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Content
March 2012, Volume 8, Issue 3
- 1-9 Mechanistic Basis of Branch-Site Selection in Filamentous Bacteria
by David M Richards & Antje M Hempel & Klas Flärdh & Mark J Buttner & Martin Howard - 1-9 Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB
by Elif Nihal Korkmaz & Ruth Nussinov & Türkan Haliloğlu - 1-10 Neural Network Mechanisms Underlying Stimulus Driven Variability Reduction
by Gustavo Deco & Etienne Hugues - 1-10 Traffic Instabilities in Self-Organized Pedestrian Crowds
by Mehdi Moussaïd & Elsa G Guillot & Mathieu Moreau & Jérôme Fehrenbach & Olivier Chabiron & Samuel Lemercier & Julien Pettré & Cécile Appert-Rolland & Pierre Degond & Guy Theraulaz - 1-10 Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data
by Alexander R Macalalad & Michael C Zody & Patrick Charlebois & Niall J Lennon & Ruchi M Newman & Christine M Malboeuf & Elizabeth M Ryan & Christian L Boutwell & Karen A Power & Doug E Brackney & Kendra N Pesko & Joshua Z Levin & Gregory D Ebel & Todd M Allen & Bruce W Birren & Matthew R Henn - 1-14 Uncovering the Dynamics of Cardiac Systems Using Stochastic Pacing and Frequency Domain Analyses
by Mathieu Lemay & Enno de Lange & Jan P Kucera - 1-14 Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery
by András Lörincz & Zsolt Palotai & Gábor Szirtes - 1-15 Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion
by Graciano Dieck Kattas & Xiao-Ke Xu & Michael Small - 1-15 Feedforward Inhibition and Synaptic Scaling – Two Sides of the Same Coin?
by Christian Keck & Cristina Savin & Jörg Lücke - 1-15 Impact of Network Structure and Cellular Response on Spike Time Correlations
by James Trousdale & Yu Hu & Eric Shea-Brown & Krešimir Josić - 1-16 Ensemble Models of Neutrophil Trafficking in Severe Sepsis
by Sang O K Song & Justin Hogg & Zhi-Yong Peng & Robert Parker & John A Kellum & Gilles Clermont - 1-16 Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations
by Giulia Morra & Raffaello Potestio & Cristian Micheletti & Giorgio Colombo - 1-16 Depression-Biased Reverse Plasticity Rule Is Required for Stable Learning at Top-Down Connections
by Kendra S Burbank & Gabriel Kreiman - 1-18 Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics
by Ruben Coen-Cagli & Peter Dayan & Odelia Schwartz - 1-27 State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data
by Hideaki Shimazaki & Shun-ichi Amari & Emery N Brown & Sonja Grün
February 2012, Volume 8, Issue 2
- 1-6 Early Warning Signals for Critical Transitions: A Generalized Modeling Approach
by Steven J Lade & Thilo Gross - 1-10 Paradoxical Evidence Integration in Rapid Decision Processes
by Johannes Rüter & Nicolas Marcille & Henning Sprekeler & Wulfram Gerstner & Michael H Herzog - 1-11 Comparison of Insertional RNA Editing in Myxomycetes
by Cai Chen & David Frankhouser & Ralf Bundschuh - 1-11 Joint Analysis of Multiple Metagenomic Samples
by Yael Baran & Eran Halperin - 1-11 Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1
by Xueyang Feng & You Xu & Yixin Chen & Yinjie J Tang - 1-11 Human Visual Search Does Not Maximize the Post-Saccadic Probability of Identifying Targets
by Camille Morvan & Laurence T Maloney - 1-12 Noise and Robustness in Phyllotaxis
by Vincent Mirabet & Fabrice Besnard & Teva Vernoux & Arezki Boudaoud - 1-13 Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina
by Pranidhi Sood & Robert J Johnston Jr. & Edo Kussell - 1-13 Use It and Improve It or Lose It: Interactions between Arm Function and Use in Humans Post-stroke
by Yukikazu Hidaka & Cheol E Han & Steven L Wolf & Carolee J Winstein & Nicolas Schweighofer - 1-15 Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data
