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Content
November 2015, Volume 11, Issue 11
- 1-17 Quantifying Stochastic Noise in Cultured Circadian Reporter Cells
by Peter C St. John & Francis J Doyle III - 1-20 Dynamic Redox Regulation of IL-4 Signaling
by Gaurav Dwivedi & Margaret A Gran & Pritha Bagchi & Melissa L Kemp - 1-20 A Unifying Probabilistic View of Associative Learning
by Samuel J Gershman - 1-21 Beyond the E-Value: Stratified Statistics for Protein Domain Prediction
by Alejandro Ochoa & John D Storey & Manuel Llinás & Mona Singh - 1-21 On the Adjacency Matrix of RyR2 Cluster Structures
by Mark A Walker & Tobias Kohl & Stephan E Lehnart & Joseph L Greenstein & W J Lederer & Raimond L Winslow - 1-22 Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition
by Jonathan Cannon & Nancy Kopell & Timothy Gardner & Jeffrey Markowitz - 1-22 A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation
by Lin-Tai Da & Chao E & Baogen Duan & Chuanbiao Zhang & Xin Zhou & Jin Yu - 1-23 Computational Modelling of Metastasis Development in Renal Cell Carcinoma
by Etienne Baratchart & Sébastien Benzekry & Andreas Bikfalvi & Thierry Colin & Lindsay S Cooley & Raphäel Pineau & Emeline J Ribot & Olivier Saut & Wilfried Souleyreau - 1-23 Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model
by Guido Gigante & Gustavo Deco & Shimon Marom & Paolo Del Giudice - 1-24 Learning of Chunking Sequences in Cognition and Behavior
by Jordi Fonollosa & Emre Neftci & Mikhail Rabinovich - 1-24 Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns
by Andrea Maesani & Pavan Ramdya & Steeve Cruchet & Kyle Gustafson & Richard Benton & Dario Floreano - 1-25 Parallel Representation of Value-Based and Finite State-Based Strategies in the Ventral and Dorsal Striatum
by Makoto Ito & Kenji Doya - 1-25 The Encoding of Decision Difficulty and Movement Time in the Primate Premotor Cortex
by Marina Martinez-Garcia & Andrea Insabato & Mario Pannunzi & Jose L Pardo-Vazquez & Carlos Acuña & Gustavo Deco - 1-25 Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum
by Miriam Grace & Marc-Thorsten Hütt - 1-25 Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution
by M Senthil Kumar & Joshua B Plotkin & Sridhar Hannenhalli - 1-26 Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach
by Joanne L Dunster & Francoise Mazet & Michael J Fry & Jonathan M Gibbins & Marcus J Tindall - 1-26 Bayesian Estimation of Conditional Independence Graphs Improves Functional Connectivity Estimates
by Max Hinne & Ronald J Janssen & Tom Heskes & Marcel AJ van Gerven - 1-26 Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction
by Benjamin D Heavner & Nathan D Price - 1-26 Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics
by Jonathan W Armond & Edward F Harry & Andrew D McAinsh & Nigel J Burroughs - 1-27 The Elementary Operations of Human Vision Are Not Reducible to Template-Matching
by Peter Neri - 1-27 Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics
by Tri Hieu Nim & Le Luo & Jacob K White & Marie-Véronique Clément & Lisa Tucker-Kellogg - 1-27 Differences in Visual-Spatial Input May Underlie Different Compression Properties of Firing Fields for Grid Cell Modules in Medial Entorhinal Cortex
by Florian Raudies & Michael E Hasselmo - 1-27 SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data
by Zhongyang Zhang & Ke Hao - 1-28 Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding
by Satohiro Tajima & Toru Yanagawa & Naotaka Fujii & Taro Toyoizumi - 1-28 Learning to Estimate Dynamical State with Probabilistic Population Codes
