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Content
March 2017, Volume 13, Issue 3
- 1-18 Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis
by Andrew F Brouwer & Rafael Meza & Marisa C Eisenberg - 1-19 A human judgment approach to epidemiological forecasting
by David C Farrow & Logan C Brooks & Sangwon Hyun & Ryan J Tibshirani & Donald S Burke & Roni Rosenfeld - 1-19 Bistable front dynamics in a contractile medium: Travelling wave fronts and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions
by Rashmi Priya & Guillermo A Gomez & Srikanth Budnar & Bipul R Acharya & Andras Czirok & Alpha S Yap & Zoltan Neufeld - 1-20 Systematic identification of phosphorylation-mediated protein interaction switches
by Matthew J Betts & Oliver Wichmann & Mathias Utz & Timon Andre & Evangelia Petsalaki & Pablo Minguez & Luca Parca & Frederick P Roth & Anne-Claude Gavin & Peer Bork & Robert B Russell - 1-20 Multiregional integration in the brain during resting-state fMRI activity
by Etay Hay & Petra Ritter & Nancy J Lobaugh & Anthony R McIntosh - 1-22 PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction
by Zhu-Hong You & Zhi-An Huang & Zexuan Zhu & Gui-Ying Yan & Zheng-Wei Li & Zhenkun Wen & Xing Chen - 1-22 Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N
by Polydefkis Diamantis & Oliver T Unke & Markus Meuwly - 1-23 Phylodynamics on local sexual contact networks
by David A Rasmussen & Roger Kouyos & Huldrych F Günthard & Tanja Stadler - 1-25 Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation
by Junjiajia Long & Steven W Zucker & Thierry Emonet - 1-26 Fast online deconvolution of calcium imaging data
by Johannes Friedrich & Pengcheng Zhou & Liam Paninski - 1-26 Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration
by Michiel J M Niesen & Connie Y Wang & Reid C Van Lehn & Thomas F Miller III - 1-27 Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells
by Aurélien Naldi & Romain M Larive & Urszula Czerwinska & Serge Urbach & Philippe Montcourrier & Christian Roy & Jérôme Solassol & Gilles Freiss & Peter J Coopman & Ovidiu Radulescu - 1-28 Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment
by Marie Devaine & Jean Daunizeau - 1-28 A model for brain life history evolution
by Mauricio González-Forero & Timm Faulwasser & Laurent Lehmann - 1-30 A critical analysis of computational protein design with sparse residue interaction graphs
by Swati Jain & Jonathan D Jou & Ivelin S Georgiev & Bruce R Donald - 1-30 Geometry can provide long-range mechanical guidance for embryogenesis
by Mahamar Dicko & Pierre Saramito & Guy B Blanchard & Claire M Lye & Bénédicte Sanson & Jocelyn Étienne - 1-31 Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study
by Emma Saulnier & Olivier Gascuel & Samuel Alizon
February 2017, Volume 13, Issue 2
- 1-1 Correction: Psychotic Experiences and Overhasty Inferences Are Related to Maladaptive Learning
by Heiner Stuke & Hannes Stuke & Veith Andreas Weilnhammer & Katharina Schmack - 1-6 Ten Simple Rules for Developing a Successful Research Proposal in Brazil
by Dyoni M de Oliveira & Marcos S Buckeridge & Wanderley D dos Santos - 1-8 Ten Simple Rules on How to Organize a Scientific Retreat
by Julia Ponomarenko & Romina Garrido & Roderic Guigó - 1-14 ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
by Stephanie Evans & Kieran Alden & Lourdes Cucurull-Sanchez & Christopher Larminie & Mark C Coles & Marika C Kullberg & Jon Timmis - 1-17 Predicting Structure-Function Relations and Survival following Surgical and Bronchoscopic Lung Volume Reduction Treatment of Emphysema
by Jarred R Mondoñedo & Béla Suki - 1-20 Two dynamic regimes in the human gut microbiome
by Sean M Gibbons & Sean M Kearney & Chris S Smillie & Eric J Alm - 1-20 Early and Real-Time Detection of Seasonal Influenza Onset
