PLOS Computational Biology

2005 - 2025

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Volume 8, issue 12, 2012

Chapter 9: Analyses Using Disease Ontologies pp. 1-12

Nigam H Shah, Tyler Cole and Mark A Musen

Chapter 8: Biological Knowledge Assembly and Interpretation pp. 1-12

Ju Han Kim

Chapter 2: Data-Driven View of Disease Biology pp. 1-8

Casey S Greene and Olga G Troyanskaya

A Comparison of Computational Models for Eukaryotic Cell Shape and Motility pp. 1-17

William R Holmes and Leah Edelstein-Keshet

SnIPRE: Selection Inference Using a Poisson Random Effects Model pp. 1-14

Kirsten E Eilertson, James G Booth and Carlos D Bustamante

Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density pp. 1-13

Claudia Coronnello, Ryan Hartmaier, Arshi Arora, Luai Huleihel, Kusum V Pandit, Abha S Bais, Michael Butterworth, Naftali Kaminski, Gary D Stormo, Steffi Oesterreich and Panayiotis V Benos

Chapter 13: Mining Electronic Health Records in the Genomics Era pp. 1-15

Joshua C Denny

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking pp. 1-10

Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund and Morten Nielsen

Chapter 10: Mining Genome-Wide Genetic Markers pp. 1-9

Xiang Zhang, Shunping Huang, Zhaojun Zhang and Wei Wang

Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought pp. 1-9

Ting Xiang, Debajyoti Ray, Terry Lohrenz, Peter Dayan and P Read Montague

Volume 8, issue 11, 2012

Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis pp. 1-24

Lars Reichl, Dominik Heide, Siegrid Löwel, Justin C Crowley, Matthias Kaschube and Fred Wolf

Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies pp. 1-26

Lars Reichl, Dominik Heide, Siegrid Löwel, Justin C Crowley, Matthias Kaschube and Fred Wolf

Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles pp. 1-14

Gergely Boza, Ádám Kun, István Scheuring and Ulf Dieckmann

Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay pp. 1-14

Filippo Cacace, Paola Paci, Valerio Cusimano, Alfredo Germani and Lorenzo Farina

Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens pp. 1-13

Renske M A Vroomans, Athanasius F M Marée, Rob J de Boer and Joost B Beltman

Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation pp. 1-17

Anupam Saxena, Hod Lipson and Francisco J Valero-Cuevas

How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population pp. 1-11

Nicolas Perony, Claudio J Tessone, Barbara König and Frank Schweitzer

Volume 8, issue 10, 2012

Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations pp. 1-10

Noah S Bieler, Tuomas P J Knowles, Daan Frenkel and Robert Vácha

Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection pp. 1-10

Jan H Peters and Bert L de Groot

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures pp. 1-12

Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, Lada Biedermannova, Jiri Sochor and Jiri Damborsky

Very Slow Search and Reach: Failure to Maximize Expected Gain in an Eye-Hand Coordination Task pp. 1-12

Hang Zhang, Camille Morvan, Louis-Alexandre Etezad-Heydari and Laurence T Maloney

Coding and Decoding with Adapting Neurons: A Population Approach to the Peri-Stimulus Time Histogram pp. 1-14

Richard Naud and Wulfram Gerstner

Estimating the Hidden Burden of Bovine Tuberculosis in Great Britain pp. 1-14

Andrew J K Conlan, Trevelyan J McKinley, Katerina Karolemeas, Ellen Brooks Pollock, Anthony V Goodchild, Andrew P Mitchell, Colin P D Birch, Richard S Clifton-Hadley and James L N Wood

Seven Years; It's Time for a Change pp. 1-2

Philip E Bourne

Analysis of Slow (Theta) Oscillations as a Potential Temporal Reference Frame for Information Coding in Sensory Cortices pp. 1-13

