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April 2015, Volume 11, Issue 4
- 1-21 NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation
by Juliane Siebourg-Polster & Daria Mudrak & Mario Emmenlauer & Pauli Rämö & Christoph Dehio & Urs Greber & Holger Fröhlich & Niko Beerenwinkel - 1-21 Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
by Tomáš Trnka & Stanislav Kozmon & Igor Tvaroška & Jaroslav Koča - 1-21 Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery
by Sébastien Giguère & François Laviolette & Mario Marchand & Denise Tremblay & Sylvain Moineau & Xinxia Liang & Éric Biron & Jacques Corbeil - 1-21 Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models
by Timo R Maarleveld & Meike T Wortel & Brett G Olivier & Bas Teusink & Frank J Bruggeman - 1-21 General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks
by Joon-Young Moon & UnCheol Lee & Stefanie Blain-Moraes & George A Mashour - 1-21 A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome
by Susan Dina Ghiassian & Jörg Menche & Albert-László Barabási - 1-21 Quantifying Spike Train Oscillations: Biases, Distortions and Solutions
by Ayala Matzner & Izhar Bar-Gad - 1-21 Twisting Right to Left: A…A Mismatch in a CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation
by Noorain Khan & Narendar Kolimi & Thenmalarchelvi Rathinavelan - 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 Spatial and Functional Heterogeneities Shape Collective Behavior of Tumor-Immune Networks
by Daniel K Wells & Yishan Chuang & Louis M Knapp & Dirk Brockmann & William L Kath & Joshua N Leonard - 1-22 Embodied Choice: How Action Influences Perceptual Decision Making
by Nathan F Lepora & Giovanni Pezzulo - 1-22 Cell-Specific Cardiac Electrophysiology Models
by Willemijn Groenendaal & Francis A Ortega & Armen R Kherlopian & Andrew C Zygmunt & Trine Krogh-Madsen & David J Christini - 1-23 Dual Dimensionality Reduction Reveals Independent Encoding of Motor Features in a Muscle Synergy for Insect Flight Control
by Simon Sponberg & Thomas L Daniel & Adrienne L Fairhall - 1-24 The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition
by Xiliang Zheng & Jin Wang - 1-25 The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information
by Daniel Bendor - 1-27 Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences
by Jian Tian & Jaie C Woodard & Anna Whitney & Eugene I Shakhnovich - 1-30 A Bayesian Ensemble Approach for Epidemiological Projections
by Tom Lindström & Michael Tildesley & Colleen Webb - 1-31 The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction
by Ross S Williamson & Maneesh Sahani & Jonathan W Pillow - 1-36 Mixed Signal Learning by Spike Correlation Propagation in Feedback Inhibitory Circuits
by Naoki Hiratani & Tomoki Fukai
March 2015, Volume 11, Issue 3
- 1-9 Integrating Interactive Computational Modeling in Biology Curricula
by Tomáš Helikar & Christine E Cutucache & Lauren M Dahlquist & Tyler A Herek & Joshua J Larson & Jim A Rogers - 1-11 Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists
by Marco D Visser & Sean M McMahon & Cory Merow & Philip M Dixon & Sydne Record & Eelke Jongejans - 1-12 Proportionality: A Valid Alternative to Correlation for Relative Data
by David Lovell & Vera Pawlowsky-Glahn & Juan José Egozcue & Samuel Marguerat & Jürg Bähler - 1-14 PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population
by Oren E Livne & Lide Han & Gorka Alkorta-Aranburu & William Wentworth-Sheilds & Mark Abney & Carole Ober & Dan L Nicolae - 1-16 Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles
by Jérôme R D Soiné & Christoph A Brand & Jonathan Stricker & Patrick W Oakes & Margaret L Gardel & Ulrich S Schwarz - 1-16 Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals
by Thomas Obadia & Romain Silhol & Lulla Opatowski & Laura Temime & Judith Legrand & Anne C M Thiébaut & Jean-Louis Herrmann & Éric Fleury & Didier Guillemot & Pierre-Yves Boëlle & on behalf of the I-Bird Study Group - 1-17 Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
by Kristen Fortney & Joshua Griesman & Max Kotlyar & Chiara Pastrello & Marc Angeli & Ming Sound-Tsao & Igor Jurisica - 1-18 Physiology of Layer 5 Pyramidal Neurons in Mouse Primary Visual Cortex: Coincidence Detection through Bursting
by Adam S Shai & Costas A Anastassiou & Matthew E Larkum & Christof Koch - 1-18 An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments
by Alejandro Torres-Sánchez & Jesús Gómez-Gardeñes & Fernando Falo - 1-18 Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting
by Davide Albanese & Carlotta De Filippo & Duccio Cavalieri & Claudio Donati - 1-19 Predicting Epidemic Risk from Past Temporal Contact Data
by Eugenio Valdano & Chiara Poletto & Armando Giovannini & Diana Palma & Lara Savini & Vittoria Colizza - 1-21 Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles
by Minseung Kim & Violeta Zorraquino & Ilias Tagkopoulos - 1-21 Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision
by Adrian M Haith & David M Huberdeau & John W Krakauer - 1-23 When Can Species Abundance Data Reveal Non-neutrality?
