7

Laia Sadeghi, Carolina Bonilla, Annelie Strålfors, Karl Ekwall and J Peter Svensson

Volume 7, issue 7, 2011

Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases pp. 1-14

Michael D Daily, George N Phillips and Qiang Cui

A Dynamical Model Reveals Gene Co-Localizations in Nucleus pp. 1-16

Jing Kang, Bing Xu, Ye Yao, Wei Lin, Conor Hennessy, Peter Fraser and Jianfeng Feng

Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models pp. 1-16

Iulian Pruteanu-Malinici, Daniel L Mace and Uwe Ohler

Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site pp. 1-16

Julia Romanowska, J Andrew McCammon and Joanna Trylska

The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics pp. 1-16

Qian Wang, Kao-Chen Liang, Arkadiusz Czader, M Neal Waxham and Margaret S Cheung

In vivo Conditions Induce Faithful Encoding of Stimuli by Reducing Nonlinear Synchronization in Vestibular Sensory Neurons pp. 1-17

Adam D Schneider, Kathleen E Cullen and Maurice J Chacron

A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells pp. 1-13

Tian Hong, Jianhua Xing, Liwu Li and John J Tyson

Stimulus-Dependent State Transition between Synchronized Oscillation and Randomly Repetitive Burst in a Model Cerebellar Granular Layer pp. 1-15

Takeru Honda, Tadashi Yamazaki, Shigeru Tanaka, Soichi Nagao and Tetsuro Nishino

MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets pp. 1-15

Kristen M Naegle, Roy E Welsch, Michael B Yaffe, Forest M White and Douglas A Lauffenburger

Optimal Stimulus Shapes for Neuronal Excitation pp. 1-9

Daniel B Forger, David Paydarfar and John R Clay

Modelling the Effects of Population Structure on Childhood Disease: The Case of Varicella pp. 1-9

Romain Silhol and Pierre-Yves Boëlle

Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties pp. 1-18

Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev

Prediction of Cell Penetrating Peptides by Support Vector Machines pp. 1-12

William S Sanders, C Ian Johnston, Susan M Bridges, Shane C Burgess and Kenneth O Willeford

Cadherin-Dependent Cell Morphology in an Epithelium: Constructing a Quantitative Dynamical Model pp. 1-12

Ian M Gemp, Richard W Carthew and Sascha Hilgenfeldt

Bayesian Inference for Genomic Data Integration Reduces Misclassification Rate in Predicting Protein-Protein Interactions pp. 1-10

Chuanhua Xing and David B Dunson

Indirect Reciprocity under Incomplete Observation pp. 1-10

Mitsuhiro Nakamura and Naoki Masuda

Volume 7, issue 6, 2011

Eurekometrics: Analyzing the Nature of Discovery pp. 1-2

Samuel Arbesman and Nicholas A Christakis

Ten Simple Rules for Building and Maintaining a Scientific Reputation pp. 1-2

Philip E Bourne and Virginia Barbour

The Origin of Behavioral Bursts in Decision-Making Circuitry pp. 1-9

Amanda Sorribes, Beatriz G Armendariz, Diego Lopez-Pigozzi, Cristina Murga and Gonzalo G de Polavieja

International Society for Computational Biology Honors Michael Ashburner and Olga Troyanskaya with Top Bioinformatics/Computational Biology Awards for 2011 pp. 1-4

Justin Mullins and Morrison McKay Bj

Generation of Diverse Biological Forms through Combinatorial Interactions between Tissue Polarity and Growth pp. 1-22

Richard Kennaway, Enrico Coen, Amelia Green and Andrew Bangham

Heterogeneous Host Susceptibility Enhances Prevalence of Mixed-Genotype Micro-Parasite Infections pp. 1-15

Wopke van der Werf, Lia Hemerik, Just M Vlak and Mark P Zwart

Extracting Message Inter-Departure Time Distributions from the Human Electroencephalogram pp. 1-8

Bratislav Mišić, Vasily A Vakorin, Nataša Kovačević, Tomáš Paus and Anthony R McIntosh

Neurobiologically Realistic Determinants of Self-Organized Criticality in Networks of Spiking Neurons pp. 1-14

Mikail Rubinov, Olaf Sporns, Jean-Philippe Thivierge and Michael Breakspear

The Binding of Learning to Action in Motor Adaptation pp. 1-14

Luis Nicolas Gonzalez Castro, Craig Bryant Monsen and Maurice A Smith

Generative Embedding for Model-Based Classification of fMRI Data pp. 1-19

Kay H Brodersen, Thomas M Schofield, Alexander P Leff, Cheng Soon Ong, Ekaterina I Lomakina, Joachim M Buhmann and Klaas E Stephan

Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics pp. 1-13

Erik M Volz, Joel C Miller, Alison Galvani and Lauren Ancel Meyers

How Haptic Size Sensations Improve Distance Perception pp. 1-13

Peter W Battaglia, Daniel Kersten and Paul R Schrater

Changes of Mind in an Attractor Network of Decision-Making pp. 1-13

Larissa Albantakis and Gustavo Deco

Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex pp. 1-16

Ruhollah Moussavi-Baygi, Yousef Jamali, Reza Karimi and Mohammad R K Mofrad

Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line pp. 1-11

Velia Siciliano, Filippo Menolascina, Lucia Marucci, Chiara Fracassi, Immacolata Garzilli, Maria Nicoletta Moretti and Diego di Bernardo

Volume 7, issue 5, 2011

Temporal Encoding in a Nervous System pp. 1-19

Zane N Aldworth, Alexander G Dimitrov, Graham I Cummins, Tomáš Gedeon and John P Miller

Attracting Dynamics of Frontal Cortex Ensembles during Memory-Guided Decision-Making pp. 1-19

Emili Balaguer-Ballester, Christopher C Lapish, Jeremy K Seamans and Daniel Durstewitz

Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability pp. 1-14

Alistair N Boettiger, Peter L Ralph and Steven N Evans

How Structure Determines Correlations in Neuronal Networks pp. 1-14

Volker Pernice, Benjamin Staude, Stefano Cardanobile and Stefan Rotter

Cellularly-Driven Differences in Network Synchronization Propensity Are Differentially Modulated by Firing Frequency pp. 1-14

Christian G Fink, Victoria Booth and Michal Zochowski

Feedback Control Architecture and the Bacterial Chemotaxis Network pp. 1-15

Abdullah Hamadeh, Mark A J Roberts, Elias August, Patrick E McSharry, Philip K Maini, Judith P Armitage and Antonis Papachristodoulou

Ten Simple Rules for Providing a Scientific Web Resource pp. 1-3

Sebastian J Schultheiss

Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo pp. 1-11

Pawel Krupinski, Vijay Chickarmane and Carsten Peterson

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein pp. 1-11

Daniel-Adriano Silva, Gregory R Bowman, Alejandro Sosa-Peinado and Xuhui Huang

Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases pp. 1-6

Frank Emmert-Streib and Galina V Glazko

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35 pp. 1-18

Jessica Nasica-Labouze, Massimiliano Meli, Philippe Derreumaux, Giorgio Colombo and Normand Mousseau

Simulation of the Undiseased Human Cardiac Ventricular Action Potential: Model Formulation and Experimental Validation pp. 1-29

Thomas O'Hara, László Virág, András Varró and Yoram Rudy

Spatial Learning and Action Planning in a Prefrontal Cortical Network Model pp. 1-21

Louis-Emmanuel Martinet, Denis Sheynikhovich, Karim Benchenane and Angelo Arleo

Speed/Accuracy Trade-Off between the Habitual and the Goal-Directed Processes pp. 1-21

Mehdi Keramati, Amir Dezfouli and Payam Piray

Volume 7, issue 4, 2011

Cell-Sorting at the A/P Boundary in the Drosophila Wing Primordium: A Computational Model to Consolidate Observed Non-Local Effects of Hh Signaling pp. 1-12

Sabine Schilling, Maria Willecke, Tinri Aegerter-Wilmsen, Olaf A Cirpka, Konrad Basler and Christian von Mering

Linking Microscopic Spatial Patterns of Tissue Destruction in Emphysema to Macroscopic Decline in Stiffness Using a 3D Computational Model pp. 1-9

Harikrishnan Parameswaran, Arnab Majumdar and Béla Suki

In Silico Elucidation of the Recognition Dynamics of Ubiquitin pp. 1-9

Dong Long and Rafael Brüschweiler

A Third Measure-Metastable State in the Dynamics of Spontaneous Shape Change in Healthy Human's White Cells pp. 1-8

Karen A Selz

Minimum Information About a Simulation Experiment (MIASE) pp. 1-4

Dagmar Waltemath, Richard Adams, Daniel A Beard, Frank T Bergmann, Upinder S Bhalla, Randall Britten, Vijayalakshmi Chelliah, Michael T Cooling, Jonathan Cooper, Edmund J Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter Hunter, Edda Klipp, Camille Laibe, Andrew K Miller, Ion Moraru, David Nickerson, Poul Nielsen, Macha Nikolski, Sven Sahle, Herbert M Sauro, Henning Schmidt, Jacky L Snoep, Dominic Tolle, Olaf Wolkenhauer and Nicolas Le Novère

