PLOS Computational Biology

2005 - 2022

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Volume 10, issue 12, 2014

Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments pp. 1-9

Christoph Zechner and Heinz Koeppl

Thermodynamic Costs of Information Processing in Sensory Adaptation pp. 1-9

Pablo Sartori, Léo Granger, Chiu Fan Lee and Jordan M Horowitz

Hippocampal Remapping Is Constrained by Sparseness rather than Capacity pp. 1-12

Axel Kammerer and Christian Leibold

Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure pp. 1-10

Ritwik K Niyogi, Peter Shizgal and Peter Dayan

Contradictory Behavioral Biases Result from the Influence of Past Stimuli on Perception pp. 1-10

Ofri Raviv, Itay Lieder, Yonatan Loewenstein and Merav Ahissar

“Bioinformatics: Introduction and Methods,” a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education pp. 1-10

Yang Ding, Meng Wang, Yao He, Adam Yongxin Ye, Xiaoxu Yang, Fenglin Liu, Yuqi Meng, Ge Gao and Liping Wei

Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models pp. 1-10

Tadashi Ando and Jeffrey Skolnick

Vesicular Stomatitis Virus Polymerase's Strong Affinity to Its Template Suggests Exotic Transcription Models pp. 1-10

Xiaolin Tang, Mourad Bendjennat and Saveez Saffarian

Molecular Insights into the Dynamics of Pharmacogenetically Important N-Terminal Variants of the Human β2-Adrenergic Receptor pp. 1-10

Ganesh Shahane, Chirag Parsania, Durba Sengupta and Manali Joshi

Yielding Elastic Tethers Stabilize Robust Cell Adhesion pp. 1-8

Matt J Whitfield, Jonathon P Luo and Wendy E Thomas

Ten Simple Rules for Finishing Your PhD pp. 1-4

Jacopo Marino, Melanie I Stefan and Sarah Blackford

A Reaction-Diffusion Model of Cholinergic Retinal Waves pp. 1-14

Benjamin Lansdell, Kevin Ford and J Nathan Kutz

Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation pp. 1-14

Lin Chen, Javad Noorbakhsh, Rhys M Adams, Joseph Samaniego-Evans, Germaine Agollah, Dmitry Nevozhay, Jennie Kuzdzal-Fick, Pankaj Mehta and Gábor Balázsi

The Social Bayesian Brain: Does Mentalizing Make a Difference When We Learn? pp. 1-14

Marie Devaine, Guillaume Hollard and Jean Daunizeau

Protein-Protein Docking with Dynamic Residue Protonation States pp. 1-14

Krishna Praneeth Kilambi, Kavan Reddy and Jeffrey J Gray

Dynamics from Seconds to Hours in Hodgkin-Huxley Model with Time-Dependent Ion Concentrations and Buffer Reservoirs pp. 1-20

Niklas Hübel and Markus A Dahlem

The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets pp. 1-20

Evandro Ferrada

Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid pp. 1-20

Robert Ietswaart, Florian Szardenings, Kenn Gerdes and Martin Howard

Live Imaging-Based Model Selection Reveals Periodic Regulation of the Stochastic G1/S Phase Transition in Vertebrate Axial Development pp. 1-16

Mayu Sugiyama, Takashi Saitou, Hiroshi Kurokawa, Asako Sakaue-Sawano, Takeshi Imamura, Atsushi Miyawaki and Tadahiro Iimura

Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons pp. 1-16

Jean-Pierre Rospars, Alexandre Grémiaux, David Jarriault, Antoine Chaffiol, Christelle Monsempes, Nina Deisig, Sylvia Anton, Philippe Lucas and Dominique Martinez

Dissecting Dynamic Genetic Variation That Controls Temporal Gene Response in Yeast pp. 1-16

Avital Brodt, Maya Botzman, Eyal David and Irit Gat-Viks

Disrupted Calcium Release as a Mechanism for Atrial Alternans Associated with Human Atrial Fibrillation pp. 1-16

Kelly C Chang, Jason D Bayer and Natalia A Trayanova

Symmetry Restoring Bifurcation in Collective Decision-Making pp. 1-11

Natalia Zabzina, Audrey Dussutour, Richard P Mann, David J T Sumpter and Stamatios C Nicolis

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration pp. 1-15

Alexandra Gavryushkina, David Welch, Tanja Stadler and Alexei J Drummond

Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences pp. 1-15

Alex N Nguyen Ba, Bob Strome, Jun Jie Hua, Jonathan Desmond, Isabelle Gagnon-Arsenault, Eric L Weiss, Christian R Landry and Alan M Moses

Bilinearity in Spatiotemporal Integration of Synaptic Inputs pp. 1-15

Songting Li, Nan Liu, Xiao-hui Zhang, Douglas Zhou and David Cai

Volume 10, issue 11, 2014

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models pp. 1-18

Veronika Boskova, Sebastian Bonhoeffer and Tanja Stadler

Spinal Mechanisms May Provide a Combination of Intermittent and Continuous Control of Human Posture: Predictions from a Biologically Based Neuromusculoskeletal Model pp. 1-18

Leonardo Abdala Elias, Renato Naville Watanabe and André Fabio Kohn

Power Laws from Linear Neuronal Cable Theory: Power Spectral Densities of the Soma Potential, Soma Membrane Current and Single-Neuron Contribution to the EEG pp. 1-26

Klas H Pettersen, Henrik Lindén, Tom Tetzlaff and Gaute T Einevoll

Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model pp. 1-10

Arne Weigenand, Michael Schellenberger Costa, Hong-Viet Victor Ngo, Jens Christian Claussen and Thomas Martinetz

Ten Simple Rules to Achieve Conference Speaker Gender Balance pp. 1-3

Jennifer L Martin

Effect of Global Cardiac Ischemia on Human Ventricular Fibrillation: Insights from a Multi-scale Mechanistic Model of the Human Heart pp. 1-15

Ivan V Kazbanov, Richard H Clayton, Martyn P Nash, Chris P Bradley, David J Paterson, Martin P Hayward, Peter Taggart and Alexander V Panfilov

