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September 2010, Volume 6, Issue 9
- 1-11 Regression Analysis for Constraining Free Parameters in Electrophysiological Models of Cardiac Cells
by Amrita X Sarkar & Eric A Sobie - 1-11 Evolution and Optimality of Similar Neural Mechanisms for Perception and Action during Search
by Sheng Zhang & Miguel P Eckstein - 1-11 Occurrence and Treatment of Bone Atrophic Non-Unions Investigated by an Integrative Approach
by Liesbet Geris & Anita A C Reed & Jos Vander Sloten & A Hamish R W Simpson & Hans Van Oosterwyck - 1-12 High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions
by Phaedra Agius & Aaron Arvey & William Chang & William Stafford Noble & Christina Leslie - 1-14 A Dynamic Neural Field Model of Mesoscopic Cortical Activity Captured with Voltage-Sensitive Dye Imaging
by Valentin Markounikau & Christian Igel & Amiram Grinvald & Dirk Jancke - 1-14 Finding the “Dark Matter” in Human and Yeast Protein Network Prediction and Modelling
by Juan A G Ranea & Ian Morilla & Jon G Lees & Adam J Reid & Corin Yeats & Andrew B Clegg & Francisca Sanchez-Jimenez & Christine Orengo
August 2010, Volume 6, Issue 8
- 1-7 Probability Matching as a Computational Strategy Used in Perception
by David R Wozny & Ulrik R Beierholm & Ladan Shams - 1-10 A Mechanistic View of the Role of E3 in Sumoylation
by Melda Tozluoğlu & Ezgi Karaca & Ruth Nussinov & Türkan Haliloğlu - 1-10 Correlation of Influenza Virus Excess Mortality with Antigenic Variation: Application to Rapid Estimation of Influenza Mortality Burden
by Aiping Wu & Yousong Peng & Xiangjun Du & Yuelong Shu & Taijiao Jiang - 1-10 Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data
by Kakajan Komurov & Michael A White & Prahlad T Ram - 1-11 Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites
by Wolfram Möbius & Ulrich Gerland - 1-11 A Model for a Correlated Random Walk Based on the Ordered Extension of Pseudopodia
by Peter J M Van Haastert - 1-13 Reinforcement Learning on Slow Features of High-Dimensional Input Streams
by Robert Legenstein & Niko Wilbert & Laurenz Wiskott - 1-21 Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors
by Thomas C Whisenant & David T Ho & Ryan W Benz & Jeffrey S Rogers & Robyn M Kaake & Elizabeth A Gordon & Lan Huang & Pierre Baldi & Lee Bardwell
July 2010, Volume 6, Issue 7
- 1-10 RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins
by Hilal Kazan & Debashish Ray & Esther T Chan & Timothy R Hughes & Quaid Morris - 1-12 Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human
by James R Wagner & Bing Ge & Dmitry Pokholok & Kevin L Gunderson & Tomi Pastinen & Mathieu Blanchette - 1-12 The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein
by Michael C Prentiss & David J Wales & Peter G Wolynes - 1-13 Avalanches in a Stochastic Model of Spiking Neurons
by Marc Benayoun & Jack D Cowan & Wim van Drongelen & Edward Wallace - 1-14 Organization of Cellular Receptors into a Nanoscale Junction during HIV-1 Adhesion
by Terrence M Dobrowsky & Brian R Daniels & Robert F Siliciano & Sean X Sun & Denis Wirtz - 1-15 Risk-Sensitive Optimal Feedback Control Accounts for Sensorimotor Behavior under Uncertainty
by Arne J Nagengast & Daniel A Braun & Daniel M Wolpert - 1-15 Do Humans Optimally Exploit Redundancy to Control Step Variability in Walking?