by Omar Al Hammal & David Alonso & Rampal S Etienne & Stephen J Cornell - 1-23 Mapping Shape to Visuomotor Mapping: Learning and Generalisation of Sensorimotor Behaviour Based on Contextual Information
by Loes C J van Dam & Marc O Ernst - 1-23 On the Firing Rate Dependency of the Phase Response Curve of Rat Purkinje Neurons In Vitro
by João Couto & Daniele Linaro & E De Schutter & Michele Giugliano - 1-23 Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer
by Christopher R S Banerji & Simone Severini & Carlos Caldas & Andrew E Teschendorff - 1-24 Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model
by Alistair M Senior & Michael A Charleston & Mathieu Lihoreau & Jerome Buhl & David Raubenheimer & Stephen J Simpson - 1-28 Theory of Choice in Bandit, Information Sampling and Foraging Tasks
by Bruno B Averbeck - 1-28 Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells
by Fiete Haack & Heiko Lemcke & Roland Ewald & Tareck Rharass & Adelinde M Uhrmacher - 1-28 Improved Estimation and Interpretation of Correlations in Neural Circuits
by Dimitri Yatsenko & Krešimir Josić & Alexander S Ecker & Emmanouil Froudarakis & R James Cotton & Andreas S Tolias - 1-29 Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data
by Alan L Hutchison & Mark Maienschein-Cline & Andrew H Chiang & S M Ali Tabei & Herman Gudjonson & Neil Bahroos & Ravi Allada & Aaron R Dinner - 1-31 Identifying and Tracking Simulated Synaptic Inputs from Neuronal Firing: Insights from In Vitro Experiments
by Maxim Volgushev & Vladimir Ilin & Ian H Stevenson - 1-32 Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief
by Giles W Story & Ivo Vlaev & Peter Dayan & Ben Seymour & Ara Darzi & Raymond J Dolan - 1-38 On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain
by Adrien Wohrer & Christian K Machens
February 2015, Volume 11, Issue 2
- 1-3 How to Write a Presubmission Inquiry
by Thomas Lengauer & Ruth Nussinov - 1-7 Ethical Challenges of Big Data in Public Health
by Effy Vayena & Marcel Salathé & Lawrence C Madoff & John S Brownstein - 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 - 1-13 PathVisio 3: An Extendable Pathway Analysis Toolbox
by Martina Kutmon & Martijn P van Iersel & Anwesha Bohler & Thomas Kelder & Nuno Nunes & Alexander R Pico & Chris T Evelo - 1-15 When Less Is More: Non-monotonic Spike Sequence Processing in Neurons
by Hinrich Arnoldt & Shuwen Chang & Sven Jahnke & Birk Urmersbach & Holger Taschenberger & Marc Timme - 1-17 A Theoretical Justification for Single Molecule Peptide Sequencing
by Jagannath Swaminathan & Alexander A Boulgakov & Edward M Marcotte - 1-18 ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
by Xavier Didelot & Daniel J Wilson - 1-19 Computer Simulations Suggest a Key Role of Membranous Nanodomains in Biliary Lipid Secretion
by Johannes Eckstein & Nikolaus Berndt & Hermann-Georg Holzhütter - 1-20 Heterogeneous CD8+ T Cell Migration in the Lymph Node in the Absence of Inflammation Revealed by Quantitative Migration Analysis