by Miguel Won & Manuel Marques-Pita & Carlota Louro & Joana Gonçalves-Sá - 1-20 The genotype-phenotype map of an evolving digital organism
by Miguel A Fortuna & Luis Zaman & Charles Ofria & Andreas Wagner - 1-20 graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
by Dongjun Chung & Hang J Kim & Hongyu Zhao - 1-23 Insect Bio-inspired Neural Network Provides New Evidence on How Simple Feature Detectors Can Enable Complex Visual Generalization and Stimulus Location Invariance in the Miniature Brain of Honeybees
by Mark Roper & Chrisantha Fernando & Lars Chittka - 1-23 Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression
by Berta Verd & Anton Crombach & Johannes Jaeger - 1-25 A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons
by Yen-Fu Chen & Hsiu-Chuan Lin & Kai-Neng Chuang & Chih-Hsu Lin & Hsueh-Chi S Yen & Chen-Hsiang Yeang - 1-25 Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome
by Jannis Schuecker & Maximilian Schmidt & Sacha J van Albada & Markus Diesmann & Moritz Helias - 1-25 Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
by David Henriques & Alejandro F Villaverde & Miguel Rocha & Julio Saez-Rodriguez & Julio R Banga - 1-26 Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression
by William Poole & Kalle Leinonen & Ilya Shmulevich & Theo A Knijnenburg & Brady Bernard - 1-28 The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt
by Sophie K Kay & Heather A Harrington & Sarah Shepherd & Keith Brennan & Trevor Dale & James M Osborne & David J Gavaghan & Helen M Byrne - 1-29 A mathematical model of calcium dynamics in HSY cells
by Jung Min Han & Akihiko Tanimura & Vivien Kirk & James Sneyd - 1-30 Testing the limits of gradient sensing
by Vinal Lakhani & Timothy C Elston - 1-31 On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs
by Felipe Gerhard & Moritz Deger & Wilson Truccolo - 1-32 Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise
by Johannes Burge & Priyank Jaini - 1-34 Elucidation of molecular kinetic schemes from macroscopic traces using system identification
by Miguel Fribourg & Diomedes E Logothetis & Javier González-Maeso & Stuart C Sealfon & Belén Galocha-Iragüen & Fernando Las-Heras Andrés & Vladimir Brezina - 1-34 Comparing individual-based approaches to modelling the self-organization of multicellular tissues
by James M Osborne & Alexander G Fletcher & Joe M Pitt-Francis & Philip K Maini & David J Gavaghan - 1-40 Mindboggling morphometry of human brains
by Arno Klein & Satrajit S Ghosh & Forrest S Bao & Joachim Giard & Yrjö Häme & Eliezer Stavsky & Noah Lee & Brian Rossa & Martin Reuter & Elias Chaibub Neto & Anisha Keshavan
January 2017, Volume 13, Issue 1
- 1-5 Ten Simple Rules for Developing Usable Software in Computational Biology
by Markus List & Peter Ebert & Felipe Albrecht - 1-12 Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing
by Mary Regina Boland & Konrad J Karczewski & Nicholas P Tatonetti - 1-13 Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation
by Stewart Heitmann & Michael Rule & Wilson Truccolo & Bard Ermentrout - 1-15 The Power of Malaria Vaccine Trials Using Controlled Human Malaria Infection
by Luc E Coffeng & Cornelus C Hermsen & Robert W Sauerwein & Sake J de Vlas - 1-16 Efficient Switches in Biology and Computer Science
by Luca Cardelli & Rosa D Hernansaiz-Ballesteros & Neil Dalchau & Attila Csikász-Nagy - 1-16 Coevolutionary dynamics of phenotypic diversity and contingent cooperation
by Te Wu & Long Wang & Feng Fu - 1-18 Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
by Fabian Fröhlich & Barbara Kaltenbacher & Fabian J Theis & Jan Hasenauer - 1-18 THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites
by Hsiao-Han Chang & Colin J Worby & Adoke Yeka & Joaniter Nankabirwa & Moses R Kamya & Sarah G Staedke & Grant Dorsey & Maxwell Murphy & Daniel E Neafsey & Anna E Jeffreys & Christina Hubbart & Kirk A Rockett & Roberto Amato & Dominic P Kwiatkowski & Caroline O Buckee & Bryan Greenhouse - 1-19 Structure-Function Network Mapping and Its Assessment via Persistent Homology
by Hualou Liang & Hongbin Wang - 1-19 Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses
by Ignacio A Rodriguez-Brenes & Andrew Hofacre & Hung Fan & Dominik Wodarz - 1-19 Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility
by David Lamparter & Daniel Marbach & Rico Rueedi & Sven Bergmann & Zoltán Kutalik - 1-20 Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome
by Erik Andrews & Yue Wang & Tian Xia & Wenqing Cheng & Chao Cheng - 1-20 Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies
by Cox Lwaka Tamba & Yuan-Li Ni & Yuan-Ming Zhang - 1-21 A Looping-Based Model for Quenching Repression
by Yaroslav Pollak & Sarah Goldberg & Roee Amit - 1-21 A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models
by Christoph Zimmer & Reza Yaesoubi & Ted Cohen - 1-22 Self-organised criticality in the evolution of a thermodynamic model of rodent thermoregulatory huddling
by Stuart P Wilson - 1-23 Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains
by Qixuan Wang & William R Holmes & Julian Sosnik & Thomas Schilling & Qing Nie - 1-23 Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst
by William R Holmes & Nabora Soledad Reyes de Mochel & Qixuan Wang & Huijing Du & Tao Peng & Michael Chiang & Olivier Cinquin & Ken Cho & Qing Nie - 1-24 Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients
by Oliver Pohl & Marius Hintsche & Zahra Alirezaeizanjani & Maximilian Seyrich & Carsten Beta & Holger Stark - 1-24 Could a Neuroscientist Understand a Microprocessor?
by Eric Jonas & Konrad Paul Kording - 1-25 Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing
by Edward S Lee & Paul G Thomas & Jeff E Mold & Andrew J Yates - 1-26 Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans
by Ho-Yon Hwang & Jiou Wang - 1-26 Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies
by Tanmay A Gokhale & Jong M Kim & Robert D Kirkton & Nenad Bursac & Craig S Henriquez - 1-26 Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?
by Christopher M Siwy & Christopher Lockhart & Dmitri K Klimov - 1-27 Modelling Systemic Iron Regulation during Dietary Iron Overload and Acute Inflammation: Role of Hepcidin-Independent Mechanisms
by Mihaela Enculescu & Christoph Metzendorf & Richard Sparla & Maximilian Hahnel & Johannes Bode & Martina U Muckenthaler & Stefan Legewie - 1-27 Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations
by Christian Donner & Klaus Obermayer & Hideaki Shimazaki - 1-28 Suboptimal Criterion Learning in Static and Dynamic Environments
by Elyse H Norton & Stephen M Fleming & Nathaniel D Daw & Michael S Landy - 1-29 Multiple Choice Neurodynamical Model of the Uncertain Option Task
by Andrea Insabato & Mario Pannunzi & Gustavo Deco - 1-30 Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model
by Chen Zhao & Jeffrey S Isenberg & Aleksander S Popel - 1-31 Real Time Multiplicative Memory Amplification Mediated by Whole-Cell Scaling of Synaptic Response in Key Neurons
by Iris Reuveni & Sourav Ghosh & Edi Barkai - 1-31 The Flash-Lag Effect as a Motion-Based Predictive Shift
by Mina A Khoei & Guillaume S Masson & Laurent U Perrinet - 1-34 Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
by Sheng Wang & Siqi Sun & Zhen Li & Renyu Zhang & Jinbo Xu - 1-36 A New Approach to Model Pitch Perception Using Sparse Coding
by Oded Barzelay & Miriam Furst & Omri Barak
December 2016, Volume 12, Issue 12
- 1-1 Correction: Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets
by The PLOS Computational Biology Staff - 1-1 Correction: Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement
by The PLOS Computational Biology Staff - 1-13 Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs
by Nadezda Kryuchkova-Mostacci & Marc Robinson-Rechavi - 1-15 Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist
by Brian Drawert & Andreas Hellander & Ben Bales & Debjani Banerjee & Giovanni Bellesia & Bernie J Daigle Jr. & Geoffrey Douglas & Mengyuan Gu & Anand Gupta & Stefan Hellander & Chris Horuk & Dibyendu Nath & Aviral Takkar & Sheng Wu & Per Lötstedt & Chandra Krintz & Linda R Petzold - 1-17 Stability of Cross-Feeding Polymorphisms in Microbial Communities
by Ivana Gudelj & Margie Kinnersley & Peter Rashkov & Karen Schmidt & Frank Rosenzweig - 1-18 Systematic Approximations to Susceptible-Infectious-Susceptible Dynamics on Networks
by Matt J Keeling & Thomas House & Alison J Cooper & Lorenzo Pellis - 1-20 Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series
by Anna Klimovskaia & Stefan Ganscha & Manfred Claassen - 1-20 Novel Models of Visual Topographic Map Alignment in the Superior Colliculus
by Ruben A Tikidji-Hamburyan & Tarek A El-Ghazawi & Jason W Triplett - 1-20 Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level
by Kawai Leung & Aylia Mohammadi & William S Ryu & Ilya Nemenman - 1-22 When Optimal Feedback Control Is Not Enough: Feedforward Strategies Are Required for Optimal Control with Active Sensing
by Sang-Hoon Yeo & David W Franklin & Daniel M Wolpert - 1-23 Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology
by James C Schaff & Fei Gao & Ye Li & Igor L Novak & Boris M Slepchenko - 1-24 Competing Mechanistic Hypotheses of Acetaminophen-Induced Hepatotoxicity Challenged by Virtual Experiments
by Andrew K Smith & Brenden K Petersen & Glen E P Ropella & Ryan C Kennedy & Neil Kaplowitz & Murad Ookhtens & C Anthony Hunt - 1-24 The Hamiltonian Brain: Efficient Probabilistic Inference with Excitatory-Inhibitory Neural Circuit Dynamics
by Laurence Aitchison & Máté Lengyel - 1-25 Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites
by Angela Re & Levi Waldron & Alessandro Quattrone - 1-26 Human Inferences about Sequences: A Minimal Transition Probability Model
by Florent Meyniel & Maxime Maheu & Stanislas Dehaene - 1-26 The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems
by Andrew White & Malachi Tolman & Howard D Thames & Hubert Rodney Withers & Kathy A Mason & Mark K Transtrum - 1-27 Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models
by Ryan C Williamson & Benjamin R Cowley & Ashok Litwin-Kumar & Brent Doiron & Adam Kohn & Matthew A Smith & Byron M Yu - 1-27 Utility and Limitations of Using Gene Expression Data to Identify Functional Associations
by Sahra Uygun & Cheng Peng & Melissa D Lehti-Shiu & Robert L Last & Shin-Han Shiu - 1-29 Decoding Single Molecule Time Traces with Dynamic Disorder
by Wonseok Hwang & Il-Buem Lee & Seok-Cheol Hong & Changbong Hyeon - 1-29 Temporal Dynamics and Developmental Maturation of Salience, Default and Central-Executive Network Interactions Revealed by Variational Bayes Hidden Markov Modeling
by Srikanth Ryali & Kaustubh Supekar & Tianwen Chen & John Kochalka & Weidong Cai & Jonathan Nicholas & Aarthi Padmanabhan & Vinod Menon - 1-30 Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
by Andrew F Neuwald & Stephen F Altschul - 1-30 Encoding in Balanced Networks: Revisiting Spike Patterns and Chaos in Stimulus-Driven Systems
by Guillaume Lajoie & Kevin K Lin & Jean-Philippe Thivierge & Eric Shea-Brown - 1-31 m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks
by Song-Yao Zhang & Shao-Wu Zhang & Lian Liu & Jia Meng & Yufei Huang - 1-31 Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos
by Jonathan Desponds & Huy Tran & Teresa Ferraro & Tanguy Lucas & Carmina Perez Romero & Aurelien Guillou & Cecile Fradin & Mathieu Coppey & Nathalie Dostatni & Aleksandra M Walczak - 1-31 Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex
by Benjamin R Cowley & Matthew A Smith & Adam Kohn & Byron M Yu - 1-32 Zipf’s Law Arises Naturally When There Are Underlying, Unobserved Variables
by Laurence Aitchison & Nicola Corradi & Peter E Latham - 1-33 Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data
by Simeon Carstens & Michael Nilges & Michael Habeck
November 2016, Volume 12, Issue 11
- 1-1 Correction: Multi-level Modeling of Light-Induced Stomatal Opening Offers New Insights into Its Regulation by Drought
by The PLOS Computational Biology Staff - 1-12 NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents
by Sophia S Liu & Adam J Hockenberry & Andrea Lancichinetti & Michael C Jewett & Luís A N Amaral - 1-14 Machine Learning for Characterization of Insect Vector Feeding
by Denis S Willett & Justin George & Nora S Willett & Lukasz L Stelinski & Stephen L Lapointe - 1-15 A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging
by Sagi Snir & Bridgett M vonHoldt & Matteo Pellegrini - 1-15 Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle
by Peter Rashkov & Ian P Barrett & Robert E Beardmore & Claus Bendtsen & Ivana Gudelj - 1-16 Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion
by Mahdi Golkaram & Stefan Hellander & Brian Drawert & Linda R Petzold - 1-18 Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway
by Kazunari Iwamoto & Yuki Shindo & Koichi Takahashi - 1-20 Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference
by Kieran R Campbell & Christopher Yau - 1-22 Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning
by Jonathan A Michaels & Benjamin Dann & Hansjörg Scherberger - 1-23 High-Frequency Resonance in the Gerbil Medial Superior Olive
by Jason Mikiel-Hunter & Vibhakar Kotak & John Rinzel - 1-26 Drivers of Inter-individual Variation in Dengue Viral Load Dynamics
by Rotem Ben-Shachar & Scott Schmidler & Katia Koelle - 1-28 Do Vascular Networks Branch Optimally or Randomly across Spatial Scales?
by Elif Tekin & David Hunt & Mitchell G Newberry & Van M Savage - 1-29 Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan
by Elizabeth N Davison & Benjamin O Turner & Kimberly J Schlesinger & Michael B Miller & Scott T Grafton & Danielle S Bassett & Jean M Carlson - 1-30 Interrogating Emergent Transport Properties for Molecular Motor Ensembles: A Semi-analytical Approach
by Shreyas Bhaban & Donatello Materassi & Mingang Li & Thomas Hays & Murti Salapaka - 1-30 Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks
by Hulda S Haraldsdóttir & Ronan M T Fleming - 1-31 As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy
by Mona Habibi & Jörg Rottler & Steven S Plotkin - 1-32 Error-Robust Modes of the Retinal Population Code
by Jason S Prentice & Olivier Marre & Mark L Ioffe & Adrianna R Loback & Gašper Tkačik & Michael J Berry II - 1-34 Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1
by Jeffrey S Seely & Matthew T Kaufman & Stephen I Ryu & Krishna V Shenoy & John P Cunningham & Mark M Churchland - 1-34 Improved Measures of Integrated Information
by Max Tegmark - 1-35 WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning
by George L Sutphin & J Matthew Mahoney & Keith Sheppard & David O Walton & Ron Korstanje - 1-35 Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay
by Adam F Prasanphanich & Douglas E White & Margaret A Gran & Melissa L Kemp - 1-38 Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue
by Geir Halnes & Tuomo Mäki-Marttunen & Daniel Keller & Klas H Pettersen & Ole A Andreassen & Gaute T Einevoll - 1-46 Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains
by Arno Onken & Jian K Liu & P P Chamanthi R Karunasekara & Ioannis Delis & Tim Gollisch & Stefano Panzeri
