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Content
March 2017, Volume 13, Issue 3
- 1-26 Fast online deconvolution of calcium imaging data
by Johannes Friedrich & Pengcheng Zhou & Liam Paninski - 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 - 1-31 Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study
by Emma Saulnier & Olivier Gascuel & Samuel Alizon
February 2017, Volume 13, Issue 2
- 1-6 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 - 1-17 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 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 - 1-25 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 - 1-28 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 - 1-31 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 - 1-40 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
- 1-15 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 - 1-19 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 Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models
by Christoph Zimmer & Reza Yaesoubi & Ted Cohen - 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 - 1-25 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 - 1-27 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 - 1-31 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
- 1-13 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 - 1-22 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 - 1-31 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
- 1-12 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 Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle
by Peter Rashkov & Ian P Barrett & Robert E Beardmore & Claus Bendtsen & Ivana Gudelj - 1-18 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 - 1-26 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 - 1-32 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 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
October 2016, Volume 12, Issue 10
- 1-4 Ten Simple Rules for Developing a MOOC
by David T Manallack & Elizabeth Yuriev - 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 - 1-20 Mechano-chemical Interactions in Cardiac Sarcomere Contraction: A Computational Modeling Study
by Lauren J Dupuis & Joost Lumens & Theo Arts & Tammo Delhaas - 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 - 1-26 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 - 1-18 The Computational Properties of a Simplified Cortical Column Model
by Nicholas Cain & Ramakrishnan Iyer & Christof Koch & Stefan Mihalas - 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 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 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 - 1-25 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 - 1-30 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 - 1-13 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 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 - 1-28 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 - 1-38 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 - 1-13 Reinforcement Learning Explains Conditional Cooperation and Its Moody Cousin
by Takahiro Ezaki & Yutaka Horita & Masanori Takezawa & Naoki Masuda - 1-16 Disease Surveillance on Complex Social Networks
by Jose L Herrera & Ravi Srinivasan & John S Brownstein & Alison P Galvani & Lauren Ancel Meyers - 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