by Jonathan B Dingwell & Joby John & Joseph P Cusumano - 1-16 A Threshold Equation for Action Potential Initiation
by Jonathan Platkiewicz & Romain Brette - 1-17 The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment
by Stephen F Altschul & John C Wootton & Elena Zaslavsky & Yi-Kuo Yu - 1-19 More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology
by Wing-Cheong Wong & Sebastian Maurer-Stroh & Frank Eisenhaber - 1-19 A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature
by Domonkos Tikk & Philippe Thomas & Peter Palaga & Jörg Hakenberg & Ulf Leser - 1-19 Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis
by Yonghua Wang & Yan Li & Zhi Ma & Wei Yang & Chunzhi Ai
June 2010, Volume 6, Issue 6
- 1-9 Optimal Drug Synergy in Antimicrobial Treatments
by Joseph Peter Torella & Remy Chait & Roy Kishony - 1-11 Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families
by Kyle Ellrott & Lukasz Jaroszewski & Weizhong Li & John C Wooley & Adam Godzik - 1-11 The 20S Proteasome Splicing Activity Discovered by SpliceMet
by Juliane Liepe & Michele Mishto & Kathrin Textoris-Taube & Katharina Janek & Christin Keller & Petra Henklein & Peter Michael Kloetzel & Alexey Zaikin - 1-12 Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues
by Rebecca Strawn & Milan Melichercik & Michael Green & Thomas Stockner & Jannette Carey & Rüdiger Ettrich - 1-12 Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology
by Timothy R Lezon & Ivet Bahar - 1-13 Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows
by Yishai Shimoni & Marc Y Fink & Soon-gang Choi & Stuart C Sealfon - 1-13 Fast- or Slow-inactivated State Preference of Na+ Channel Inhibitors: A Simulation and Experimental Study
by Robert Karoly & Nora Lenkey & Andras O Juhasz & E Sylvester Vizi & Arpad Mike - 1-13 Combinatorial Gene Regulation Using Auto-Regulation
by Rutger Hermsen & Bas Ursem & Pieter Rein ten Wolde - 1-15 Slope-Based Stochastic Resonance: How Noise Enables Phasic Neurons to Encode Slow Signals
by Yan Gai & Brent Doiron & John Rinzel - 1-22 Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures
by Nicholas J P Wiebe & Irmtraud M Meyer
May 2010, Volume 6, Issue 5
- 1-7 Making Informed Choices about Microarray Data Analysis
by Mark Reimers - 1-9 Game Theory of Social Distancing in Response to an Epidemic
by Timothy C Reluga - 1-9 Analysis and Computational Dissection of Molecular Signature Multiplicity
by Alexander Statnikov & Constantin F Aliferis - 1-11 Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation
by Jochen S Hub & Marcus B Kubitzki & Bert L de Groot - 1-11 A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies
by Oliver Stegle & Leopold Parts & Richard Durbin & John Winn - 1-11 Chemotactic Response and Adaptation Dynamics in Escherichia coli
by Diana Clausznitzer & Olga Oleksiuk & Linda Løvdok & Victor Sourjik & Robert G Endres - 1-12 Assimilating Seizure Dynamics
by Ghanim Ullah & Steven J Schiff - 1-13 Mathematical Modelling of DNA Replication Reveals a Trade-off between Coherence of Origin Activation and Robustness against Rereplication
by Anneke Brümmer & Carlos Salazar & Vittoria Zinzalla & Lilia Alberghina & Thomas Höfer - 1-16 Inductive Game Theory and the Dynamics of Animal Conflict
by Simon DeDeo & David C Krakauer & Jessica C Flack - 1-20 Influence of Low-Level Stimulus Features, Task Dependent Factors, and Spatial Biases on Overt Visual Attention
by Sepp Kollmorgen & Nora Nortmann & Sylvia Schröder & Peter König
April 2010, Volume 6, Issue 4
