PLOS Computational Biology

2005 - 2025

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Volume 11, issue 12, 2015

Distinctive Behaviors of Druggable Proteins in Cellular Networks pp. 1-18

Costas Mitsopoulos, Amanda C Schierz, Paul Workman and Bissan Al-Lazikani

Computer Simulations Imply Forelimb-Dominated Underwater Flight in Plesiosaurs pp. 1-18

Shiqiu Liu, Adam S Smith, Yuting Gu, Jie Tan, C Karen Liu and Greg Turk

Protein Connectivity in Chemotaxis Receptor Complexes pp. 1-21

Stephan Eismann and Robert G Endres

Anxiety-Like Behavioural Inhibition Is Normative under Environmental Threat-Reward Correlations pp. 1-20

Dominik R Bach

Structural and Energetic Characterization of the Ankyrin Repeat Protein Family pp. 1-20

R Gonzalo Parra, Rocío Espada, Nina Verstraete and Diego U Ferreiro

Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction pp. 1-20

Tatjana Braun, Julia Koehler Leman and Oliver F Lange

Sources of Variability in a Synthetic Gene Oscillator pp. 1-23

Alan Veliz-Cuba, Andrew J Hirning, Adam A Atanas, Faiza Hussain, Flavia Vancia, Krešimir Josić and Matthew R Bennett

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility pp. 1-28

Pradeep Anand Ravindranath, Stefano Forli, David S Goodsell, Arthur J Olson and Michel F Sanner

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome pp. 1-14

István Bartha, Antonio Rausell, Paul J McLaren, Pejman Mohammadi, Manuel Tardaguila, Nimisha Chaturvedi, Jacques Fellay and Amalio Telenti

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set pp. 1-36

Matthew Hall, Mark Woolhouse and Andrew Rambaut

The Essential Complexity of Auditory Receptive Fields pp. 1-33

Ivar L Thorson, Jean Liénard and Stephen V David

Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks pp. 1-12

Henrik Ronellenfitsch, Jana Lasser, Douglas C Daly and Eleni Katifori

Mirrored STDP Implements Autoencoder Learning in a Network of Spiking Neurons pp. 1-25

Kendra S Burbank

Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-Step Task pp. 1-25

Thomas Akam, Rui Costa and Peter Dayan

Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation pp. 1-22

Brenda N Vo, Christopher C Drovandi, Anthony N Pettitt and Graeme J Pettet

Formation and Maintenance of Robust Long-Term Information Storage in the Presence of Synaptic Turnover pp. 1-22

Michael Fauth, Florentin Wörgötter and Christian Tetzlaff

A Functional Cartography of Cognitive Systems pp. 1-26

Marcelo G Mattar, Michael W Cole, Sharon L Thompson-Schill and Danielle S Bassett

Clustered Desynchronization from High-Frequency Deep Brain Stimulation pp. 1-26

Dan Wilson and Jeff Moehlis

Maximizing Sensory Dynamic Range by Tuning the Cortical State to Criticality pp. 1-15

Shree Hari Gautam, Thanh T Hoang, Kylie McClanahan, Stephen K Grady and Woodrow L Shew

Volume 11, issue 11, 2015

Reputation Effects in Public and Private Interactions pp. 1-11

Hisashi Ohtsuki, Yoh Iwasa and Martin A Nowak

Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics pp. 1-14

Laura Hindersin and Arne Traulsen

A Bio-inspired Collision Avoidance Model Based on Spatial Information Derived from Motion Detectors Leads to Common Routes pp. 1-28

Olivier J N Bertrand, Jens P Lindemann and Martin Egelhaaf

Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding pp. 1-28

Satohiro Tajima, Toru Yanagawa, Naotaka Fujii and Taro Toyoizumi

Learning to Estimate Dynamical State with Probabilistic Population Codes pp. 1-28

Joseph G Makin, Benjamin K Dichter and Philip N Sabes

Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics pp. 1-27

Tri Hieu Nim, Le Luo, Jacob K White, Marie-Véronique Clément and Lisa Tucker-Kellogg

Differences in Visual-Spatial Input May Underlie Different Compression Properties of Firing Fields for Grid Cell Modules in Medial Entorhinal Cortex pp. 1-27

