Printed from https://ideas.repec.org/s/plo/pcbi0013.html
Content
July 2016, Volume 12, Issue 7
- 1-17 How People Use Social Information to Find out What to Want in the Paradigmatic Case of Inter-temporal Preferences
by Michael Moutoussis & Raymond J Dolan & Peter Dayan - 1-18 Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data
by Yuheng Lu & Christina S Leslie - 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 - 1-23 Dynamic Reweighting of Auditory Modulation Filters
by Eva R M Joosten & Shihab A Shamma & Christian Lorenzi & Peter Neri - 1-26 Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
by Edoardo Pasolli & Duy Tin Truong & Faizan Malik & Levi Waldron & Nicola Segata - 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 - 1-29 Modeling Electrophysiological Coupling and Fusion between Human Mesenchymal Stem Cells and Cardiomyocytes
by Joshua Mayourian & Ruben M Savizky & Eric A Sobie & Kevin D Costa - 1-33 Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling
by Manikandan Narayanan & Andrew J Martins & John S Tsang - 1-34 ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains
by Emiliano Torre & Carlos Canova & Michael Denker & George Gerstein & Moritz Helias & Sonja Grün - 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 MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
by Daniel H Huson & Sina Beier & Isabell Flade & Anna Górska & Mohamed El-Hadidi & Suparna Mitra & Hans-Joachim Ruscheweyh & Rewati Tappu - 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 - 1-16 Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks
by Anthony Szedlak & Nicholas Smith & Li Liu & Giovanni Paternostro & Carlo Piermarocchi - 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 - 1-23 Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level
by Xinge Jessie Jeng & Zhongyin John Daye & Wenbin Lu & Jung-Ying Tzeng - 1-25 The Computational Development of Reinforcement Learning during Adolescence
by Stefano Palminteri & Emma J Kilford & Giorgio Coricelli & Sarah-Jayne Blakemore - 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 - 1-31 Formal Models of the Network Co-occurrence Underlying Mental Operations
by Danilo Bzdok & Gaël Varoquaux & Olivier Grisel & Michael Eickenberg & Cyril Poupon & Bertrand Thirion - 1-32 Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering
by Elisa Boari de Lima & Wagner Meira Júnior & Raquel Cardoso de Melo-Minardi - 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 - 1-15 Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance
by Hannah E Clapham & Than Ha Quyen & Duong Thi Hue Kien & Ilaria Dorigatti & Cameron P Simmons & Neil M Ferguson - 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 - 1-18 Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models
by Hugo Jacquin & Amy Gilson & Eugene Shakhnovich & Simona Cocco & Rémi Monasson - 1-21 Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties
by Andrew F Neuwald & Stephen F Altschul - 1-22 Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
by Jerome Kelleher & Alison M Etheridge & Gilean McVean - 1-23 Evaluation of the Phase-Dependent Rhythm Control of Human Walking Using Phase Response Curves
by Tetsuro Funato & Yuki Yamamoto & Shinya Aoi & Takashi Imai & Toshio Aoyagi & Nozomi Tomita & Kazuo Tsuchiya - 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 - 1-27 Tuning Curves for Arm Posture Control in Motor Cortex Are Consistent with Random Connectivity
by Hagai Lalazar & L F Abbott & Eilon Vaadia - 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
- 1-14 Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System
by Maulik K Nariya & Johnny Israeli & Jack J Shi & Eric J Deeds - 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 Traveling Pulses for a Two-Species Chemotaxis Model
by Casimir Emako & Charlène Gayrard & Axel Buguin & Luís Neves de Almeida & Nicolas Vauchelet - 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 - 1-23 A Geometrically-Constrained Mathematical Model of Mammary Gland Ductal Elongation Reveals Novel Cellular Dynamics within the Terminal End Bud
by Ingrid Paine & Arnaud Chauviere & John Landua & Amulya Sreekumar & Vittorio Cristini & Jeffrey Rosen & Michael T Lewis - 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 - 1-30 Problem Solving as Probabilistic Inference with Subgoaling: Explaining Human Successes and Pitfalls in the Tower of Hanoi
by Francesco Donnarumma & Domenico Maisto & Giovanni Pezzulo - 1-33 Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory
by Evgeni V Nikolaev & Eduardo D Sontag - 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 - 1-19 Distinguishing Antimicrobial Models with Different Resistance Mechanisms via Population Pharmacodynamic Modeling
by Matthieu Jacobs & Nicolas Grégoire & William Couet & Jurgen B Bulitta - 1-19 Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference
by Michael D Karcher & Julia A Palacios & Trevor Bedford & Marc A Suchard & Vladimir N Minin - 1-20 Causal Inference for Spatial Constancy across Saccades
by Jeroen Atsma & Femke Maij & Mathieu Koppen & David E Irwin & W Pieter Medendorp - 1-20 Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data
by Andrej Kuritzin & Tabea Kischka & Jürgen Schmitz & Gennady Churakov - 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 - 1-27 Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability
by Sam F Greenbury & Steffen Schaper & Sebastian E Ahnert & Ard A Louis - 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
- 1-16 FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks
by Ting Wang & Zhao Ren & Ying Ding & Zhou Fang & Zhe Sun & Matthew L MacDonald & Robert A Sweet & Jieru Wang & Wei Chen - 1-18 A Feedback Model of Attention Explains the Diverse Effects of Attention on Neural Firing Rates and Receptive Field Structure
by Thomas Miconi & Rufin VanRullen - 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 - 1-24 Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia
by Javier Macia & Romilde Manzoni & Núria Conde & Arturo Urrios & Eulàlia de Nadal & Ricard Solé & Francesc Posas - 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 - 1-26 Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction
by Yong Liu & Min Wu & Chunyan Miao & Peilin Zhao & Xiao-Li Li - 1-38 Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons
by Skander Mensi & Olivier Hagens & Wulfram Gerstner & Christian Pozzorini
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 - 1-14 Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates
by Marco A Deriu & Gianvito Grasso & Jack A Tuszynski & Diego Gallo & Umberto Morbiducci & Andrea Danani - 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 - 1-20 Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change
by Kai J Miller & Gerwin Schalk & Dora Hermes & Jeffrey G Ojemann & Rajesh P N Rao - 1-22 Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities
by Maria E Tomasso & Micheal J Tarver & Deepa Devarajan & Steven T Whitten - 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 Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance
by Keng Boon Wee & Raphael Tze Chuen Lee & Jing Lin & Zacharias Aloysius Dwi Pramono & Sebastian Maurer-Stroh - 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 - 1-14 The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome
by István Bartha & Antonio Rausell & Paul J McLaren & Pejman Mohammadi & Manuel Tardaguila & Nimisha Chaturvedi & Jacques Fellay & Amalio Telenti - 1-15 Maximizing Sensory Dynamic Range by Tuning the Cortical State to Criticality
by Shree Hari Gautam & Thanh T Hoang & Kylie McClanahan & Stephen K Grady & Woodrow L Shew - 1-18 Distinctive Behaviors of Druggable Proteins in Cellular Networks
by Costas Mitsopoulos & Amanda C Schierz & Paul Workman & Bissan Al-Lazikani - 1-18 Computer Simulations Imply Forelimb-Dominated Underwater Flight in Plesiosaurs
by Shiqiu Liu & Adam S Smith & Yuting Gu & Jie Tan & C Karen Liu & Greg Turk - 1-20 Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction
by Tatjana Braun & Julia Koehler Leman & Oliver F Lange - 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 - 1-21 Protein Connectivity in Chemotaxis Receptor Complexes
by Stephan Eismann & Robert G Endres - 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 - 1-26 A Functional Cartography of Cognitive Systems
by Marcelo G Mattar & Michael W Cole & Sharon L Thompson-Schill & Danielle S Bassett - 1-26 Clustered Desynchronization from High-Frequency Deep Brain Stimulation
by Dan Wilson & Jeff Moehlis - 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 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 - 1-25 Parallel Representation of Value-Based and Finite State-Based Strategies in the Ventral and Dorsal Striatum
by Makoto Ito & Kenji Doya - 1-25 The Encoding of Decision Difficulty and Movement Time in the Primate Premotor Cortex
by Marina Martinez-Garcia & Andrea Insabato & Mario Pannunzi & Jose L Pardo-Vazquez & Carlos Acuña & Gustavo Deco - 1-26 Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach
by Joanne L Dunster & Francoise Mazet & Michael J Fry & Jonathan M Gibbins & Marcus J Tindall - 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 Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics
by Tri Hieu Nim & Le Luo & Jacob K White & Marie-Véronique Clément & Lisa Tucker-Kellogg - 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 - 1-28 A Bio-inspired Collision Avoidance Model Based on Spatial Information Derived from Motion Detectors Leads to Common Routes
by Olivier J N Bertrand & Jens P Lindemann & Martin Egelhaaf - 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 TRANSIT - A Software Tool for Himar1 TnSeq Analysis
by Michael A DeJesus & Chaitra Ambadipudi & Richard Baker & Christopher Sassetti & Thomas R Ioerger - 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 - 1-24 A Common Mechanism Underlying Food Choice and Social Decisions
by Ian Krajbich & Todd Hare & Björn Bartling & Yosuke Morishima & Ernst Fehr - 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 - 1-26 SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing
by Noushin Niknafs & Violeta Beleva-Guthrie & Daniel Q Naiman & Rachel Karchin - 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 - 1-29 The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex
by Joel Z Leibo & Qianli Liao & Fabio Anselmi & Tomaso Poggio - 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 - 1-37 Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
by Sean L Seyler & Avishek Kumar & M F Thorpe & Oliver Beckstein - 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 - 1-13 Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions
by Claudio Altafini & Giuseppe Facchetti - 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 Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance
by Daniel Nichol & Peter Jeavons & Alexander G Fletcher & Robert A Bonomo & Philip K Maini & Jerome L Paul & Robert A Gatenby & Alexander RA Anderson & Jacob G Scott - 1-19 The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
by Stephan Köhler & Friederike Schmid & Giovanni Settanni - 1-20 Social Feedback and the Emergence of Rank in Animal Society
by Elizabeth A Hobson & Simon DeDeo - 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 Dynamic Integration of Value Information into a Common Probability Currency as a Theory for Flexible Decision Making
by Vassilios Christopoulos & Paul R Schrater - 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 Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures
by Brinda Vallat & Carlos Madrid-Aliste & Andras Fiser - 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 Flexible Modeling of Epidemics with an Empirical Bayes Framework
by Logan C Brooks & David C Farrow & Sangwon Hyun & Ryan J Tibshirani & Roni Rosenfeld - 1-18 Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks
by Mitchell G Newberry & Daniel B Ennis & Van M Savage - 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