- 1-9 Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions
by Dirk Helbing & Attila Szolnoki & Matjaž Perc & György Szabó - 1-10 A Reaction-Diffusion Model of Human Brain Development
by Julien Lefèvre & Jean-François Mangin - 1-10 Independent Component Analysis in Spiking Neurons
by Cristina Savin & Prashant Joshi & Jochen Triesch - 1-10 Flow-Based Cytometric Analysis of Cell Cycle via Simulated Cell Populations
by M Rowan Brown & Huw D Summers & Paul Rees & Paul J Smith & Sally C Chappell & Rachel J Errington - 1-11 Dynamics and Control of Diseases in Networks with Community Structure
by Marcel Salathé & James H Jones - 1-11 Predicting Odor Pleasantness with an Electronic Nose
by Rafi Haddad & Abebe Medhanie & Yehudah Roth & David Harel & Noam Sobel - 1-12 Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data
by Eric Samorodnitsky & B Franklin Pugh - 1-12 Quantifying Aggregated Uncertainty in Plasmodium falciparum Malaria Prevalence and Populations at Risk via Efficient Space-Time Geostatistical Joint Simulation
by Peter W Gething & Anand P Patil & Simon I Hay - 1-13 Learning “graph-mer” Motifs that Predict Gene Expression Trajectories in Development
by Xuejing Li & Casandra Panea & Chris H Wiggins & Valerie Reinke & Christina Leslie - 1-13 New Insights into the Genetic Control of Gene Expression using a Bayesian Multi-tissue Approach
by Enrico Petretto & Leonardo Bottolo & Sarah R Langley & Matthias Heinig & Chris McDermott-Roe & Rizwan Sarwar & Michal Pravenec & Norbert Hübner & Timothy J Aitman & Stuart A Cook & Sylvia Richardson - 1-13 Signatures of Arithmetic Simplicity in Metabolic Network Architecture
by William J Riehl & Paul L Krapivsky & Sidney Redner & Daniel Segrè - 1-13 Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets
by Manikandan Narayanan & Adrian Vetta & Eric E Schadt & Jun Zhu - 1-15 The Origins of Time-Delay in Template Biopolymerization Processes
by Luis Mier-y-Terán-Romero & Mary Silber & Vassily Hatzimanikatis - 1-16 Simulating Microdosimetry in a Virtual Hepatic Lobule
by John Wambaugh & Imran Shah - 1-16 Coordinate Dependence of Variability Analysis
by Dagmar Sternad & Se-Woong Park & Hermann Müller & Neville Hogan - 1-21 Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model
by Daniel Ting & Guoli Wang & Maxim Shapovalov & Rajib Mitra & Michael I Jordan & Roland L Dunbrack Jr
March 2010, Volume 6, Issue 3
- 1-9 The Impact of Contact Tracing in Clustered Populations
by Thomas House & Matt J Keeling - 1-10 Detailed Simulations of Cell Biology with Smoldyn 2.1
by Steven S Andrews & Nathan J Addy & Roger Brent & Adam P Arkin - 1-11 Estimating the Stoichiometry of HIV Neutralization
by Carsten Magnus & Roland R Regoes - 1-11 Estimating the Stochastic Bifurcation Structure of Cellular Networks
by Carl Song & Hilary Phenix & Vida Abedi & Matthew Scott & Brian P Ingalls & Mads Kærn & Theodore J Perkins - 1-13 Slower Visuomotor Corrections with Unchanged Latency are Consistent with Optimal Adaptation to Increased Endogenous Noise in the Elderly
by Michael Sherback & Francisco J Valero-Cuevas & Raffaello D'Andrea - 1-14 Comparing Families of Dynamic Causal Models
by Will D Penny & Klaas E Stephan & Jean Daunizeau & Maria J Rosa & Karl J Friston & Thomas M Schofield & Alex P Leff - 1-15 Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods
by Christelle Reynès & Hélène Host & Anne-Claude Camproux & Guillaume Laconde & Florence Leroux & Anne Mazars & Benoit Deprez & Robin Fahraeus & Bruno O Villoutreix & Olivier Sperandio - 1-15 Non-Linear Neuronal Responses as an Emergent Property of Afferent Networks: A Case Study of the Locust Lobula Giant Movement Detector