Computational Thinking in Life Science Education pp. 1-5

Amir Rubinstein and Benny Chor

Evolution of All-or-None Strategies in Repeated Public Goods Dilemmas pp. 1-5

Flávio Pinheiro, Vítor V Vasconcelos, Francisco C Santos and Jorge M Pacheco

Pattern of Tick Aggregation on Mice: Larger Than Expected Distribution Tail Enhances the Spread of Tick-Borne Pathogens pp. 1-12

Luca Ferreri, Mario Giacobini, Paolo Bajardi, Luigi Bertolotti, Luca Bolzoni, Valentina Tagliapietra, Annapaola Rizzoli and Roberto Rosà

High-Fidelity Coding with Correlated Neurons pp. 1-25

Rava Azeredo da Silveira and Michael J Berry

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns pp. 1-14

Marcin J Skwark, Daniele Raimondi, Mirco Michel and Arne Elofsson

Statistical Computations Underlying the Dynamics of Memory Updating pp. 1-13

Samuel J Gershman, Angela Radulescu, Kenneth A Norman and Yael Niv

Global Disease Monitoring and Forecasting with Wikipedia pp. 1-16

Nicholas Generous, Geoffrey Fairchild, Alina Deshpande, Sara Y Del Valle and Reid Priedhorsky

Herpes Simplex Virus-2 Genital Tract Shedding Is Not Predictable over Months or Years in Infected Persons pp. 1-16

Varsha Dhankani, J Nathan Kutz and Joshua T Schiffer

Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification pp. 1-20

Junaid Hassan, Linda L Bergaust, I David Wheat and Lars R Bakken

Volume 10, issue 10, 2014

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article pp. 1-5

Harriet Dashnow, Andrew Lonsdale and Philip E Bourne

The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion pp. 1-12

Nicole Dölker, Maria W Górna, Ludovico Sutto, Antonio S Torralba, Giulio Superti-Furga and Francesco L Gervasio

A Reappraisal of How to Build Modular, Reusable Models of Biological Systems pp. 1-7

Maxwell L Neal, Michael T Cooling, Lucian P Smith, Christopher T Thompson, Herbert M Sauro, Brian E Carlson, Daniel L Cook and John H Gennari

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations pp. 1-7

Hai Fang

Predicting Chemical Environments of Bacteria from Receptor Signaling pp. 1-14

Diana Clausznitzer, Gabriele Micali, Silke Neumann, Victor Sourjik and Robert G Endres

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models pp. 1-14

Matthew N Benedict, Michael B Mundy, Christopher S Henry, Nicholas Chia and Nathan D Price

Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics pp. 1-19

Michael J Prerau, Katie E Hartnack, Gabriel Obregon-Henao, Aaron Sampson, Margaret Merlino, Karen Gannon, Matt T Bianchi, Jeffrey M Ellenbogen and Patrick L Purdon

Rhythmic Manipulation of Objects with Complex Dynamics: Predictability over Chaos pp. 1-19

Bahman Nasseroleslami, Christopher J Hasson and Dagmar Sternad

Putting Theory to the Test: Which Regulatory Mechanisms Can Drive Realistic Growth of a Root? pp. 1-19

Dirk De Vos, Kris Vissenberg, Jan Broeckhove and Gerrit T S Beemster

Synaptic Size Dynamics as an Effectively Stochastic Process pp. 1-17

Adiel Statman, Maya Kaufman, Amir Minerbi, Noam E Ziv and Naama Brenner

Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro pp. 1-17

Sophia Rudorf, Michael Thommen, Marina V Rodnina and Reinhard Lipowsky

Improving Contact Prediction along Three Dimensions pp. 1-13

Christoph Feinauer, Marcin J Skwark, Andrea Pagnani and Erik Aurell

Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery pp. 1-13

Jose A Seoane, Colin Campbell, Ian N M Day, Juan P Casas and Tom R Gaunt

Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells pp. 1-11

Christian L Althaus, Beda Joos, Alan S Perelson and Huldrych F Günthard

Phosphate Sink Containing Two-Component Signaling Systems as Tunable Threshold Devices pp. 1-11

Munia Amin, Varun B Kothamachu, Elisenda Feliu, Birgit E Scharf, Steven L Porter and Orkun S Soyer

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling pp. 1-11

Kei Moritsugu, Tohru Terada and Akinori Kidera

Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers pp. 1-11

Heidi Koldsø, David Shorthouse, Jean Hélie and Mark S P Sansom

Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis pp. 1-16

Nathalie Poupin, François Mariotti, Jean-François Huneau, Dominique Hermier and Hélène Fouillet

Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment pp. 1-27

Robert Legenstein and Wolfgang Maass

Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble pp. 1-10

Mary A. Rohrdanz, Wenwei Zheng, Bradley Lambeth, Jocelyne Vreede and Cecilia Clementi

Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups pp. 1-10

Amos Korman, Efrat Greenwald and Ofer Feinerman

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions pp. 1-10

Boryana Doyle, Geoffrey Fudenberg, Maxim Imakaev and Leonid A Mirny

Establishing and Managing a Global Student Network pp. 1-3

Avinash Shanmugam and Geoff Macintyre

Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections pp. 1-15

Frédéric Crevecoeur and Stephen H Scott

Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle pp. 1-15

Mary Hongying Cheng and Ivet Bahar

FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units pp. 1-6

Gang Peng, Yu Fan and Wenyi Wang

Volume 10, issue 9, 2014

Multi-state Modeling of Biomolecules pp. 1-9

Melanie I Stefan, Thomas M Bartol, Terrence J Sejnowski and Mary B Kennedy

Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma pp. 1-18

Marti Bernardo-Faura, Stefan Massen, Christine S Falk, Nathan R Brady and Roland Eils

Seasonally Dependent Relationships between Indicators of Malaria Transmission and Disease Provided by Mathematical Model Simulations pp. 1-10