Florian Raudies and Michael E Hasselmo

From Sensory Signals to Modality-Independent Conceptual Representations: A Probabilistic Language of Thought Approach pp. 1-32

Goker Erdogan, Ilker Yildirim and Robert A Jacobs

Beyond the E-Value: Stratified Statistics for Protein Domain Prediction pp. 1-21

Alejandro Ochoa, John D Storey, Manuel Llinás and Mona Singh

A Unifying Probabilistic View of Associative Learning pp. 1-20

Samuel J Gershman

Dynamic Redox Regulation of IL-4 Signaling pp. 1-20

Gaurav Dwivedi, Margaret A Gran, Pritha Bagchi and Melissa L Kemp

Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model pp. 1-23

Guido Gigante, Gustavo Deco, Shimon Marom and Paolo Del Giudice

Quantifying Stochastic Noise in Cultured Circadian Reporter Cells pp. 1-17

Peter C St. John and Francis J Doyle

Remodeling and Tenacity of Inhibitory Synapses: Relationships with Network Activity and Neighboring Excitatory Synapses pp. 1-29

Anna Rubinski and Noam E Ziv

Bayesian Estimation of Conditional Independence Graphs Improves Functional Connectivity Estimates pp. 1-26

Max Hinne, Ronald J Janssen, Tom Heskes and Marcel AJ van Gerven

Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach pp. 1-26

Joanne L Dunster, Francoise Mazet, Michael J Fry, Jonathan M Gibbins and Marcus J Tindall

Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics pp. 1-26

Jonathan W Armond, Edward F Harry, Andrew D McAinsh and Nigel J Burroughs

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires pp. 1-16

Mikhail Shugay, Dmitriy V Bagaev, Maria A Turchaninova, Dmitriy A Bolotin, Olga V Britanova, Ekaterina V Putintseva, Mikhail V Pogorelyy, Vadim I Nazarov, Ivan V Zvyagin, Vitalina I Kirgizova, Kirill I Kirgizov, Elena V Skorobogatova and Dmitriy M Chudakov

Improving Collective Estimations Using Resistance to Social Influence pp. 1-16

Gabriel Madirolas and Gonzalo G de Polavieja

Lévy Walks Suboptimal under Predation Risk pp. 1-16

Masato S Abe and Masakazu Shimada

The Encoding of Decision Difficulty and Movement Time in the Primate Premotor Cortex pp. 1-25

Marina Martinez-Garcia, Andrea Insabato, Mario Pannunzi, Jose L Pardo-Vazquez, Carlos Acuña and Gustavo Deco

Parallel Representation of Value-Based and Finite State-Based Strategies in the Ventral and Dorsal Striatum pp. 1-25

Makoto Ito and Kenji Doya

Neuromechanistic Model of Auditory Bistability pp. 1-34

James Rankin, Elyse Sussman and John Rinzel

Volume 11, issue 10, 2015

A Generative Statistical Algorithm for Automatic Detection of Complex Postures pp. 1-23

Stanislav Nagy, Marc Goessling, Yali Amit and David Biron

Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making pp. 1-23

Laurence Aitchison, Dan Bang, Bahador Bahrami and Peter E Latham

TRANSIT - A Software Tool for Himar1 TnSeq Analysis pp. 1-17

Michael A DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher Sassetti and Thomas R Ioerger

Dendritic Pooling of Noisy Threshold Processes Can Explain Many Properties of a Collision-Sensitive Visual Neuron pp. 1-17

Matthias S Keil

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling pp. 1-20

Armin Meier and Johannes Söding

Ten Simple Rules for Protecting Research Integrity pp. 1-6

David M Shaw and Thomas C Erren

The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks pp. 1-21

Michael Chevalier, Ophelia Venturelli and Hana El-Samad

A Common Mechanism Underlying Food Choice and Social Decisions pp. 1-24

Ian Krajbich, Todd Hare, Björn Bartling, Yosuke Morishima and Ernst Fehr

Primary Visual Cortex as a Saliency Map: A Parameter-Free Prediction and Its Test by Behavioral Data pp. 1-39

