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July 2015, Volume 11, Issue 7
- 1-20 Optimal Prediction of Moving Sound Source Direction in the Owl
by Weston Cox & Brian J Fischer - 1-21 Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
by Hanlun Jiang & Fu Kit Sheong & Lizhe Zhu & Xin Gao & Julie Bernauer & Xuhui Huang - 1-22 Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models
by Richard R Stein & Debora S Marks & Chris Sander - 1-23 Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
by Marharyta Petukh & Minghui Li & Emil Alexov - 1-23 Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks
by Saket Navlakha & Alison L Barth & Ziv Bar-Joseph - 1-23 Adaptive Synaptogenesis Constructs Neural Codes That Benefit Discrimination
by Blake T Thomas & Davis W Blalock & William B Levy - 1-23 Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences
by Alexander M Sevy & Tim M Jacobs & James E Crowe Jr. & Jens Meiler - 1-25 A Diffusive Homeostatic Signal Maintains Neural Heterogeneity and Responsiveness in Cortical Networks
by Yann Sweeney & Jeanette Hellgren Kotaleski & Matthias H Hennig - 1-27 Geometry of the Gene Expression Space of Individual Cells
by Yael Korem & Pablo Szekely & Yuval Hart & Hila Sheftel & Jean Hausser & Avi Mayo & Michael E Rothenberg & Tomer Kalisky & Uri Alon - 1-30 Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina
by Jian K Liu & Tim Gollisch - 1-38 Asynchronous Rate Chaos in Spiking Neuronal Circuits
by Omri Harish & David Hansel
June 2015, Volume 11, Issue 6
- 1-3 Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation
by Philip E Bourne & Steven E Brenner & Michael B Eisen - 1-3 2015 ISCB Overton Prize Awarded to Curtis Huttenhower
by Christiana N Fogg & Diane E Kovats - 1-13 Computational Biology: Moving into the Future One Click at a Time
by Christiana N Fogg & Diane E Kovats - 1-15 Antibiotic Restriction Might Facilitate the Emergence of Multi-drug Resistance
by Uri Obolski & Gideon Y Stein & Lilach Hadany - 1-16 Posterior Probability Matching and Human Perceptual Decision Making
by Richard F Murray & Khushbu Patel & Alan Yee - 1-18 Behavioural Contagion Explains Group Cohesion in a Social Crustacean
by Pierre Broly & Jean-Louis Deneubourg - 1-18 BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
by Catalina A Vallejos & John C Marioni & Sylvia Richardson - 1-19 Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks
by Xiaoke Ma & Long Gao & Georgios Karamanlidis & Peng Gao & Chi Fung Lee & Lorena Garcia-Menendez & Rong Tian & Kai Tan - 1-21 Is Model Fitting Necessary for Model-Based fMRI?
by Robert C Wilson & Yael Niv - 1-21 Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation
by Gabriele Micali & Gerardo Aquino & David M Richards & Robert G Endres - 1-24 Energy Efficient Sparse Connectivity from Imbalanced Synaptic Plasticity Rules
by João Sacramento & Andreas Wichert & Mark C W van Rossum - 1-25 Encoder-Decoder Optimization for Brain-Computer Interfaces
by Josh Merel & Donald M Pianto & John P Cunningham & Liam Paninski - 1-25 The Sense of Confidence during Probabilistic Learning: A Normative Account
by Florent Meyniel & Daniel Schlunegger & Stanislas Dehaene - 1-26 Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait
by Kerry E Boyle & Hilary Monaco & Dave van Ditmarsch & Maxime Deforet & Joao B Xavier - 1-27 Measuring Fisher Information Accurately in Correlated Neural Populations
by Ingmar Kanitscheider & Ruben Coen-Cagli & Adam Kohn & Alexandre Pouget - 1-31 The Decay of Motor Memories Is Independent of Context Change Detection
by Andrew E Brennan & Maurice A Smith - 1-32 High Stimulus-Related Information in Barrel Cortex Inhibitory Interneurons