Erin M Stuckey, Thomas Smith and Nakul Chitnis

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer pp. 1-10

Jinyu Li, Giulia Rossetti, Jens Dreyer, Simone Raugei, Emiliano Ippoliti, Bernhard Lüscher and Paolo Carloni

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform pp. 1-10

N Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D Richman, Dennis R Burton, Pascal Poignard, Davey M Smith and Sergei L Kosakovsky Pond

Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis pp. 1-10

Hong Yang, Elias W Krumholz, Evan D Brutinel, Nagendra P Palani, Michael J Sadowsky, Andrew M Odlyzko, Jeffrey A Gralnick and Igor G L Libourel

eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models pp. 1-15

Michal Brylinski

A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer pp. 1-15

Sijia Huang, Cameron Yee, Travers Ching, Herbert Yu and Lana X Garmire

Environmental Statistics and Optimal Regulation pp. 1-12

David A Sivak and Matt Thomson

A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data pp. 1-8

Qing Xie, Qi Liu, Fengbiao Mao, Wanshi Cai, Honghu Wu, Mingcong You, Zhen Wang, Bingyu Chen, Zhong Sheng Sun and Jinyu Wu

Phase Transitions in the Multi-cellular Regulatory Behavior of Pancreatic Islet Excitability pp. 1-14

Thomas H Hraha, Matthew J Westacott, Marina Pozzoli, Aleena M Notary, P Mason McClatchey and Richard K P Benninger

Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies pp. 1-14

Diana Chang and Alon Keinan

Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages pp. 1-19

Tamás Székely, Kevin Burrage, Marc Mangel and Michael B Bonsall

Inferring on the Intentions of Others by Hierarchical Bayesian Learning pp. 1-19

Andreea O Diaconescu, Christoph Mathys, Lilian A E Weber, Jean Daunizeau, Lars Kasper, Ekaterina I Lomakina, Ernst Fehr and Klaas E Stephan

The Time Scale of Evolutionary Innovation pp. 1-7

Krishnendu Chatterjee, Andreas Pavlogiannis, Ben Adlam and Martin A Nowak

Ten Simple Rules for Better Figures pp. 1-7

Nicolas P Rougier, Michael Droettboom and Philip E Bourne

Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method pp. 1-16

Simone Vincenzi, Marc Mangel, Alain J Crivelli, Stephan Munch and Hans J Skaug

Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets pp. 1-11

Jean-Baptiste Pettit, Raju Tomer, Kaia Achim, Sylvia Richardson, Lamiae Azizi and John Marioni

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing pp. 1-11

Yun-Ching Chen, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace Yeo, Violeta Beleva-Guthrie, Hannah Carter, Peter D Stenson, David N Cooper, Biao Li, Sean Mooney and Rachel Karchin

NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles pp. 1-11

Shunichi Kosugi, Hiroshi Yanagawa, Ryohei Terauchi and Satoshi Tabata

Pupil-Linked Arousal Determines Variability in Perceptual Decision Making pp. 1-13

Peter R Murphy, Joachim Vandekerckhove and Sander Nieuwenhuis

Quantifying the Impact and Extent of Undocumented Biomedical Synonymy pp. 1-17

David R Blair, Kanix Wang, Svetlozar Nestorov, James A Evans and Andrey Rzhetsky

Volume 10, issue 8, 2014

The Upside of Failure: How Regional Student Groups Learn from Their Mistakes pp. 1-3

Tarun Mishra, R Gonzalo Parra and Thomas Abeel

Memory Capacity of Networks with Stochastic Binary Synapses pp. 1-15

Alexis M Dubreuil, Yali Amit and Nicolas Brunel

Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes pp. 1-15

Anne-Florence Bitbol and David J Schwab

A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells pp. 1-15

Pengxing Cao, Xiahui Tan, Graham Donovan, Michael J Sanderson and James Sneyd

Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens pp. 1-9

Delphine Pessoa, Caetano Souto-Maior, Erida Gjini, Joao S Lopes, Bruno Ceña, Cláudia T Codeço and M Gabriela M Gomes

Dynamic Mechanisms of Neocortical Focal Seizure Onset pp. 1-18

Yujiang Wang, Marc Goodfellow, Peter Neal Taylor and Gerold Baier

Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era pp. 1-2

Qiang Cui and Ruth Nussinov

Phenotypic Signatures Arising from Unbalanced Bacterial Growth pp. 1-10

Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz and Lingchong You

Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque pp. 1-19

Fang-Chieh Chou, Jan Lipfert and Rhiju Das

Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth pp. 1-19

Sébastien Benzekry, Clare Lamont, Afshin Beheshti, Amanda Tracz, John M L Ebos, Lynn Hlatky and Philip Hahnfeldt

Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus pp. 1-14

Nik J Cunniffe, Francisco F Laranjeira, Franco M Neri, R Erik DeSimone and Christopher A Gilligan

Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro pp. 1-14

René F M van Oers, Elisabeth G Rens, Danielle J LaValley, Cynthia A Reinhart-King and Roeland M H Merks

Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection pp. 1-14

Miri Adler, Avi Mayo and Uri Alon

Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network pp. 1-7

Frantisek Honti, Stephen Meader and Caleb Webber

Collective Learning and Optimal Consensus Decisions in Social Animal Groups pp. 1-11

Albert B Kao, Noam Miller, Colin Torney, Andrew Hartnett and Iain D Couzin

Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism pp. 1-11

Rui Xia, Selina Vattathil and Paul Scheet

Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis pp. 1-11

Shuo Gu, Daniel-Adriano Silva, Luming Meng, Alexander Yue and Xuhui Huang

Sparsity and Compressed Coding in Sensory Systems pp. 1-11

Victor J Barranca, Gregor Kovačič, Douglas Zhou and David Cai

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data pp. 1-16

Yuan Zhang, Yanni Sun and James R Cole

Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment pp. 1-16

Johannes Textor, Sarah E Henrickson, Judith N Mandl, Ulrich H von Andrian, Jürgen Westermann, Rob J de Boer and Joost B Beltman