Li Zhaoping and Li Zhe

PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps pp. 1-27

Radhakrishna Bettadapura, Muhibur Rasheed, Antje Vollrath and Chandrajit Bajaj

Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks pp. 1-28

Christian L Vestergaard and Mathieu Génois

Ten Simple Rules for Establishing International Research Collaborations pp. 1-7

Richard de Grijs

Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism pp. 1-34

Dimitrije Marković, Jan Gläscher, Peter Bossaerts, John O’Doherty and Stefan J Kiebel

Establishing a Statistical Link between Network Oscillations and Neural Synchrony pp. 1-25

Pengcheng Zhou, Shawn D Burton, Adam C Snyder, Matthew A Smith, Nathaniel N Urban and Robert E Kass

Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data pp. 1-30

Daniel Soudry, Suraj Keshri, Patrick Stinson, Min-hwan Oh, Garud Iyengar and Liam Paninski

ENCORE: Software for Quantitative Ensemble Comparison pp. 1-16

Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma and Kresten Lindorff-Larsen

Emergence of Shared Intentionality Is Coupled to the Advance of Cumulative Culture pp. 1-12

Simon Angus and Jonathan Newton

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways pp. 1-37

Sean L Seyler, Avishek Kumar, M F Thorpe and Oliver Beckstein

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing pp. 1-26

Noushin Niknafs, Violeta Beleva-Guthrie, Daniel Q Naiman and Rachel Karchin

The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex pp. 1-29

Joel Z Leibo, Qianli Liao, Fabio Anselmi and Tomaso Poggio

Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models pp. 1-22

Niraj Kumar, Abhyudai Singh and Rahul V Kulkarni

Analyzing and Quantifying the Gain-of-Function Enhancement of IP3 Receptor Gating by Familial Alzheimer’s Disease-Causing Mutants in Presenilins pp. 1-22

Don-On Daniel Mak, King-Ho Cheung, Patrick Toglia, J Kevin Foskett and Ghanim Ullah

Volume 11, issue 9, 2015

Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations pp. 1-37

Sacha Jennifer van Albada, Moritz Helias and Markus Diesmann

A Theory of Cheap Control in Embodied Systems pp. 1-22

Guido Montúfar, Keyan Ghazi-Zahedi and Nihat Ay

You Are Not Working for Me; I Am Working with You pp. 1-8

Florian Markowetz

Dynamic Integration of Value Information into a Common Probability Currency as a Theory for Flexible Decision Making pp. 1-26

Vassilios Christopoulos and Paul R Schrater

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm pp. 1-26

Rudy Clausen, Buyong Ma, Ruth Nussinov and Amarda Shehu

The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption pp. 1-19

Stephan Köhler, Friederike Schmid and Giovanni Settanni

Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance pp. 1-19

Daniel Nichol, Peter Jeavons, Alexander G Fletcher, Robert A Bonomo, Philip K Maini, Jerome L Paul, Robert A Gatenby, Alexander RA Anderson and Jacob G Scott

A Method to Constrain Genome-Scale Models with 13C Labeling Data pp. 1-34

Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam Arkin and Jay D Keasling

Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca2+ Release Patterns in Cardiomyocytes pp. 1-31

Vijay Rajagopal, Gregory Bass, Cameron G Walker, David J Crossman, Amorita Petzer, Anthony Hickey, Ivo Siekmann, Masahiko Hoshijima, Mark H Ellisman, Edmund J Crampin and Christian Soeller

Prospective Optimization with Limited Resources pp. 1-28

Joseph Snider, Dongpyo Lee, Howard Poizner and Sergei Gepshtein

Ten Simple Rules for a Computational Biologist’s Laboratory Notebook pp. 1-5

Santiago Schnell

How to Grow a Computational Biology Lab pp. 1-5

Alice Carolyn McHardy

Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions pp. 1-13

Claudio Altafini and Giuseppe Facchetti

Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model pp. 1-27

Greg Jensen, Fabian Muñoz, Yelda Alkan, Vincent P Ferrera and Herbert S Terrace

Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model pp. 1-18

Naiqian Zhang, Haiyun Wang, Yun Fang, Jun Wang, Xiaoqi Zheng and X Shirley Liu

Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty pp. 1-23

Thembi Mdluli, Gregery T Buzzard and Ann E Rundell

Social Feedback and the Emergence of Rank in Animal Society pp. 1-20

Elizabeth A Hobson and Simon DeDeo

Volume 11, issue 8, 2015

A Bayesian Attractor Model for Perceptual Decision Making pp. 1-35

Sebastian Bitzer, Jelle Bruineberg and Stefan J Kiebel

Flexible Modeling of Epidemics with an Empirical Bayes Framework pp. 1-18

Logan C Brooks, David C Farrow, Sangwon Hyun, Ryan J Tibshirani and Roni Rosenfeld