by Vicente Reyes-Puerta & Suam Kim & Jyh-Jang Sun & Barbara Imbrosci & Werner Kilb & Heiko J Luhmann - 1-38 Monte Carlo Planning Method Estimates Planning Horizons during Interactive Social Exchange
by Andreas Hula & P Read Montague & Peter Dayan - 1-46 Stochastic Dynamics Underlying Cognitive Stability and Flexibility
by Kai Ueltzhöffer & Diana J N Armbruster-Genç & Christian J Fiebach
May 2015, Volume 11, Issue 5
- 1-5 Power Law Scaling in Human and Empty Room MEG Recordings
by Manfred G Kitzbichler & Edward T Bullmore - 1-13 Metapopulation Persistence in Random Fragmented Landscapes
by Jacopo Grilli & György Barabás & Stefano Allesina - 1-17 The Effect of Incentives and Meta-incentives on the Evolution of Cooperation
by Isamu Okada & Hitoshi Yamamoto & Fujio Toriumi & Tatsuya Sasaki - 1-18 Accurate Computation of Survival Statistics in Genome-Wide Studies
by Fabio Vandin & Alexandra Papoutsaki & Benjamin J Raphael & Eli Upfal - 1-19 Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities
by Victor Garcia & Kirsten Richter & Frederik Graw & Annette Oxenius & Roland R Regoes - 1-19 Maintaining Homeostasis by Decision-Making
by Christoph W Korn & Dominik R Bach - 1-19 Sharing and Specificity of Co-expression Networks across 35 Human Tissues
by Emma Pierson & the GTEx Consortium & Daphne Koller & Alexis Battle & Sara Mostafavi - 1-21 Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
by Jonathan R Karr & Alex H Williams & Jeremy D Zucker & Andreas Raue & Bernhard Steiert & Jens Timmer & Clemens Kreutz & DREAM8 Parameter Estimation Challenge Consortium & Simon Wilkinson & Brandon A Allgood & Brian M Bot & Bruce R Hoff & Michael R Kellen & Markus W Covert & Gustavo A Stolovitzky & Pablo Meyer - 1-21 SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
by Manu Setty & Christina S Leslie - 1-22 Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints
by Alon Diament & Tamir Tuller - 1-25 Predicting Cortical Dark/Bright Asymmetries from Natural Image Statistics and Early Visual Transforms
by Emily A Cooper & Anthony M Norcia - 1-25 Sparse and Compositionally Robust Inference of Microbial Ecological Networks
by Zachary D Kurtz & Christian L Müller & Emily R Miraldi & Dan R Littman & Martin J Blaser & Richard A Bonneau - 1-29 Forecasting the 2013–2014 Influenza Season Using Wikipedia
by Kyle S Hickmann & Geoffrey Fairchild & Reid Priedhorsky & Nicholas Generous & James M Hyman & Alina Deshpande & Sara Y Del Valle - 1-31 Convex Clustering: An Attractive Alternative to Hierarchical Clustering
by Gary K Chen & Eric C Chi & John Michael O Ranola & Kenneth Lange
April 2015, Volume 11, Issue 4
- 1-4 Ten Simple Rules to Win a Nobel Prize
by Richard J Roberts - 1-6 Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research
by Anne-Laure Boulesteix - 1-7 Ten Simple Rules for a Successful Cross-Disciplinary Collaboration
by 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 & Charlotte M Deane - 1-15 The Serotype Distribution among Healthy Carriers before Vaccination Is Essential for Predicting the Impact of Pneumococcal Conjugate Vaccine on Invasive Disease
by Stefan Flasche & Olivier Le Polain de Waroux & Katherine L O’Brien & W John Edmunds - 1-16 Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity
by Paul Egan & Jeffrey Moore & Christian Schunn & Jonathan Cagan & Philip LeDuc - 1-19 MAGMA: Generalized Gene-Set Analysis of GWAS Data
by Christiaan A de Leeuw & Joris M Mooij & Tom Heskes & Danielle Posthuma - 1-20 Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees
by 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 & Chris Bailey-Kellogg - 1-21 Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