Bursts and Heavy Tails in Temporal and Sequential Dynamics of Foraging Decisions pp. 1-13

Kanghoon Jung, Hyeran Jang, Jerald D Kralik and Jaeseung Jeong

Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment pp. 1-13

Eric L Haseltine, Sandra De Meyer, Inge Dierynck, Doug J Bartels, Anne Ghys, Andrew Davis, Eileen Z Zhang, Ann M Tigges, Joan Spanks, Gaston Picchio, Tara L Kieffer and James C Sullivan

Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution pp. 1-17

Priscilla Ambrosi, Juan Sebastian Chahda, Hannah R Koslen, Hillel J Chiel and Claudia Mieko Mizutani

Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images pp. 1-12

Umut Güçlü and Marcel A J van Gerven

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis pp. 1-12

Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W Newell, John Ramey, Mark M Davis, Spyros A Kalams, Stephen C De Rosa and Raphael Gottardo

Volume 10, issue 7, 2014

Computational Modeling and Analysis of Iron Release from Macrophages pp. 1-19

Alka A Potdar, Joydeep Sarkar, Nupur K Das, Paroma Ghosh, Miklos Gratzl, Paul L Fox and Gerald M Saidel

Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics pp. 1-19

Salim Akhter Chowdhury, Stanley E Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A Schäffer and Russell Schwartz

CCAST: A Model-Based Gating Strategy to Isolate Homogeneous Subpopulations in a Heterogeneous Population of Single Cells pp. 1-14

Benedict Anchang, Mary T Do, Xi Zhao and Sylvia K Plevritis

PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape pp. 1-14

Yong Wang, Chun Tang, Erkang Wang and Jin Wang

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial pp. 1-7

Benjamin T Miller, Rishi P Singh, Vinushka Schalk, Yuri Pevzner, Jingjun Sun, Carrie S Miller, Stefan Boresch, Toshiko Ichiye, Bernard R Brooks and H Lee Woodcock

Correlated Inter-Domain Motions in Adenylate Kinase pp. 1-7

Santiago Esteban-Martín, Robert Bryn Fenwick, Jörgen Ådén, Benjamin Cossins, Carlos W Bertoncini, Victor Guallar, Magnus Wolf-Watz and Xavier Salvatella

Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding pp. 1-7

Frank C Pickard Iv, Benjamin T Miller, Vinushka Schalk, Michael G Lerner, H Lee Woodcock and Bernard R Brooks

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes pp. 1-16

Richard Lonsdale, Sarah L Rouse, Mark S P Sansom and Adrian J Mulholland

Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials pp. 1-11

Fabrizio Pucci and Marianne Rooman

LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry pp. 1-11

Jacob D Durrant and Rommie E Amaro

Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor pp. 1-11

Anton Arkhipov, Yibing Shan, Eric T Kim and David E Shaw

Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling pp. 1-17

Tom Serge Weber, Irene Jaehnert, Christian Schichor, Michal Or-Guil and Jorge Carneiro

ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics pp. 1-17

Jan Hasenauer, Christine Hasenauer, Tim Hucho and Fabian J Theis

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape pp. 1-13

Huiyong Sun, Youyong Li, Sheng Tian, Junmei Wang and Tingjun Hou

Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation pp. 1-13

Aniket Magarkar, Nawel Mele, Noha Abdel-Rahman, Sarah Butcher, Mika Torkkeli, Ritva Serimaa, Arja Paananen, Markus Linder and Alex Bunker

Modeling Higher-Order Correlations within Cortical Microcolumns pp. 1-12

Urs Köster, Jascha Sohl-Dickstein, Charles M Gray and Bruno A Olshausen

CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion pp. 1-12

Christophe Restif, Carolina Ibáñez-Ventoso, Mehul M Vora, Suzhen Guo, Dimitris Metaxas and Monica Driscoll

Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock pp. 1-12

Karl Fogelmark and Carl Troein

Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex pp. 1-12

Suchin S Gururangan, Alexander J Sadovsky and Jason N MacLean

Brain and Behavior in Decision-Making pp. 1-8

Peter Cassey, Andrew Heathcote and Scott D Brown

Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity pp. 1-25

Isaure Chauvot de Beauchêne, Ariane Allain, Nicolas Panel, Elodie Laine, Alain Trouvé, Patrice Dubreuil and Luba Tchertanov

Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities pp. 1-3

Jeroen de Ridder, Pieter Meysman, Olugbenga Oluwagbemi and Thomas Abeel

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features pp. 1-15

Mahmoud Ghandi, Dongwon Lee, Morteza Mohammad-Noori and Michael A Beer

Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior pp. 1-15

Adam M Gifford, Yale E Cohen and Alan A Stocker

On the Use of Human Mobility Proxies for Modeling Epidemics pp. 1-15

Michele Tizzoni, Paolo Bajardi, Adeline Decuyper, Guillaume Kon Kam King, Christian M Schneider, Vincent Blondel, Zbigniew Smoreda, Marta C González and Vittoria Colizza

Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks pp. 1-15

Robert Ton, Gustavo Deco and Andreas Daffertshofer

Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication" pp. 1-2

Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort and Peer Bork

A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges pp. 1-10

James Kaufman, Justin Lessler, April Harry, Stefan Edlund, Kun Hu, Judith Douglas, Christian Thoens, Bernd Appel, Annemarie Käsbohrer and Matthias Filter

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells pp. 1-10

Andrew McDavid, Lucas Dennis, Patrick Danaher, Greg Finak, Michael Krouse, Alice Wang, Philippa Webster, Joseph Beechem and Raphael Gottardo

Volume 10, issue 6, 2014

A Novel Cell Traction Force Microscopy to Study Multi-Cellular System pp. 1-15

Xin Tang, Alireza Tofangchi, Sandeep V Anand and Taher A Saif

Ten Simple Rules for Approaching a New Job pp. 1-3

Philip E Bourne

A New Online Computational Biology Curriculum pp. 1-3

David B Searls

International Society for Computational Biology Honors Dana Pe'er with Top Bioinformatics/Computational Biology Award for 2014 pp. 1-3

