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July 2016, Volume 12, Issue 7
- 1-6 Ten Simple Rules for Writing a Postdoctoral Fellowship
by Ke Yuan & Lei Cai & Siu Ping Ngok & Li Ma & Crystal M Botham - 1-8 Ten Simple Rules for Curating and Facilitating Small Workshops
by Greg J McInerny - 1-13 Reinforcement Learning Explains Conditional Cooperation and Its Moody Cousin
by Takahiro Ezaki & Yutaka Horita & Masanori Takezawa & Naoki Masuda - 1-20 Ancestral Reconstruction
by Jeffrey B Joy & Richard H Liang & Rosemary M McCloskey & T Nguyen & Art F Y Poon - 1-21 Intrinsic Valuation of Information in Decision Making under Uncertainty
by Daniel Bennett & Stefan Bode & Maja Brydevall & Hayley Warren & Carsten Murawski - 1-22 Metagenome and Metatranscriptome Analyses Using Protein Family Profiles
by Cuncong Zhong & Anna Edlund & Youngik Yang & Jeffrey S McLean & Shibu Yooseph - 1-28 Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion
by Fabian Fröhlich & Philipp Thomas & Atefeh Kazeroonian & Fabian J Theis & Ramon Grima & Jan Hasenauer - 1-39 Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering
by Chuan Gao & Ian C McDowell & Shiwen Zhao & Christopher D Brown & Barbara E Engelhardt
June 2016, Volume 12, Issue 6
- 1-8 Ten Simple Rules for Effective Statistical Practice
by Robert E Kass & Brian S Caffo & Marie Davidian & Xiao-Li Meng & Bin Yu & Nancy Reid - 1-10 Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability
by Bastian Schiffthaler & Myrto Kostadima & NGS Trainer Consortium & Nicolas Delhomme & Gabriella Rustici - 1-12 Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers
by Michelle D Brazas & B F Francis Ouellette - 1-14 Computing Average Passive Forces in Sarcomeres in Length-Ramp Simulations
by Gudrun Schappacher-Tilp & Timothy Leonard & Gertrud Desch & Walter Herzog - 1-16 Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits
by Gentian Buzi & Mustafa Khammash - 1-18 Stochastic Simulation of Biomolecular Networks in Dynamic Environments
by Margaritis Voliotis & Philipp Thomas & Ramon Grima & Clive G Bowsher - 1-19 Computationally Efficient Implementation of a Novel Algorithm for the General Unified Threshold Model of Survival (GUTS)
by Carlo Albert & Sören Vogel & Roman Ashauer - 1-20 Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data
by John D O’Brien & Zamin Iqbal & Jason Wendler & Lucas Amenga-Etego - 1-27 Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches
by Tobias Sikosek & Heinrich Krobath & Hue Sun Chan - 1-28 Interplay between Graph Topology and Correlations of Third Order in Spiking Neuronal Networks
by Stojan Jovanović & Stefan Rotter - 1-33 Modeling Inter-trial Variability of Saccade Trajectories: Effects of Lesions of the Oculomotor Part of the Fastigial Nucleus
by Thomas Eggert & Farrel R Robinson & Andreas Straube - 1-33 Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases
by David Lee & Sayoni Das & Natalie L Dawson & Dragana Dobrijevic & John Ward & Christine Orengo - 1-43 An Introduction to Programming for Bioscientists: A Python-Based Primer
by Berk Ekmekci & Charles E McAnany & Cameron Mura
May 2016, Volume 12, Issue 5
- 1-4 Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)
by Lonnie Welch & Cath Brooksbank & Russell Schwartz & Sarah L Morgan & Bruno Gaeta & Alastair M Kilpatrick & Daniel Mietchen & Benjamin L Moore & Nicola Mulder & Mark Pauley & William Pearson & Predrag Radivojac & Naomi Rosenberg & Anne Rosenwald & Gabriella Rustici & Tandy Warnow - 1-7 The Maximum Entropy Fallacy Redux?
by Erik Aurell - 1-10 Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?