by Edward J Banigan & Tajie H Harris & David A Christian & Christopher A Hunter & Andrea J Liu - 1-20 Protein Sectors: Statistical Coupling Analysis versus Conservation
by Tiberiu Teşileanu & Lucy J Colwell & Stanislas Leibler - 1-20 Critical Slowing Down Governs the Transition to Neuron Spiking
by Christian Meisel & Andreas Klaus & Christian Kuehn & Dietmar Plenz - 1-21 Correlations and Functional Connections in a Population of Grid Cells
by Benjamin Dunn & Maria Mørreaunet & Yasser Roudi - 1-22 HIV Competition Dynamics over Sexual Networks: First Comer Advantage Conserves Founder Effects
by Bence Ferdinandy & Enys Mones & Tamás Vicsek & Viktor Müller - 1-23 Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage
by Ishutesh Jain & Mandar M Inamdar & Ranjith Padinhateeri - 1-23 Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity
by Adrián Ponce-Alvarez & Gustavo Deco & Patric Hagmann & Gian Luca Romani & Dante Mantini & Maurizio Corbetta - 1-24 Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information
by Daniel M Keenan & Amy W Quinkert & Donald W Pfaff - 1-27 Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis
by Andrew J K Conlan & Ellen Brooks Pollock & Trevelyan J McKinley & Andrew P Mitchell & Gareth J Jones & Martin Vordermeier & James L N Wood - 1-28 Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions
by Vladimir Potapov & Jenifer B Kaplan & Amy E Keating - 1-32 The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure
by Benjamin Allen & Christine Sample & Yulia Dementieva & Ruben C Medeiros & Christopher Paoletti & Martin A Nowak - 1-34 A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination
by Laura R González-Ramírez & Omar J Ahmed & Sydney S Cash & C Eugene Wayne & Mark A Kramer
January 2015, Volume 11, Issue 1
- 1-7 150 Years of the Mass Action Law
by Eberhard O Voit & Harald A Martens & Stig W Omholt - 1-10 GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells
by Alboukadel Kassambara & Thierry Rème & Michel Jourdan & Thierry Fest & Dirk Hose & Karin Tarte & Bernard Klein - 1-12 Modulation of Elementary Calcium Release Mediates a Transition from Puffs to Waves in an IP3R Cluster Model
by Martin Rückl & Ian Parker & Jonathan S Marchant & Chamakuri Nagaiah & Friedrich W Johenning & Sten Rüdiger - 1-15 Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate
by Regina S Salvat & Andrew S Parker & Yoonjoo Choi & Chris Bailey-Kellogg & Karl E Griswold - 1-15 A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso
by Erick A Perez Alday & Michael A Colman & Philip Langley & Timothy D Butters & Jonathan Higham & Antony J Workman & Jules C Hancox & Henggui Zhang - 1-17 Orientation Selectivity in Inhibition-Dominated Networks of Spiking Neurons: Effect of Single Neuron Properties and Network Dynamics
by Sadra Sadeh & Stefan Rotter - 1-18 Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda
by Ioannis Andrianakis & Ian R Vernon & Nicky McCreesh & Trevelyan J McKinley & Jeremy E Oakley & Rebecca N Nsubuga & Michael Goldstein & Richard G White - 1-20 Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