by Sergi Bermúdez i Badia & Ulysses Bernardet & Paul F M J Verschure - 1-15 Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance
by Bernie J Daigle Jr & Alicia Deng & Tracey McLaughlin & Samuel W Cushman & Margaret C Cam & Gerald Reaven & Philip S Tsao & Russ B Altman - 1-17 Parameter Estimation and Model Selection in Computational Biology
by Gabriele Lillacci & Mustafa Khammash - 1-17 Investigating Homology between Proteins using Energetic Profiles
by James O Wrabl & Vincent J Hilser - 1-25 Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation
by Julian M L Budd & Krisztina Kovács & Alex S Ferecskó & Péter Buzás & Ulf T Eysel & Zoltán F Kisvárday
February 2010, Volume 6, Issue 2
- 1-11 Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks
by Sashi Marella & Bard Ermentrout - 1-11 Explicit Kinetic Heterogeneity: Mathematical Models for Interpretation of Deuterium Labeling of Heterogeneous Cell Populations
by Vitaly V Ganusov & José A M Borghans & Rob J De Boer - 1-12 Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture
by Ju Han & Hang Chang & Orsi Giricz & Genee Y Lee & Frederick L Baehner & Joe W Gray & Mina J Bissell & Paraic A Kenny & Bahram Parvin - 1-13 Spatial Simulations of Myxobacterial Development
by Antony B Holmes & Sara Kalvala & David E Whitworth - 1-14 Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease
by Neema L Salimi & Bosco Ho & David A Agard
January 2010, Volume 6, Issue 1
- 1-8 Network-Free Inference of Knockout Effects in Yeast
by Tal Peleg & Nir Yosef & Eytan Ruppin & Roded Sharan - 1-9 Associating Genes and Protein Complexes with Disease via Network Propagation
by Oron Vanunu & Oded Magger & Eytan Ruppin & Tomer Shlomi & Roded Sharan - 1-9 Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains
by Isabella Daidone & Hannes Neuweiler & Sören Doose & Markus Sauer & Jeremy C Smith - 1-10 A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules
by Wei Zhang & Jun Zhu & Eric E Schadt & Jun S Liu - 1-11 A Neurophysiologically Plausible Population Code Model for Feature Integration Explains Visual Crowding
by Ronald van den Berg & Jos B T M Roerdink & Frans W Cornelissen - 1-12 Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration
by Anna Dvorkin & Henry Szechtman & Ilan Golani - 1-13 Protein Interaction Networks—More Than Mere Modules
by Stefan Pinkert & Jörg Schultz & Jörg Reichardt - 1-13 SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models
by Aroop Sircar & Jeffrey J Gray - 1-18 Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments
by Lukas Burger & Erik van Nimwegen - 1-25 Axonal Velocity Distributions in Neural Field Equations
by Ingo Bojak & David T J Liley
December 2009, Volume 5, Issue 12
- 1-7 Calculating Evolutionary Dynamics in Structured Populations
by Charles G Nathanson & Corina E Tarnita & Martin A Nowak - 1-7 Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation
by Jorge M Pacheco & Flávio L Pinheiro & Francisco C Santos - 1-8 Inferring Binding Energies from Selected Binding Sites
by Yue Zhao & David Granas & Gary D Stormo - 1-9 Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task
by Ian H Stevenson & Hugo L Fernandes & Iris Vilares & Kunlin Wei & Konrad P Körding - 1-10 Effective Reduced Diffusion-Models: A Data Driven Approach to the Analysis of Neuronal Dynamics
by Gustavo Deco & Daniel Martí & Anders Ledberg & Ramon Reig & Maria V Sanchez Vives - 1-11 Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