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data pp. 1-18

Pengyi Yang, Xiaofeng Zheng, Vivek Jayaswal, Guang Hu, Jean Yee Hwa Yang and Raja Jothi

Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks pp. 1-18

Mitchell G Newberry, Daniel B Ennis and Savage Van M

Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations pp. 1-23

Paul M Harrison, Laurent Badel, Mark J Wall and Magnus J E Richardson

A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks pp. 1-23

Alireza Alemi, Carlo Baldassi, Nicolas Brunel and Riccardo Zecchina

Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses pp. 1-40

Gabriel Koch Ocker, Ashok Litwin-Kumar and Brent Doiron

Structure Learning in Bayesian Sensorimotor Integration pp. 1-27

Tim Genewein, Eduard Hez, Zeynab Razzaghpanah and Daniel A Braun

Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures pp. 1-16

Brinda Vallat, Carlos Madrid-Aliste and Andras Fiser

Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions pp. 1-16

Assaf Amitai, Mathias Toulouze, Karine Dubrana and David Holcman

Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks pp. 1-16

Claudia Schillings, Mikael Sunnåker, Jörg Stelling and Christoph Schwab

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction pp. 1-19

Jonas Paulsen, Odin Gramstad and Philippe Collas

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data pp. 1-26

Alexey A Gritsenko, Marc Hulsman, Marcel J T Reinders and Dick de Ridder

Asymmetric Evolutionary Games pp. 1-26

Alex McAvoy and Christoph Hauert

Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling pp. 1-26

Adrián Ponce-Alvarez, Biyu J He, Patric Hagmann and Gustavo Deco

The Beta Cell in Its Cluster: Stochastic Graphs of Beta Cell Connectivity in the Islets of Langerhans pp. 1-29

Deborah A Striegel, Manami Hara and Vipul Periwal

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast pp. 1-22

Zing Tsung-Yeh Tsai, Shin-Han Shiu and Huai-Kuang Tsai

Volume 11, issue 7, 2015

A Diffusive Homeostatic Signal Maintains Neural Heterogeneity and Responsiveness in Cortical Networks pp. 1-25

Yann Sweeney, Jeanette Hellgren Kotaleski and Matthias H Hennig

Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method pp. 1-23

Marharyta Petukh, Minghui Li and Emil Alexov

Adaptive Synaptogenesis Constructs Neural Codes That Benefit Discrimination pp. 1-23

Blake T Thomas, Davis W Blalock and William B Levy

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences pp. 1-23

Alexander M Sevy, Tim M Jacobs, James E Crowe and Jens Meiler

Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks pp. 1-23

Saket Navlakha, Alison L Barth and Ziv Bar-Joseph

Optimal Prediction of Moving Sound Source Direction in the Owl pp. 1-20

Weston Cox and Brian J Fischer

Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina pp. 1-30

Jian K Liu and Tim Gollisch

Measuring Asymmetry in Time-Stamped Phylogenies pp. 1-16

Bethany L Dearlove and Simon D W Frost

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement pp. 1-21

Hanlun Jiang, Fu Kit Sheong, Lizhe Zhu, Xin Gao, Julie Bernauer and Xuhui Huang

Asynchronous Rate Chaos in Spiking Neuronal Circuits pp. 1-38

Omri Harish and David Hansel

Geometry of the Gene Expression Space of Individual Cells pp. 1-27

Yael Korem, Pablo Szekely, Yuval Hart, Hila Sheftel, Jean Hausser, Avi Mayo, Michael E Rothenberg, Tomer Kalisky and Uri Alon