Christoph Kayser, Robin A A Ince and Stefano Panzeri

Volume 8, issue 9, 2012

High-throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications pp. 1-12

Ping-Chang Lee, Chao-Chun Chuang, Ann-Shyn Chiang and Yu-Tai Ching

Spike-based Decision Learning of Nash Equilibria in Two-Player Games pp. 1-12

Johannes Friedrich and Walter Senn

Risk-Sensitivity in Bayesian Sensorimotor Integration pp. 1-7

Jordi Grau-Moya, Pedro A Ortega and Daniel A Braun

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts pp. 1-17

Tobias Sikosek, Erich Bornberg-Bauer and Hue Sun Chan

Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function pp. 1-8

Michael A Jamros, Leandro C Oliveira, Paul C Whitford, José N Onuchic, Joseph A Adams and Patricia A Jennings

Ten Simple Rules To Commercialize Scientific Research pp. 1-3

Anthony C Fletcher and Philip E Bourne

Predicting the Extension of Biomedical Ontologies pp. 1-16

Catia Pesquita and Francisco M Couto

Dependencies among Editing Sites in Serotonin 2C Receptor mRNA pp. 1-13

Liran Carmel, Eugene V Koonin and Stella Dracheva

Spike-Timing Dependence of Structural Plasticity Explains Cooperative Synapse Formation in the Neocortex pp. 1-13

Moritz Deger, Moritz Helias, Stefan Rotter and Markus Diesmann

Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease pp. 1-10

Omar Haq, Michael Andrec, Alexandre V Morozov and Ronald M Levy

Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study pp. 1-9

Iskra Staneva, Yongqi Huang, Zhirong Liu and Stefan Wallin

Volume 8, issue 8, 2012

Locust Dynamics: Behavioral Phase Change and Swarming pp. 1-11

Chad M Topaz, Maria R D'Orsogna, Leah Edelstein-Keshet and Andrew J Bernoff

Decorrelation of Neural-Network Activity by Inhibitory Feedback pp. 1-29

Tom Tetzlaff, Moritz Helias, Gaute T Einevoll and Markus Diesmann

The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles pp. 1-14

Deena M A Gendoo and Paul M Harrison

The Roots of Bioinformatics in ISMB pp. 1-10

Todd A Gibson

Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics pp. 1-15

Reuben H Kraft, Phillip Justin Mckee, Amy M Dagro and Scott T Grafton

Design and Implementation of a Genomics Field Trip Program Aimed at Secondary School Students pp. 1-1

Jennifer McQueen, Jody J Wright and Joanne A Fox

Volume 8, issue 7, 2012

Assessing Drug Target Association Using Semantic Linked Data pp. 1-10

Bin Chen, Ying Ding and David J Wild

Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation pp. 1-13

Jason Flannick, Joshua M Korn, Pierre Fontanillas, George B Grant, Eric Banks, Mark A Depristo and David Altshuler

Coding Conspecific Identity and Motion in the Electric Sense pp. 1-16

Na Yu, Ginette Hupé, Charles Garfinkle, John E Lewis and André Longtin

Which of Our Modeling Predictions Are Robust? pp. 1-5

Rob J De Boer

Automated Tracking of Whiskers in Videos of Head Fixed Rodents pp. 1-8

Nathan G Clack, Daniel H O'Connor, Daniel Huber, Leopoldo Petreanu, Andrew Hires, Simon Peron, Karel Svoboda and Eugene W Myers

Why SIT Works: Normal Function Despite Typical Myofiber Pattern in Situs Inversus Totalis (SIT) Hearts Derived by Shear-induced Myofiber Reorientation pp. 1-11

Marieke Pluijmert, Wilco Kroon, Alessandro C Rossi, Peter H M Bovendeerd and Tammo Delhaas

Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data pp. 1-12

Haipeng Xing, Yifan Mo, Will Liao and Michael Q Zhang

Volume 8, issue 6, 2012

Modeling Boundary Vector Cell Firing Given Optic Flow as a Cue pp. 1-17

Florian Raudies and Michael E Hasselmo

Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees pp. 1-17

Eftychios A Pnevmatikakis, Keith Kelleher, Rebecca Chen, Petter Saggau, Krešimir Josić and Liam Paninski