by Tomáš Trnka & Stanislav Kozmon & Igor Tvaroška & Jaroslav Koča - 1-21 Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery
by Sébastien Giguère & François Laviolette & Mario Marchand & Denise Tremblay & Sylvain Moineau & Xinxia Liang & Éric Biron & Jacques Corbeil - 1-21 Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models
by Timo R Maarleveld & Meike T Wortel & Brett G Olivier & Bas Teusink & Frank J Bruggeman - 1-21 A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome
by Susan Dina Ghiassian & Jörg Menche & Albert-László Barabási - 1-21 Quantifying Spike Train Oscillations: Biases, Distortions and Solutions
by Ayala Matzner & Izhar Bar-Gad - 1-22 Metrics for Assessing Cytoskeletal Orientational Correlations and Consistency
by Nancy K Drew & Mackenzie A Eagleson & Danny B Baldo Jr. & Kevin Kit Parker & Anna Grosberg - 1-22 Embodied Choice: How Action Influences Perceptual Decision Making
by Nathan F Lepora & Giovanni Pezzulo - 1-22 Cell-Specific Cardiac Electrophysiology Models
by Willemijn Groenendaal & Francis A Ortega & Armen R Kherlopian & Andrew C Zygmunt & Trine Krogh-Madsen & David J Christini - 1-23 Dual Dimensionality Reduction Reveals Independent Encoding of Motor Features in a Muscle Synergy for Insect Flight Control
by Simon Sponberg & Thomas L Daniel & Adrienne L Fairhall - 1-24 The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition
by Xiliang Zheng & Jin Wang - 1-25 The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information
by Daniel Bendor - 1-27 Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences
by Jian Tian & Jaie C Woodard & Andrew Whitney & Eugene I Shakhnovich - 1-30 A Bayesian Ensemble Approach for Epidemiological Projections
by Tom Lindström & Michael Tildesley & Colleen Webb - 1-31 The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction
by Ross S Williamson & Maneesh Sahani & Jonathan W Pillow
March 2015, Volume 11, Issue 3
- 1-11 Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists
by Marco D Visser & Sean M McMahon & Cory Merow & Philip M Dixon & Sydne Record & Eelke Jongejans - 1-12 Proportionality: A Valid Alternative to Correlation for Relative Data
by David Lovell & Vera Pawlowsky-Glahn & Juan José Egozcue & Samuel Marguerat & Jürg Bähler - 1-14 PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population
by Oren E Livne & Lide Han & Gorka Alkorta-Aranburu & William Wentworth-Sheilds & Mark Abney & Carole Ober & Dan L Nicolae - 1-16 Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles
by Jérôme R D Soiné & Christoph A Brand & Jonathan Stricker & Patrick W Oakes & Margaret L Gardel & Ulrich S Schwarz - 1-16 Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals
by Thomas Obadia & Romain Silhol & Lulla Opatowski & Laura Temime & Judith Legrand & Anne C M Thiébaut & Jean-Louis Herrmann & Éric Fleury & Didier Guillemot & Pierre-Yves Boëlle & on behalf of the I-Bird Study Group - 1-17 Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
by Kristen Fortney & Joshua Griesman & Max Kotlyar & Chiara Pastrello & Marc Angeli & Ming Sound-Tsao & Igor Jurisica - 1-18 Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting
by Davide Albanese & Carlotta De Filippo & Duccio Cavalieri & Claudio Donati - 1-19 Predicting Epidemic Risk from Past Temporal Contact Data
by Eugenio Valdano & Chiara Poletto & Armando Giovannini & Diana Palma & Lara Savini & Vittoria Colizza - 1-21 Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles
by Minseung Kim & Violeta Zorraquino & Ilias Tagkopoulos - 1-21 Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision
by Adrian M Haith & David M Huberdeau & John W Krakauer - 1-23 When Can Species Abundance Data Reveal Non-neutrality?