by João F Matias Rodrigues & Andreas Wagner - 1-11 Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data
by Alexander Mitsos & Ioannis N Melas & Paraskeuas Siminelakis & Aikaterini D Chairakaki & Julio Saez-Rodriguez & Leonidas G Alexopoulos - 1-11 Model of Transcriptional Activation by MarA in Escherichia coli
by Michael E Wall & David A Markowitz & Judah L Rosner & Robert G Martin - 1-13 Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
by Alexandra M Schnoes & Shoshana D Brown & Igor Dodevski & Patricia C Babbitt - 1-16 Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases
by Kai Wang & Manikandan Narayanan & Hua Zhong & Martin Tompa & Eric E Schadt & Jun Zhu - 1-16 Hyperbolic Planforms in Relation to Visual Edges and Textures Perception
by Pascal Chossat & Olivier Faugeras - 1-18 Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
by John A Capra & Roman A Laskowski & Janet M Thornton & Mona Singh & Thomas A Funkhouser - 1-19 Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation
by Brian J Schmidt & Jason A Papin & Michael B Lawrence
November 2009, Volume 5, Issue 11
- 1-8 Discovery of Regulatory Elements is Improved by a Discriminatory Approach
by Eivind Valen & Albin Sandelin & Ole Winther & Anders Krogh - 1-12 A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen
by Omer Dushek & Raibatak Das & Daniel Coombs - 1-12 Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model
by Samuel Bandara & Johannes P Schlöder & Roland Eils & Hans Georg Bock & Tobias Meyer - 1-13 Attention Increases the Temporal Precision of Conscious Perception: Verifying the Neural-ST2 Model
by Srivas Chennu & Patrick Craston & Brad Wyble & Howard Bowman - 1-13 Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation
by Arno Onken & Steffen Grünewälder & Matthias H J Munk & Klaus Obermayer - 1-13 A Novel Extended Granger Causal Model Approach Demonstrates Brain Hemispheric Differences during Face Recognition Learning
by Tian Ge & Keith M Kendrick & Jianfeng Feng - 1-16 A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton
by Raibatak Das & Christopher W Cairo & Daniel Coombs - 1-16 Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators
by Eric A Zilli & Motoharu Yoshida & Babak Tahvildari & Lisa M Giocomo & Michael E Hasselmo
October 2009, Volume 5, Issue 10
- 1-4 Getting Started in Gene Expression Microarray Analysis
by Donna K Slonim & Itai Yanai - 1-10 The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation
by Jin Liu & Ruth Nussinov - 1-10 ‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators
by Marc Hafner & Heinz Koeppl & Martin Hasler & Andreas Wagner - 1-11 Grasping Objects with Environmentally Induced Position Uncertainty
by Vassilios N Christopoulos & Paul R Schrater - 1-13 Perturbation-based Markovian Transmission Model for Probing Allosteric Dynamics of Large Macromolecular Assembling: A Study of GroEL-GroES
by Hsiao-Mei Lu & Jie Liang - 1-15 Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
by Mateusz Sikora & Joanna I Sułkowska & Marek Cieplak - 1-16 Gene Circuit Analysis of the Terminal Gap Gene huckebein
by Maksat Ashyraliyev & Ken Siggens & Hilde Janssens & Joke Blom & Michael Akam & Johannes Jaeger - 1-26 Towards a Mathematical Theory of Cortical Micro-circuits
by Dileep George & Jeff Hawkins
September 2009, Volume 5, Issue 9
- 1-6 Chemically Based Mathematical Model for Development of Cerebral Cortical Folding Patterns
by Deborah A Striegel & Monica K Hurdal - 1-6 Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?