Christiana N Fogg and Diane E Kovats

Place Cell Rate Remapping by CA3 Recurrent Collaterals pp. 1-10

Trygve Solstad, Hosam N Yousif and Terrence J Sejnowski

On the Origins of Suboptimality in Human Probabilistic Inference pp. 1-23

Luigi Acerbi, Sethu Vijayakumar and Daniel M Wolpert

Identifying Crucial Parameter Correlations Maintaining Bursting Activity pp. 1-23

Anca Doloc-Mihu and Ronald L Calabrese

An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation pp. 1-21

Jerry S Chen, Abygail M Gumbayan, Robert W Zeller and Joseph M Mahaffy

Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE) pp. 1-13

Doron Shem-Tov and Eran Halperin

An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes pp. 1-13

Kevin J Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H Kohn and Luay Nakhleh

Unsupervised Learning of Cone Spectral Classes from Natural Images pp. 1-13

Noah C Benson, Jeremy R Manning and David H Brainard

Optimal Sampling Strategies for Detecting Zoonotic Disease Epidemics pp. 1-13

Jake M Ferguson, Jessica B Langebrake, Vincent L Cannataro, Andres J Garcia, Elizabeth A Hamman, Maia Martcheva and Craig W Osenberg

Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses pp. 1-11

Nadine Töpfer, Federico Scossa, Alisdair Fernie and Zoran Nikoloski

The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro, with Negative Feedback through PPM1A Upregulation pp. 1-16

Junjie Wang, Lisa Tucker-Kellogg, Inn Chuan Ng, Ruirui Jia, P S Thiagarajan, Jacob K White and Hanry Yu

A Unifying Mechanistic Model of Selective Attention in Spiking Neurons pp. 1-16

Bruce Bobier, Terrence C Stewart and Chris Eliasmith

Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference pp. 1-16

Guocai Chen, Michael J Cairelli, Halil Kilicoglu, Dongwook Shin and Thomas C Rindflesch

A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks pp. 1-16

Ankit Gupta, Corentin Briat and Mustafa Khammash

Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization pp. 1-16

Narjes Javaheri, Roland Dries and Jaap Kaandorp

CGBayesNets: Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data pp. 1-7

Michael J McGeachie, Hsun-Hsien Chang and Scott T Weiss

AprioriGWAS, a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects pp. 1-14

Qingrun Zhang, Quan Long and Jurg Ott

Model Selection in Systems Biology Depends on Experimental Design pp. 1-14

Daniel Silk, Paul D W Kirk, Chris P Barnes, Tina Toni and Michael P H Stumpf

The Effects of Theta Precession on Spatial Learning and Simplicial Complex Dynamics in a Topological Model of the Hippocampal Spatial Map pp. 1-14

Mamiko Arai, Vicky Brandt and Yuri Dabaghian

Negative Example Selection for Protein Function Prediction: The NoGO Database pp. 1-12

Noah Youngs, Duncan Penfold-Brown, Richard Bonneau and Dennis Shasha

Volume 10, issue 5, 2014

Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4+T Cells in HIV-1 Infection pp. 1-12

Rodolphe Thiébaut, Julia Drylewicz, Mélanie Prague, Christine Lacabaratz, Stéphanie Beq, Ana Jarne, Thérèse Croughs, Rafick-Pierre Sekaly, Michael M Lederman, Irini Sereti, Daniel Commenges and Yves Lévy

Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks pp. 1-12

Eric A Yen, Aaron Tsay, Jerome Waldispuhl and Jackie Vogel

From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0 pp. 1-25

Masafumi Oizumi, Larissa Albantakis and Giulio Tononi

Barriers to Cooperation Aid Ideological Rigidity and Threaten Societal Collapse pp. 1-8

Marko Jusup, Tadasu Matsuo and Yoh Iwasa

Spatial Generalization in Operant Learning: Lessons from Professional Basketball pp. 1-8

Tal Neiman and Yonatan Loewenstein

In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks pp. 1-14

Filippo Menolascina, Gianfranco Fiore, Emanuele Orabona, Luca De Stefano, Mike Ferry, Jeff Hasty, Mario di Bernardo and Diego di Bernardo

Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells pp. 1-13

Sven Dähne, Niko Wilbert and Laurenz Wiskott

A Computational Framework for Analyzing Stochasticity in Gene Expression pp. 1-13

Marc S Sherman and Barak A Cohen

Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation pp. 1-13

Marcus J Tindall and Angela Clerk

Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data pp. 1-17

Ciira wa Maina, Antti Honkela, Filomena Matarese, Korbinian Grote, Hendrik G Stunnenberg, George Reid, Neil D Lawrence and Magnus Rattray

Predicting the Responses of Repetitively Firing Neurons to Current Noise pp. 1-17

Charles J Wilson, David Barraza, Todd Troyer and Michael A Farries

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones pp. 1-17

Ignacio J General, Ying Liu, Mandy E Blackburn, Wenzhi Mao, Lila M Gierasch and Ivet Bahar

Combined Role of Seizure-Induced Dendritic Morphology Alterations and Spine Loss in Newborn Granule Cells with Mossy Fiber Sprouting on the Hyperexcitability of a Computer Model of the Dentate Gyrus pp. 1-11

Julian Tejada, Norberto Garcia-Cairasco and Antonio C Roque

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments? pp. 1-11

Drazen Petrov and Bojan Zagrovic

Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions pp. 1-9

Daphna Rothschild, Erez Dekel, Jean Hausser, Anat Bren, Guy Aidelberg, Pablo Szekely and Uri Alon

Optimism as a Prior Belief about the Probability of Future Reward pp. 1-9

Aistis Stankevicius, Quentin J M Huys, Aditi Kalra and Peggy Seriès

The Changing Geometry of a Fitness Landscape Along an Adaptive Walk pp. 1-10

Devin Greene and Kristina Crona

Slow Noise in the Period of a Biological Oscillator Underlies Gradual Trends and Abrupt Transitions in Phasic Relationships in Hybrid Neural Networks pp. 1-21