by Joseph G Makin & Benjamin K Dichter & Philip N Sabes - 1-28 Computational Model of MicroRNA Control of HIF-VEGF Pathway: Insights into the Pathophysiology of Ischemic Vascular Disease and Cancer
by Chen Zhao & Aleksander S Popel - 1-28 A Bio-inspired Collision Avoidance Model Based on Spatial Information Derived from Motion Detectors Leads to Common Routes
by Olivier J N Bertrand & Jens P Lindemann & Martin Egelhaaf - 1-29 Remodeling and Tenacity of Inhibitory Synapses: Relationships with Network Activity and Neighboring Excitatory Synapses
by Anna Rubinski & Noam E Ziv - 1-29 Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration
by David P A Cohen & Loredana Martignetti & Sylvie Robine & Emmanuel Barillot & Andrei Zinovyev & Laurence Calzone - 1-32 From Sensory Signals to Modality-Independent Conceptual Representations: A Probabilistic Language of Thought Approach
by Goker Erdogan & Ilker Yildirim & Robert A Jacobs - 1-34 Neuromechanistic Model of Auditory Bistability
by James Rankin & Elyse Sussman & John Rinzel - 1-35 Multiscale Embedded Gene Co-expression Network Analysis
by Won-Min Song & Bin Zhang
October 2015, Volume 11, Issue 10
- 1-6 Ten Simple Rules for Protecting Research Integrity
by David M Shaw & Thomas C Erren - 1-7 Ten Simple Rules for Establishing International Research Collaborations
by Richard de Grijs - 1-12 Emergence of Shared Intentionality Is Coupled to the Advance of Cumulative Culture
by Simon D Angus & Jonathan Newton - 1-15 Combining Search, Social Media, and Traditional Data Sources to Improve Influenza Surveillance
by Mauricio Santillana & André T Nguyen & Mark Dredze & Michael J Paul & Elaine O Nsoesie & John S Brownstein - 1-16 ENCORE: Software for Quantitative Ensemble Comparison
by Matteo Tiberti & Elena Papaleo & Tone Bengtsen & Wouter Boomsma & Kresten Lindorff-Larsen - 1-17 TRANSIT - A Software Tool for Himar1 TnSeq Analysis
by Michael A DeJesus & Chaitra Ambadipudi & Richard Baker & Christopher Sassetti & Thomas R Ioerger - 1-17 Dendritic Pooling of Noisy Threshold Processes Can Explain Many Properties of a Collision-Sensitive Visual Neuron
by Matthias S Keil - 1-19 Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
by Rong Shen & Wei Han & Giacomo Fiorin & Shahidul M Islam & Klaus Schulten & Benoît Roux - 1-19 Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
by Predrag Kukic & Arvind Kannan & Maurits J J Dijkstra & Sanne Abeln & Carlo Camilloni & Michele Vendruscolo - 1-20 Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling
by Armin Meier & Johannes Söding - 1-20 Oxygen-Driven Tumour Growth Model: A Pathology-Relevant Mathematical Approach
by Juan A Delgado-SanMartin & Jennifer I Hare & Alessandro P S de Moura & James W T Yates - 1-21 Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes
by Sivan Leviyang & Vitaly V Ganusov - 1-21 The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks
by Michael Chevalier & Ophelia Venturelli & Hana El-Samad - 1-22 Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration
by Ioana Niculescu & Johannes Textor & Rob J de Boer - 1-22 Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models
by Niraj Kumar & Abhyudai Singh & Rahul V Kulkarni - 1-22 Analyzing and Quantifying the Gain-of-Function Enhancement of IP3 Receptor Gating by Familial Alzheimer’s Disease-Causing Mutants in Presenilins
by Don-On Daniel Mak & King-Ho Cheung & Patrick Toglia & J Kevin Foskett & Ghanim Ullah - 1-22 Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis
by Philipp S Orekhov & Daniel Klose & Armen Y Mulkidjanian & Konstantin V Shaitan & Martin Engelhard & Johann P Klare & Heinz-Jürgen Steinhoff - 1-23 A Generative Statistical Algorithm for Automatic Detection of Complex Postures
by Stanislav Nagy & Marc Goessling & Yali Amit & David Biron - 1-23 Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components
by Bruce S Gardiner & Kelvin K L Wong & Grand R Joldes & Addison J Rich & Chin Wee Tan & Antony W Burgess & David W Smith - 1-23 Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making
by Laurence Aitchison & Dan Bang & Bahador Bahrami & Peter E Latham - 1-24 A Common Mechanism Underlying Food Choice and Social Decisions
by Ian Krajbich & Todd Hare & Björn Bartling & Yosuke Morishima & Ernst Fehr - 1-24 Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
by Lane W Votapka & Rommie E Amaro - 1-25 Establishing a Statistical Link between Network Oscillations and Neural Synchrony
by Pengcheng Zhou & Shawn D Burton & Adam C Snyder & Matthew A Smith & Nathaniel N Urban & Robert E Kass - 1-26 Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry
by Peter K Koo & Matthew Weitzman & Chandran R Sabanaygam & Kenneth L van Golen & Simon G J Mochrie - 1-26 SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing
by Noushin Niknafs & Violeta Beleva-Guthrie & Daniel Q Naiman & Rachel Karchin - 1-27 PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps
by Radhakrishna Bettadapura & Muhibur Rasheed & Antje Vollrath & Chandrajit Bajaj - 1-28 Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks
by Christian L Vestergaard & Mathieu Génois - 1-29 The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex
by Joel Z Leibo & Qianli Liao & Fabio Anselmi & Tomaso Poggio - 1-29 Cell Invasion Dynamics into a Three Dimensional Extracellular Matrix Fibre Network
by Min-Cheol Kim & Jordan Whisler & Yaron R Silberberg & Roger D Kamm & H Harry Asada - 1-29 An Adapting Auditory-motor Feedback Loop Can Contribute to Generating Vocal Repetition
by Jason D Wittenbach & Kristofer E Bouchard & Michael S Brainard & Dezhe Z Jin - 1-29 A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water
by Xiongwu Wu & Bernard R Brooks - 1-30 A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis
by Alexander D Malkin & Robert P Sheehan & Shibin Mathew & William J Federspiel & Heinz Redl & Gilles Clermont - 1-30 Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data
by Daniel Soudry & Suraj Keshri & Patrick Stinson & Min-hwan Oh & Garud Iyengar & Liam Paninski - 1-31 Modelling Odor Decoding in the Antennal Lobe by Combining Sequential Firing Rate Models with Bayesian Inference
by Dario Cuevas Rivera & Sebastian Bitzer & Stefan J Kiebel - 1-34 Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism
by Dimitrije Marković & Jan Gläscher & Peter Bossaerts & John O’Doherty & Stefan J Kiebel - 1-37 Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
by Sean L Seyler & Avishek Kumar & M F Thorpe & Oliver Beckstein - 1-39 Primary Visual Cortex as a Saliency Map: A Parameter-Free Prediction and Its Test by Behavioral Data
by Li Zhaoping & Li Zhe
September 2015, Volume 11, Issue 9
- 1-5 How to Grow a Computational Biology Lab
by Alice Carolyn McHardy - 1-5 Ten Simple Rules for a Computational Biologist’s Laboratory Notebook
by Santiago Schnell - 1-8 You Are Not Working for Me; I Am Working with You
by Florian Markowetz - 1-13 Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions
by Claudio Altafini & Giuseppe Facchetti - 1-13 ReproPhylo: An Environment for Reproducible Phylogenomics
by Amir Szitenberg & Max John & Mark L Blaxter & David H Lunt - 1-14 Bioinformatics in Africa: The Rise of Ghana?
