Printed from https://ideas.repec.org/s/plo/pcbi0012.html
Content
November 2015, Volume 11, Issue 11
- 1-16 VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
by 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 & Dmitriy M Chudakov - 1-16 Lévy Walks Suboptimal under Predation Risk
by Masato S Abe & Masakazu Shimada - 1-16 Improving Collective Estimations Using Resistance to Social Influence
by Gabriel Madirolas & Gonzalo G de Polavieja - 1-17 Quantifying Stochastic Noise in Cultured Circadian Reporter Cells
by Peter C St. John & Francis J Doyle III - 1-20 Dynamic Redox Regulation of IL-4 Signaling
by Gaurav Dwivedi & Margaret A Gran & Pritha Bagchi & Melissa L Kemp - 1-20 A Unifying Probabilistic View of Associative Learning
by Samuel J Gershman - 1-21 Beyond the E-Value: Stratified Statistics for Protein Domain Prediction
by Alejandro Ochoa & John D Storey & Manuel Llinás & Mona Singh - 1-23 Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model
by Guido Gigante & Gustavo Deco & Shimon Marom & Paolo Del Giudice - 1-26 Bayesian Estimation of Conditional Independence Graphs Improves Functional Connectivity Estimates
by Max Hinne & Ronald J Janssen & Tom Heskes & Marcel AJ van Gerven - 1-26 Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics
by Jonathan W Armond & Edward F Harry & Andrew D McAinsh & Nigel J Burroughs - 1-27 Differences in Visual-Spatial Input May Underlie Different Compression Properties of Firing Fields for Grid Cell Modules in Medial Entorhinal Cortex
by Florian Raudies & Michael E Hasselmo - 1-28 Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding
by Satohiro Tajima & Toru Yanagawa & Naotaka Fujii & Taro Toyoizumi - 1-28 Learning to Estimate Dynamical State with Probabilistic Population Codes
by Joseph G Makin & Benjamin K Dichter & Philip N Sabes - 1-29 Remodeling and Tenacity of Inhibitory Synapses: Relationships with Network Activity and Neighboring Excitatory Synapses
by Anna Rubinski & Noam E Ziv - 1-32 From Sensory Signals to Modality-Independent Conceptual Representations: A Probabilistic Language of Thought Approach
by Goker Erdogan & Ilker Yildirim & Robert A Jacobs - 1-34 Neuromechanistic Model of Auditory Bistability
by James Rankin & Elyse Sussman & John Rinzel
October 2015, Volume 11, Issue 10
- 1-6 Ten Simple Rules for Protecting Research Integrity
by David M Shaw & Thomas C Erren - 1-7 Ten Simple Rules for Establishing International Research Collaborations
by Richard de Grijs - 1-12 Emergence of Shared Intentionality Is Coupled to the Advance of Cumulative Culture
by Simon D Angus & Jonathan Newton - 1-16 ENCORE: Software for Quantitative Ensemble Comparison
by Matteo Tiberti & Elena Papaleo & Tone Bengtsen & Wouter Boomsma & Kresten Lindorff-Larsen - 1-17 Dendritic Pooling of Noisy Threshold Processes Can Explain Many Properties of a Collision-Sensitive Visual Neuron
by Matthias S Keil - 1-20 Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling
by Armin Meier & Johannes Söding - 1-21 The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks
by Michael Chevalier & Ophelia Venturelli & Hana El-Samad - 1-22 Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models
by Niraj Kumar & Abhyudai Singh & Rahul V Kulkarni - 1-22 Analyzing and Quantifying the Gain-of-Function Enhancement of IP3 Receptor Gating by Familial Alzheimer’s Disease-Causing Mutants in Presenilins
by Don-On Daniel Mak & King-Ho Cheung & Patrick Toglia & J Kevin Foskett & Ghanim Ullah - 1-23 A Generative Statistical Algorithm for Automatic Detection of Complex Postures
by Stanislav Nagy & Marc Goessling & Yali Amit & David Biron - 1-23 Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making
by Laurence Aitchison & Dan Bang & Bahador Bahrami & Peter E Latham - 1-25 Establishing a Statistical Link between Network Oscillations and Neural Synchrony
by Pengcheng Zhou & Shawn D Burton & Adam C Snyder & Matthew A Smith & Nathaniel N Urban & Robert E Kass - 1-27 PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps
by Radhakrishna Bettadapura & Muhibur Rasheed & Antje Vollrath & Chandrajit Bajaj - 1-28 Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks
by Christian L Vestergaard & Mathieu Génois - 1-30 Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data
by Daniel Soudry & Suraj Keshri & Patrick Stinson & Min-hwan Oh & Garud Iyengar & Liam Paninski - 1-34 Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism
by Dimitrije Marković & Jan Gläscher & Peter Bossaerts & John O’Doherty & Stefan J Kiebel - 1-39 Primary Visual Cortex as a Saliency Map: A Parameter-Free Prediction and Its Test by Behavioral Data
by Li Zhaoping & Li Zhe
September 2015, Volume 11, Issue 9
- 1-5 How to Grow a Computational Biology Lab
by Alice Carolyn McHardy - 1-5 Ten Simple Rules for a Computational Biologist’s Laboratory Notebook
by Santiago Schnell - 1-8 You Are Not Working for Me; I Am Working with You
by Florian Markowetz - 1-18 Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model
by Naiqian Zhang & Haiyun Wang & Yun Fang & Jun Wang & Xiaoqi Zheng & X Shirley Liu - 1-19 The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
by Stephan Köhler & Friederike Schmid & Giovanni Settanni - 1-22 A Theory of Cheap Control in Embodied Systems
by Guido Montúfar & Keyan Ghazi-Zahedi & Nihat Ay - 1-23 Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty
by Thembi Mdluli & Gregery T Buzzard & Ann E Rundell - 1-26 Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm
by Rudy Clausen & Buyong Ma & Ruth Nussinov & Amarda Shehu - 1-27 Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model
by Greg Jensen & Fabian Muñoz & Yelda Alkan & Vincent P Ferrera & Herbert S Terrace - 1-28 Prospective Optimization with Limited Resources
by Joseph Snider & Dongpyo Lee & Howard Poizner & Sergei Gepshtein - 1-31 Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca2+ Release Patterns in Cardiomyocytes