Umeshkanta S Thounaojam, Jianxia Cui, Sharon E Norman, Robert J Butera and Carmen C Canavier

Inferring Host Gene Subnetworks Involved in Viral Replication pp. 1-22

Deborah Chasman, Brandi Gancarz, Linhui Hao, Michael Ferris, Paul Ahlquist and Mark Craven

Paving the Way Towards a Successful and Fulfilling Career in Computational Biology pp. 1-3

Olugbenga Oluwagbemi, Marion Adebiyi, Segun Fatumo and Geoff Macintyre

Ten Simple Rules for Internship in a Pharmaceutical Company pp. 1-3

Bin Chen

2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers pp. 1-3

Christiana N Fogg and Diane E Kovats

Learn from the Best pp. 1-3

Virginie Bernard, Sebastian J Schultheiss and Magali Michaut

Mathematical Modeling Reveals Kinetics of Lymphocyte Recirculation in the Whole Organism pp. 1-15

Vitaly V Ganusov and Jeremy Auerbach

NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT pp. 1-15

Michael V LeVine and Harel Weinstein

In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation pp. 1-15

Jussi T Koivumäki, Gunnar Seemann, Mary M Maleckar and Pasi Tavi

A Signature of Attractor Dynamics in the CA3 Region of the Hippocampus pp. 1-15

César Rennó-Costa, John E Lisman and Paul F M J Verschure

Volume 10, issue 4, 2014

Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics pp. 1-15

Jeffrey P Perley, Judith Mikolajczak, Marietta L Harrison, Gregery T Buzzard and Ann E Rundell

Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics pp. 1-15

Wan Yang, Alicia Karspeck and Jeffrey Shaman

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis pp. 1-6

Remco Bouckaert, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A Suchard, Andrew Rambaut and Alexei J Drummond

Active Learning to Understand Infectious Disease Models and Improve Policy Making pp. 1-10

Lander Willem, Sean Stijven, Ekaterina Vladislavleva, Jan Broeckhove, Philippe Beutels and Niel Hens

Glutamate-Bound NMDARs Arising from In Vivo-like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model pp. 1-21

Matteo Farinella, Daniel T Ruedt, Padraig Gleeson, Frederic Lanore and R Angus Silver

Continuous Attractor Network Model for Conjunctive Position-by-Velocity Tuning of Grid Cells pp. 1-18

Bailu Si, Sandro Romani and Misha Tsodyks

Influence of Wiring Cost on the Large-Scale Architecture of Human Cortical Connectivity pp. 1-24

David Samu, Anil K Seth and Thomas Nowotny

Feedback Signals in Myelodysplastic Syndromes: Increased Self-Renewal of the Malignant Clone Suppresses Normal Hematopoiesis pp. 1-9

Thomas Walenda, Thomas Stiehl, Hanna Braun, Julia Fröbel, Anthony D Ho, Thomas Schroeder, Tamme W Goecke, Björn Rath, Ulrich Germing, Anna Marciniak-Czochra and Wolfgang Wagner

ISMB 2014—The Premier Conference for the World's Computational Biologists pp. 1-2

Christiana N Fogg and Diane E Kovats

Mechanisms of Zero-Lag Synchronization in Cortical Motifs pp. 1-17

Leonardo L Gollo, Claudio Mirasso, Olaf Sporns and Michael Breakspear

Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin pp. 1-13

Qing-Miao Nie, Akio Togashi, Takeshi N Sasaki, Mitsunori Takano, Masaki Sasai and Tomoki P Terada

Agent-Based Modeling of Oxygen-Responsive Transcription Factors in Escherichia coli pp. 1-13

Hao Bai, Matthew D Rolfe, Wenjing Jia, Simon Coakley, Robert K Poole, Jeffrey Green and Mike Holcombe

Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method pp. 1-16

Ke Tang, Jinfeng Zhang and Jie Liang

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems pp. 1-16

Justin S Hogg, Leonard A Harris, Lori J Stover, Niketh S Nair and James R Faeder

Evolutionary Game Dynamics in Populations with Heterogenous Structures pp. 1-16

Wes Maciejewski, Feng Fu and Christoph Hauert

Phylodynamic Inference for Structured Epidemiological Models pp. 1-16

David A Rasmussen, Erik M Volz and Katia Koelle

Bayesian Analysis for Inference of an Emerging Epidemic: Citrus Canker in Urban Landscapes pp. 1-16

Franco M Neri, Alex R Cook, Gavin J Gibson, Tim R Gottwald and Christopher A Gilligan

Phylogenetic Quantification of Intra-tumour Heterogeneity pp. 1-11

Roland F Schwarz, Anne Trinh, Botond Sipos, James D Brenton, Nick Goldman and Florian Markowetz

The Evolution of Multivariate Maternal Effects pp. 1-11

Bram Kuijper, Rufus A Johnstone and Stuart Townley

A Toolbox for Representational Similarity Analysis pp. 1-11

Hamed Nili, Cai Wingfield, Alexander Walther, Li Su, William Marslen-Wilson and Nikolaus Kriegeskorte

Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors pp. 1-11

Lars Boukharta, Hugo Gutiérrez- de-Terán and Johan Åqvist

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids pp. 1-7

Sergio Ruiz-Carmona, Daniel Alvarez-Garcia, Nicolas Foloppe, A Beatriz Garmendia-Doval, Szilveszter Juhos, Peter Schmidtke, Xavier Barril, Roderick E Hubbard and S David Morley

Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment pp. 1-14

Kirill Serkh and Daniel B Forger

Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals pp. 1-1

Robert Brown and Bogdan Pasaniuc

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible pp. 1-12

Paul J McMurdie and Susan Holmes

Prediction and Prioritization of Rare Oncogenic Mutations in the Cancer Kinome Using Novel Features and Multiple Classifiers pp. 1-12