by J Matthew Mahoney & Jaclyn Taroni & Viktor Martyanov & Tammara A Wood & Casey S Greene & Patricia A Pioli & Monique E Hinchcliff & Michael L Whitfield - 1-22 Computation in Dynamically Bounded Asymmetric Systems
by Ueli Rutishauser & Jean-Jacques Slotine & Rodney Douglas - 1-28 Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions
by Massimo Lai & Denis Brun & Stuart J Edelstein & Nicolas Le Novère - 1-29 The Formation of Multi-synaptic Connections by the Interaction of Synaptic and Structural Plasticity and Their Functional Consequences
by Michael Fauth & Florentin Wörgötter & Christian Tetzlaff - 1-34 A Probabilistic Palimpsest Model of Visual Short-term Memory
by Loic Matthey & Paul M Bays & Peter Dayan
December 2014, Volume 10, Issue 12
- 1-4 Ten Simple Rules for Finishing Your PhD
by Jacopo Marino & Melanie I Stefan & Sarah Blackford - 1-8 Yielding Elastic Tethers Stabilize Robust Cell Adhesion
by Matt J Whitfield & Jonathon P Luo & Wendy E Thomas - 1-9 Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments
by Christoph Zechner & Heinz Koeppl - 1-9 Thermodynamic Costs of Information Processing in Sensory Adaptation
by Pablo Sartori & Léo Granger & Chiu Fan Lee & Jordan M Horowitz - 1-10 Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models
by Tadashi Ando & Jeffrey Skolnick - 1-10 Molecular Insights into the Dynamics of Pharmacogenetically Important N-Terminal Variants of the Human β2-Adrenergic Receptor
by Ganesh Shahane & Chirag Parsania & Durba Sengupta & Manali Joshi - 1-10 Vesicular Stomatitis Virus Polymerase's Strong Affinity to Its Template Suggests Exotic Transcription Models
by Xiaolin Tang & Mourad Bendjennat & Saveez Saffarian - 1-10 Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure
by Ritwik K Niyogi & Peter Shizgal & Peter Dayan - 1-10 Contradictory Behavioral Biases Result from the Influence of Past Stimuli on Perception
by Ofri Raviv & Itay Lieder & Yonatan Loewenstein & Merav Ahissar - 1-10 “Bioinformatics: Introduction and Methods,” a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education
by Yang Ding & Meng Wang & Yao He & Adam Yongxin Ye & Xiaoxu Yang & Fenglin Liu & Yuqi Meng & Ge Gao & Liping Wei - 1-11 Symmetry Restoring Bifurcation in Collective Decision-Making
by Natalia Zabzina & Audrey Dussutour & Richard P Mann & David J T Sumpter & Stamatios C Nicolis - 1-12 Hippocampal Remapping Is Constrained by Sparseness rather than Capacity
by Axel Kammerer & Christian Leibold - 1-14 A Reaction-Diffusion Model of Cholinergic Retinal Waves
by Benjamin Lansdell & Kevin Ford & J Nathan Kutz - 1-14 Protein-Protein Docking with Dynamic Residue Protonation States
by Krishna Praneeth Kilambi & Kavan Reddy & Jeffrey J Gray - 1-14 Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation
by Lin Chen & Javad Noorbakhsh & Rhys M Adams & Joseph Samaniego-Evans & Germaine Agollah & Dmitry Nevozhay & Jennie Kuzdzal-Fick & Pankaj Mehta & Gábor Balázsi - 1-14 The Social Bayesian Brain: Does Mentalizing Make a Difference When We Learn?