by Vijay Rajagopal & Gregory Bass & Cameron G Walker & David J Crossman & Amorita Petzer & Anthony Hickey & Ivo Siekmann & Masahiko Hoshijima & Mark H Ellisman & Edmund J Crampin & Christian Soeller - 1-34 A Method to Constrain Genome-Scale Models with 13C Labeling Data
by Héctor García Martín & Vinay Satish Kumar & Daniel Weaver & Amit Ghosh & Victor Chubukov & Aindrila Mukhopadhyay & Adam Arkin & Jay D Keasling - 1-37 Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations
by Sacha Jennifer van Albada & Moritz Helias & Markus Diesmann
August 2015, Volume 11, Issue 8
- 1-16 Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks
by Claudia Schillings & Mikael Sunnåker & Jörg Stelling & Christoph Schwab - 1-16 Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions
by Assaf Amitai & Mathias Toulouze & Karine Dubrana & David Holcman - 1-18 Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data
by Pengyi Yang & Xiaofeng Zheng & Vivek Jayaswal & Guang Hu & Jean Yee Hwa Yang & Raja Jothi - 1-19 Manifold Based Optimization for Single-Cell 3D Genome Reconstruction
by Jonas Paulsen & Odin Gramstad & Philippe Collas - 1-22 Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast
by Zing Tsung-Yeh Tsai & Shin-Han Shiu & Huai-Kuang Tsai - 1-23 A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks
by Alireza Alemi & Carlo Baldassi & Nicolas Brunel & Riccardo Zecchina - 1-23 Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations
by Paul M Harrison & Laurent Badel & Mark J Wall & Magnus J E Richardson - 1-26 Asymmetric Evolutionary Games
by Alex McAvoy & Christoph Hauert - 1-26 Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data
by Alexey A Gritsenko & Marc Hulsman & Marcel J T Reinders & Dick de Ridder - 1-26 Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling
by Adrián Ponce-Alvarez & Biyu J He & Patric Hagmann & Gustavo Deco - 1-27 Structure Learning in Bayesian Sensorimotor Integration
by Tim Genewein & Eduard Hez & Zeynab Razzaghpanah & Daniel A Braun - 1-29 The Beta Cell in Its Cluster: Stochastic Graphs of Beta Cell Connectivity in the Islets of Langerhans
by Deborah A Striegel & Manami Hara & Vipul Periwal - 1-35 A Bayesian Attractor Model for Perceptual Decision Making
by Sebastian Bitzer & Jelle Bruineberg & Stefan J Kiebel - 1-40 Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses
by Gabriel Koch Ocker & Ashok Litwin-Kumar & Brent Doiron
July 2015, Volume 11, Issue 7
- 1-16 Measuring Asymmetry in Time-Stamped Phylogenies
by Bethany L Dearlove & Simon D W Frost - 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 - 1-25 A Diffusive Homeostatic Signal Maintains Neural Heterogeneity and Responsiveness in Cortical Networks
by Yann Sweeney & Jeanette Hellgren Kotaleski & Matthias H Hennig - 1-30 Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina
by Jian K Liu & Tim Gollisch
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 - 1-15 Antibiotic Restriction Might Facilitate the Emergence of Multi-drug Resistance
by Uri Obolski & Gideon Y Stein & Lilach Hadany - 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 - 1-21 Is Model Fitting Necessary for Model-Based fMRI?
by Robert C Wilson & Yael Niv - 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 - 1-26 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 - 1-19 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 - 1-21 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
- 1-6 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 - 1-19 MAGMA: Generalized Gene-Set Analysis of GWAS Data
by Christiaan A de Leeuw & Joris M Mooij & Tom Heskes & Danielle Posthuma - 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 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 - 1-25 The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information
by Daniel Bendor - 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
- 1-12 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 - 1-18 Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting
by Davide Albanese & Carlotta De Filippo & Duccio Cavalieri & Claudio Donati - 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 Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer
by Christopher R S Banerji & Simone Severini & Carlos Caldas & Andrew E Teschendorff - 1-28 Theory of Choice in Bandit, Information Sampling and Foraging Tasks
by Bruno B Averbeck - 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 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 - 1-34 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 - 1-18 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 - 1-34 A Probabilistic Palimpsest Model of Visual Short-term Memory
by Loic Matthey & Paul M Bays & Peter Dayan
December 2014, Volume 10, Issue 12
- 1-9 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 - 1-14 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 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
November 2014, Volume 10, Issue 11
- 1-3 Ten Simple Rules to Achieve Conference Speaker Gender Balance
by Jennifer L Martin - 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 - 1-14 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
October 2014, Volume 10, Issue 10
- 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 - 1-14 Predicting Chemical Environments of Bacteria from Receptor Signaling
by Diana Clausznitzer & Gabriele Micali & Silke Neumann & Victor Sourjik & Robert G Endres - 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 - 1-11 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 - 1-12 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
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 - 1-11 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 - 1-14 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 - 1-19 Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque
by Fang-Chieh Chou & Jan Lipfert & Rhiju Das
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 - 1-12 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 - 1-14 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 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