ManChon U, Eric Talevich, Samiksha Katiyar, Khaled Rasheed and Natarajan Kannan

Ten Simple Rules for the Care and Feeding of Scientific Data pp. 1-5

Alyssa Goodman, Alberto Pepe, Alexander W Blocker, Christine L Borgman, Kyle Cranmer, Merce Crosas, Rosanne Di Stefano, Yolanda Gil, Paul Groth, Margaret Hedstrom, David W Hogg, Vinay Kashyap, Ashish Mahabal, Aneta Siemiginowska and Aleksandra Slavkovic

Volume 10, issue 3, 2014

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields pp. 1-12

Jianzhu Ma, Sheng Wang, Zhiyong Wang and Jinbo Xu

Modeling Mutual Exclusivity of Cancer Mutations pp. 1-12

Ewa Szczurek and Niko Beerenwinkel

Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating pp. 1-14

Ramya Gamini, Wei Han, John E Stone and Klaus Schulten

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding pp. 1-14

Shaun Mahony, Matthew D Edwards, Esteban O Mazzoni, Richard I Sherwood, Akshay Kakumanu, Carolyn A Morrison, Hynek Wichterle and David K Gifford

Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model pp. 1-14

Wondimu Teka, Toma M Marinov and Fidel Santamaria

Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach pp. 1-14

Fabian Konrath, Johannes Witt, Thomas Sauter and Dagmar Kulms

Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains pp. 1-19

Vladimir Kazeev, Mustafa Khammash, Michael Nip and Christoph Schwab

Dynamic Alignment Models for Neural Coding pp. 1-19

Sepp Kollmorgen and Richard H R Hahnloser

Slowness and Sparseness Have Diverging Effects on Complex Cell Learning pp. 1-11

Jörn-Philipp Lies, Ralf M Häfner and Matthias Bethge

Universal Count Correction for High-Throughput Sequencing pp. 1-11

Tatsunori B Hashimoto, Matthew D Edwards and David K Gifford

Computational Analyses of Synergism in Small Molecular Network Motifs pp. 1-16

Yili Zhang, Paul Smolen, Douglas A Baxter and John H Byrne

Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems pp. 1-16

Samanthe M Lyons, Wenlong Xu, June Medford and Ashok Prasad

Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins pp. 1-17

Lit-Hsin Loo, Danai Laksameethanasan and Yi-Ling Tung

Behavioral Lateralization and Optimal Route Choice in Flying Budgerigars pp. 1-13

Partha S Bhagavatula, Charles Claudianos, Michael R Ibbotson and Mandyam V Srinivasan

Global Quantitative Modeling of Chromatin Factor Interactions pp. 1-13

Jian Zhou and Olga G Troyanskaya

Comprehensive Analyses of Ventricular Myocyte Models Identify Targets Exhibiting Favorable Rate Dependence pp. 1-13

Megan A Cummins, Pavan J Dalal, Marco Bugana, Stefano Severi and Eric A Sobie

Spatiotemporal Computations of an Excitable and Plastic Brain: Neuronal Plasticity Leads to Noise-Robust and Noise-Constructive Computations pp. 1-20

Hazem Toutounji and Gordon Pipa

Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities pp. 1-9

Arnaud Messé, David Rudrauf, Habib Benali and Guillaume Marrelec

Correction of Distortion in Flattened Representations of the Cortical Surface Allows Prediction of V1-V3 Functional Organization from Anatomy pp. 1-9

Noah C Benson, Omar H Butt, David H Brainard and Geoffrey K Aguirre

Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation pp. 1-18

Michael Pargett, Ann E Rundell, Gregery T Buzzard and David M Umulis

Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver pp. 1-18

Lars Ole Schwen, Markus Krauss, Christoph Niederalt, Felix Gremse, Fabian Kiessling, Andrea Schenk, Tobias Preusser and Lars Kuepfer

If You Can't Measure It, You Can't Manage It pp. 1-4

Jean Peccoud

An In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway pp. 1-26

James Lu, Katrin Hübner, M Nazeem Nanjee, Eliot A Brinton and Norman A Mazer

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies pp. 1-10

Lonnie Welch, Fran Lewitter, Russell Schwartz, Cath Brooksbank, Predrag Radivojac, Bruno Gaeta and Maria Victoria Schneider

Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases pp. 1-10

Teresa Szczepińska, Jan Kutner, Michał Kopczyński, Krzysztof Pawłowski, Andrzej Dziembowski, Andrzej Kudlicki, Krzysztof Ginalski and Maga Rowicka

STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning pp. 1-22

David Kappel, Bernhard Nessler and Wolfgang Maass

Ten Simple Rules for Effective Computational Research pp. 1-3

James M Osborne, Miguel O Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J McInerny, Gary R Mirams, Joe Pitt-Francis, Biswa Sengupta, David W Wright, Christian A Yates, David J Gavaghan, Stephen Emmott and Charlotte Deane

Crossing Borders for Science pp. 1-3

Sebastian J Schultheiss, Joshua SungWoo Yang, Wataru Iwasaki, Shu-Hsi Lin, Angela Jean and Magali Michaut

Volume 10, issue 2, 2014

A Unified View of “How Allostery Works” pp. 1-12

Chung-Jung Tsai and Ruth Nussinov

Compact Modeling of Allosteric Multisite Proteins: Application to a Cell Size Checkpoint pp. 1-12

Germán Enciso, Douglas R Kellogg and Arturo Vargas

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species pp. 1-12

Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu and Mikko Arvas

A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes pp. 1-12

Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino and Michele Caselle

Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia pp. 1-14

Patrick W Sheppard, Xiaoyun Sun, Mustafa Khammash and Rona G Giffard

A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses pp. 1-14

Frederick A Matsen Iv, Christopher T Small, Khanh Soliven, Gregory A Engel, Mostafa M Feeroz, Xiaoxing Wang, Karen L Craig, M Kamrul Hasan, Michael Emerman, Maxine L Linial and Lisa Jones-Engel

GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans pp. 1-11

Oscar Lao, Fan Liu, Andreas Wollstein and Manfred Kayser

In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics pp. 1-13

Pascal Carrivain, Maria Barbi and Jean-Marc Victor

Learning Gene Networks under SNP Perturbations Using eQTL Datasets pp. 1-20

Lingxue Zhang and Seyoung Kim

A Unified Model of Heading and Path Perception in Primate MSTd pp. 1-20

Oliver W Layton and N Andrew Browning

Combining Experiments and Simulations Using the Maximum Entropy Principle pp. 1-9

Wouter Boomsma, Jesper Ferkinghoff-Borg and Kresten Lindorff-Larsen

Modelling Individual Differences in the Form of Pavlovian Conditioned Approach Responses: A Dual Learning Systems Approach with Factored Representations pp. 1-18

Florian Lesaint, Olivier Sigaud, Shelly B Flagel, Terry E Robinson and Mehdi Khamassi

A Network Characteristic That Correlates Environmental and Genetic Robustness pp. 1-23

Zeina Shreif and Vipul Periwal

Mathematical Modeling of the Phoenix Rising Pathway pp. 1-10

Chad Liu, Chuan-Yuan Li and Fan Yuan

Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations pp. 1-10

James C Gumbart, Morgan Beeby, Grant J Jensen and Benoît Roux

The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes pp. 1-22

Yu Hu, Joel Zylberberg and Eric Shea-Brown

A Virtual Infection Model Quantifies Innate Effector Mechanisms and Candida albicans Immune Escape in Human Blood pp. 1-15

Kerstin Hünniger, Teresa Lehnert, Kristin Bieber, Ronny Martin, Marc Thilo Figge and Oliver Kurzai

Workshops: A Great Way to Enhance and Supplement a Degree pp. 1-3

Segun Fatumo, Sayane Shome and Geoff Macintyre

Volume 10, issue 1, 2014

Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures pp. 1-12

Yi-Fei Huang and G Brian Golding

Machine Learning Estimates of Natural Product Conformational Energies pp. 1-8

Matthias Rupp, Matthias R Bauer, Rainer Wilcken, Andreas Lange, Michael Reutlinger, Frank M Boeckler and Gisbert Schneider

Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses pp. 1-14

Mehdi Adibi, James S McDonald, Colin W G Clifford and Ehsan Arabzadeh

Interference and Shaping in Sensorimotor Adaptations with Rewards pp. 1-20

Ran Darshan, Arthur Leblois and David Hansel

Coarse-Grained Molecular Simulation of Epidermal Growth Factor Receptor Protein Tyrosine Kinase Multi-Site Self-Phosphorylation pp. 1-20

John G Koland

Environmental Influence on the Evolution of Morphological Complexity in Machines pp. 1-17

Joshua E Auerbach and Josh C Bongard

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks pp. 1-13

Axel von Kamp and Steffen Klamt

Stress and Strain Provide Positional and Directional Cues in Development pp. 1-13

Behruz Bozorg, Pawel Krupinski and Henrik Jönsson

Competition for Antigen between Th1 and Th2 Responses Determines the Timing of the Immune Response Switch during Mycobaterium avium Subspecies paratuberulosis Infection in Ruminants pp. 1-13

Gesham Magombedze, Shigetoshi Eda and Vitaly V Ganusov

The Role of Thalamic Population Synchrony in the Emergence of Cortical Feature Selectivity pp. 1-13

Sean T Kelly, Jens Kremkow, Jianzhong Jin, Yushi Wang, Qi Wang, Jose-Manuel Alonso and Garrett B Stanley

Task-Specific Response Strategy Selection on the Basis of Recent Training Experience pp. 1-16

Jacqueline M Fulvio, C Shawn Green and Paul R Schrater

Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data pp. 1-16

Nicole Bohme Carnegie, Rui Wang, Vladimir Novitsky and Victor De Gruttola

VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data pp. 1-16

Jean Daunizeau, Vincent Adam and Lionel Rigoux

Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting pp. 1-11

Aaron C Miller, Linnea A Polgreen and Philip M Polgreen

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations pp. 1-11

Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D Wieben, Jaroslav Zendulka, Jan Brezovsky and Jiri Damborsky

Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency pp. 1-18

Biswa Sengupta, Simon Barry Laughlin and Jeremy Edward Niven

De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function pp. 1-18

Areum Han, Peter Stoilov, Anthony J Linares, Yu Zhou, Xiang-Dong Fu and Douglas L Black

Current Practice in Software Development for Computational Neuroscience and How to Improve It pp. 1-9

Marc-Oliver Gewaltig and Robert Cannon

Leadership and Path Characteristics during Walks Are Linked to Dominance Order and Individual Traits in Dogs pp. 1-9

Zsuzsa Ákos, Róbert Beck, Máté Nagy, Tamás Vicsek and Enikő Kubinyi

The Making of the Women in Biology Forum (WiB) at Bioclues pp. 1-2

Reeta Rani Singhania, Dhatri Madduru, Pranathi Pappu, Sameera Panchangam, Renuka Suravajhala and Mohanalatha Chandrasekharan

Fast Reconstruction of Compact Context-Specific Metabolic Network Models pp. 1-10

Nikos Vlassis, Maria Pires Pacheco and Thomas Sauter

Searching for Collective Behavior in a Large Network of Sensory Neurons pp. 1-23

Gašper Tkačik, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek and Michael J Berry

The Correlation Structure of Local Neuronal Networks Intrinsically Results from Recurrent Dynamics pp. 1-21

Moritz Helias, Tom Tetzlaff and Markus Diesmann

Intrinsic Noise Induces Critical Behavior in Leaky Markovian Networks Leading to Avalanching pp. 1-15

Garrett Jenkinson and John Goutsias

Ten Simple Rules for Writing Research Papers pp. 1-3

Weixiong Zhang

Bioinformatics Projects Supporting Life-Sciences Learning in High Schools pp. 1-6

Isabel Marques, Paulo Almeida, Renato Alves, Maria João Dias, Ana Godinho and José B Pereira-Leal