by Santiago Treviño III & Yudong Sun & Tim F Cooper & Kevin E Bassler - 1-17 Multi-Scale Modeling of HIV Infection in vitro and APOBEC3G-Based Anti-Retroviral Therapy
by Iraj Hosseini & Feilim Mac Gabhann
January 2012, Volume 8, Issue 1
- 1-2 A Review of 2011 for PLoS Computational Biology
by Rosemary Dickin & Chris James Hall & Laura K Taylor & Andrew M Collings & Ruth Nussinov & Philip E Bourne - 1-6 Computational and Statistical Analysis of Protein Mass Spectrometry Data
by William Stafford Noble & Michael J MacCoss - 1-8 Failure of Adaptive Self-Organized Criticality during Epileptic Seizure Attacks
by Christian Meisel & Alexander Storch & Susanne Hallmeyer-Elgner & Ed Bullmore & Thilo Gross - 1-9 Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies
by Nicoló Fusi & Oliver Stegle & Neil D Lawrence - 1-11 Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism
by Fiona Achcar & Eduard J Kerkhoven & The SilicoTryp Consortium & Barbara M Bakker & Michael P Barrett & Rainer Breitling - 1-11 A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser
by Justin Hsia & William J Holtz & Daniel C Huang & Murat Arcak & Michel M Maharbiz - 1-12 Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection
by Richard P Mann & Andrea Perna & Daniel Strömbom & Roman Garnett & James E Herbert-Read & David J T Sumpter & Ashley J W Ward - 1-12 Balancing Feed-Forward Excitation and Inhibition via Hebbian Inhibitory Synaptic Plasticity
by Yotam Luz & Maoz Shamir - 1-12 Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress
by Patrick D McMullen & Erin Z Aprison & Peter B Winter & Luis A N Amaral & Richard I Morimoto & Ilya Ruvinsky - 1-13 A Dynamic View of Domain-Motif Interactions
by Eyal Akiva & Gilgi Friedlander & Zohar Itzhaki & Hanah Margalit - 1-13 Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding
by Iain H Moal & Paul A Bates - 1-13 Senescent Cells in Growing Tumors: Population Dynamics and Cancer Stem Cells
by Caterina A M La Porta & Stefano Zapperi & James P Sethna - 1-14 Prediction by Promoter Logic in Bacterial Quorum Sensing
by Navneet Rai & Rajat Anand & Krishna Ramkumar & Varun Sreenivasan & Sugat Dabholkar & K V Venkatesh & Mukund Thattai - 1-14 Adjusting Phenotypes by Noise Control
by Kyung H Kim & Herbert M Sauro - 1-15 Protein Design Using Continuous Rotamers
by Pablo Gainza & Kyle E Roberts & Bruce R Donald - 1-15 Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins
by Weihong Zhang & Debabani Ganguly & Jianhan Chen - 1-15 Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana
by Michael Seifert & André Gohr & Marc Strickert & Ivo Grosse - 1-18 Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer
by Xinan Yang & Kelly Regan & Yong Huang & Qingbei Zhang & Jianrong Li & Tanguy Y Seiwert & Ezra E W Cohen & H Rosie Xing & Yves A Lussier - 1-20 Membrane Properties and the Balance between Excitation and Inhibition Control Gamma-Frequency Oscillations Arising from Feedback Inhibition
by Michael N Economo & John A White
December 2011, Volume 7, Issue 12
- 1-6 BeadArray Expression Analysis Using Bioconductor
by Matthew E Ritchie & Mark J Dunning & Mike L Smith & Wei Shi & Andy G Lynch - 1-6 Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
by Dov Greenbaum & Andrea Sboner & Xinmeng Jasmine Mu & Mark Gerstein - 1-7 Computational Mass Spectrometry–Based Proteomics
by Lukas Käll & Olga Vitek - 1-8 Joint Ancestry and Association Testing in Admixed Individuals
by Daniel Shriner & Adebowale Adeyemo & Charles N Rotimi - 1-8 Chemotaxis when Bacteria Remember: Drift versus Diffusion
by Sakuntala Chatterjee & Rava Azeredo da Silveira & Yariv Kafri - 1-9 Genetic Co-Occurrence Network across Sequenced Microbes
by Pan-Jun Kim & Nathan D Price - 1-10 Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes
by Amin R Mazloom & Ruth Dannenfelser & Neil R Clark & Arsen V Grigoryan & Kathryn M Linder & Timothy J Cardozo & Julia C Bond & Aislyn D W Boran & Ravi Iyengar & Anna Malovannaya & Rainer B Lanz & Avi Ma'ayan - 1-11 Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry
by Pranesh Padmanabhan & Narendra M Dixit - 1-11 Radial and Spiral Stream Formation in Proteus mirabilis Colonies
by Chuan Xue & Elena O Budrene & Hans G Othmer - 1-11 Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model
by Edward B Baskerville & Andy P Dobson & Trevor Bedford & Stefano Allesina & T Michael Anderson & Mercedes Pascual - 1-13 Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps)
by Zhichao Liu & Qiang Shi & Don Ding & Reagan Kelly & Hong Fang & Weida Tong - 1-14 Balanced Synaptic Input Shapes the Correlation between Neural Spike Trains
by Ashok Litwin-Kumar & Anne-Marie M Oswald & Nathaniel N Urban & Brent Doiron - 1-15 Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers
by Andrew T Kwon & Alice Yi Chou & David J Arenillas & Wyeth W Wasserman - 1-16 Increased Vulnerability of Human Ventricle to Re-entrant Excitation in hERG-linked Variant 1 Short QT Syndrome
by Ismail Adeniran & Mark J McPate & Harry J Witchel & Jules C Hancox & Henggui Zhang - 1-18 A Hierarchical Neuronal Model for Generation and Online Recognition of Birdsongs
by Izzet B Yildiz & Stefan J Kiebel - 1-25 Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons
by Dejan Pecevski & Lars Buesing & Wolfgang Maass
November 2011, Volume 7, Issue 11
- 1-6 High Degree of Heterogeneity in Alzheimer's Disease Progression Patterns
by Natalia L Komarova & Craig J Thalhauser - 1-8 How Landscape Heterogeneity Frames Optimal Diffusivity in Searching Processes
by E P Raposo & F Bartumeus & M G E da Luz & P J Ribeiro-Neto & T A Souza & G M Viswanathan - 1-9 The What and Where of Adding Channel Noise to the Hodgkin-Huxley Equations
by Joshua H Goldwyn & Eric Shea-Brown - 1-9 Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits
by Rutger Hermsen & David W Erickson & Terence Hwa - 1-9 Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study
by Zhuo Song & Yang Cao & David C Samuels - 1-11 A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules
by Alexandra Jilkine & Sigurd B Angenent & Lani F Wu & Steven J Altschuler - 1-13 Trade-Offs and Constraints in Allosteric Sensing
by Bruno MC Martins & Peter S Swain - 1-14 Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy
by Seyed Yahya Anvar & Allan Tucker & Veronica Vinciotti & Andrea Venema & Gert-Jan B van Ommen & Silvere M van der Maarel & Vered Raz & Peter A C ‘t Hoen - 1-17 Representational Switching by Dynamical Reorganization of Attractor Structure in a Network Model of the Prefrontal Cortex
by Yuichi Katori & Kazuhiro Sakamoto & Naohiro Saito & Jun Tanji & Hajime Mushiake & Kazuyuki Aihara - 1-18 Optimizing Experimental Design for Comparing Models of Brain Function
by Jean Daunizeau & Kerstin Preuschoff & Karl Friston & Klaas Stephan - 1-22 Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons
by Lars Buesing & Johannes Bill & Bernhard Nessler & Wolfgang Maass
October 2011, Volume 7, Issue 10
- 1-2 Teaching Bioinformatics at the Secondary School Level
by Fran Lewitter & Philip E Bourne - 1-3 Ten Simple Rules for Developing a Short Bioinformatics Training Course
by Allegra Via & Javier De Las Rivas & Teresa K Attwood & David Landsman & Michelle D Brazas & Jack A M Leunissen & Anna Tramontano & Maria Victoria Schneider - 1-3 Ten Simple Rules for Getting Involved in Your Scientific Community
by Magali Michaut - 1-7 A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms
by Suzanne Renick Gallagher & William Coon & Kristin Donley & Abby Scott & Debra S Goldberg - 1-7 Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation
by César Augusto F de Oliveira & Barry J Grant & Michelle Zhou & J Andrew McCammon - 1-8 Three People Can Synchronize as Coupled Oscillators during Sports Activities
by Keiko Yokoyama & Yuji Yamamoto - 1-9 Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models
by Jeffrey D Fitzgerald & Ryan J Rowekamp & Lawrence C Sincich & Tatyana O Sharpee - 1-10 The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers
by Sean A Rands - 1-10 Coupled Information Diffusion–Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs
by François Rebaudo & Olivier Dangles - 1-10 Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer
by Anup Dewanji & Jihyoun Jeon & Rafael Meza & E Georg Luebeck - 1-11 Using Structure to Explore the Sequence Alignment Space of Remote Homologs
by Andrew Kuziemko & Barry Honig & Donald Petrey - 1-12 Estimating the Relevance of World Disturbances to Explain Savings, Interference and Long-Term Motor Adaptation Effects
by Max Berniker & Konrad P Kording - 1-12 Formation of Regulatory Modules by Local Sequence Duplication
by Armita Nourmohammad & Michael Lässig - 1-12 Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response
by Yaakov Maman & Ran Nir-Paz & Yoram Louzoun - 1-13 Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex
by Anurag Sethi & Byron Goldstein & S Gnanakaran - 1-13 A Neurodynamic Account of Spontaneous Behaviour
by Jun Namikawa & Ryunosuke Nishimoto & Jun Tani - 1-13 Integrated Information Increases with Fitness in the Evolution of Animats
by Jeffrey A Edlund & Nicolas Chaumont & Arend Hintze & Christof Koch & Giulio Tononi & Christoph Adami - 1-14 Coexistence of Lateral and Co-Tuned Inhibitory Configurations in Cortical Networks
by Robert B Levy & Alex D Reyes - 1-14 Grid Cells, Place Cells, and Geodesic Generalization for Spatial Reinforcement Learning
by Nicholas J Gustafson & Nathaniel D Daw - 1-14 Automatic Morphological Subtyping Reveals New Roles of Caspases in Mitochondrial Dynamics
by Jyh-Ying Peng & Chung-Chih Lin & Yen-Jen Chen & Lung-Sen Kao & Young-Chau Liu & Chung-Chien Chou & Yi-Hung Huang & Fang-Rong Chang & Yang-Chang Wu & Yuh-Show Tsai & Chun-Nan Hsu - 1-14 Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity
by Hyun Joo & Archana G Chavan & Ryan Day & Kristin P Lennox & Paul Sukhanov & David B Dahl & Marina Vannucci & Jerry Tsai - 1-14 Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release
by Heidi Koldsø & Pernille Noer & Julie Grouleff & Henriette Elisabeth Autzen & Steffen Sinning & Birgit Schiøtt - 1-14 Barriers to Diffusion in Dendrites and Estimation of Calcium Spread Following Synaptic Inputs
by Armin Biess & Eduard Korkotian & David Holcman - 1-14 A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization
by Neil Dalchau & Andrew Phillips & Leonard D Goldstein & Mark Howarth & Luca Cardelli & Stephen Emmott & Tim Elliott & Joern M Werner - 1-15 Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis
by Anna Divoli & Eneida A Mendonça & James A Evans & Andrey Rzhetsky - 1-15 Brain Rhythms Reveal a Hierarchical Network Organization
by G Karl Steinke & Roberto F Galán - 1-16 Metabolic Regulation in Progression to Autoimmune Diabetes
by Marko Sysi-Aho & Andrey Ermolov & Peddinti V Gopalacharyulu & Abhishek Tripathi & Tuulikki Seppänen-Laakso & Johanna Maukonen & Ismo Mattila & Suvi T Ruohonen & Laura Vähätalo & Laxman Yetukuri & Taina Härkönen & Erno Lindfors & Janne Nikkilä & Jorma Ilonen & Olli Simell & Maria Saarela & Mikael Knip & Samuel Kaski & Eriika Savontaus & Matej Orešič - 1-16 Receptive Field Inference with Localized Priors
by Mijung Park & Jonathan W Pillow - 1-16 Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks
by Mark Hallen & Bochong Li & Yu Tanouchi & Cheemeng Tan & Mike West & Lingchong You - 1-16 Accelerated Profile HMM Searches
by Sean R Eddy - 1-16 The Dynamics of Supply and Demand in mRNA Translation
