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Content
July 2016, Volume 12, Issue 7
- 1-17 How People Use Social Information to Find out What to Want in the Paradigmatic Case of Inter-temporal Preferences
by Michael Moutoussis & Raymond J Dolan & Peter Dayan - 1-18 Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data
by Yuheng Lu & Christina S Leslie - 1-20 Ancestral Reconstruction
by Jeffrey B Joy & Richard H Liang & Rosemary M McCloskey & T Nguyen & Art F Y Poon - 1-21 Intrinsic Valuation of Information in Decision Making under Uncertainty
by Daniel Bennett & Stefan Bode & Maja Brydevall & Hayley Warren & Carsten Murawski - 1-21 Near Equilibrium Calculus of Stem Cells in Application to the Airway Epithelium Lineage
by Zheng Sun & Maksim V Plikus & Natalia L Komarova - 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 - 1-23 A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation
by Pei-Chi Yang & Britton W Boras & Mao-Tsuen Jeng & Steffen S Docken & Timothy J Lewis & Andrew D McCulloch & Robert D Harvey & Colleen E Clancy - 1-24 A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism
by Nathan Mih & Elizabeth Brunk & Aarash Bordbar & Bernhard O Palsson - 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 - 1-28 Properties of Neurons in External Globus Pallidus Can Support Optimal Action Selection
by Rafal Bogacz & Eduardo Martin Moraud & Azzedine Abdi & Peter J Magill & Jérôme Baufreton - 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 - 1-29 Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling
by Javier Estrada & Natalie Andrew & Daniel Gibson & Frederick Chang & Florian Gnad & Jeremy Gunawardena - 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
- 1-2 Program Bytes: Satellite Meetings, SIGs, and AKEs at ISMB 2016
by Christiana N Fogg & Diane E Kovats - 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 Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
by Samuel Hertig & Naomi R Latorraca & Ron O Dror - 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 A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis
by David P Noren & Byron L Long & Raquel Norel & Kahn Rrhissorrakrai & Kenneth Hess & Chenyue Wendy Hu & Alex J Bisberg & Andre Schultz & Erik Engquist & Li Liu & Xihui Lin & Gregory M Chen & Honglei Xie & Geoffrey A M Hunter & Paul C Boutros & Oleg Stepanov & DREAM 9 AML-OPC Consortium & Thea Norman & Stephen H Friend & Gustavo Stolovitzky & Steven Kornblau & Amina A Qutub - 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 - 1-17 Graded, Dynamically Routable Information Processing with Synfire-Gated Synfire Chains
by Zhuo Wang & Andrew T Sornborger & Louis Tao - 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 - 1-19 How to Estimate Epidemic Risk from Incomplete Contact Diaries Data?
by Rossana Mastrandrea & Alain Barrat - 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 - 1-20 Filopodial-Tension Model of Convergent-Extension of Tissues
by Julio M Belmonte & Maciej H Swat & James A Glazier - 1-22 Model Constrained by Visual Hierarchy Improves Prediction of Neural Responses to Natural Scenes
by Ján Antolík & Sonja B Hofer & James A Bednar & Thomas D Mrsic-Flogel - 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 Adaptive Spike Threshold Enables Robust and Temporally Precise Neuronal Encoding
by Chao Huang & Andrey Resnik & Tansu Celikel & Bernhard Englitz - 1-25 The Computational Development of Reinforcement Learning during Adolescence
by Stefano Palminteri & Emma J Kilford & Giorgio Coricelli & Sarah-Jayne Blakemore - 1-25 Electrophysiology of Heart Failure Using a Rabbit Model: From the Failing Myocyte to Ventricular Fibrillation
by Aditya V S Ponnaluri & Luigi E Perotti & Michael Liu & Zhilin Qu & James N Weiss & Daniel B Ennis & William S Klug & Alan Garfinkel - 1-25 Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
by Daniel L Parton & Patrick B Grinaway & Sonya M Hanson & Kyle A Beauchamp & John D Chodera - 1-27 Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches
by Tobias Sikosek & Heinrich Krobath & Hue Sun Chan - 1-28 Mechanistic Mathematical Modeling Tests Hypotheses of the Neurovascular Coupling in fMRI
by Karin Lundengård & Gunnar Cedersund & Sebastian Sten & Felix Leong & Alexander Smedberg & Fredrik Elinder & Maria Engström - 1-28 Interplay between Graph Topology and Correlations of Third Order in Spiking Neuronal Networks
by Stojan Jovanović & Stefan Rotter - 1-29 Learning Universal Computations with Spikes
by Dominik Thalmeier & Marvin Uhlmann & Hilbert J Kappen & Raoul-Martin Memmesheimer - 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 - 1-37 Competitive Dynamics in MSTd: A Mechanism for Robust Heading Perception Based on Optic Flow
by Oliver W Layton & Brett R Fajen - 1-41 Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis
by Rebeca Campos-Sánchez & Marzia A Cremona & Alessia Pini & Francesca Chiaromonte & Kateryna D Makova - 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 - 1-20 A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett’s Esophagus
by Kit Curtius & Chao-Jen Wong & William D Hazelton & Andrew M Kaz & Amitabh Chak & Joseph E Willis & William M Grady & E Georg Luebeck - 1-20 Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks
by Song Feng & Julien F Ollivier & Orkun S Soyer - 1-21 Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties
by Andrew F Neuwald & Stephen F Altschul - 1-21 A Single Mechanism Can Account for Human Perception of Depth in Mixed Correlation Random Dot Stereograms
by Sid Henriksen & Bruce G Cumming & Jenny C A Read - 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 Structural Determinants of Misfolding in Multidomain Proteins
by Pengfei Tian & Robert B Best - 1-28 Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression
by John Wiedenhoeft & Eric Brugel & Alexander Schliep - 1-29 Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions
by Natalie S Scholes & Robert O J Weinzierl - 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 The Evolution of Quorum Sensing as a Mechanism to Infer Kinship
by Jonas Schluter & Armin P Schoech & Kevin R Foster & Sara Mitri - 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 - 1-19 Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors
by David N Quan & Chen-Yu Tsao & Hsuan-Chen Wu & William E Bentley - 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 Mechanical Stress Induces Remodeling of Vascular Networks in Growing Leaves
by Yohai Bar-Sinai & Jean-Daniel Julien & Eran Sharon & Shahaf Armon & Naomi Nakayama & Mokhtar Adda-Bedia & Arezki Boudaoud - 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 An Electrostatic Funnel in the GABA-Binding Pathway
by Timothy S Carpenter & Felice C Lightstone - 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 - 1-29 Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees
by Eben Kenah & Tom Britton & M Elizabeth Halloran & Ira M Longini Jr - 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 - 1-35 MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks
by Konstantin Popov & James Komianos & Garegin A Papoian - 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
- 1-2 ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing
by Bonnie Berger & Terry Gaasterland & Thomas Lengauer & Christine Orengo & Bruno Gaeta & Scott Markel & Alfonso Valencia - 1-8 Systems Approaches to the Eukaryotic Stress Response
by Christine Vogel - 1-13 H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation
by Jinzen Ikebe & Shun Sakuraba & Hidetoshi Kono - 1-14 SMOG 2: A Versatile Software Package for Generating Structure-Based Models
by Jeffrey K Noel & Mariana Levi & Mohit Raghunathan & Heiko Lammert & Ryan L Hayes & José N Onuchic & Paul C Whitford - 1-17 Dynamic Modelling Reveals ‘Hotspots’ on the Pathway to Enzyme-Substrate Complex Formation
by Shane E Gordon & Daniel K Weber & Matthew T Downton & John Wagner & Matthew A Perugini - 1-17 Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses
by Nicolas Dérian & Bertrand Bellier & Hang Phuong Pham & Eliza Tsitoura & Dorothea Kazazi & Christophe Huret & Penelope Mavromara & David Klatzmann & Adrien Six - 1-17 Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces
by Cristiano De Michele & Paolo De Los Rios & Giuseppe Foffi & Francesco Piazza - 1-18 Stability of Ensemble Models Predicts Productivity of Enzymatic Systems
by Matthew K Theisen & Jimmy G Lafontaine Rivera & James C Liao - 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 - 1-21 Noise Expands the Response Range of the Bacillus subtilis Competence Circuit
by Andrew Mugler & Mark Kittisopikul & Luke Hayden & Jintao Liu & Chris H Wiggins & Gürol M Süel & Aleksandra M Walczak - 1-23 Pathway-Based Genomics Prediction using Generalized Elastic Net
by Artem Sokolov & Daniel E Carlin & Evan O Paull & Robert Baertsch & Joshua M Stuart - 1-23 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
by Ramya Raviram & Pedro P Rocha & Christian L Müller & Emily R Miraldi & Sana Badri & Yi Fu & Emily Swanzey & Charlotte Proudhon & Valentina Snetkova & Richard Bonneau & Jane A Skok - 1-23 Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search
by G Matthew Fricke & Kenneth A Letendre & Melanie E Moses & Judy L Cannon - 1-25 Annealed Importance Sampling for Neural Mass Models
by Will Penny & Biswa Sengupta - 1-25 Quantitative Analysis of Axonal Branch Dynamics in the Developing Nervous System
by Kelsey Chalmers & Elizabeth M Kita & Ethan K Scott & Geoffrey J Goodhill - 1-25 A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry
by Bonnie Nijhof & Anna Castells-Nobau & Louis Wolf & Jolanda M Scheffer-de Gooyert & Ignacio Monedero & Laura Torroja & Lluis Coromina & Jeroen A W M van der Laak & Annette Schenck - 1-25 Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb
by Anat Kahan & Yoram Ben-Shaul - 1-26 Stability and Competition in Multi-spike Models of Spike-Timing Dependent Plasticity
by Baktash Babadi & L F Abbott - 1-27 A Sensorimotor Model for Computing Intended Reach Trajectories
by Cevat Üstün - 1-27 Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability
by Sam F Greenbury & Steffen Schaper & Sebastian E Ahnert & Ard A Louis - 1-27 Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection
by Andreas Milias-Argeitis & Ana Paula Oliveira & Luca Gerosa & Laura Falter & Uwe Sauer & John Lygeros - 1-28 Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies
by Nils Giordano & Francis Mairet & Jean-Luc Gouzé & Johannes Geiselmann & Hidde de Jong - 1-30 Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome
by Matthieu Gilson & Ruben Moreno-Bote & Adrián Ponce-Alvarez & Petra Ritter & Gustavo Deco - 1-33 Reconstruction of Tissue-Specific Metabolic Networks Using CORDA
by André Schultz & Amina A Qutub
February 2016, Volume 12, Issue 2
- 1-6 The 2015 Bioinformatics Open Source Conference (BOSC 2015)
by Nomi L Harris & Peter J A Cock & Hilmar Lapp & Brad Chapman & Rob Davey & Christopher Fields & Karsten Hokamp & Monica Munoz-Torres - 1-6 Ten Simple Rules for Selecting a Bio-ontology
by James Malone & Robert Stevens & Simon Jupp & Tom Hancocks & Helen Parkinson & Cath Brooksbank - 1-12 Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns
by Benjamin D Dalziel & Ottar N Bjørnstad & Willem G van Panhuis & Donald S Burke & C Jessica E Metcalf & Bryan T Grenfell - 1-14 Oligomers of Heat-Shock Proteins: Structures That Don’t Imply Function
by William M Jacobs & Tuomas P J Knowles & Daan Frenkel - 1-15 The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt
by Nicola J Mulder & Alan Christoffels & Tulio de Oliveira & Junaid Gamieldien & Scott Hazelhurst & Fourie Joubert & Judit Kumuthini & Ché S Pillay & Jacky L Snoep & Özlem Tastan Bishop & Nicki Tiffin - 1-16 FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks
by Ting Wang & Zhao Ren & Ying Ding & Zhou Fang & Zhe Sun & Matthew L MacDonald & Robert A Sweet & Jieru Wang & Wei Chen - 1-16 Quantifying Transmission Investment in Malaria Parasites
by Megan A Greischar & Nicole Mideo & Andrew F Read & Ottar N Bjørnstad - 1-18 A Feedback Model of Attention Explains the Diverse Effects of Attention on Neural Firing Rates and Receptive Field Structure