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models pp. 1-22

Richard R Stein, Debora S Marks and Chris Sander

Volume 11, issue 6, 2015

Behavioural Contagion Explains Group Cohesion in a Social Crustacean pp. 1-18

Pierre Broly and Jean-Louis Deneubourg

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data pp. 1-18

Catalina A Vallejos, John C Marioni and Sylvia Richardson

Energy Efficient Sparse Connectivity from Imbalanced Synaptic Plasticity Rules pp. 1-24

João Sacramento, Andreas Wichert and Mark C W van Rossum

Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation pp. 1-21

Gabriele Micali, Gerardo Aquino, David M Richards and Robert G Endres

Is Model Fitting Necessary for Model-Based fMRI? pp. 1-21

Robert C Wilson and Yael Niv

Measuring Fisher Information Accurately in Correlated Neural Populations pp. 1-27

Ingmar Kanitscheider, Ruben Coen-Cagli, Adam Kohn and Alexandre Pouget

Computational Biology: Moving into the Future One Click at a Time pp. 1-13

Christiana N Fogg and Diane E Kovats

High Stimulus-Related Information in Barrel Cortex Inhibitory Interneurons pp. 1-32

Vicente Reyes-Puerta, Suam Kim, Jyh-Jang Sun, Barbara Imbrosci, Werner Kilb and Heiko J Luhmann

Posterior Probability Matching and Human Perceptual Decision Making pp. 1-16

Richard F Murray, Khushbu Patel and Alan Yee

Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks pp. 1-19

Xiaoke Ma, Long Gao, Georgios Karamanlidis, Peng Gao, Chi Fung Lee, Lorena Garcia-Menendez, Rong Tian and Kai Tan

The Decay of Motor Memories Is Independent of Context Change Detection pp. 1-31

Andrew E Brennan and Maurice A Smith

Stochastic Dynamics Underlying Cognitive Stability and Flexibility pp. 1-46

Kai Ueltzhöffer, Diana J N Armbruster-Genç and Christian J Fiebach

Encoder-Decoder Optimization for Brain-Computer Interfaces pp. 1-25

Josh Merel, Donald M Pianto, John P Cunningham and Liam Paninski

The Sense of Confidence during Probabilistic Learning: A Normative Account pp. 1-25

Florent Meyniel, Daniel Schlunegger and Stanislas Dehaene

Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait pp. 1-26

Kerry E Boyle, Hilary Monaco, Dave van Ditmarsch, Maxime Deforet and Joao B Xavier

Monte Carlo Planning Method Estimates Planning Horizons during Interactive Social Exchange pp. 1-38

Andreas Hula, P Read Montague and Peter Dayan

Antibiotic Restriction Might Facilitate the Emergence of Multi-drug Resistance pp. 1-15

Uri Obolski, Gideon Y Stein and Lilach Hadany

Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation pp. 1-3

Philip E Bourne, Steven E Brenner and Michael B Eisen

2015 ISCB Overton Prize Awarded to Curtis Huttenhower pp. 1-3

Christiana N Fogg and Diane E Kovats

Volume 11, issue 5, 2015

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models pp. 1-21

Jonathan R Karr, Alex H Williams, Jeremy D Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, Parameter Estimation Challenge Consortium Dream8, Simon Wilkinson, Brandon A Allgood, Brian M Bot, Bruce R Hoff, Michael R Kellen, Markus W Covert, Gustavo A Stolovitzky and Pablo Meyer

SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps pp. 1-21

Manu Setty and Christina S Leslie

Accurate Computation of Survival Statistics in Genome-Wide Studies pp. 1-18

Fabio Vandin, Alexandra Papoutsaki, Benjamin J Raphael and Eli Upfal

The Effect of Incentives and Meta-incentives on the Evolution of Cooperation pp. 1-17

Isamu Okada, Hitoshi Yamamoto, Fujio Toriumi and Tatsuya Sasaki

Power Law Scaling in Human and Empty Room MEG Recordings pp. 1-5

Manfred G Kitzbichler and Edward T Bullmore

Metapopulation Persistence in Random Fragmented Landscapes pp. 1-13

Jacopo Grilli, György Barabás and Stefano Allesina

Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities pp. 1-19

Victor Garcia, Kirsten Richter, Frederik Graw, Annette Oxenius and Roland R Regoes