by Chris A Brackley & M Carmen Romano & Marco Thiel - 1-16 Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability
by Kirsten H ten Tusscher & Paulien Hogeweg - 1-19 NHE Inhibition Does Not Improve Na+ or Ca2+ Overload During Reperfusion: Using Modeling to Illuminate the Mechanisms Underlying a Therapeutic Failure
by Byron N Roberts & David J Christini - 1-19 Representation of Dynamical Stimuli in Populations of Threshold Neurons
by Tatjana Tchumatchenko & Fred Wolf - 1-32 A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation
by Susan D Hester & Julio M Belmonte & J Scott Gens & Sherry G Clendenon & James A Glazier
September 2011, Volume 7, Issue 9
- 1-3 Ten Simple Rules for Getting Help from Online Scientific Communities
by Giovanni M Dall'Olio & Jacopo Marino & Michael Schubert & Kevin L Keys & Melanie I Stefan & Colin S Gillespie & Pierre Poulain & Khader Shameer & Robert Sugar & Brandon M Invergo & Lars J Jensen & Jaume Bertranpetit & Hafid Laayouni - 1-9 A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes
by Miklos Csuros & Igor B Rogozin & Eugene V Koonin - 1-10 Signalling and the Evolution of Cooperative Foraging in Dynamic Environments
by Colin J Torney & Andrew Berdahl & Iain D Couzin - 1-11 Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions
by Adi Shklarsh & Gil Ariel & Elad Schneidman & Eshel Ben-Jacob - 1-11 LsrR Quorum Sensing “Switch” Is Revealed by a Bottom-Up Approach
by Sara Hooshangi & William E Bentley - 1-11 Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network
by Jérémie Bourdon & Damien Eveillard & Anne Siegel - 1-11 Filament Depolymerization Can Explain Chromosome Pulling during Bacterial Mitosis
by Edward J Banigan & Michael A Gelbart & Zemer Gitai & Ned S Wingreen & Andrea J Liu - 1-12 A Combined Experimental and Mathematical Approach for Molecular-based Optimization of Irinotecan Circadian Delivery
by Annabelle Ballesta & Sandrine Dulong & Chadi Abbara & Boris Cohen & Alper Okyar & Jean Clairambault & Francis Levi - 1-12 An Integrated Disease/Pharmacokinetic/Pharmacodynamic Model Suggests Improved Interleukin-21 Regimens Validated Prospectively for Mouse Solid Cancers
by Moran Elishmereni & Yuri Kheifetz & Henrik Søndergaard & Rune Viig Overgaard & Zvia Agur - 1-13 Determinants of the Spatiotemporal Dynamics of the 2009 H1N1 Pandemic in Europe: Implications for Real-Time Modelling
by Stefano Merler & Marco Ajelli & Andrea Pugliese & Neil M Ferguson - 1-14 Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations
by Lipi Thukral & Isabella Daidone & Jeremy C Smith - 1-14 A Model for the Origin and Properties of Flicker-Induced Geometric Phosphenes
by Michael Rule & Matthew Stoffregen & Bard Ermentrout - 1-15 Neuromotor Noise, Error Tolerance and Velocity-Dependent Costs in Skilled Performance
by Dagmar Sternad & Masaki O Abe & Xiaogang Hu & Hermann Müller - 1-15 Network-Based Prediction and Analysis of HIV Dependency Factors
by T M Murali & Matthew D Dyer & David Badger & Brett M Tyler & Michael G Katze - 1-18 Time Scale Hierarchies in the Functional Organization of Complex Behaviors
by Dionysios Perdikis & Raoul Huys & Viktor K Jirsa
August 2011, Volume 7, Issue 8
- 1-6 Biomedical Cloud Computing With Amazon Web Services
by Vincent A Fusaro & Prasad Patil & Erik Gafni & Dennis P Wall & Peter J Tonellato - 1-7 Podbat: A Novel Genomic Tool Reveals Swr1-Independent H2A.Z Incorporation at Gene Coding Sequences through Epigenetic Meta-Analysis
by Laia Sadeghi & Carolina Bonilla & Annelie Strålfors & Karl Ekwall & J Peter Svensson - 1-9 Binding Free Energy Landscape of Domain-Peptide Interactions
by Iskra Staneva & Stefan Wallin - 1-9 Evolutionary Accessibility of Mutational Pathways