October 2016, Volume 12, Issue 10
- 1-4 Ten Simple Rules for Developing a MOOC
by David T Manallack & Elizabeth Yuriev - 1-15 Retrospective Parameter Estimation and Forecast of Respiratory Syncytial Virus in the United States
by Julia Reis & Jeffrey Shaman - 1-18 Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements
by Samuel M D Oliveira & Antti Häkkinen & Jason Lloyd-Price & Huy Tran & Vinodh Kandavalli & Andre S Ribeiro - 1-18 rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
by Lars Hahn & Chris-André Leimeister & Rachid Ounit & Stefano Lonardi & Burkhard Morgenstern - 1-19 Glucose Oscillations Can Activate an Endogenous Oscillator in Pancreatic Islets
by Joseph P McKenna & Raghuram Dhumpa & Nikita Mukhitov & Michael G Roper & Richard Bertram - 1-20 Mechano-chemical Interactions in Cardiac Sarcomere Contraction: A Computational Modeling Study
by Lauren J Dupuis & Joost Lumens & Theo Arts & Tammo Delhaas - 1-20 SARAH Domain-Mediated MST2-RASSF Dimeric Interactions
by Goar Sánchez-Sanz & Bartłomiej Tywoniuk & David Matallanas & David Romano & Lan K Nguyen & Boris N Kholodenko & Edina Rosta & Walter Kolch & Nicolae-Viorel Buchete - 1-21 A Parsimonious Model of the Rabbit Action Potential Elucidates the Minimal Physiological Requirements for Alternans and Spiral Wave Breakup
by Richard A Gray & Pras Pathmanathan - 1-21 Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair
by Mae L Woods & Chris P Barnes - 1-21 Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections
by Jason Karslake & Jeff Maltas & Peter Brumm & Kevin B Wood - 1-22 PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse
by Kerstin Reuter & Alexander Biehl & Laurena Koch & Volkhard Helms - 1-22 The Spatial Dynamics of Predators and the Benefits and Costs of Sharing Information
by Matthieu Barbier & James R Watson - 1-22 Structural Identifiability of Dynamic Systems Biology Models
by Alejandro F Villaverde & Antonio Barreiro & Antonis Papachristodoulou - 1-23 Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches
by Ruben Perez-Carrasco & Pilar Guerrero & James Briscoe & Karen M Page - 1-24 Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction
by Daniel Machado & Markus J Herrgård & Isabel Rocha - 1-25 Functional Connectivity’s Degenerate View of Brain Computation
by Guillaume Marrelec & Arnaud Messé & Alain Giron & David Rudrauf - 1-26 Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
by Hansaim Lim & Aleksandar Poleksic & Yuan Yao & Hanghang Tong & Di He & Luke Zhuang & Patrick Meng & Lei Xie - 1-28 Likelihood-Based Inference of B Cell Clonal Families
by Duncan K Ralph & Frederick A Matsen IV - 1-34 Identifying Anatomical Origins of Coexisting Oscillations in the Cortical Microcircuit
by Hannah Bos & Markus Diesmann & Moritz Helias - 1-34 How Do Efficient Coding Strategies Depend on Origins of Noise in Neural Circuits?
by Braden A W Brinkman & Alison I Weber & Fred Rieke & Eric Shea-Brown - 1-41 Forgetting in Reinforcement Learning Links Sustained Dopamine Signals to Motivation
by Ayaka Kato & Kenji Morita
September 2016, Volume 12, Issue 9
- 1-11 A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains
by Florian C Rieger & Peter Virnau - 1-13 The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community
by Xiaokan Guo & James Q Boedicker - 1-14 Novel Covariance-Based Neutrality Test of Time-Series Data Reveals Asymmetries in Ecological and Economic Systems
by Alex D Washburne & Joshua W Burby & Daniel Lacker - 1-17 How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates
by Fabian Paul & Thomas R Weikl - 1-17 Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline
by Hao Chen & Mai Chan Lau & Michael Thomas Wong & Evan W Newell & Michael Poidinger & Jinmiao Chen - 1-17 Bipartite Community Structure of eQTLs