by Thomas Miconi & Rufin VanRullen - 1-18 What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast
by Artémis Llamosi & Andres M Gonzalez-Vargas & Cristian Versari & Eugenio Cinquemani & Giancarlo Ferrari-Trecate & Pascal Hersen & Gregory Batt - 1-19 Cortical Resonance Frequencies Emerge from Network Size and Connectivity
by Caroline A Lea-Carnall & Marcelo A Montemurro & Nelson J Trujillo-Barreto & Laura M Parkes & Wael El-Deredy - 1-21 Non-monotonic Temporal-Weighting Indicates a Dynamically Modulated Evidence-Integration Mechanism
by Zohar Z Bronfman & Noam Brezis & Marius Usher - 1-21 On the Origins and Control of Community Types in the Human Microbiome
by Travis E Gibson & Amir Bashan & Hong-Tai Cao & Scott T Weiss & Yang-Yu Liu - 1-22 Non-monotonic Response to Monotonic Stimulus: Regulation of Glyoxylate Shunt Gene-Expression Dynamics in Mycobacterium tuberculosis
by Joao A Ascensao & Pratik Datta & Baris Hancioglu & Eduardo Sontag & Maria L Gennaro & Oleg A Igoshin - 1-22 Ensemble Tractography
by Hiromasa Takemura & Cesar F Caiafa & Brian A Wandell & Franco Pestilli - 1-23 Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin
by Tiziano Dallavilla & Laurence Abrami & Patrick A Sandoz & Georgios Savoglidis & Vassily Hatzimanikatis & F Gisou van der Goot - 1-24 Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia
by Javier Macia & Romilde Manzoni & Núria Conde & Arturo Urrios & Eulàlia de Nadal & Ricard Solé & Francesc Posas - 1-25 Evolution of Cooperation in Social Dilemmas on Complex Networks
by Swami Iyer & Timothy Killingback - 1-25 Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories
by Rory M Donovan & Jose-Juan Tapia & Devin P Sullivan & James R Faeder & Robert F Murphy & Markus Dittrich & Daniel M Zuckerman - 1-26 Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction
by Yong Liu & Min Wu & Chunyan Miao & Peilin Zhao & Xiao-Li Li - 1-27 Recovery of Dynamics and Function in Spiking Neural Networks with Closed-Loop Control
by Ioannis Vlachos & Taşkin Deniz & Ad Aertsen & Arvind Kumar - 1-28 Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies
by Benedikt Frieg & Boris Görg & Nadine Homeyer & Verena Keitel & Dieter Häussinger & Holger Gohlke - 1-29 PSAMM: A Portable System for the Analysis of Metabolic Models
by Jon Lund Steffensen & Keith Dufault-Thompson & Ying Zhang - 1-31 A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers
by Yasin Şenbabaoğlu & Selçuk Onur Sümer & Francisco Sánchez-Vega & Debra Bemis & Giovanni Ciriello & Nikolaus Schultz & Chris Sander - 1-32 Control of βAR- and N-methyl-D-aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons
by Andrew Chay & Ilaria Zamparo & Andreas Koschinski & Manuela Zaccolo & Kim T Blackwell - 1-38 Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons
by Skander Mensi & Olivier Hagens & Wulfram Gerstner & Christian Pozzorini
January 2016, Volume 12, Issue 1
- 1-9 Ten Simple Rules for a Bioinformatics Journal Club
by Andrew Lonsdale & Jocelyn Sietsma Penington & Timothy Rice & Michael Walker & Harriet Dashnow - 1-13 Social Norms of Cooperation in Small-Scale Societies
by Fernando P Santos & Francisco C Santos & Jorge M Pacheco - 1-14 Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates
by Marco A Deriu & Gianvito Grasso & Jack A Tuszynski & Diego Gallo & Umberto Morbiducci & Andrea Danani - 1-16 Neurally Encoding Time for Olfactory Navigation
by In Jun Park & Andrew M Hein & Yuriy V Bobkov & Matthew A Reidenbach & Barry W Ache & Jose C Principe - 1-18 Measuring Integrated Information from the Decoding Perspective
by Masafumi Oizumi & Shun-ichi Amari & Toru Yanagawa & Naotaka Fujii & Naotsugu Tsuchiya - 1-18 A Quick Introduction to Version Control with Git and GitHub
by John D Blischak & Emily R Davenport & Greg Wilson - 1-20 Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics
by David Lamparter & Daniel Marbach & Rico Rueedi & Zoltán Kutalik & Sven Bergmann - 1-20 Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance?