by Thomas K Karikari - 1-14 An Emerging Allee Effect Is Critical for Tumor Initiation and Persistence
by Katrin Böttger & Haralambos Hatzikirou & Anja Voss-Böhme & Elisabetta Ada Cavalcanti-Adam & Miguel A Herrero & Andreas Deutsch - 1-15 Early Characterization of the Severity and Transmissibility of Pandemic Influenza Using Clinical Episode Data from Multiple Populations
by Pete Riley & Michal Ben-Nun & Jon A Linker & Angelia A Cost & Jose L Sanchez & Dylan George & David P Bacon & Steven Riley - 1-18 Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model
by Naiqian Zhang & Haiyun Wang & Yun Fang & Jun Wang & Xiaoqi Zheng & X Shirley Liu - 1-19 Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance
by Daniel Nichol & Peter Jeavons & Alexander G Fletcher & Robert A Bonomo & Philip K Maini & Jerome L Paul & Robert A Gatenby & Alexander RA Anderson & Jacob G Scott - 1-19 The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
by Stephan Köhler & Friederike Schmid & Giovanni Settanni - 1-20 Explaining the Timing of Natural Scene Understanding with a Computational Model of Perceptual Categorization
by Imri Sofer & Sébastien M Crouzet & Thomas Serre - 1-20 Social Feedback and the Emergence of Rank in Animal Society
by Elizabeth A Hobson & Simon DeDeo - 1-21 A Self-Organising Model of Thermoregulatory Huddling
by Jonathan Glancy & Roderich Groß & James V Stone & Stuart P Wilson - 1-22 A Theory of Cheap Control in Embodied Systems
by Guido Montúfar & Keyan Ghazi-Zahedi & Nihat Ay - 1-23 Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty
by Thembi Mdluli & Gregery T Buzzard & Ann E Rundell - 1-24 miRTex: A Text Mining System for miRNA-Gene Relation Extraction
by Gang Li & Karen E Ross & Cecilia N Arighi & Yifan Peng & Cathy H Wu & K Vijay-Shanker - 1-26 Dynamic Integration of Value Information into a Common Probability Currency as a Theory for Flexible Decision Making
by Vassilios Christopoulos & Paul R Schrater - 1-26 Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm
by Rudy Clausen & Buyong Ma & Ruth Nussinov & Amarda Shehu - 1-27 Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model
by Greg Jensen & Fabian Muñoz & Yelda Alkan & Vincent P Ferrera & Herbert S Terrace - 1-28 Prospective Optimization with Limited Resources
by Joseph Snider & Dongpyo Lee & Howard Poizner & Sergei Gepshtein - 1-31 Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca2+ Release Patterns in Cardiomyocytes
by Vijay Rajagopal & Gregory Bass & Cameron G Walker & David J Crossman & Amorita Petzer & Anthony Hickey & Ivo Siekmann & Masahiko Hoshijima & Mark H Ellisman & Edmund J Crampin & Christian Soeller - 1-34 A Method to Constrain Genome-Scale Models with 13C Labeling Data
by Héctor García Martín & Vinay Satish Kumar & Daniel Weaver & Amit Ghosh & Victor Chubukov & Aindrila Mukhopadhyay & Adam Arkin & Jay D Keasling - 1-37 Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations
by Sacha Jennifer van Albada & Moritz Helias & Markus Diesmann
August 2015, Volume 11, Issue 8
- 1-13 Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees
by Kirill Lykov & Xuejin Li & Huan Lei & Igor V Pivkin & George Em Karniadakis - 1-16 Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures
by Brinda Vallat & Carlos Madrid-Aliste & Andras Fiser - 1-16 Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks
by Claudia Schillings & Mikael Sunnåker & Jörg Stelling & Christoph Schwab - 1-16 Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions
by Assaf Amitai & Mathias Toulouze & Karine Dubrana & David Holcman - 1-18 Flexible Modeling of Epidemics with an Empirical Bayes Framework