by John Platig & Peter J Castaldi & Dawn DeMeo & John Quackenbush - 1-17 Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes
by Abibatou Mbodj & E Hilary Gustafson & Lucia Ciglar & Guillaume Junion & Aitor Gonzalez & Charles Girardot & Laurent Perrin & Eileen E M Furlong & Denis Thieffry - 1-18 The Computational Properties of a Simplified Cortical Column Model
by Nicholas Cain & Ramakrishnan Iyer & Christof Koch & Stefan Mihalas - 1-19 SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis
by Maria Kogadeeva & Nicola Zamboni - 1-19 M-Track: A New Software for Automated Detection of Grooming Trajectories in Mice
by Sheldon L Reeves & Kelsey E Fleming & Lin Zhang & Annalisa Scimemi - 1-20 The Statistical Determinants of the Speed of Motor Learning
by Kang He & You Liang & Farnaz Abdollahi & Moria Fisher Bittmann & Konrad Kording & Kunlin Wei - 1-20 Including Thermal Fluctuations in Actomyosin Stable States Increases the Predicted Force per Motor and Macroscopic Efficiency in Muscle Modelling
by Lorenzo Marcucci & Takumi Washio & Toshio Yanagida - 1-22 The Edge of Stability: Response Times and Delta Oscillations in Balanced Networks
by Grant Gillary & Ernst Niebur - 1-22 Statistical Analysis of Tract-Tracing Experiments Demonstrates a Dense, Complex Cortical Network in the Mouse
by Rolf J F Ypma & Edward T Bullmore - 1-23 Stimulation-Based Control of Dynamic Brain Networks
by Sarah Feldt Muldoon & Fabio Pasqualetti & Shi Gu & Matthew Cieslak & Scott T Grafton & Jean M Vettel & Danielle S Bassett - 1-23 SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
by Nicola De Maio & Chieh-Hsi Wu & Daniel J Wilson - 1-23 Forecasting Human African Trypanosomiasis Prevalences from Population Screening Data Using Continuous Time Models
by Harwin de Vries & Albert P M Wagelmans & Epco Hasker & Crispin Lumbala & Pascal Lutumba & Sake J de Vlas & Joris van de Klundert - 1-24 Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation
by Carlos S N Brito & Wulfram Gerstner - 1-25 Direct Correlation between Motile Behavior and Protein Abundance in Single Cells
by Yann S Dufour & Sébastien Gillet & Nicholas W Frankel & Douglas B Weibel & Thierry Emonet - 1-27 Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement
by Lars Lau Raket & Britta Grimme & Gregor Schöner & Christian Igel & Bo Markussen - 1-28 Learning Reward Uncertainty in the Basal Ganglia
by John G Mikhael & Rafal Bogacz - 1-30 Error Correction and the Structure of Inter-Trial Fluctuations in a Redundant Movement Task
by Joby John & Jonathan B Dingwell & Joseph P Cusumano - 1-30 A Computational Model of Hepatic Energy Metabolism: Understanding Zonated Damage and Steatosis in NAFLD
by William B Ashworth & Nathan A Davies & I David L Bogle - 1-34 Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection
by Mark N Read & Jacqueline Bailey & Jon Timmis & Tatyana Chtanova
August 2016, Volume 12, Issue 8
- 1-6 The Virtuous Cycle of a Data Ecosystem
by Bradley Voytek - 1-12 metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns
by Charles Joly Beauparlant & Fabien C Lamaze & Astrid Deschênes & Rawane Samb & Audrey Lemaçon & Pascal Belleau & Steve Bilodeau & Arnaud Droit - 1-13 Defining the Product Chemical Space of Monoterpenoid Synthases
by Boxue Tian & C Dale Poulter & Matthew P Jacobson - 1-14 Predicted Molecular Effects of Sequence Variants Link to System Level of Disease
by Jonas Reeb & Maximilian Hecht & Yannick Mahlich & Yana Bromberg & Burkhard Rost - 1-15 Evolutionary Games of Multiplayer Cooperation on Graphs
by Jorge Peña & Bin Wu & Jordi Arranz & Arne Traulsen - 1-15 Comparison of Detailed and Simplified Models of Human Atrial Myocytes to Recapitulate Patient Specific Properties