by Omar Al Hammal & David Alonso & Rampal S Etienne & Stephen J Cornell - 1-23 Mapping Shape to Visuomotor Mapping: Learning and Generalisation of Sensorimotor Behaviour Based on Contextual Information
by Loes C J van Dam & Marc O Ernst - 1-23 Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer
by Christopher R S Banerji & Simone Severini & Carlos Caldas & Andrew E Teschendorff - 1-24 Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model
by Alistair M Senior & Michael A Charleston & Mathieu Lihoreau & Camille Buhl & David Raubenheimer & Stephen J Simpson - 1-28 Theory of Choice in Bandit, Information Sampling and Foraging Tasks
by Bruno B Averbeck - 1-28 Improved Estimation and Interpretation of Correlations in Neural Circuits
by Dimitri Yatsenko & Krešimir Josić & Alexander S Ecker & Emmanouil Froudarakis & R James Cotton & Andreas S Tolias - 1-29 Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data
by Alan L Hutchison & Mark Maienschein-Cline & Andrew H Chiang & S M Ali Tabei & Herman Gudjonson & Neil Bahroos & Ravi Allada & Aaron R Dinner - 1-31 Identifying and Tracking Simulated Synaptic Inputs from Neuronal Firing: Insights from In Vitro Experiments
by Maxim Volgushev & Vladimir Ilin & Ian H Stevenson - 1-32 Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief
by Giles W Story & Ivo Vlaev & Peter Dayan & Ben Seymour & Ara Darzi & Raymond J Dolan - 1-38 On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain
by Adrien Wohrer & Christian K Machens
February 2015, Volume 11, Issue 2
- 1-12 Co-evolutionary Dynamics of Collective Action with Signaling for a Quorum
by Jorge M Pacheco & Vítor V Vasconcelos & Francisco C Santos & Brian Skyrms - 1-17 A Theoretical Justification for Single Molecule Peptide Sequencing
by Jagannath Swaminathan & Alexander A Boulgakov & Edward M Marcotte - 1-20 Heterogeneous CD8+ T Cell Migration in the Lymph Node in the Absence of Inflammation Revealed by Quantitative Migration Analysis
by Edward J Banigan & Tajie H Harris & David A Christian & Christopher A Hunter & Andrea J Liu - 1-20 Protein Sectors: Statistical Coupling Analysis versus Conservation
by Tiberiu Teşileanu & Lucy J Colwell & Stanislas Leibler - 1-20 Critical Slowing Down Governs the Transition to Neuron Spiking
by Christian Meisel & Andreas Klaus & Christian Kuehn & Dietmar Plenz - 1-21 Correlations and Functional Connections in a Population of Grid Cells
by Benjamin Dunn & Maria Mørreaunet & Yasser Roudi - 1-23 Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage
by Ishutesh Jain & Mandar M Inamdar & Ranjith Padinhateeri - 1-23 Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity
by Adrián Ponce-Alvarez & Gustavo Deco & Patric Hagmann & Gian Luca Romani & Dante Mantini & Maurizio Corbetta - 1-24 Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information
by Daniel M Keenan & Amy W Quinkert & Donald W Pfaff - 1-27 Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis
by Andrew J K Conlan & Ellen Brooks Pollock & Trevelyan J McKinley & Andrew P Mitchell & Gareth J Jones & Martin Vordermeier & James L N Wood - 1-28 Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions
by Vladimir Potapov & Jenifer B Kaplan & Amy E Keating - 1-32 The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure
by Benjamin Allen & Christine Sample & Yulia Dementieva & Ruben C Medeiros & Christopher Paoletti & Martin A Nowak - 1-34 A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination
by Laura R González-Ramírez & Omar J Ahmed & Sydney S Cash & C Eugene Wayne & Mark A Kramer
January 2015, Volume 11, Issue 1
- 1-7 150 Years of the Mass Action Law
by Eberhard O Voit & Harald A Martens & Stig W Omholt - 1-10 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
by Alboukadel Kassambara & Thierry Rème & Michel Jourdan & Thierry Fest & Dirk Hose & Karin Tarte & Bernard Klein - 1-12 Modulation of Elementary Calcium Release Mediates a Transition from Puffs to Waves in an IP3R Cluster Model
by Martin Rückl & Ian Parker & Jonathan S Marchant & Chamakuri Nagaiah & Friedrich W Johenning & Sten Rüdiger - 1-15 Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate
by Regina S Salvat & Andrew S Parker & Yoonjoo Choi & Chris Bailey-Kellogg & Karl E Griswold - 1-15 A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso
by Erick A Perez Alday & Michael A Colman & Philip Langley & Timothy D Butters & Jonathan Higham & Antony J Workman & Jules C Hancox & Henggui Zhang - 1-17 Orientation Selectivity in Inhibition-Dominated Networks of Spiking Neurons: Effect of Single Neuron Properties and Network Dynamics
by Sadra Sadeh & Stefan Rotter - 1-18 Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda
by Ioannis Andrianakis & Ian R Vernon & Nicky McCreesh & Trevelyan J McKinley & Jeremy E Oakley & Rebecca N Nsubuga & Michael Goldstein & Richard G White - 1-20 Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
by J Matthew Mahoney & Jaclyn Taroni & Viktor Martyanov & Tammara A Wood & Casey S Greene & Patricia A Pioli & Monique E Hinchcliff & Michael L Whitfield - 1-28 Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions
by Massimo Lai & Denis Brun & Stuart J Edelstein & Nicolas Le Novère - 1-29 The Formation of Multi-synaptic Connections by the Interaction of Synaptic and Structural Plasticity and Their Functional Consequences
by Michael Fauth & Florentin Wörgötter & Christian Tetzlaff - 1-34 A Probabilistic Palimpsest Model of Visual Short-term Memory
by Loic Matthey & Paul M Bays & Peter Dayan
December 2014, Volume 10, Issue 12
- 1-4 Ten Simple Rules for Finishing Your PhD
by Jacopo Marino & Melanie I Stefan & Sarah Blackford - 1-9 Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments
by Christoph Zechner & Heinz Koeppl - 1-10 Vesicular Stomatitis Virus Polymerase's Strong Affinity to Its Template Suggests Exotic Transcription Models
by Xiaolin Tang & Mourad Bendjennat & Saveez Saffarian - 1-10 Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure
by Ritwik K Niyogi & Peter Shizgal & Peter Dayan - 1-10 Contradictory Behavioral Biases Result from the Influence of Past Stimuli on Perception
by Ofri Raviv & Itay Lieder & Yonatan Loewenstein & Merav Ahissar - 1-11 Symmetry Restoring Bifurcation in Collective Decision-Making
by Natalia Zabzina & Audrey Dussutour & Richard P Mann & David J T Sumpter & Stamatios C Nicolis - 1-12 Hippocampal Remapping Is Constrained by Sparseness rather than Capacity
by Axel Kammerer & Christian Leibold - 1-14 Protein-Protein Docking with Dynamic Residue Protonation States
by Krishna Praneeth Kilambi & Kavan Reddy & Jeffrey J Gray - 1-14 Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation
by Lin Chen & Javad Noorbakhsh & Rhys M Adams & Joseph Samaniego-Evans & Germaine Agollah & Dmitry Nevozhay & Jennie Kuzdzal-Fick & Pankaj Mehta & Gábor Balázsi - 1-14 The Social Bayesian Brain: Does Mentalizing Make a Difference When We Learn?