by Marie Devaine & Guillaume Hollard & Jean Daunizeau - 1-15 Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
by Alexandra Gavryushkina & David Welch & Tanja Stadler & Alexei J Drummond - 1-15 Bilinearity in Spatiotemporal Integration of Synaptic Inputs
by Songting Li & Nan Liu & Xiao-hui Zhang & Douglas Zhou & David Cai - 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 Disrupted Calcium Release as a Mechanism for Atrial Alternans Associated with Human Atrial Fibrillation
by Kelly C Chang & Jason D Bayer & Natalia A Trayanova - 1-16 Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons
by Jean-Pierre Rospars & Alexandre Grémiaux & David Jarriault & Antoine Chaffiol & Christelle Monsempes & Nina Deisig & Sylvia Anton & Philippe Lucas & Dominique Martinez - 1-16 Dissecting Dynamic Genetic Variation That Controls Temporal Gene Response in Yeast
by Avital Brodt & Maya Botzman & Eyal David & Irit Gat-Viks - 1-16 Live Imaging-Based Model Selection Reveals Periodic Regulation of the Stochastic G1/S Phase Transition in Vertebrate Axial Development
by Mayu Sugiyama & Takashi Saitou & Hiroshi Kurokawa & Asako Sakaue-Sawano & Takeshi Imamura & Atsushi Miyawaki & Tadahiro Iimura - 1-20 Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid
by Robert Ietswaart & Florian Szardenings & Kenn Gerdes & Martin Howard - 1-20 The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets
by Evandro Ferrada - 1-20 Dynamics from Seconds to Hours in Hodgkin-Huxley Model with Time-Dependent Ion Concentrations and Buffer Reservoirs
by Niklas Hübel & Markus A Dahlem
November 2014, Volume 10, Issue 11
- 1-3 Ten Simple Rules to Achieve Conference Speaker Gender Balance
by Jennifer L Martin - 1-5 Computational Thinking in Life Science Education
by Amir Rubinstein & Benny Chor - 1-5 Evolution of All-or-None Strategies in Repeated Public Goods Dilemmas
by Flávio L Pinheiro & Vítor V Vasconcelos & Francisco C Santos & Jorge M Pacheco - 1-10 Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model
by Arne Weigenand & Michael Schellenberger Costa & Hong-Viet Victor Ngo & Jens Christian Claussen & Thomas Martinetz - 1-12 Pattern of Tick Aggregation on Mice: Larger Than Expected Distribution Tail Enhances the Spread of Tick-Borne Pathogens
by Luca Ferreri & Mario Giacobini & Paolo Bajardi & Luigi Bertolotti & Luca Bolzoni & Valentina Tagliapietra & Annapaola Rizzoli & Roberto Rosà - 1-13 Statistical Computations Underlying the Dynamics of Memory Updating
by Samuel J Gershman & Angela Radulescu & Kenneth A Norman & Yael Niv - 1-14 Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
by Marcin J Skwark & Daniele Raimondi & Mirco Michel & Arne Elofsson - 1-15 Effect of Global Cardiac Ischemia on Human Ventricular Fibrillation: Insights from a Multi-scale Mechanistic Model of the Human Heart
by Ivan V Kazbanov & Richard H Clayton & Martyn P Nash & Chris P Bradley & David J Paterson & Martin P Hayward & Peter Taggart & Alexander V Panfilov - 1-16 Herpes Simplex Virus-2 Genital Tract Shedding Is Not Predictable over Months or Years in Infected Persons
by Varsha Dhankani & J Nathan Kutz & Joshua T Schiffer - 1-16 Global Disease Monitoring and Forecasting with Wikipedia
by Nicholas Generous & Geoffrey Fairchild & Alina Deshpande & Sara Y Del Valle & Reid Priedhorsky - 1-18 Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models
by Veronika Boskova & Sebastian Bonhoeffer & Tanja Stadler - 1-18 Spinal Mechanisms May Provide a Combination of Intermittent and Continuous Control of Human Posture: Predictions from a Biologically Based Neuromusculoskeletal Model
by Leonardo Abdala Elias & Renato Naville Watanabe & André Fabio Kohn - 1-20 Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification
by Junaid Hassan & Linda L Bergaust & I David Wheat & Lars R Bakken - 1-25 High-Fidelity Coding with Correlated Neurons
by Rava Azeredo da Silveira & Michael J Berry II - 1-26 Power Laws from Linear Neuronal Cable Theory: Power Spectral Densities of the Soma Potential, Soma Membrane Current and Single-Neuron Contribution to the EEG