by Logan C Brooks & David C Farrow & Sangwon Hyun & Ryan J Tibshirani & Roni Rosenfeld - 1-18 Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks
by Mitchell G Newberry & Daniel B Ennis & Van M Savage - 1-18 Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data
by Pengyi Yang & Xiaofeng Zheng & Vivek Jayaswal & Guang Hu & Jean Yee Hwa Yang & Raja Jothi - 1-19 Manifold Based Optimization for Single-Cell 3D Genome Reconstruction
by Jonas Paulsen & Odin Gramstad & Philippe Collas - 1-20 Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets
by Songjian Lu & Kevin N Lu & Shi-Yuan Cheng & Bo Hu & Xiaojun Ma & Nicholas Nystrom & Xinghua Lu - 1-20 Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling
by Åsmund Flobak & Anaïs Baudot & Elisabeth Remy & Liv Thommesen & Denis Thieffry & Martin Kuiper & Astrid Lægreid - 1-20 Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria
by Rajesh Balagam & Oleg A Igoshin - 1-22 Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast
by Zing Tsung-Yeh Tsai & Shin-Han Shiu & Huai-Kuang Tsai - 1-23 A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks
by Alireza Alemi & Carlo Baldassi & Nicolas Brunel & Riccardo Zecchina - 1-23 Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations
by Paul M Harrison & Laurent Badel & Mark J Wall & Magnus J E Richardson - 1-24 Automatic Adaptation to Fast Input Changes in a Time-Invariant Neural Circuit
by Arjun Bharioke & Dmitri B Chklovskii - 1-26 Asymmetric Evolutionary Games
by Alex McAvoy & Christoph Hauert - 1-26 Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data
by Alexey A Gritsenko & Marc Hulsman & Marcel J T Reinders & Dick de Ridder - 1-26 Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling
by Adrián Ponce-Alvarez & Biyu J He & Patric Hagmann & Gustavo Deco - 1-27 Structure Learning in Bayesian Sensorimotor Integration
by Tim Genewein & Eduard Hez & Zeynab Razzaghpanah & Daniel A Braun - 1-29 The Beta Cell in Its Cluster: Stochastic Graphs of Beta Cell Connectivity in the Islets of Langerhans
by Deborah A Striegel & Manami Hara & Vipul Periwal - 1-35 A Bayesian Attractor Model for Perceptual Decision Making
by Sebastian Bitzer & Jelle Bruineberg & Stefan J Kiebel - 1-40 Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses
by Gabriel Koch Ocker & Ashok Litwin-Kumar & Brent Doiron
July 2015, Volume 11, Issue 7
- 1-16 Measuring Asymmetry in Time-Stamped Phylogenies
by Bethany L Dearlove & Simon D W Frost - 1-17 Forecasting Influenza Epidemics in Hong Kong
by Wan Yang & Benjamin J Cowling & Eric H Y Lau & Jeffrey Shaman - 1-20 Optimal Prediction of Moving Sound Source Direction in the Owl
by Weston Cox & Brian J Fischer - 1-20 Stability of Neuronal Networks with Homeostatic Regulation
by Daniel Harnack & Miha Pelko & Antoine Chaillet & Yacine Chitour & Mark CW van Rossum - 1-21 Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes
by Lu Zhang & Daniel-Adriano Silva & Fátima Pardo-Avila & Dong Wang & Xuhui Huang - 1-21 Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
by Hanlun Jiang & Fu Kit Sheong & Lizhe Zhu & Xin Gao & Julie Bernauer & Xuhui Huang - 1-22 Modeling Inhibitory Interneurons in Efficient Sensory Coding Models
by Mengchen Zhu & Christopher J Rozell - 1-22 Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models
by Richard R Stein & Debora S Marks & Chris Sander - 1-23 Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
by Marharyta Petukh & Minghui Li & Emil Alexov - 1-23 Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks
by Saket Navlakha & Alison L Barth & Ziv Bar-Joseph - 1-23 Fast Simulation of Mechanical Heterogeneity in the Electrically Asynchronous Heart Using the MultiPatch Module
by John Walmsley & Theo Arts & Nicolas Derval & Pierre Bordachar & Hubert Cochet & Sylvain Ploux & Frits W Prinzen & Tammo Delhaas & Joost Lumens - 1-23 Adaptive Synaptogenesis Constructs Neural Codes That Benefit Discrimination
by Blake T Thomas & Davis W Blalock & William B Levy - 1-23 Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences
by Alexander M Sevy & Tim M Jacobs & James E Crowe Jr. & Jens Meiler - 1-25 A Diffusive Homeostatic Signal Maintains Neural Heterogeneity and Responsiveness in Cortical Networks
by Yann Sweeney & Jeanette Hellgren Kotaleski & Matthias H Hennig - 1-27 Geometry of the Gene Expression Space of Individual Cells
by Yael Korem & Pablo Szekely & Yuval Hart & Hila Sheftel & Jean Hausser & Avi Mayo & Michael E Rothenberg & Tomer Kalisky & Uri Alon - 1-30 Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina
by Jian K Liu & Tim Gollisch - 1-38 Asynchronous Rate Chaos in Spiking Neuronal Circuits
by Omri Harish & David Hansel
June 2015, Volume 11, Issue 6
- 1-2 ISMB/ECCB Rebooted: 2015 Brings Major Update to the Meeting Program
by Christiana N Fogg & Diane E Kovats - 1-3 Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation
by Philip E Bourne & Steven E Brenner & Michael B Eisen - 1-3 2015 ISCB Overton Prize Awarded to Curtis Huttenhower
by Christiana N Fogg & Diane E Kovats - 1-13 Computational Biology: Moving into the Future One Click at a Time
by Christiana N Fogg & Diane E Kovats - 1-15 Antibiotic Restriction Might Facilitate the Emergence of Multi-drug Resistance
by Uri Obolski & Gideon Y Stein & Lilach Hadany - 1-16 Posterior Probability Matching and Human Perceptual Decision Making
by Richard F Murray & Khushbu Patel & Alan Yee - 1-18 Behavioural Contagion Explains Group Cohesion in a Social Crustacean
by Pierre Broly & Jean-Louis Deneubourg - 1-18 BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
by Catalina A Vallejos & John C Marioni & Sylvia Richardson - 1-19 Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks
by Xiaoke Ma & Long Gao & Georgios Karamanlidis & Peng Gao & Chi Fung Lee & Lorena Garcia-Menendez & Rong Tian & Kai Tan - 1-20 Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection
by Ruian Ke & Claude Loverdo & Hangfei Qi & Ren Sun & James O Lloyd-Smith - 1-21 Is Model Fitting Necessary for Model-Based fMRI?
by Robert C Wilson & Yael Niv - 1-21 Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation
by Gabriele Micali & Gerardo Aquino & David M Richards & Robert G Endres - 1-21 Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes
by Hanae Shimo & Satya Nanda Vel Arjunan & Hiroaki Machiyama & Taiko Nishino & Makoto Suematsu & Hideaki Fujita & Masaru Tomita & Koichi Takahashi - 1-22 Spatio-temporal Dynamics and Mechanisms of Stress Granule Assembly
by Daisuke Ohshima & Kyoko Arimoto-Matsuzaki & Taichiro Tomida & Mutsuhiro Takekawa & Kazuhisa Ichikawa - 1-24 Energy Efficient Sparse Connectivity from Imbalanced Synaptic Plasticity Rules
by João Sacramento & Andreas Wichert & Mark C W van Rossum - 1-25 Encoder-Decoder Optimization for Brain-Computer Interfaces
by Josh Merel & Donald M Pianto & John P Cunningham & Liam Paninski - 1-25 The Sense of Confidence during Probabilistic Learning: A Normative Account
by Florent Meyniel & Daniel Schlunegger & Stanislas Dehaene - 1-26 Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait
by Kerry E Boyle & Hilary Monaco & Dave van Ditmarsch & Maxime Deforet & Joao B Xavier - 1-27 Measuring Fisher Information Accurately in Correlated Neural Populations