by Jasper Franke & Alexander Klözer & J Arjan G M de Visser & Joachim Krug - 1-11 Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series
by David A Rasmussen & Oliver Ratmann & Katia Koelle - 1-13 Effective Stimuli for Constructing Reliable Neuron Models
by Shaul Druckmann & Thomas K Berger & Felix Schürmann & Sean Hill & Henry Markram & Idan Segev - 1-14 Statistical Inference for Multi-Pathogen Systems
by Sourya Shrestha & Aaron A King & Pejman Rohani - 1-14 Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9
by Vlad Cojocaru & Kia Balali-Mood & Mark S P Sansom & Rebecca C Wade - 1-15 A Neurocomputational Model of Stimulus-Specific Adaptation to Oddball and Markov Sequences
by Robert Mill & Martin Coath & Thomas Wennekers & Susan L Denham - 1-15 Alterations in Brain Connectivity Underlying Beta Oscillations in Parkinsonism
by Rosalyn J Moran & Nicolas Mallet & Vladimir Litvak & Raymond J Dolan & Peter J Magill & Karl J Friston & Peter Brown - 1-16 Understanding Auditory Spectro-Temporal Receptive Fields and Their Changes with Input Statistics by Efficient Coding Principles
by Lingyun Zhao & Li Zhaoping
July 2011, Volume 7, Issue 7
- 1-9 Modelling the Effects of Population Structure on Childhood Disease: The Case of Varicella
by Romain Silhol & Pierre-Yves Boëlle - 1-9 Optimal Stimulus Shapes for Neuronal Excitation
by Daniel B Forger & David Paydarfar & John R Clay - 1-10 Bayesian Inference for Genomic Data Integration Reduces Misclassification Rate in Predicting Protein-Protein Interactions
by Chuanhua Xing & David B Dunson - 1-10 Indirect Reciprocity under Incomplete Observation
by Mitsuhiro Nakamura & Naoki Masuda - 1-12 Prediction of Cell Penetrating Peptides by Support Vector Machines
by William S Sanders & C Ian Johnston & Susan M Bridges & Shane C Burgess & Kenneth O Willeford - 1-12 Cadherin-Dependent Cell Morphology in an Epithelium: Constructing a Quantitative Dynamical Model
by Ian M Gemp & Richard W Carthew & Sascha Hilgenfeldt - 1-13 A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells
by Tian Hong & Jianhua Xing & Liwu Li & John J Tyson - 1-14 Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases
by Michael D Daily & George N Phillips Jr. & Qiang Cui - 1-15 Stimulus-Dependent State Transition between Synchronized Oscillation and Randomly Repetitive Burst in a Model Cerebellar Granular Layer
by Takeru Honda & Tadashi Yamazaki & Shigeru Tanaka & Soichi Nagao & Tetsuro Nishino - 1-15 MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets
by Kristen M Naegle & Roy E Welsch & Michael B Yaffe & Forest M White & Douglas A Lauffenburger - 1-16 The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics
by Qian Wang & Kao-Chen Liang & Arkadiusz Czader & M Neal Waxham & Margaret S Cheung - 1-16 A Dynamical Model Reveals Gene Co-Localizations in Nucleus
by Jing Kang & Bing Xu & Ye Yao & Wei Lin & Conor Hennessy & Peter Fraser & Jianfeng Feng - 1-16 Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site
by Julia Romanowska & J Andrew McCammon & Joanna Trylska - 1-16 Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models
by Iulian Pruteanu-Malinici & Daniel L Mace & Uwe Ohler - 1-17 In vivo Conditions Induce Faithful Encoding of Stimuli by Reducing Nonlinear Synchronization in Vestibular Sensory Neurons
by Adam D Schneider & Kathleen E Cullen & Maurice J Chacron - 1-18 Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties
by Etay Hay & Sean Hill & Felix Schürmann & Henry Markram & Idan Segev
June 2011, Volume 7, Issue 6
- 1-2 Eurekometrics: Analyzing the Nature of Discovery
by Samuel Arbesman & Nicholas A Christakis - 1-2 Ten Simple Rules for Building and Maintaining a Scientific Reputation
by Philip E Bourne & Virginia Barbour - 1-4 International Society for Computational Biology Honors Michael Ashburner and Olga Troyanskaya with Top Bioinformatics/Computational Biology Awards for 2011