by Stefano Allesina & Mercedes Pascual - 1-9 A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels
by Steven H Wu & Michael A Black & Robyn A North & Kelly R Atkinson & Allen G Rodrigo - 1-12 Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities
by Rui-Ru Ji & Heshani de Silva & Yisheng Jin & Robert E Bruccoleri & Jian Cao & Aiqing He & Wenjun Huang & Paul S Kayne & Isaac M Neuhaus & Karl-Heinz Ott & Becky Penhallow & Mark I Cockett & Michael G Neubauer & Nathan O Siemers & Petra Ross-Macdonald - 1-12 Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning
by Samuel A Danziger & Roberta Baronio & Lydia Ho & Linda Hall & Kirsty Salmon & G Wesley Hatfield & Peter Kaiser & Richard H Lathrop - 1-15 Interrogating and Predicting Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein
by Jennifer L Lahti & Adam P Silverman & Jennifer R Cochran - 1-15 Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification
by Stephen A Stanhope & Srikumar Sengupta & Johan den Boon & Paul Ahlquist & Michael A Newton - 1-16 Parallel Computational Subunits in Dentate Granule Cells Generate Multiple Place Fields
by Balázs Ujfalussy & Tamás Kiss & Péter Érdi - 1-16 A Structured Model of Video Reproduces Primary Visual Cortical Organisation
by Pietro Berkes & Richard E Turner & Maneesh Sahani
August 2009, Volume 5, Issue 8
- 1-8 Nash Equilibria in Multi-Agent Motor Interactions
by Daniel A Braun & Pedro A Ortega & Daniel M Wolpert - 1-9 Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data
by Joost Van Durme & Sebastian Maurer-Stroh & Rodrigo Gallardo & Hannah Wilkinson & Frederic Rousseau & Joost Schymkowitz - 1-10 A Generalized Framework for Quantifying the Dynamics of EEG Event-Related Desynchronization
by Steven Lemm & Klaus-Robert Müller & Gabriel Curio - 1-10 Computation of Conformational Coupling in Allosteric Proteins
by Brian A Kidd & David Baker & Wendy E Thomas - 1-10 Geometric De-noising of Protein-Protein Interaction Networks
by Oleksii Kuchaiev & Marija Rašajski & Desmond J Higham & Nataša Pržulj - 1-11 A Self-Organizing Algorithm for Modeling Protein Loops
by Pu Liu & Fangqiang Zhu & Dmitrii N Rassokhin & Dimitris K Agrafiotis - 1-12 FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies
by Oliver C Redfern & Benoît H Dessailly & Timothy J Dallman & Ian Sillitoe & Christine A Orengo - 1-12 Investigating CTL Mediated Killing with a 3D Cellular Automaton
by Frederik Graw & Roland R Regoes - 1-13 Detection of Functional Modes in Protein Dynamics
by Jochen S Hub & Bert L de Groot - 1-17 Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens
by Leighton Pritchard & Hui Liu & Clare Booth & Emma Douglas & Patrice François & Jacques Schrenzel & Peter E Hedley & Paul R J Birch & Ian K Toth - 1-20 Evolutionary Triplet Models of Structured RNA
by Robert K Bradley & Ian Holmes - 1-24 Qualia: The Geometry of Integrated Information
by David Balduzzi & Giulio Tononi
July 2009, Volume 5, Issue 7
- 1-9 Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels
by Guido Gigante & Maurizio Mattia & Jochen Braun & Paolo Del Giudice - 1-10 Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation
by Daniel Geberth & Marc-Thorsten Hütt - 1-10 Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors
by Andrew J Olaharski & Nina Gonzaludo & Hans Bitter & David Goldstein & Stephan Kirchner & Hirdesh Uppal & Kyle Kolaja - 1-10 Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs
by Flávio Codeço Coelho & Claudia T Codeço - 1-12 Semantic Similarity in Biomedical Ontologies
by Catia Pesquita & Daniel Faria & André O Falcão & Phillip Lord & Francisco M Couto
June 2009, Volume 5, Issue 6
- 1-4 Ten Simple Rules for Choosing between Industry and Academia
by David B Searls - 1-9 Exploring the Free Energy Landscape: From Dynamics to Networks and Back
by Diego Prada-Gracia & Jesús Gómez-Gardeñes & Pablo Echenique & Fernando Falo - 1-11 A Probabilistic Model of RNA Conformational Space
by Jes Frellsen & Ida Moltke & Martin Thiim & Kanti V Mardia & Jesper Ferkinghoff-Borg & Thomas Hamelryck - 1-11 Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening
by Nobuyoshi Nagamine & Takayuki Shirakawa & Yusuke Minato & Kentaro Torii & Hiroki Kobayashi & Masaya Imoto & Yasubumi Sakakibara - 1-12 The Effect of Ongoing Exposure Dynamics in Dose Response Relationships
by Josep M Pujol & Joseph E Eisenberg & Charles N Haas & James S Koopman - 1-14 Taking the Lag out of Jet Lag through Model-Based Schedule Design
by Dennis A Dean , II & Daniel B Forger & Elizabeth B Klerman - 1-14 Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences
by Zhang Zhang & Jeffrey P Townsend
May 2009, Volume 5, Issue 5
- 1-11 SHRiMP: Accurate Mapping of Short Color-space Reads
by Stephen M Rumble & Phil Lacroute & Adrian V Dalca & Marc Fiume & Arend Sidow & Michael Brudno - 1-13 How to Get the Most out of Your Curation Effort
by Andrey Rzhetsky & Hagit Shatkay & W John Wilbur - 1-14 Functional Brain Networks Develop from a “Local to Distributed” Organization
by Damien A Fair & Alexander L Cohen & Jonathan D Power & Nico U F Dosenbach & Jessica A Church & Francis M Miezin & Bradley L Schlaggar & Steven E Petersen - 1-15 Fast Statistical Alignment
by Robert K Bradley & Adam Roberts & Michael Smoot & Sudeep Juvekar & Jaeyoung Do & Colin Dewey & Ian Holmes & Lior Pachter - 1-16 Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings
by Quentin J M Huys & Liam Paninski - 1-16 A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family
by Gregory D Friedland & Nils-Alexander Lakomek & Christian Griesinger & Jens Meiler & Tanja Kortemme - 1-18 Prediction of Protein Binding Regions in Disordered Proteins
by Bálint Mészáros & István Simon & Zsuzsanna Dosztányi - 1-18 Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't
by Yasser Roudi & Sheila Nirenberg & Peter E Latham
April 2009, Volume 5, Issue 4
- 1-2 Ten Simple Rules To Combine Teaching and Research
by Quentin Vicens & Philip E Bourne - 1-4 Webb Miller and Trey Ideker To Receive Top International Bioinformatics Awards for 2009 from the International Society for Computational Biology
by B J Morrison McKay & Clare Sansom - 1-6 Polymorphism Data Can Reveal the Origin of Species Abundance Statistics
by Yosef E Maruvka & Nadav M Shnerb - 1-11 Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
by James Robert White & Niranjan Nagarajan & Mihai Pop - 1-12 Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons
by Cheng Ly & Brent Doiron - 1-14 Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis
by Gitanjali Yadav & Rajesh S Gokhale & Debasisa Mohanty - 1-16 Natural Image Coding in V1: How Much Use Is Orientation Selectivity?
