PLOS Computational Biology

2005 - 2025

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Volume 11, issue 12, 2015

Protein Connectivity in Chemotaxis Receptor Complexes pp. 1-21

Stephan Eismann and Robert G Endres

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

Matthew Hall, Mark Woolhouse and Andrew Rambaut

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

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

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

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

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

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

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

Ivar L Thorson, Jean Liénard and Stephen V David

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

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

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

Volume 11, issue 11, 2015

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

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

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

Hisashi Ohtsuki, Yoh Iwasa and Martin A Nowak

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

Neuromechanistic Model of Auditory Bistability pp. 1-34

James Rankin, Elyse Sussman and John Rinzel

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

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

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

Peter C St. John and Francis J Doyle

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

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

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

Anna Rubinski and Noam E Ziv

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

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

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

Volume 11, issue 10, 2015

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

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

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

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

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

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

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

Armin Meier and Johannes Söding

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

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

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

Richard de Grijs

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

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

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

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

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

Simon Angus and Jonathan Newton

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

David M Shaw and Thomas C Erren

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

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

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

Christian L Vestergaard and Mathieu Génois

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

Michael Chevalier, Ophelia Venturelli and Hana El-Samad

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

Volume 11, issue 9, 2015

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

Florian Markowetz

Prospective Optimization with Limited Resources pp. 1-28

Joseph Snider, Dongpyo Lee, Howard Poizner and Sergei Gepshtein

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

Claudio Altafini and Giuseppe Facchetti

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

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

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

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

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

Elizabeth A Hobson and Simon DeDeo

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

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

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

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

Volume 11, issue 8, 2015

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

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

Gabriel Koch Ocker, Ashok Litwin-Kumar and Brent Doiron

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

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

Sebastian Bitzer, Jelle Bruineberg and Stefan J Kiebel

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

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

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

Structure Learning in Bayesian Sensorimotor Integration pp. 1-27

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

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

Jonas Paulsen, Odin Gramstad and Philippe Collas

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

Volume 11, issue 7, 2015

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

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

Richard R Stein, Debora S Marks and Chris Sander

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

Yann Sweeney, Jeanette Hellgren Kotaleski and Matthias H Hennig

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

Bethany L Dearlove and Simon D W Frost

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

Jian K Liu and Tim Gollisch

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

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

Weston Cox and Brian J Fischer

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

Volume 11, issue 6, 2015

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

Uri Obolski, Gideon Y Stein and Lilach Hadany

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

Richard F Murray, Khushbu Patel and Alan Yee

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

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

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

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

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

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

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

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

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

Andreas Hula, P Read Montague and Peter Dayan

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

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

Andrew E Brennan and Maurice A Smith

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

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

Christiana N Fogg and Diane E Kovats

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

Volume 11, issue 5, 2015

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

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

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

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

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

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

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

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

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

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

Alon Diament and Tamir Tuller

Volume 11, issue 4, 2015

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

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

Anne-Laure Boulesteix

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

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

Daniel Bendor

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

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

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

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 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

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

Tom Lindström, Michael Tildesley and Colleen Webb

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

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

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

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

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

Volume 11, issue 3, 2015

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Volume 11, issue 2, 2015

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

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

Jagannath Swaminathan, Alexander A Boulgakov and Edward M Marcotte

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

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

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

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

Benjamin Dunn, Maria Mørreaunet and Yasser Roudi

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

Vladimir Potapov, Jenifer B Kaplan and Amy E Keating

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

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

Volume 11, issue 1, 2015

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

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

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

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

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

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

Eberhard O Voit, Harald A Martens and Stig W Omholt

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

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

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