by Justin Mullins & BJ Morrison McKay - 1-8 Extracting Message Inter-Departure Time Distributions from the Human Electroencephalogram
by Bratislav Mišić & Vasily A Vakorin & Nataša Kovačević & Tomáš Paus & Anthony R McIntosh - 1-9 The Origin of Behavioral Bursts in Decision-Making Circuitry
by Amanda Sorribes & Beatriz G Armendariz & Diego Lopez-Pigozzi & Cristina Murga & Gonzalo G de Polavieja - 1-11 Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line
by Velia Siciliano & Filippo Menolascina & Lucia Marucci & Chiara Fracassi & Immacolata Garzilli & Maria Nicoletta Moretti & Diego di Bernardo - 1-13 Changes of Mind in an Attractor Network of Decision-Making
by Larissa Albantakis & Gustavo Deco - 1-13 Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics
by Erik M Volz & Joel C Miller & Alison Galvani & Lauren Ancel Meyers - 1-13 How Haptic Size Sensations Improve Distance Perception
by Peter W Battaglia & Daniel Kersten & Paul R Schrater - 1-14 Neurobiologically Realistic Determinants of Self-Organized Criticality in Networks of Spiking Neurons
by Mikail Rubinov & Olaf Sporns & Jean-Philippe Thivierge & Michael Breakspear - 1-14 The Binding of Learning to Action in Motor Adaptation
by Luis Nicolas Gonzalez Castro & Craig Bryant Monsen & Maurice A Smith - 1-15 Heterogeneous Host Susceptibility Enhances Prevalence of Mixed-Genotype Micro-Parasite Infections
by Wopke van der Werf & Lia Hemerik & Just M Vlak & Mark P Zwart - 1-16 Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex
by Ruhollah Moussavi-Baygi & Yousef Jamali & Reza Karimi & Mohammad R K Mofrad - 1-19 Generative Embedding for Model-Based Classification of fMRI Data
by Kay H Brodersen & Thomas M Schofield & Alexander P Leff & Cheng Soon Ong & Ekaterina I Lomakina & Joachim M Buhmann & Klaas E Stephan - 1-22 Generation of Diverse Biological Forms through Combinatorial Interactions between Tissue Polarity and Growth
by Richard Kennaway & Enrico Coen & Amelia Green & Andrew Bangham
May 2011, Volume 7, Issue 5
- 1-3 Ten Simple Rules for Providing a Scientific Web Resource
by Sebastian J Schultheiss - 1-6 Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases
by Frank Emmert-Streib & Galina V Glazko - 1-11 Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo
by Pawel Krupinski & Vijay Chickarmane & Carsten Peterson - 1-11 A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein
by Daniel-Adriano Silva & Gregory R Bowman & Alejandro Sosa-Peinado & Xuhui Huang - 1-14 How Structure Determines Correlations in Neuronal Networks
by Volker Pernice & Benjamin Staude & Stefano Cardanobile & Stefan Rotter - 1-14 Cellularly-Driven Differences in Network Synchronization Propensity Are Differentially Modulated by Firing Frequency
by Christian G Fink & Victoria Booth & Michal Zochowski - 1-14 Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability
by Alistair N Boettiger & Peter L Ralph & Steven N Evans - 1-15 Feedback Control Architecture and the Bacterial Chemotaxis Network
by Abdullah Hamadeh & Mark A J Roberts & Elias August & Patrick E McSharry & Philip K Maini & Judith P Armitage & Antonis Papachristodoulou - 1-18 A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35
by Jessica Nasica-Labouze & Massimiliano Meli & Philippe Derreumaux & Giorgio Colombo & Normand Mousseau - 1-19 Temporal Encoding in a Nervous System
by Zane N Aldworth & Alexander G Dimitrov & Graham I Cummins & Tomáš Gedeon & John P Miller - 1-19 Attracting Dynamics of Frontal Cortex Ensembles during Memory-Guided Decision-Making
by Emili Balaguer-Ballester & Christopher C Lapish & Jeremy K Seamans & Daniel Durstewitz - 1-21 Spatial Learning and Action Planning in a Prefrontal Cortical Network Model