by Daniel M Lombardo & Flavio H Fenton & Sanjiv M Narayan & Wouter-Jan Rappel - 1-17 Structure Prediction of RNA Loops with a Probabilistic Approach
by Jun Li & Jian Zhang & Jun Wang & Wenfei Li & Wei Wang - 1-17 Inference of Gene Regulatory Network Based on Local Bayesian Networks
by Fei Liu & Shao-Wu Zhang & Wei-Feng Guo & Ze-Gang Wei & Luonan Chen - 1-20 Impact of Heterogeneity in Sexual Behavior on Effectiveness in Reducing HIV Transmission with Test-and-Treat Strategy
by Ganna Rozhnova & Maarten F Schim van der Loeff & Janneke C M Heijne & Mirjam E Kretzschmar - 1-22 Autonomous Optimization of Targeted Stimulation of Neuronal Networks
by Sreedhar S Kumar & Jan Wülfing & Samora Okujeni & Joschka Boedecker & Martin Riedmiller & Ulrich Egert - 1-23 Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks
by Brendan Chambers & Jason N MacLean - 1-23 Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes
by Mohammad Soltani & Cesar A Vargas-Garcia & Duarte Antunes & Abhyudai Singh - 1-26 Malaria Incidence Rates from Time Series of 2-Wave Panel Surveys
by Marcia C Castro & Mathieu Maheu-Giroux & Christinah Chiyaka & Burton H Singer - 1-27 Flow-Based Network Analysis of the Caenorhabditis elegans Connectome
by Karol A Bacik & Michael T Schaub & Mariano Beguerisse-Díaz & Yazan N Billeh & Mauricio Barahona - 1-28 Neuromotor Noise Is Malleable by Amplifying Perceived Errors
by Christopher J Hasson & Zhaoran Zhang & Masaki O Abe & Dagmar Sternad - 1-28 Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data
by Daphne Ezer & Victoria Moignard & Berthold Göttgens & Boris Adryan - 1-28 Modeling of Large-Scale Functional Brain Networks Based on Structural Connectivity from DTI: Comparison with EEG Derived Phase Coupling Networks and Evaluation of Alternative Methods along the Modeling Path
by Holger Finger & Marlene Bönstrup & Bastian Cheng & Arnaud Messé & Claus Hilgetag & Götz Thomalla & Christian Gerloff & Peter König - 1-28 The Representation of Prediction Error in Auditory Cortex
by Jonathan Rubin & Nachum Ulanovsky & Israel Nelken & Naftali Tishby - 1-31 Inverse Stochastic Resonance in Cerebellar Purkinje Cells
by Anatoly Buchin & Sarah Rieubland & Michael Häusser & Boris S Gutkin & Arnd Roth - 1-34 When Does Model-Based Control Pay Off?
by Wouter Kool & Fiery A Cushman & Samuel J Gershman - 1-34 Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells
by Ruth Merkle & Bernhard Steiert & Florian Salopiata & Sofia Depner & Andreas Raue & Nao Iwamoto & Max Schelker & Helge Hass & Marvin Wäsch & Martin E Böhm & Oliver Mücke & Daniel B Lipka & Christoph Plass & Wolf D Lehmann & Clemens Kreutz & Jens Timmer & Marcel Schilling & Ursula Klingmüller - 1-35 The Complexity of Dynamics in Small Neural Circuits
by Diego Fasoli & Anna Cattani & Stefano Panzeri - 1-38 A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases
by Tamra Heberling & Lisa Davis & Jakub Gedeon & Charles Morgan & Tomáš Gedeon
July 2016, Volume 12, Issue 7
- 1-3 Computing Biology
by Ruth Nussinov & Jason A Papin - 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 - 1-11 Ten Simple Rules for Taking Advantage of Git and GitHub
by Yasset Perez-Riverol & Laurent Gatto & Rui Wang & Timo Sachsenberg & Julian Uszkoreit & Felipe da Veiga Leprevost & Christian Fufezan & Tobias Ternent & Stephen J Eglen & Daniel S Katz & Tom J Pollard & Alexander Konovalov & Robert M Flight & Kai Blin & Juan Antonio Vizcaíno - 1-13 Reinforcement Learning Explains Conditional Cooperation and Its Moody Cousin
by Takahiro Ezaki & Yutaka Horita & Masanori Takezawa & Naoki Masuda - 1-13 The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation
by Julian Weichsel & Phillip L Geissler - 1-16 Disease Surveillance on Complex Social Networks
by Jose L Herrera & Ravi Srinivasan & John S Brownstein & Alison P Galvani & Lauren Ancel Meyers