by Ingmar Kanitscheider & Ruben Coen-Cagli & Adam Kohn & Alexandre Pouget - 1-28 A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury
by Cordelia Ziraldo & Alexey Solovyev & Ana Allegretti & Shilpa Krishnan & M Kristi Henzel & Gwendolyn A Sowa & David Brienza & Gary An & Qi Mi & Yoram Vodovotz - 1-28 Inferring Regulatory Networks from Experimental Morphological Phenotypes: A Computational Method Reverse-Engineers Planarian Regeneration
by Daniel Lobo & Michael Levin - 1-29 Automated High-Throughput Characterization of Single Neurons by Means of Simplified Spiking Models
by Christian Pozzorini & Skander Mensi & Olivier Hagens & Richard Naud & Christof Koch & Wulfram Gerstner - 1-31 The Decay of Motor Memories Is Independent of Context Change Detection
by Andrew E Brennan & Maurice A Smith - 1-32 High Stimulus-Related Information in Barrel Cortex Inhibitory Interneurons
by Vicente Reyes-Puerta & Suam Kim & Jyh-Jang Sun & Barbara Imbrosci & Werner Kilb & Heiko J Luhmann - 1-38 Monte Carlo Planning Method Estimates Planning Horizons during Interactive Social Exchange
by Andreas Hula & P Read Montague & Peter Dayan - 1-46 Stochastic Dynamics Underlying Cognitive Stability and Flexibility
by Kai Ueltzhöffer & Diana J N Armbruster-Genç & Christian J Fiebach
May 2015, Volume 11, Issue 5
- 1-2 Comment on “Broadband Criticality of Human Brain Network Synchronization” by Kitzbichler MG, Smith ML, Christensen SR, Bullmore E (2009) PLoS Comput Biol 5: e1000314
by Simon Farmer - 1-5 Power Law Scaling in Human and Empty Room MEG Recordings
by Manfred G Kitzbichler & Edward T Bullmore - 1-13 Metapopulation Persistence in Random Fragmented Landscapes
by Jacopo Grilli & György Barabás & Stefano Allesina - 1-17 The Effect of Incentives and Meta-incentives on the Evolution of Cooperation
by Isamu Okada & Hitoshi Yamamoto & Fujio Toriumi & Tatsuya Sasaki - 1-18 Accurate Computation of Survival Statistics in Genome-Wide Studies
by Fabio Vandin & Alexandra Papoutsaki & Benjamin J Raphael & Eli Upfal - 1-19 Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling
by David W P Dolan & Anze Zupanic & Glyn Nelson & Philip Hall & Satomi Miwa & Thomas B L Kirkwood & Daryl P Shanley - 1-19 Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities
by Victor Garcia & Kirsten Richter & Frederik Graw & Annette Oxenius & Roland R Regoes - 1-19 Maintaining Homeostasis by Decision-Making
by Christoph W Korn & Dominik R Bach - 1-19 Sharing and Specificity of Co-expression Networks across 35 Human Tissues
by Emma Pierson & the GTEx Consortium & Daphne Koller & Alexis Battle & Sara Mostafavi - 1-21 An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse
by Daniel Keller & Norbert Babai & Olexiy Kochubey & Yunyun Han & Henry Markram & Felix Schürmann & Ralf Schneggenburger - 1-21 Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
by Jonathan R Karr & Alex H Williams & Jeremy D Zucker & Andreas Raue & Bernhard Steiert & Jens Timmer & Clemens Kreutz & DREAM8 Parameter Estimation Challenge Consortium & Simon Wilkinson & Brandon A Allgood & Brian M Bot & Bruce R Hoff & Michael R Kellen & Markus W Covert & Gustavo A Stolovitzky & Pablo Meyer - 1-21 SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
by Manu Setty & Christina S Leslie - 1-22 Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations
by Zhi Yang Tam & Jan Gruber & Barry Halliwell & Rudiyanto Gunawan - 1-22 Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints
by Alon Diament & Tamir Tuller - 1-25 Predicting Cortical Dark/Bright Asymmetries from Natural Image Statistics and Early Visual Transforms