by Louis-Emmanuel Martinet & Denis Sheynikhovich & Karim Benchenane & Angelo Arleo - 1-21 Speed/Accuracy Trade-Off between the Habitual and the Goal-Directed Processes
by Mehdi Keramati & Amir Dezfouli & Payam Piray - 1-29 Simulation of the Undiseased Human Cardiac Ventricular Action Potential: Model Formulation and Experimental Validation
by Thomas O'Hara & László Virág & András Varró & Yoram Rudy
April 2011, Volume 7, Issue 4
- 1-4 Minimum Information About a Simulation Experiment (MIASE)
by Dagmar Waltemath & Richard Adams & Daniel A Beard & Frank T Bergmann & Upinder S Bhalla & Randall Britten & Vijayalakshmi Chelliah & Michael T Cooling & Jonathan Cooper & Edmund J Crampin & Alan Garny & Stefan Hoops & Michael Hucka & Peter Hunter & Edda Klipp & Camille Laibe & Andrew K Miller & Ion Moraru & David Nickerson & Poul Nielsen & Macha Nikolski & Sven Sahle & Herbert M Sauro & Henning Schmidt & Jacky L Snoep & Dominic Tolle & Olaf Wolkenhauer & Nicolas Le Novère - 1-8 A Third Measure-Metastable State in the Dynamics of Spontaneous Shape Change in Healthy Human's White Cells
by Karen A Selz - 1-9 Linking Microscopic Spatial Patterns of Tissue Destruction in Emphysema to Macroscopic Decline in Stiffness Using a 3D Computational Model
by Harikrishnan Parameswaran & Arnab Majumdar & Béla Suki - 1-9 In Silico Elucidation of the Recognition Dynamics of Ubiquitin
by Dong Long & Rafael Brüschweiler - 1-11 A Mathematical Framework for Estimating Pathogen Transmission Fitness and Inoculum Size Using Data from a Competitive Mixtures Animal Model
by James M McCaw & Nimalan Arinaminpathy & Aeron C Hurt & Jodie McVernon & Angela R McLean - 1-12 Cell-Sorting at the A/P Boundary in the Drosophila Wing Primordium: A Computational Model to Consolidate Observed Non-Local Effects of Hh Signaling
by Sabine Schilling & Maria Willecke & Tinri Aegerter-Wilmsen & Olaf A Cirpka & Konrad Basler & Christian von Mering - 1-15 A Stochastic Model of Latently Infected Cell Reactivation and Viral Blip Generation in Treated HIV Patients
by Jessica M Conway & Daniel Coombs
March 2011, Volume 7, Issue 3
- 1-5 The Roots of Bioinformatics in Theoretical Biology
by Paulien Hogeweg - 1-9 Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts
by Luis E C Rocha & Fredrik Liljeros & Petter Holme - 1-9 Animal Interactions and the Emergence of Territoriality
by Luca Giuggioli & Jonathan R Potts & Stephen Harris - 1-11 Learning from Sensory and Reward Prediction Errors during Motor Adaptation
by Jun Izawa & Reza Shadmehr - 1-12 Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells
by Rachel Cavill & Atanas Kamburov & James K Ellis & Toby J Athersuch & Marcus S C Blagrove & Ralf Herwig & Timothy M D Ebbels & Hector C Keun - 1-12 Dynamic Phenotypic Clustering in Noisy Ecosystems
by Morten Ernebjerg & Roy Kishony - 1-13 Flexible Cognitive Strategies during Motor Learning
by Jordan A Taylor & Richard B Ivry - 1-13 Inferring Visuomotor Priors for Sensorimotor Learning
by Edward J A Turnham & Daniel A Braun & Daniel M Wolpert - 1-13 Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding
by Dana Bar-On & Esther Nachliel & Menachem Gutman & Uri Ashery - 1-13 A Granger Causality Measure for Point Process Models of Ensemble Neural Spiking Activity
by Sanggyun Kim & David Putrino & Soumya Ghosh & Emery N Brown - 1-13 Identifying Causal Genes and Dysregulated Pathways in Complex Diseases
by Yoo-Ah Kim & Stefan Wuchty & Teresa M Przytycka - 1-14 Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations
by Lars Skjaerven & Barry Grant & Arturo Muga & Knut Teigen & J Andrew McCammon & Nathalie Reuter & Aurora Martinez - 1-16 Blockade of Neuronal α7-nAChR by α-Conotoxin ImI Explained by Computational Scanning and Energy Calculations
by Rilei Yu & David J Craik & Quentin Kaas