A Stochastic Model of Latently Infected Cell Reactivation and Viral Blip Generation in Treated HIV Patients pp. 1-15

Jessica M Conway and Daniel Coombs

A Mathematical Framework for Estimating Pathogen Transmission Fitness and Inoculum Size Using Data from a Competitive Mixtures Animal Model pp. 1-11

James M McCaw, Nimalan Arinaminpathy, Aeron C Hurt, Jodie McVernon and Angela R McLean

Volume 7, issue 3, 2011

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study pp. 1-21

Elijah Roberts, Andrew Magis, Julio O Ortiz, Wolfgang Baumeister and Zaida Luthey-Schulten

Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts pp. 1-9

Luis Rocha, Fredrik Liljeros and Petter Holme

Animal Interactions and the Emergence of Territoriality pp. 1-9

Luca Giuggioli, Jonathan R Potts and Stephen Harris

The Roots of Bioinformatics in Theoretical Biology pp. 1-5

Paulien Hogeweg

Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells pp. 1-12

Rachel Cavill, Atanas Kamburov, James K Ellis, Toby J Athersuch, Marcus S C Blagrove, Ralf Herwig, Timothy M D Ebbels and Hector C Keun

Dynamic Phenotypic Clustering in Noisy Ecosystems pp. 1-12

Morten Ernebjerg and Roy Kishony

Learning from Sensory and Reward Prediction Errors during Motor Adaptation pp. 1-11

Jun Izawa and Reza Shadmehr

Blockade of Neuronal α7-nAChR by α-Conotoxin ImI Explained by Computational Scanning and Energy Calculations pp. 1-16

Rilei Yu, David J Craik and Quentin Kaas

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases pp. 1-13

Yoo-Ah Kim, Stefan Wuchty and Teresa M Przytycka

Flexible Cognitive Strategies during Motor Learning pp. 1-13

Jordan A Taylor and Richard B Ivry

Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding pp. 1-13

Dana Bar-On, Esther Nachliel, Menachem Gutman and Uri Ashery

A Granger Causality Measure for Point Process Models of Ensemble Neural Spiking Activity pp. 1-13

Sanggyun Kim, David Putrino, Soumya Ghosh and Emery N Brown

Inferring Visuomotor Priors for Sensorimotor Learning pp. 1-13

Edward J A Turnham, Daniel A Braun and Daniel M Wolpert

Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation pp. 1-17

Daniele Linaro, Marco Storace and Michele Giugliano

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli pp. 1-20

Melody K Morris, Julio Saez-Rodriguez, David C Clarke, Peter K Sorger and Douglas A Lauffenburger

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations pp. 1-14

Lars Skjaerven, Barry Grant, Arturo Muga, Knut Teigen, J Andrew McCammon, Nathalie Reuter and Aurora Martinez

Causal Modeling Using Network Ensemble Simulations of Genetic and Gene Expression Data Predicts Genes Involved in Rheumatoid Arthritis pp. 1-19

Heming Xing, Paul D McDonagh, Jadwiga Bienkowska, Tanya Cashorali, Karl Runge, Robert E Miller, Dave DeCaprio, Bruce Church, Ronenn Roubenoff, Iya G Khalil and John Carulli

A Compact Statistical Model of the Song Syntax in Bengalese Finch pp. 1-19

Dezhe Z Jin and Alexay A Kozhevnikov

Volume 7, issue 2, 2011

Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation pp. 1-18

David M Holloway, Francisco J P Lopes, Luciano da Fontoura Costa, Bruno A N Travençolo, Nina Golyandina, Konstantin Usevich and Alexander V Spirov

Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics pp. 1-12

Amber M Smith, Frederick R Adler, Julie L McAuley, Ryan N Gutenkunst, Ruy M Ribeiro, Jonathan A McCullers and Alan S Perelson

A Mathematical Framework for Protein Structure Comparison pp. 1-10

Wei Liu, Anuj Srivastava and Jinfeng Zhang

A Hybrid Model of Mammalian Cell Cycle Regulation pp. 1-10

Rajat Singhania, R Michael Sramkoski, James W Jacobberger and John J Tyson

Transition from Persistent to Anti-Persistent Correlations in Postural Sway Indicates Velocity-Based Control pp. 1-10

Didier Delignières, Kjerstin Torre and Pierre-Louis Bernard

Power-Law Input-Output Transfer Functions Explain the Contrast-Response and Tuning Properties of Neurons in Visual Cortex pp. 1-21