Sharing and Specificity of Co-expression Networks across 35 Human Tissues pp. 1-19

Emma Pierson, the GTEx Consortium, Daphne Koller, Alexis Battle and Sara Mostafavi

Maintaining Homeostasis by Decision-Making pp. 1-19

Christoph W Korn and Dominik R Bach

Sparse and Compositionally Robust Inference of Microbial Ecological Networks pp. 1-25

Zachary D Kurtz, Christian L Müller, Emily R Miraldi, Dan R Littman, Martin J Blaser and Richard A Bonneau

Predicting Cortical Dark/Bright Asymmetries from Natural Image Statistics and Early Visual Transforms pp. 1-25

Emily A Cooper and Anthony M Norcia

Convex Clustering: An Attractive Alternative to Hierarchical Clustering pp. 1-31

Gary K Chen, Eric C Chi, John Michael O Ranola and Kenneth Lange

Forecasting the 2013–2014 Influenza Season Using Wikipedia pp. 1-29

Kyle S Hickmann, Geoffrey Fairchild, Reid Priedhorsky, Nicholas Generous, James M Hyman, Alina Deshpande and Sara Y Del Valle

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints pp. 1-22

Alon Diament and Tamir Tuller

Volume 11, issue 4, 2015

Embodied Choice: How Action Influences Perceptual Decision Making pp. 1-22

Nathan F Lepora and Giovanni Pezzulo

Metrics for Assessing Cytoskeletal Orientational Correlations and Consistency pp. 1-22

Nancy K Drew, Mackenzie A Eagleson, Danny B Baldo, Kevin Kit Parker and Anna Grosberg

Cell-Specific Cardiac Electrophysiology Models pp. 1-22

Willemijn Groenendaal, Francis A Ortega, Armen R Kherlopian, Andrew C Zygmunt, Trine Krogh-Madsen and David J Christini

The Serotype Distribution among Healthy Carriers before Vaccination Is Essential for Predicting the Impact of Pneumococcal Conjugate Vaccine on Invasive Disease pp. 1-15

Stefan Flasche, Olivier Le Polain de Waroux, Katherine L O’Brien and W John Edmunds

Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity pp. 1-16

Paul Egan, Jeffrey Moore, Christian Schunn, Jonathan Cagan and Philip LeDuc

A Bayesian Ensemble Approach for Epidemiological Projections pp. 1-30

Tom Lindström, Michael Tildesley and Colleen Webb

MAGMA: Generalized Gene-Set Analysis of GWAS Data pp. 1-19

Christiaan A de Leeuw, Joris M Mooij, Tom Heskes and Danielle Posthuma

The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction pp. 1-31

Ross S Williamson, Maneesh Sahani and Jonathan W Pillow

Ten Simple Rules for a Successful Cross-Disciplinary Collaboration pp. 1-7

Bernhard Knapp, Rémi Bardenet, Miguel O Bernabeu, Rafel Bordas, Maria Bruna, Ben Calderhead, Jonathan Cooper, Alexander G Fletcher, Derek Groen, Bram Kuijper, Joanna Lewis, Greg McInerny, Timo Minssen, James Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A Yates, David Gavaghan and Charlotte M Deane

The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information pp. 1-25

Daniel Bendor

Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences pp. 1-27

Jian Tian, Jaie C Woodard, Andrew Whitney and Eugene I Shakhnovich

The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition pp. 1-24

Xiliang Zheng and Jin Wang

Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research pp. 1-6

Anne-Laure Boulesteix

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2 pp. 1-21

Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška and Jaroslav Koča

Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery pp. 1-21

Sébastien Giguère, François Laviolette, Mario Marchand, Denise Tremblay, Sylvain Moineau, Xinxia Liang, Éric Biron and Jacques Corbeil

A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome pp. 1-21

Susan Dina Ghiassian, Jörg Menche and Albert-László Barabási

Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models pp. 1-21

Timo R Maarleveld, Meike T Wortel, Brett G Olivier, Bas Teusink and Frank J Bruggeman