by Troy Day & Andrew F Read - 1-20 Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change
by Kai J Miller & Gerwin Schalk & Dora Hermes & Jeffrey G Ojemann & Rajesh P N Rao - 1-22 Computational Modeling, Formal Analysis, and Tools for Systems Biology
by Ezio Bartocci & Pietro Lió - 1-22 Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities
by Maria E Tomasso & Micheal J Tarver & Deepa Devarajan & Steven T Whitten - 1-23 Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles
by Olga Kononova & Joost Snijder & Yaroslav Kholodov & Kenneth A Marx & Gijs J L Wuite & Wouter H Roos & Valeri Barsegov - 1-24 Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes
by Junaid Hassan & Zhi Qu & Linda L Bergaust & Lars R Bakken - 1-24 Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance
by Keng Boon Wee & Raphael Tze Chuen Lee & Jing Lin & Zacharias Aloysius Dwi Pramono & Sebastian Maurer-Stroh - 1-24 Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines
by Andrea N Kravats & Sam Tonddast-Navaei & George Stan - 1-24 Long-Lasting Sparks: Multi-Metastability and Release Competition in the Calcium Release Unit Network
by Zhen Song & Alain Karma & James N Weiss & Zhilin Qu - 1-25 Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
by Duncan K Ralph & Frederick A Matsen IV - 1-26 A Network Model to Describe the Terminal Differentiation of B Cells
by Akram Méndez & Luis Mendoza
December 2015, Volume 11, Issue 12
- 1-12 Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks
by Henrik Ronellenfitsch & Jana Lasser & Douglas C Daly & Eleni Katifori - 1-14 The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome
by István Bartha & Antonio Rausell & Paul J McLaren & Pejman Mohammadi & Manuel Tardaguila & Nimisha Chaturvedi & Jacques Fellay & Amalio Telenti - 1-15 Maximizing Sensory Dynamic Range by Tuning the Cortical State to Criticality
by Shree Hari Gautam & Thanh T Hoang & Kylie McClanahan & Stephen K Grady & Woodrow L Shew - 1-17 MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells
by Richard Moore & Hsu Kiang Ooi & Taek Kang & Leonidas Bleris & Lan Ma - 1-17 Operational Principles for the Dynamics of the In Vitro ParA-ParB System
by Lavisha Jindal & Eldon Emberly - 1-18 Distinctive Behaviors of Druggable Proteins in Cellular Networks
by Costas Mitsopoulos & Amanda C Schierz & Paul Workman & Bissan Al-Lazikani - 1-18 Computer Simulations Imply Forelimb-Dominated Underwater Flight in Plesiosaurs
by Shiqiu Liu & Adam S Smith & Yuting Gu & Jie Tan & C Karen Liu & Greg Turk - 1-20 Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction
by Tatjana Braun & Julia Koehler Leman & Oliver F Lange - 1-20 Anxiety-Like Behavioural Inhibition Is Normative under Environmental Threat-Reward Correlations
by Dominik R Bach - 1-20 Structural and Energetic Characterization of the Ankyrin Repeat Protein Family
by R Gonzalo Parra & Rocío Espada & Nina Verstraete & Diego U Ferreiro - 1-21 Protein Connectivity in Chemotaxis Receptor Complexes
by Stephan Eismann & Robert G Endres - 1-22 Formation and Maintenance of Robust Long-Term Information Storage in the Presence of Synaptic Turnover
by Michael Fauth & Florentin Wörgötter & Christian Tetzlaff - 1-22 Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation
by Brenda N Vo & Christopher C Drovandi & Anthony N Pettitt & Graeme J Pettet - 1-23 Sources of Variability in a Synthetic Gene Oscillator
by Alan Veliz-Cuba & Andrew J Hirning & Adam A Atanas & Faiza Hussain & Flavia Vancia & Krešimir Josić & Matthew R Bennett - 1-24 Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
by Wei Zhang & Jae-Woong Chang & Lilong Lin & Kay Minn & Baolin Wu & Jeremy Chien & Jeongsik Yong & Hui Zheng & Rui Kuang - 1-24 Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations
by Frances Hutchings & Cheol E Han & Simon S Keller & Bernd Weber & Peter N Taylor & Marcus Kaiser - 1-25 Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-Step Task
by Thomas Akam & Rui Costa & Peter Dayan - 1-25 Mirrored STDP Implements Autoencoder Learning in a Network of Spiking Neurons
by Kendra S Burbank - 1-26 A Functional Cartography of Cognitive Systems
by Marcelo G Mattar & Michael W Cole & Sharon L Thompson-Schill & Danielle S Bassett - 1-26 Computational Identification of Mechanistic Factors That Determine the Timing and Intensity of the Inflammatory Response
by Sridevi Nagaraja & Jaques Reifman & Alexander Y Mitrophanov - 1-26 Capabilities and Limitations of Tissue Size Control through Passive Mechanical Forces
by Jochen Kursawe & Pavel A Brodskiy & Jeremiah J Zartman & Ruth E Baker & Alexander G Fletcher - 1-26 Clustered Desynchronization from High-Frequency Deep Brain Stimulation
by Dan Wilson & Jeff Moehlis - 1-28 AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
by Pradeep Anand Ravindranath & Stefano Forli & David S Goodsell & Arthur J Olson & Michel F Sanner - 1-29 Computational Models Describing Possible Mechanisms for Generation of Excessive Beta Oscillations in Parkinson’s Disease
by Alex Pavlides & S John Hogan & Rafal Bogacz - 1-30 How Obstacles Perturb Population Fronts and Alter Their Genetic Structure
by Wolfram Möbius & Andrew W Murray & David R Nelson - 1-32 Multistability in Large Scale Models of Brain Activity
by Mathieu Golos & Viktor Jirsa & Emmanuel Daucé - 1-33 The Essential Complexity of Auditory Receptive Fields
by Ivar L Thorson & Jean Liénard & Stephen V David - 1-35 Where’s the Noise? Key Features of Spontaneous Activity and Neural Variability Arise through Learning in a Deterministic Network
by Christoph Hartmann & Andreea Lazar & Bernhard Nessler & Jochen Triesch - 1-36 Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set
by Matthew Hall & Mark Woolhouse & Andrew Rambaut - 1-43 Complete Firing-Rate Response of Neurons with Complex Intrinsic Dynamics
by Maximilian Puelma Touzel & Fred Wolf
November 2015, Volume 11, Issue 11
- 1-11 Reputation Effects in Public and Private Interactions
by Hisashi Ohtsuki & Yoh Iwasa & Martin A Nowak - 1-14 Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics
by Laura Hindersin & Arne Traulsen - 1-16 VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
by Mikhail Shugay & Dmitriy V Bagaev & Maria A Turchaninova & Dmitriy A Bolotin & Olga V Britanova & Ekaterina V Putintseva & Mikhail V Pogorelyy & Vadim I Nazarov & Ivan V Zvyagin & Vitalina I Kirgizova & Kirill I Kirgizov & Elena V Skorobogatova & Dmitriy M Chudakov - 1-16 Lévy Walks Suboptimal under Predation Risk
by Masato S Abe & Masakazu Shimada - 1-16 Improving Collective Estimations Using Resistance to Social Influence
by Gabriel Madirolas & Gonzalo G de Polavieja