by Erik van Nimwegen - 1-12 Optimal Current Transfer in Dendrites
by Alex D Bird & Hermann Cuntz - 1-14 To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter
by Arthur Bernard & Jean-Baptiste André & Nicolas Bredeche - 1-16 The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach
by Pascal Giehr & Charalampos Kyriakopoulos & Gabriella Ficz & Verena Wolf & Jörn Walter - 1-22 Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
by Jerome Kelleher & Alison M Etheridge & Gilean McVean - 1-24 Neuroprosthetic Decoder Training as Imitation Learning
by Josh Merel & David Carlson & Liam Paninski & John P Cunningham - 1-26 Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics
by Lisa M Breckels & Sean B Holden & David Wojnar & Claire M Mulvey & Andy Christoforou & Arnoud Groen & Matthew W B Trotter & Oliver Kohlbacher & Kathryn S Lilley & Laurent Gatto - 1-28 Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression
by John Wiedenhoeft & Eric Brugel & Alexander Schliep - 1-34 Bridging Mechanistic and Phenomenological Models of Complex Biological Systems
by Mark K Transtrum & Peng Qiu
April 2016, Volume 12, Issue 4
- 1-15 A Robust Feedforward Model of the Olfactory System
by Yilun Zhang & Tatyana O Sharpee - 1-17 The Development of Audio-Visual Integration for Temporal Judgements
by Wendy J Adams - 1-18 Detecting Presymptomatic Infection Is Necessary to Forecast Major Epidemics in the Earliest Stages of Infectious Disease Outbreaks
by Robin N Thompson & Christopher A Gilligan & Nik J Cunniffe - 1-20 Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity
by Lorenzo Asti & Guido Uguzzoni & Paolo Marcatili & Andrea Pagnani - 1-21 Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery
by Robert Kalescky & Hongyu Zhou & Jin Liu & Peng Tao - 1-21 Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes
by Amit A Upadhyay & Aaron D Fleetwood & Ogun Adebali & Robert D Finn & Igor B Zhulin - 1-22 Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System
by Yael Steuerman & Irit Gat-Viks - 1-22 Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming
by Stephen Gang Wu & Yuxuan Wang & Wu Jiang & Tolutola Oyetunde & Ruilian Yao & Xuehong Zhang & Kazuyuki Shimizu & Yinjie J Tang & Forrest Sheng Bao - 1-28 AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression
by Sara Ballouz & Jesse Gillis - 1-28 Fast and Accurate Learning When Making Discrete Numerical Estimates
by Adam N Sanborn & Ulrik R Beierholm - 1-70 Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
by Tatiana Maximova & Ryan Moffatt & Buyong Ma & Ruth Nussinov & Amarda Shehu
March 2016, Volume 12, Issue 3
- 1-8 Systems Approaches to the Eukaryotic Stress Response
by Christine Vogel - 1-20 Causal Inference for Spatial Constancy across Saccades
by Jeroen Atsma & Femke Maij & Mathieu Koppen & David E Irwin & W Pieter Medendorp - 1-23 Pathway-Based Genomics Prediction using Generalized Elastic Net
by Artem Sokolov & Daniel E Carlin & Evan O Paull & Robert Baertsch & Joshua M Stuart - 1-23 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
by Ramya Raviram & Pedro P Rocha & Christian L Müller & Emily R Miraldi & Sana Badri & Yi Fu & Emily Swanzey & Charlotte Proudhon & Valentina Snetkova & Richard Bonneau & Jane A Skok - 1-23 Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search
by G Matthew Fricke & Kenneth A Letendre & Melanie E Moses & Judy L Cannon - 1-25 Annealed Importance Sampling for Neural Mass Models
by Will Penny & Biswa Sengupta - 1-25 Quantitative Analysis of Axonal Branch Dynamics in the Developing Nervous System
by Kelsey Chalmers & Elizabeth M Kita & Ethan K Scott & Geoffrey J Goodhill - 1-25 Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb
by Anat Kahan & Yoram Ben-Shaul - 1-30 Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome
by Matthieu Gilson & Ruben Moreno-Bote & Adrián Ponce-Alvarez & Petra Ritter & Gustavo Deco - 1-33 Reconstruction of Tissue-Specific Metabolic Networks Using CORDA
by André Schultz & Amina A Qutub
February 2016, Volume 12, Issue 2
- 1-18 What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast
by Artémis Llamosi & Andres M Gonzalez-Vargas & Cristian Versari & Eugenio Cinquemani & Giancarlo Ferrari-Trecate & Pascal Hersen & Gregory Batt - 1-21 Non-monotonic Temporal-Weighting Indicates a Dynamically Modulated Evidence-Integration Mechanism
by Zohar Z Bronfman & Noam Brezis & Marius Usher - 1-22 Ensemble Tractography
by Hiromasa Takemura & Cesar F Caiafa & Brian A Wandell & Franco Pestilli - 1-25 Evolution of Cooperation in Social Dilemmas on Complex Networks
by Swami Iyer & Timothy Killingback - 1-25 Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories
by Rory M Donovan & Jose-Juan Tapia & Devin P Sullivan & James R Faeder & Robert F Murphy & Markus Dittrich & Daniel M Zuckerman
January 2016, Volume 12, Issue 1
- 1-9 Ten Simple Rules for a Bioinformatics Journal Club
by Andrew Lonsdale & Jocelyn Sietsma Penington & Timothy Rice & Michael Walker & Harriet Dashnow - 1-13 Social Norms of Cooperation in Small-Scale Societies
by Fernando P Santos & Francisco C Santos & Jorge M Pacheco - 1-18 Measuring Integrated Information from the Decoding Perspective
by Masafumi Oizumi & Shun-ichi Amari & Toru Yanagawa & Naotaka Fujii & Naotsugu Tsuchiya - 1-20 Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics
by David Lamparter & Daniel Marbach & Rico Rueedi & Zoltán Kutalik & Sven Bergmann - 1-20 Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance?