Quantifying Spike Train Oscillations: Biases, Distortions and Solutions pp. 1-21

Ayala Matzner and Izhar Bar-Gad

Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees pp. 1-20

Ickwon Choi, Amy W Chung, Todd J Suscovich, Supachai Rerks-Ngarm, Punnee Pitisuttithum, Sorachai Nitayaphan, Jaranit Kaewkungwal, Robert J O'Connell, Donald Francis, Merlin L Robb, Nelson L Michael, Jerome H Kim, Galit Alter, Margaret E Ackerman and Chris Bailey-Kellogg

Ten Simple Rules to Win a Nobel Prize pp. 1-4

Richard J Roberts

Dual Dimensionality Reduction Reveals Independent Encoding of Motor Features in a Muscle Synergy for Insect Flight Control pp. 1-23

Simon Sponberg, Thomas L Daniel and Adrienne L Fairhall

Volume 11, issue 3, 2015

PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population pp. 1-14

Oren E Livne, Lide Han, Gorka Alkorta-Aranburu, William Wentworth-Sheilds, Mark Abney, Carole Ober and Dan L Nicolae

Improved Estimation and Interpretation of Correlations in Neural Circuits pp. 1-28

Dimitri Yatsenko, Krešimir Josić, Alexander S Ecker, Emmanouil Froudarakis, R James Cotton and Andreas S Tolias

Theory of Choice in Bandit, Information Sampling and Foraging Tasks pp. 1-28

Bruno B Averbeck

Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists pp. 1-11

Marco D Visser, Sean M McMahon, Cory Merow, Philip M Dixon, Sydne Record and Eelke Jongejans

Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief pp. 1-32

Giles W Story, Ivo Vlaev, Peter Dayan, Ben Seymour, Ara Darzi and Raymond J Dolan

Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles pp. 1-21

Minseung Kim, Violeta Zorraquino and Ilias Tagkopoulos

Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision pp. 1-21

Adrian M Haith, David M Huberdeau and John W Krakauer

Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting pp. 1-18

Davide Albanese, Carlotta De Filippo, Duccio Cavalieri and Claudio Donati

Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model pp. 1-24

Alistair M Senior, Michael A Charleston, Mathieu Lihoreau, Camille Buhl, David Raubenheimer and Stephen J Simpson

Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer pp. 1-23

Christopher R S Banerji, Simone Severini, Carlos Caldas and Andrew E Teschendorff

When Can Species Abundance Data Reveal Non-neutrality? pp. 1-23

Omar Al Hammal, David Alonso, Rampal S Etienne and Stephen J Cornell

Mapping Shape to Visuomotor Mapping: Learning and Generalisation of Sensorimotor Behaviour Based on Contextual Information pp. 1-23

Loes C J van Dam and Marc O Ernst

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data pp. 1-17

Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming Sound-Tsao and Igor Jurisica

Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data pp. 1-29

Alan L Hutchison, Mark Maienschein-Cline, Andrew H Chiang, S M Ali Tabei, Herman Gudjonson, Neil Bahroos, Ravi Allada and Aaron R Dinner

On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain pp. 1-38

Adrien Wohrer and Christian K Machens

Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles pp. 1-16

Jérôme R D Soiné, Christoph A Brand, Jonathan Stricker, Patrick W Oakes, Margaret L Gardel and Ulrich S Schwarz

Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals pp. 1-16

Thomas Obadia, Romain Silhol, Lulla Opatowski, Laura Temime, Judith Legrand, Anne C M Thiébaut, Jean-Louis Herrmann, Éric Fleury, Didier Guillemot, Pierre-Yves Boëlle and on behalf of the I-Bird Study Group

Proportionality: A Valid Alternative to Correlation for Relative Data pp. 1-12

David Lovell, Vera Pawlowsky-Glahn, Juan José Egozcue, Samuel Marguerat and Jürg Bähler

Predicting Epidemic Risk from Past Temporal Contact Data pp. 1-19

Eugenio Valdano, Chiara Poletto, Armando Giovannini, Diana Palma, Lara Savini and Vittoria Colizza

Identifying and Tracking Simulated Synaptic Inputs from Neuronal Firing: Insights from In Vitro Experiments pp. 1-31

Maxim Volgushev, Vladimir Ilin and Ian H Stevenson

Volume 11, issue 2, 2015

Co-evolutionary Dynamics of Collective Action with Signaling for a Quorum pp. 1-12