by Klas H Pettersen & Henrik Lindén & Tom Tetzlaff & Gaute T Einevoll
October 2014, Volume 10, Issue 10
- 1-3 Establishing and Managing a Global Student Network
by Avinash Shanmugam & Geoff Macintyre - 1-5 Ten Simple Rules for Writing a PLOS Ten Simple Rules Article
by Harriet Dashnow & Andrew Lonsdale & Philip E Bourne - 1-6 FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
by Gang Peng & Yu Fan & Wenyi Wang - 1-7 dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
by Hai Fang - 1-7 A Reappraisal of How to Build Modular, Reusable Models of Biological Systems
by Maxwell L Neal & Michael T Cooling & Lucian P Smith & Christopher T Thompson & Herbert M Sauro & Brian E Carlson & Daniel L Cook & John H Gennari - 1-10 Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble
by Mary A. Rohrdanz & Wenwei Zheng & Bradley Lambeth & Jocelyne Vreede & Cecilia Clementi - 1-10 Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups
by Amos Korman & Efrat Greenwald & Ofer Feinerman - 1-10 Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions
by Boryana Doyle & Geoffrey Fudenberg & Maxim Imakaev & Leonid A Mirny - 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 - 1-11 Phosphate Sink Containing Two-Component Signaling Systems as Tunable Threshold Devices
by Munia Amin & Varun B Kothamachu & Elisenda Feliu & Birgit E Scharf & Steven L Porter & Orkun S Soyer - 1-11 Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers
by Heidi Koldsø & David Shorthouse & Jean Hélie & Mark S P Sansom - 1-11 Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling
by Kei Moritsugu & Tohru Terada & Akinori Kidera - 1-12 The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion
by Nicole Dölker & Maria W Górna & Ludovico Sutto & Antonio S Torralba & Giulio Superti-Furga & Francesco L Gervasio - 1-13 Improving Contact Prediction along Three Dimensions
by Christoph Feinauer & Marcin J Skwark & Andrea Pagnani & Erik Aurell - 1-13 Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery
by Jose A Seoane & Colin Campbell & Ian N M Day & Juan P Casas & Tom R Gaunt - 1-14 Predicting Chemical Environments of Bacteria from Receptor Signaling
by Diana Clausznitzer & Gabriele Micali & Silke Neumann & Victor Sourjik & Robert G Endres - 1-14 Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
by Matthew N Benedict & Michael B Mundy & Christopher S Henry & Nicholas Chia & Nathan D Price - 1-15 Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle
by Mary Hongying Cheng & Ivet Bahar - 1-15 Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections
by Frédéric Crevecoeur & Stephen H Scott - 1-16 Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis
by Nathalie Poupin & François Mariotti & Jean-François Huneau & Dominique Hermier & Hélène Fouillet - 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 - 1-19 Rhythmic Manipulation of Objects with Complex Dynamics: Predictability over Chaos
by Bahman Nasseroleslami & Christopher J Hasson & Dagmar Sternad - 1-19 Putting Theory to the Test: Which Regulatory Mechanisms Can Drive Realistic Growth of a Root?
by Dirk De Vos & Kris Vissenberg & Jan Broeckhove & Gerrit T S Beemster - 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 Ten Simple Rules for Better Figures
by Nicolas P Rougier & Michael Droettboom & Philip E Bourne - 1-7 The Time Scale of Evolutionary Innovation
by Krishnendu Chatterjee & Andreas Pavlogiannis & Ben Adlam & Martin A Nowak - 1-8 A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data
by Qing Xie & Qi Liu & Fengbiao Mao & Wanshi Cai & Honghu Wu & Mingcong You & Zhen Wang & Bingyu Chen & Zhong Sheng Sun & Jinyu Wu - 1-9 Multi-state Modeling of Biomolecules
by Melanie I Stefan & Thomas M Bartol & Terrence J Sejnowski & Mary B Kennedy - 1-10 Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer
by Jinyu Li & Giulia Rossetti & Jens Dreyer & Simone Raugei & Emiliano Ippoliti & Bernhard Lüscher & Paolo Carloni - 1-10 Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis
by Hong Yang & Elias W Krumholz & Evan D Brutinel & Nagendra P Palani & Michael J Sadowsky & Andrew M Odlyzko & Jeffrey A Gralnick & Igor G L Libourel - 1-10 Seasonally Dependent Relationships between Indicators of Malaria Transmission and Disease Provided by Mathematical Model Simulations
by Erin M Stuckey & Thomas Smith & Nakul Chitnis - 1-10 IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
by N Lance Hepler & Konrad Scheffler & Steven Weaver & Ben Murrell & Douglas D Richman & Dennis R Burton & Pascal Poignard & Davey M Smith & Sergei L Kosakovsky Pond - 1-11 A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing
by Yun-Ching Chen & Christopher Douville & Cheng Wang & Noushin Niknafs & Grace Yeo & Violeta Beleva-Guthrie & Hannah Carter & Peter D Stenson & David N Cooper & Biao Li & Sean Mooney & Rachel Karchin - 1-11 Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets
by Jean-Baptiste Pettit & Raju Tomer & Kaia Achim & Sylvia Richardson & Lamiae Azizi & John Marioni - 1-11 NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles
by Shunichi Kosugi & Hiroshi Yanagawa & Ryohei Terauchi & Satoshi Tabata - 1-12 Environmental Statistics and Optimal Regulation
by David A Sivak & Matt Thomson - 1-13 Pupil-Linked Arousal Determines Variability in Perceptual Decision Making
by Peter R Murphy & Joachim Vandekerckhove & Sander Nieuwenhuis - 1-14 Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies
by Diana Chang & Alon Keinan - 1-14 Phase Transitions in the Multi-cellular Regulatory Behavior of Pancreatic Islet Excitability
by Thomas H Hraha & Matthew J Westacott & Marina Pozzoli & Aleena M Notary & P Mason McClatchey & Richard K P Benninger - 1-15 eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models
by Michal Brylinski - 1-15 A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer
by Sijia Huang & Cameron Yee & Travers Ching & Herbert Yu & Lana X Garmire - 1-16 Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method
by Simone Vincenzi & Marc Mangel & Alain J Crivelli & Stephan Munch & Hans J Skaug - 1-17 Quantifying the Impact and Extent of Undocumented Biomedical Synonymy
by David R Blair & Kanix Wang & Svetlozar Nestorov & James A Evans & Andrey Rzhetsky - 1-18 Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma
by Marti Bernardo-Faura & Stefan Massen & Christine S Falk & Nathan R Brady & Roland Eils - 1-19 Inferring on the Intentions of Others by Hierarchical Bayesian Learning
by Andreea O Diaconescu & Christoph Mathys & Lilian A E Weber & Jean Daunizeau & Lars Kasper & Ekaterina I Lomakina & Ernst Fehr & Klaas E Stephan - 1-19 Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages
by Tamás Székely Jr & Kevin Burrage & Marc Mangel & Michael B Bonsall
August 2014, Volume 10, Issue 8
- 1-2 Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era
by Qiang Cui & Ruth Nussinov - 1-3 The Upside of Failure: How Regional Student Groups Learn from Their Mistakes
by Tarun Mishra & R Gonzalo Parra & Thomas Abeel - 1-7 Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network
by Frantisek Honti & Stephen Meader & Caleb Webber - 1-9 Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens
by Delphine Pessoa & Caetano Souto-Maior & Erida Gjini & Joao S Lopes & Bruno Ceña & Cláudia T Codeço & M Gabriela M Gomes - 1-10 Phenotypic Signatures Arising from Unbalanced Bacterial Growth
by Cheemeng Tan & Robert Phillip Smith & Ming-Chi Tsai & Russell Schwartz & Lingchong You - 1-11 Sparsity and Compressed Coding in Sensory Systems
by Victor J Barranca & Gregor Kovačič & Douglas Zhou & David Cai - 1-11 Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism
by Rui Xia & Selina Vattathil & Paul Scheet - 1-11 Collective Learning and Optimal Consensus Decisions in Social Animal Groups
by Albert B Kao & Noam Miller & Colin Torney & Andrew Hartnett & Iain D Couzin - 1-11 Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