by Emily A Cooper & Anthony M Norcia - 1-25 Sparse and Compositionally Robust Inference of Microbial Ecological Networks
by Zachary D Kurtz & Christian L Müller & Emily R Miraldi & Dan R Littman & Martin J Blaser & Richard A Bonneau - 1-25 Memory Storage Fidelity in the Hippocampal Circuit: The Role of Subregions and Input Statistics
by Torsten Neher & Sen Cheng & Laurenz Wiskott - 1-27 Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins
by Tao Chen & Hue Sun Chan - 1-29 Forecasting the 2013–2014 Influenza Season Using Wikipedia
by Kyle S Hickmann & Geoffrey Fairchild & Reid Priedhorsky & Nicholas Generous & James M Hyman & Alina Deshpande & Sara Y Del Valle - 1-31 Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering
by Thomas P Prescott & Moritz Lang & Antonis Papachristodoulou - 1-31 Convex Clustering: An Attractive Alternative to Hierarchical Clustering
by Gary K Chen & Eric C Chi & John Michael O Ranola & Kenneth Lange
April 2015, Volume 11, Issue 4
- 1-4 Ten Simple Rules to Win a Nobel Prize
by Richard J Roberts - 1-5 Ten Simple Rules for a Community Computational Challenge
by Iddo Friedberg & Mark N Wass & Sean D Mooney & Predrag Radivojac - 1-6 Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research
by Anne-Laure Boulesteix - 1-6 Ten Simple (Empirical) Rules for Writing Science
by Cody J Weinberger & James A Evans & Stefano Allesina - 1-7 Ten Simple Rules for a Successful Cross-Disciplinary Collaboration
by Bernhard Knapp & Rémi Bardenet & Miguel O Bernabeu & Rafel Bordas & Maria Bruna & Ben Calderhead & Jonathan Cooper & Alexander G Fletcher & Derek Groen & Bram Kuijper & Joanna Lewis & Greg McInerny & Timo Minssen & James Osborne & Verena Paulitschke & Joe Pitt-Francis & Jelena Todoric & Christian A Yates & David Gavaghan & Charlotte M Deane - 1-10 GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
by Teresa K Atwood & Erik Bongcam-Rudloff & Michelle E Brazas & Manuel Corpas & Pascale Gaudet & Fran Lewitter & Nicola Mulder & Patricia M Palagi & Maria Victoria Schneider & Celia W G van Gelder & GOBLET Consortium - 1-15 The Serotype Distribution among Healthy Carriers before Vaccination Is Essential for Predicting the Impact of Pneumococcal Conjugate Vaccine on Invasive Disease
by Stefan Flasche & Olivier Le Polain de Waroux & Katherine L O’Brien & W John Edmunds - 1-16 Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity
by Paul Egan & Jeffrey Moore & Christian Schunn & Jonathan Cagan & Philip LeDuc - 1-17 Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study
by Nils A Berglund & Thomas J Piggot & Damien Jefferies & Richard B Sessions & Peter J Bond & Syma Khalid - 1-17 A Power-Law Dependence of Bacterial Invasion on Mammalian Host Receptors
by Tae J Lee & Jeffrey Wong & Sena Bae & Anna Jisu Lee & Allison Lopatkin & Fan Yuan & Lingchong You - 1-18 Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent
by Andy Phaiboun & Yiming Zhang & Boryung Park & Minsu Kim - 1-19 MAGMA: Generalized Gene-Set Analysis of GWAS Data
by Christiaan A de Leeuw & Joris M Mooij & Tom Heskes & Danielle Posthuma - 1-20 Simulation Predicts IGFBP2-HIF1α Interaction Drives Glioblastoma Growth
by Ka Wai Lin & Angela Liao & Amina A Qutub - 1-20 Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees
by Ickwon Choi & Amy W Chung & Todd J Suscovich & Supachai Rerks-Ngarm & Punnee Pitisuttithum & Sorachai Nitayaphan & Jaranit Kaewkungwal & Robert J O'Connell & Donald Francis & Merlin L Robb & Nelson L Michael & Jerome H Kim & Galit Alter & Margaret E Ackerman & Chris Bailey-Kellogg