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation pp. 1-11

Crina-Maria Ionescu, Radka Svobodová Vařeková, Jochen H M Prehn, Heinrich J Huber and Jaroslav Koča

The Role of Non-Native Interactions in the Folding of Knotted Proteins pp. 1-12

Tatjana Škrbić, Cristian Micheletti and Pietro Faccioli

Structural Drift: The Population Dynamics of Sequential Learning pp. 1-12

James P Crutchfield and Sean Whalen

A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts pp. 1-12

Arno Onken, Valentin Dragoi and Klaus Obermayer

A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks pp. 1-12

Daniele De Martino, Matteo Figliuzzi, Andrea De Martino and Enzo Marinari

A Report of the Curriculum Task Force of the ISCB Education Committee pp. 1-2

Lonnie R Welch, Russell Schwartz and Fran Lewitter

Fast Coding of Orientation in Primary Visual Cortex pp. 1-16

Oren Shriki, Adam Kohn and Maoz Shamir

Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations pp. 1-16

Xin Wang, Mauro A Castro, Klaas W Mulder and Florian Markowetz

Short Term Synaptic Depression Imposes a Frequency Dependent Filter on Synaptic Information Transfer pp. 1-18

Robert Rosenbaum, Jonathan Rubin and Brent Doiron

Deceleration of Fusion–Fission Cycles Improves Mitochondrial Quality Control during Aging pp. 1-18

Marc Thilo Figge, Andreas S Reichert, Michael Meyer-Hermann and Heinz D Osiewacz

MC EMiNEM Maps the Interaction Landscape of the Mediator pp. 1-10

Theresa Niederberger, Stefanie Etzold, Michael Lidschreiber, Kerstin C Maier, Dietmar E Martin, Holger Fröhlich, Patrick Cramer and Achim Tresch

Volume 8, issue 5, 2012

Optimal Control of Saccades by Spatial-Temporal Activity Patterns in the Monkey Superior Colliculus pp. 1-18

H H L M Goossens and A J van Opstal

Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments pp. 1-10

Sepideh Bazazi, Frederic Bartumeus, Joseph J Hale and Iain D Couzin

Optimality of Human Contour Integration pp. 1-17

Udo A Ernst, Sunita Mandon, Nadja Schinkel–Bielefeld, Simon D Neitzel, Andreas K Kreiter and Klaus R Pawelzik

Crossing Over…Markov Meets Mendel pp. 1-12

Saad Mneimneh

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package pp. 1-12

Alexander Favorov, Loris Mularoni, Leslie M Cope, Yulia Medvedeva, Andrey A Mironov, Vsevolod J Makeev and Sarah J Wheelan

A Spatial Model of Mosquito Host-Seeking Behavior pp. 1-13

Bree Cummins, Ricardo Cortez, Ivo M Foppa, Justin Walbeck and James M Hyman

Measuring Granger Causality between Cortical Regions from Voxelwise fMRI BOLD Signals with LASSO pp. 1-14

Wei Tang, Steven L Bressler, Chad M Sylvester, Gordon L Shulman and Maurizio Corbetta

Volume 8, issue 4, 2012

Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons pp. 1-15

Kyriaki Sidiropoulou and Panayiota Poirazi

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA pp. 1-21

Dina Zhabinskaya and Craig J Benham

Storage of Correlated Patterns in Standard and Bistable Purkinje Cell Models pp. 1-10

Claudia Clopath, Jean-Pierre Nadal and Nicolas Brunel

Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat pp. 1-7

Yihwa Kim, Robert Sinclair, Nol Chindapol, Jaap A Kaandorp and Erik De Schutter

Tension and Robustness in Multitasking Cellular Networks pp. 1-12

Jeffrey V Wong, Bochong Li and Lingchong You

Volume 8, issue 3, 2012

Ten Simple Rules for Starting a Company pp. 1-3

Anthony C Fletcher and Philip E Bourne

Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery pp. 1-14

András Lörincz, Zsolt Palotai and Gábor Szirtes

Uncovering the Dynamics of Cardiac Systems Using Stochastic Pacing and Frequency Domain Analyses pp. 1-14