Erez Persi, David Hansel, Lionel Nowak, Pascal Barone and Carl van Vreeswijk

Application of Biomarkers in Cancer Risk Management: Evaluation from Stochastic Clonal Evolutionary and Dynamic System Optimization Points of View pp. 1-7

Xiaohong Li, Patricia L Blount, Thomas L Vaughan and Brian J Reid

Pharmacodynamic Modeling of Anti-Cancer Activity of Tetraiodothyroacetic Acid in a Perfused Cell Culture System pp. 1-14

Hung-Yun Lin, Cornelia B Landersdorfer, David London, Ran Meng, Chang-Uk Lim, Cassie Lin, Sharon Lin, Heng-Yuan Tang, David Brown, Brian Van Scoy, Robert Kulawy, Lurdes Queimado, George L Drusano, Arnold Louie, Faith B Davis, Shaker A Mousa and Paul J Davis

First Principles Modeling of Nonlinear Incidence Rates in Seasonal Epidemics pp. 1-14

José M Ponciano and Marcos A Capistrán

Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions pp. 1-17

John E Pearson, Paul Krapivsky and Alan S Perelson

ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature pp. 1-3

Richard H Lathrop, Burkhard Rost, Membership Iscb, Executive Committee Iscb, Board of Directors Iscb and Public Affairs Committee Iscb

De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference pp. 1-13

Jens Keilwagen, Jan Grau, Ivan A Paponov, Stefan Posch, Marc Strickert and Ivo Grosse

Automatic Design of Digital Synthetic Gene Circuits pp. 1-13

Mario A Marchisio and Jörg Stelling

Molecular Dynamics Simulations of Forced Unbending of Integrin αVβ3 pp. 1-13

Wei Chen, Jizhong Lou, Jen Hsin, Klaus Schulten, Stephen C Harvey and Cheng Zhu

Mitigation Strategies for Pandemic Influenza A: Balancing Conflicting Policy Objectives pp. 1-11

T Déirdre Hollingsworth, Don Klinkenberg, Hans Heesterbeek and Roy M Anderson

Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations pp. 1-11

Chikako Ragan, Michael Zuker and Mark A Ragan

Volume 7, issue 1, 2011

Estimation of Parent Specific DNA Copy Number in Tumors using High-Density Genotyping Arrays pp. 1-15

Hao Chen, Haipeng Xing and Nancy R Zhang

A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt pp. 1-13

Peter Buske, Jörg Galle, Nick Barker, Gabriela Aust, Hans Clevers and Markus Loeffler

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data pp. 1-13

Thomas J Sharpton, Samantha J Riesenfeld, Steven W Kembel, Joshua Ladau, James P O'Dwyer, Jessica L Green, Jonathan A Eisen and Katherine S Pollard

From Spiking Neuron Models to Linear-Nonlinear Models pp. 1-16

Srdjan Ostojic and Nicolas Brunel

A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System pp. 1-16

Bing Liu, Jing Zhang, Pei Yi Tan, David Hsu, Anna M Blom, Benjamin Leong, Sunil Sethi, Bow Ho, Jeak Ling Ding and P S Thiagarajan

Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings pp. 1-14

Elise Payzan-LeNestour and Peter Bossaerts

Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA pp. 1-14

Dina Zhabinskaya and Craig J Benham

Impact of Sarcoplasmic Reticulum Calcium Release on Calcium Dynamics and Action Potential Morphology in Human Atrial Myocytes: A Computational Study pp. 1-14

Jussi T Koivumäki, Topi Korhonen and Pasi Tavi

Decrypting the Sequence of Structural Events during the Gating Transition of Pentameric Ligand-Gated Ion Channels Based on an Interpolated Elastic Network Model pp. 1-10

Wenjun Zheng and Anthony Auerbach

Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks pp. 1-10

Daniel M Cornforth, Timothy C Reluga, Eunha Shim, Chris T Bauch, Alison P Galvani and Lauren Ancel Meyers

A Novel Approach to Pharmacodynamic Assessment of Antimicrobial Agents: New Insights to Dosing Regimen Design pp. 1-8

Vincent H Tam and Michael Nikolaou

Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding pp. 1-8

Iain Melvin, Jason Weston, William Stafford Noble and Christina Leslie

Practical Measures of Integrated Information for Time-Series Data pp. 1-18

Adam B Barrett and Anil K Seth

Is My Network Module Preserved and Reproducible? pp. 1-29

Peter Langfelder, Rui Luo, Michael C Oldham and Steve Horvath

Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia pp. 1-2

Philip E Bourne