by Shuo Gu & Daniel-Adriano Silva & Luming Meng & Alexander Yue & Xuhui Huang - 1-12 OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis
by Greg Finak & Jacob Frelinger & Wenxin Jiang & Evan W Newell & John Ramey & Mark M Davis & Spyros A Kalams & Stephen C De Rosa & Raphael Gottardo - 1-12 Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images
by Umut Güçlü & Marcel A J van Gerven - 1-13 Bursts and Heavy Tails in Temporal and Sequential Dynamics of Foraging Decisions
by Kanghoon Jung & Hyeran Jang & Jerald D Kralik & Jaeseung Jeong - 1-13 Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment
by Eric L Haseltine & Sandra De Meyer & Inge Dierynck & Doug J Bartels & Anne Ghys & Andrew Davis & Eileen Z Zhang & Ann M Tigges & Joan Spanks & Gaston Picchio & Tara L Kieffer & James C Sullivan - 1-14 Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus
by Nik J Cunniffe & Francisco F Laranjeira & Franco M Neri & R Erik DeSimone & Christopher A Gilligan - 1-14 Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro
by René F M van Oers & Elisabeth G Rens & Danielle J LaValley & Cynthia A Reinhart-King & Roeland M H Merks - 1-14 Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection
by Miri Adler & Avi Mayo & Uri Alon - 1-15 A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells
by Pengxing Cao & Xiahui Tan & Graham Donovan & Michael J Sanderson & James Sneyd - 1-15 Memory Capacity of Networks with Stochastic Binary Synapses
by Alexis M Dubreuil & Yali Amit & Nicolas Brunel - 1-15 Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes
by Anne-Florence Bitbol & David J Schwab - 1-16 A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data
by Yuan Zhang & Yanni Sun & James R Cole - 1-16 Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment
by Johannes Textor & Sarah E Henrickson & Judith N Mandl & Ulrich H von Andrian & Jürgen Westermann & Rob J de Boer & Joost B Beltman - 1-17 Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution
by Priscilla Ambrosi & Juan Sebastian Chahda & Hannah R Koslen & Hillel J Chiel & Claudia Mieko Mizutani - 1-18 Dynamic Mechanisms of Neocortical Focal Seizure Onset
by Yujiang Wang & Marc Goodfellow & Peter Neal Taylor & Gerold Baier - 1-19 Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque
by Fang-Chieh Chou & Jan Lipfert & Rhiju Das - 1-19 Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth
by Sébastien Benzekry & Clare Lamont & Afshin Beheshti & Amanda Tracz & John M L Ebos & Lynn Hlatky & Philip Hahnfeldt
July 2014, Volume 10, Issue 7
- 1-2 Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"
by Wei-Hua Chen & Xing-Ming Zhao & Vera van Noort & Peer Bork - 1-3 Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities
by Jeroen de Ridder & Pieter Meysman & Olugbenga Oluwagbemi & Thomas Abeel - 1-7 Correlated Inter-Domain Motions in Adenylate Kinase
by Santiago Esteban-Martín & Robert Bryn Fenwick & Jörgen Ådén & Benjamin Cossins & Carlos W Bertoncini & Victor Guallar & Magnus Wolf-Watz & Xavier Salvatella - 1-7 Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial
by Benjamin T Miller & Rishi P Singh & Vinushka Schalk & Yuri Pevzner & Jingjun Sun & Carrie S Miller & Stefan Boresch & Toshiko Ichiye & Bernard R Brooks & H Lee Woodcock III - 1-7 Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding
by Frank C Pickard IV & Benjamin T Miller & Vinushka Schalk & Michael G Lerner & H Lee Woodcock III & Bernard R Brooks - 1-8 Brain and Behavior in Decision-Making
by Peter Cassey & Andrew Heathcote & Scott D Brown - 1-10 A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges
by James Kaufman & Justin Lessler & April Harry & Stefan Edlund & Kun Hu & Judith Douglas & Christian Thoens & Bernd Appel & Annemarie Käsbohrer & Matthias Filter - 1-10 Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells
by Andrew McDavid & Lucas Dennis & Patrick Danaher & Greg Finak & Michael Krouse & Alice Wang & Philippa Webster & Joseph Beechem & Raphael Gottardo