Mathieu Lemay, Enno de Lange and Jan P Kucera

State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data pp. 1-27

Hideaki Shimazaki, Shun-ichi Amari, Emery N Brown and Sonja Grün

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data pp. 1-10

Alexander R Macalalad, Michael C Zody, Patrick Charlebois, Niall J Lennon, Ruchi M Newman, Christine M Malboeuf, Elizabeth M Ryan, Christian L Boutwell, Karen A Power, Doug E Brackney, Kendra N Pesko, Joshua Z Levin, Gregory D Ebel, Todd M Allen, Bruce W Birren and Matthew R Henn

Traffic Instabilities in Self-Organized Pedestrian Crowds pp. 1-10

Mehdi Moussaïd, Elsa G Guillot, Mathieu Moreau, Jérôme Fehrenbach, Olivier Chabiron, Samuel Lemercier, Julien Pettré, Cécile Appert-Rolland, Pierre Degond and Guy Theraulaz

Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics pp. 1-18

Ruben Coen-Cagli, Peter Dayan and Odelia Schwartz

A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons pp. 1-1

Dimitrios V Vavoulis, Volko A Straub, John A D Aston and Jianfeng Feng

Volume 8, issue 2, 2012

Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina pp. 1-13

Pranidhi Sood, Robert J Johnston and Edo Kussell

Multi-Scale Modeling of HIV Infection in vitro and APOBEC3G-Based Anti-Retroviral Therapy pp. 1-17

Iraj Hosseini and Feilim Mac Gabhann

Human Visual Search Does Not Maximize the Post-Saccadic Probability of Identifying Targets pp. 1-11

Camille Morvan and Laurence T Maloney

Joint Analysis of Multiple Metagenomic Samples pp. 1-11

Yael Baran and Eran Halperin

Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1 pp. 1-11

Xueyang Feng, You Xu, Yixin Chen and Yinjie J Tang

Paradoxical Evidence Integration in Rapid Decision Processes pp. 1-10

Johannes Rüter, Nicolas Marcille, Henning Sprekeler, Wulfram Gerstner and Michael H Herzog

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data pp. 1-15

Santiago Treviño, Yudong Sun, Tim F Cooper and Kevin E Bassler

Volume 8, issue 1, 2012

Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana pp. 1-15

Michael Seifert, André Gohr, Marc Strickert and Ivo Grosse

Protein Design Using Continuous Rotamers pp. 1-15

Pablo Gainza, Kyle E Roberts and Bruce R Donald

Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies pp. 1-9

Nicoló Fusi, Oliver Stegle and Neil D Lawrence

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection pp. 1-12

Richard P Mann, Andrea Perna, Daniel Strömbom, Roman Garnett, James E Herbert-Read, David J T Sumpter and Ashley J W Ward

Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress pp. 1-12

Patrick D McMullen, Erin Z Aprison, Peter B Winter, Luis A N Amaral, Richard I Morimoto and Ilya Ruvinsky

Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism pp. 1-11

Fiona Achcar, Eduard J Kerkhoven, The SilicoTryp Consortium, Barbara M Bakker, Michael P Barrett and Rainer Breitling

Failure of Adaptive Self-Organized Criticality during Epileptic Seizure Attacks pp. 1-8

Christian Meisel, Alexander Storch, Susanne Hallmeyer-Elgner, Ed Bullmore and Thilo Gross

Adjusting Phenotypes by Noise Control pp. 1-14

Kyung H Kim and Herbert M Sauro

Prediction by Promoter Logic in Bacterial Quorum Sensing pp. 1-14

Navneet Rai, Rajat Anand, Krishna Ramkumar, Varun Sreenivasan, Sugat Dabholkar, K V Venkatesh and Mukund Thattai

A Dynamic View of Domain-Motif Interactions pp. 1-13

Eyal Akiva, Gilgi Friedlander, Zohar Itzhaki and Hanah Margalit

Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding pp. 1-13

Iain H Moal and Paul A Bates