by Troy Day & Andrew F Read - 1-24 Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes
by Junaid Hassan & Zhi Qu & Linda L Bergaust & Lars R Bakken - 1-24 Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines
by Andrea N Kravats & Sam Tonddast-Navaei & George Stan - 1-25 Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
by Duncan K Ralph & Frederick A Matsen IV
December 2015, Volume 11, Issue 12
- 1-12 Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks
by Henrik Ronellenfitsch & Jana Lasser & Douglas C Daly & Eleni Katifori - 1-18 Distinctive Behaviors of Druggable Proteins in Cellular Networks
by Costas Mitsopoulos & Amanda C Schierz & Paul Workman & Bissan Al-Lazikani - 1-20 Anxiety-Like Behavioural Inhibition Is Normative under Environmental Threat-Reward Correlations
by Dominik R Bach - 1-20 Structural and Energetic Characterization of the Ankyrin Repeat Protein Family
by R Gonzalo Parra & Rocío Espada & Nina Verstraete & Diego U Ferreiro - 1-22 Formation and Maintenance of Robust Long-Term Information Storage in the Presence of Synaptic Turnover
by Michael Fauth & Florentin Wörgötter & Christian Tetzlaff - 1-22 Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation
by Brenda N Vo & Christopher C Drovandi & Anthony N Pettitt & Graeme J Pettet - 1-23 Sources of Variability in a Synthetic Gene Oscillator
by Alan Veliz-Cuba & Andrew J Hirning & Adam A Atanas & Faiza Hussain & Flavia Vancia & Krešimir Josić & Matthew R Bennett - 1-25 Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-Step Task
by Thomas Akam & Rui Costa & Peter Dayan - 1-25 Mirrored STDP Implements Autoencoder Learning in a Network of Spiking Neurons
by Kendra S Burbank - 1-28 AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
by Pradeep Anand Ravindranath & Stefano Forli & David S Goodsell & Arthur J Olson & Michel F Sanner - 1-33 The Essential Complexity of Auditory Receptive Fields
by Ivar L Thorson & Jean Liénard & Stephen V David - 1-36 Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set
by Matthew Hall & Mark Woolhouse & Andrew Rambaut
November 2015, Volume 11, Issue 11
- 1-11 Reputation Effects in Public and Private Interactions
by Hisashi Ohtsuki & Yoh Iwasa & Martin A Nowak - 1-14 Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics
by Laura Hindersin & Arne Traulsen - 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 - 1-20 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 - 1-12 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 - 1-20 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 - 1-25 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 - 1-22 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 - 1-18 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 - 1-23 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 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
- 1-20 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 - 1-30 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 - 1-18 Behavioural Contagion Explains Group Cohesion in a Social Crustacean
by Pierre Broly & Jean-Louis Deneubourg - 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 - 1-27 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 - 1-38 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 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 - 1-21 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 - 1-22 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 - 1-30 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 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 - 1-20 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 - 1-21 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
January 2015, Volume 11, Issue 1
- 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 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 - 1-34 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 - 1-14 Protein-Protein Docking with Dynamic Residue Protonation States
by Krishna Praneeth Kilambi & Kavan Reddy & Jeffrey J Gray - 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