by Marie Devaine & Guillaume Hollard & Jean Daunizeau - 1-15 Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
by Alexandra Gavryushkina & David Welch & Tanja Stadler & Alexei J Drummond - 1-15 Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences
by Alex N Nguyen Ba & Bob Strome & Jun Jie Hua & Jonathan Desmond & Isabelle Gagnon-Arsenault & Eric L Weiss & Christian R Landry & Alan M Moses - 1-16 Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons
by Jean-Pierre Rospars & Alexandre Grémiaux & David Jarriault & Antoine Chaffiol & Christelle Monsempes & Nina Deisig & Sylvia Anton & Philippe Lucas & Dominique Martinez - 1-16 Live Imaging-Based Model Selection Reveals Periodic Regulation of the Stochastic G1/S Phase Transition in Vertebrate Axial Development
by Mayu Sugiyama & Takashi Saitou & Hiroshi Kurokawa & Asako Sakaue-Sawano & Takeshi Imamura & Atsushi Miyawaki & Tadahiro Iimura - 1-20 The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets
by Evandro Ferrada
November 2014, Volume 10, Issue 11
- 1-3 Ten Simple Rules to Achieve Conference Speaker Gender Balance
by Jennifer L Martin - 1-5 Computational Thinking in Life Science Education
by Amir Rubinstein & Benny Chor - 1-5 Evolution of All-or-None Strategies in Repeated Public Goods Dilemmas
by Flávio L Pinheiro & Vítor V Vasconcelos & Francisco C Santos & Jorge M Pacheco - 1-12 Pattern of Tick Aggregation on Mice: Larger Than Expected Distribution Tail Enhances the Spread of Tick-Borne Pathogens
by Luca Ferreri & Mario Giacobini & Paolo Bajardi & Luigi Bertolotti & Luca Bolzoni & Valentina Tagliapietra & Annapaola Rizzoli & Roberto Rosà - 1-13 Statistical Computations Underlying the Dynamics of Memory Updating
by Samuel J Gershman & Angela Radulescu & Kenneth A Norman & Yael Niv - 1-14 Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
by Marcin J Skwark & Daniele Raimondi & Mirco Michel & Arne Elofsson - 1-15 Effect of Global Cardiac Ischemia on Human Ventricular Fibrillation: Insights from a Multi-scale Mechanistic Model of the Human Heart
by Ivan V Kazbanov & Richard H Clayton & Martyn P Nash & Chris P Bradley & David J Paterson & Martin P Hayward & Peter Taggart & Alexander V Panfilov - 1-16 Herpes Simplex Virus-2 Genital Tract Shedding Is Not Predictable over Months or Years in Infected Persons
by Varsha Dhankani & J Nathan Kutz & Joshua T Schiffer - 1-16 Global Disease Monitoring and Forecasting with Wikipedia
by Nicholas Generous & Geoffrey Fairchild & Alina Deshpande & Sara Y Del Valle & Reid Priedhorsky - 1-25 High-Fidelity Coding with Correlated Neurons
by Rava Azeredo da Silveira & Michael J Berry II - 1-26 Power Laws from Linear Neuronal Cable Theory: Power Spectral Densities of the Soma Potential, Soma Membrane Current and Single-Neuron Contribution to the EEG
by Klas H Pettersen & Henrik Lindén & Tom Tetzlaff & Gaute T Einevoll
October 2014, Volume 10, Issue 10
- 1-5 Ten Simple Rules for Writing a PLOS Ten Simple Rules Article
by Harriet Dashnow & Andrew Lonsdale & Philip E Bourne - 1-6 FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
by Gang Peng & Yu Fan & Wenyi Wang - 1-10 Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups
by Amos Korman & Efrat Greenwald & Ofer Feinerman - 1-11 Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells
by Christian L Althaus & Beda Joos & Alan S Perelson & Huldrych F Günthard - 1-12 The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion
by Nicole Dölker & Maria W Górna & Ludovico Sutto & Antonio S Torralba & Giulio Superti-Furga & Francesco L Gervasio - 1-13 Improving Contact Prediction along Three Dimensions
by Christoph Feinauer & Marcin J Skwark & Andrea Pagnani & Erik Aurell - 1-13 Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery
by Jose A Seoane & Colin Campbell & Ian N M Day & Juan P Casas & Tom R Gaunt - 1-14 Predicting Chemical Environments of Bacteria from Receptor Signaling
by Diana Clausznitzer & Gabriele Micali & Silke Neumann & Victor Sourjik & Robert G Endres - 1-14 Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