by Jan Eichhorn & Fabian Sinz & Matthias Bethge - 1-21 Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
by Zheng Yang & Peter Májek & Ivet Bahar
March 2009, Volume 5, Issue 3
- 1-7 T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules
by Aidan MacNamara & Ulrich Kadolsky & Charles R M Bangham & Becca Asquith - 1-9 Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior
by Jeremy E Purvis & Ravi Radhakrishnan & Scott L Diamond - 1-10 Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter
by Boian S Alexandrov & Vladimir Gelev & Sang Wook Yoo & Alan R Bishop & Kim Ø Rasmussen & Anny Usheva - 1-10 Accurate Prediction of Peptide Binding Sites on Protein Surfaces
by Evangelia Petsalaki & Alexander Stark & Eduardo García-Urdiales & Robert B Russell - 1-10 Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
by Barry J Grant & Alemayehu A Gorfe & J Andrew McCammon - 1-11 BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis
by Allen W Bryan Jr. & Matthew Menke & Lenore J Cowen & Susan L Lindquist & Bonnie Berger - 1-12 A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis
by Gabriel Krouk & Daniel Tranchina & Laurence Lejay & Alexis A Cruikshank & Dennis Shasha & Gloria M Coruzzi & Rodrigo A Gutiérrez - 1-12 Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis
by Matthew A Hibbs & Chad L Myers & Curtis Huttenhower & David C Hess & Kai Li & Amy A Caudy & Olga G Troyanskaya - 1-13 Broadband Criticality of Human Brain Network Synchronization
by Manfred G Kitzbichler & Marie L Smith & Søren R Christensen & Ed Bullmore - 1-13 “I Look in Your Eyes, Honey”: Internal Face Features Induce Spatial Frequency Preference for Human Face Processing
by Matthias S Keil - 1-13 Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments
by Oscar Westesson & Ian Holmes - 1-15 Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation
by Emili Balaguer-Ballester & Nicholas R Clark & Martin Coath & Katrin Krumbholz & Susan L Denham - 1-15 Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy
by Arash Bahrami & Amir H Assadi & John L Markley & Hamid R Eghbalnia - 1-20 Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures
by Alberto Pascual-García & David Abia & Ángel R Ortiz & Ugo Bastolla - 1-24 Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System
by Patrick Blomquist & Anna Devor & Ulf G Indahl & Istvan Ulbert & Gaute T Einevoll & Anders M Dale
February 2009, Volume 5, Issue 2
- 1-10 Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing
by John M Higgins & David T Eddington & Sangeeta N Bhatia & L Mahadevan - 1-13 The Temporal Winner-Take-All Readout
by Maoz Shamir - 1-14 Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins
by Michael D Daily & Jeffrey J Gray
April 2009, Volume 5, Issue 1
- 1-9 Estimating the Location and Spatial Extent of a Covert Anthrax Release
by Judith Legrand & Joseph R Egan & Ian M Hall & Simon Cauchemez & Steve Leach & Neil M Ferguson
January 2009, Volume 5, Issue 1
- 1-7 Action Potential Initiation in the Hodgkin-Huxley Model
by Lucy J Colwell & Michael P Brenner - 1-12 Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks
by Adel Dayarian & Madalena Chaves & Eduardo D Sontag & Anirvan M Sengupta - 1-12 Evolutionary Sequence Modeling for Discovery of Peptide Hormones
by Kemal Sonmez & Naunihal T Zaveri & Ilan A Kerman & Sharon Burke & Charles R Neal & Xinmin Xie & Stanley J Watson & Lawrence Toll - 1-15 Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties
by Wenxu Tong & Ying Wei & Leonel F Murga & Mary Jo Ondrechen & Ronald J Williams - 1-20 Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches
by Sinisa Pajevic & Dietmar Plenz
December 2008, Volume 4, Issue 12
- 1-3 I Am Not a Scientist, I Am a Number
by Philip E Bourne & J Lynn Fink - 1-7 Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation
by Antonio Scialdone & Mario Nicodemi - 1-7 The Morphological Identity of Insect Dendrites
by Hermann Cuntz & Friedrich Forstner & Juergen Haag & Alexander Borst - 1-7 Disordered Flanks Prevent Peptide Aggregation
by Sanne Abeln & Daan Frenkel - 1-12 Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment
by Da-Wei Li & Sandipan Mohanty & Anders Irbäck & Shuanghong Huo - 1-14 Game Theory of Mind
by Wako Yoshida & Ray J Dolan & Karl J Friston - 1-14 Search Algorithms as a Framework for the Optimization of Drug Combinations
by Diego Calzolari & Stefania Bruschi & Laurence Coquin & Jennifer Schofield & Jacob D Feala & John C Reed & Andrew D McCulloch & Giovanni Paternostro