Jorge M Pacheco, Vítor V Vasconcelos, Francisco C Santos and Brian Skyrms

A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination pp. 1-34

Laura R González-Ramírez, Omar J Ahmed, Sydney S Cash, C Eugene Wayne and Mark A Kramer

Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions pp. 1-28

Vladimir Potapov, Jenifer B Kaplan and Amy E Keating

The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure pp. 1-32

Benjamin Allen, Christine Sample, Yulia Dementieva, Ruben C Medeiros, Christopher Paoletti and Martin A Nowak

Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis pp. 1-27

Andrew J K Conlan, Ellen Brooks Pollock, Trevelyan J McKinley, Andrew P Mitchell, Gareth J Jones, Martin Vordermeier and James L N Wood

Correlations and Functional Connections in a Population of Grid Cells pp. 1-21

Benjamin Dunn, Maria Mørreaunet and Yasser Roudi

Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information pp. 1-24

Daniel M Keenan, Amy W Quinkert and Donald W Pfaff

A Theoretical Justification for Single Molecule Peptide Sequencing pp. 1-17

Jagannath Swaminathan, Alexander A Boulgakov and Edward M Marcotte

Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage pp. 1-23

Ishutesh Jain, Mandar M Inamdar and Ranjith Padinhateeri

Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity pp. 1-23

Adrián Ponce-Alvarez, Gustavo Deco, Patric Hagmann, Gian Luca Romani, Dante Mantini and Maurizio Corbetta

Heterogeneous CD8+ T Cell Migration in the Lymph Node in the Absence of Inflammation Revealed by Quantitative Migration Analysis pp. 1-20

Edward J Banigan, Tajie H Harris, David A Christian, Christopher A Hunter and Andrea J Liu

Protein Sectors: Statistical Coupling Analysis versus Conservation pp. 1-20

Tiberiu Teşileanu, Lucy J Colwell and Stanislas Leibler

Critical Slowing Down Governs the Transition to Neuron Spiking pp. 1-20

Christian Meisel, Andreas Klaus, Christian Kuehn and Dietmar Plenz

Volume 11, issue 1, 2015

150 Years of the Mass Action Law pp. 1-7

Eberhard O Voit, Harald A Martens and Stig W Omholt

A Probabilistic Palimpsest Model of Visual Short-term Memory pp. 1-34

Loic Matthey, Paul M Bays and Peter Dayan

Modulation of Elementary Calcium Release Mediates a Transition from Puffs to Waves in an IP3R Cluster Model pp. 1-12

Martin Rückl, Ian Parker, Jonathan S Marchant, Chamakuri Nagaiah, Friedrich W Johenning and Sten Rüdiger

Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate pp. 1-15

Regina S Salvat, Andrew S Parker, Yoonjoo Choi, Chris Bailey-Kellogg and Karl E Griswold

A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso pp. 1-15

Erick A Perez Alday, Michael A Colman, Philip Langley, Timothy D Butters, Jonathan Higham, Antony J Workman, Jules C Hancox and Henggui Zhang

The Formation of Multi-synaptic Connections by the Interaction of Synaptic and Structural Plasticity and Their Functional Consequences pp. 1-29

Michael Fauth, Florentin Wörgötter and Christian Tetzlaff

Orientation Selectivity in Inhibition-Dominated Networks of Spiking Neurons: Effect of Single Neuron Properties and Network Dynamics pp. 1-17

Sadra Sadeh and Stefan Rotter

Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms pp. 1-20

J Matthew Mahoney, Jaclyn Taroni, Viktor Martyanov, Tammara A Wood, Casey S Greene, Patricia A Pioli, Monique E Hinchcliff and Michael L Whitfield

Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda pp. 1-18

Ioannis Andrianakis, Ian R Vernon, Nicky McCreesh, Trevelyan J McKinley, Jeremy E Oakley, Rebecca N Nsubuga, Michael Goldstein and Richard G White

GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells pp. 1-10

Alboukadel Kassambara, Thierry Rème, Michel Jourdan, Thierry Fest, Dirk Hose, Karin Tarte and Bernard Klein

Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions pp. 1-28

Massimo Lai, Denis Brun, Stuart J Edelstein and Nicolas Le Novère