by Matthew N Benedict & Michael B Mundy & Christopher S Henry & Nicholas Chia & Nathan D Price - 1-17 Synaptic Size Dynamics as an Effectively Stochastic Process
by Adiel Statman & Maya Kaufman & Amir Minerbi & Noam E Ziv & Naama Brenner - 1-17 Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro
by Sophia Rudorf & Michael Thommen & Marina V Rodnina & Reinhard Lipowsky - 1-19 Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics
by Michael J Prerau & Katie E Hartnack & Gabriel Obregon-Henao & Aaron Sampson & Margaret Merlino & Karen Gannon & Matt T Bianchi & Jeffrey M Ellenbogen & Patrick L Purdon - 1-27 Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment
by Robert Legenstein & Wolfgang Maass
September 2014, Volume 10, Issue 9
- 1-7 The Time Scale of Evolutionary Innovation
by Krishnendu Chatterjee & Andreas Pavlogiannis & Ben Adlam & Martin A Nowak - 1-9 Multi-state Modeling of Biomolecules
by Melanie I Stefan & Thomas M Bartol & Terrence J Sejnowski & Mary B Kennedy - 1-10 Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis
by Hong Yang & Elias W Krumholz & Evan D Brutinel & Nagendra P Palani & Michael J Sadowsky & Andrew M Odlyzko & Jeffrey A Gralnick & Igor G L Libourel - 1-10 IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
by N Lance Hepler & Konrad Scheffler & Steven Weaver & Ben Murrell & Douglas D Richman & Dennis R Burton & Pascal Poignard & Davey M Smith & Sergei L Kosakovsky Pond - 1-11 A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing
by 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 & Rachel Karchin - 1-11 NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles
by Shunichi Kosugi & Hiroshi Yanagawa & Ryohei Terauchi & Satoshi Tabata - 1-12 Environmental Statistics and Optimal Regulation
by David A Sivak & Matt Thomson - 1-13 Pupil-Linked Arousal Determines Variability in Perceptual Decision Making
by Peter R Murphy & Joachim Vandekerckhove & Sander Nieuwenhuis - 1-14 Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies
by Diana Chang & Alon Keinan - 1-15 eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models
by Michal Brylinski - 1-16 Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method
by Simone Vincenzi & Marc Mangel & Alain J Crivelli & Stephan Munch & Hans J Skaug - 1-17 Quantifying the Impact and Extent of Undocumented Biomedical Synonymy
by David R Blair & Kanix Wang & Svetlozar Nestorov & James A Evans & Andrey Rzhetsky - 1-19 Inferring on the Intentions of Others by Hierarchical Bayesian Learning
by Andreea O Diaconescu & Christoph Mathys & Lilian A E Weber & Jean Daunizeau & Lars Kasper & Ekaterina I Lomakina & Ernst Fehr & Klaas E Stephan
August 2014, Volume 10, Issue 8
- 1-3 The Upside of Failure: How Regional Student Groups Learn from Their Mistakes
by Tarun Mishra & R Gonzalo Parra & Thomas Abeel - 1-9 Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens
by Delphine Pessoa & Caetano Souto-Maior & Erida Gjini & Joao S Lopes & Bruno Ceña & Cláudia T Codeço & M Gabriela M Gomes - 1-10 Phenotypic Signatures Arising from Unbalanced Bacterial Growth
by Cheemeng Tan & Robert Phillip Smith & Ming-Chi Tsai & Russell Schwartz & Lingchong You - 1-11 Sparsity and Compressed Coding in Sensory Systems
by Victor J Barranca & Gregor Kovačič & Douglas Zhou & David Cai - 1-11 Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism
by Rui Xia & Selina Vattathil & Paul Scheet - 1-11 Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
by Shuo Gu & Daniel-Adriano Silva & Luming Meng & Alexander Yue & Xuhui Huang - 1-12 OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis
by Greg Finak & Jacob Frelinger & Wenxin Jiang & Evan W Newell & John Ramey & Mark M Davis & Spyros A Kalams & Stephen C De Rosa & Raphael Gottardo - 1-12 Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images
by Umut Güçlü & Marcel A J van Gerven - 1-13 Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment
by 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 & James C Sullivan - 1-14 Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus
by Nik J Cunniffe & Francisco F Laranjeira & Franco M Neri & R Erik DeSimone & Christopher A Gilligan - 1-14 Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro
by René F M van Oers & Elisabeth G Rens & Danielle J LaValley & Cynthia A Reinhart-King & Roeland M H Merks - 1-14 Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection
by Miri Adler & Avi Mayo & Uri Alon - 1-15 A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells
by Pengxing Cao & Xiahui Tan & Graham Donovan & Michael J Sanderson & James Sneyd - 1-15 Memory Capacity of Networks with Stochastic Binary Synapses
by Alexis M Dubreuil & Yali Amit & Nicolas Brunel - 1-15 Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes
by Anne-Florence Bitbol & David J Schwab - 1-16 A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data
by Yuan Zhang & Yanni Sun & James R Cole - 1-16 Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment
by Johannes Textor & Sarah E Henrickson & Judith N Mandl & Ulrich H von Andrian & Jürgen Westermann & Rob J de Boer & Joost B Beltman - 1-19 Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque
by Fang-Chieh Chou & Jan Lipfert & Rhiju Das - 1-19 Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth
by Sébastien Benzekry & Clare Lamont & Afshin Beheshti & Amanda Tracz & John M L Ebos & Lynn Hlatky & Philip Hahnfeldt
July 2014, Volume 10, Issue 7
- 1-2 Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"
by Wei-Hua Chen & Xing-Ming Zhao & Vera van Noort & Peer Bork - 1-3 Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities
by Jeroen de Ridder & Pieter Meysman & Olugbenga Oluwagbemi & Thomas Abeel - 1-7 Correlated Inter-Domain Motions in Adenylate Kinase
by Santiago Esteban-Martín & Robert Bryn Fenwick & Jörgen Ådén & Benjamin Cossins & Carlos W Bertoncini & Victor Guallar & Magnus Wolf-Watz & Xavier Salvatella - 1-8 Brain and Behavior in Decision-Making
by Peter Cassey & Andrew Heathcote & Scott D Brown - 1-10 A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges
by James Kaufman & Justin Lessler & April Harry & Stefan Edlund & Kun Hu & Judith Douglas & Christian Thoens & Bernd Appel & Annemarie Käsbohrer & Matthias Filter - 1-10 Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells
by Andrew McDavid & Lucas Dennis & Patrick Danaher & Greg Finak & Michael Krouse & Alice Wang & Philippa Webster & Joseph Beechem & Raphael Gottardo - 1-11 Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials
by Fabrizio Pucci & Marianne Rooman - 1-12 CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion
by Christophe Restif & Carolina Ibáñez-Ventoso & Mehul M Vora & Suzhen Guo & Dimitris Metaxas & Monica Driscoll - 1-12 Modeling Higher-Order Correlations within Cortical Microcolumns
by Urs Köster & Jascha Sohl-Dickstein & Charles M Gray & Bruno A Olshausen - 1-12 Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex
by Suchin S Gururangan & Alexander J Sadovsky & Jason N MacLean - 1-13 Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation
by Aniket Magarkar & Nawel Mele & Noha Abdel-Rahman & Sarah Butcher & Mika Torkkeli & Ritva Serimaa & Arja Paananen & Markus Linder & Alex Bunker - 1-14 CCAST: A Model-Based Gating Strategy to Isolate Homogeneous Subpopulations in a Heterogeneous Population of Single Cells
by Benedict Anchang & Mary T Do & Xi Zhao & Sylvia K Plevritis - 1-15 Enhanced Regulatory Sequence Prediction Using Gapped k -mer Features
by Mahmoud Ghandi & Dongwon Lee & Morteza Mohammad-Noori & Michael A Beer - 1-15 Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior
by Adam M Gifford & Yale E Cohen & Alan A Stocker - 1-15 Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks
by Robert Ton & Gustavo Deco & Andreas Daffertshofer - 1-17 Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling
by Tom Serge Weber & Irene Jaehnert & Christian Schichor & Michal Or-Guil & Jorge Carneiro - 1-17 ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
by Jan Hasenauer & Christine Hasenauer & Tim Hucho & Fabian J Theis - 1-19 Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics
by Salim Akhter Chowdhury & Stanley E Shackney & Kerstin Heselmeyer-Haddad & Thomas Ried & Alejandro A Schäffer & Russell Schwartz