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March 2011, Volume 7, Issue 3
- 1-17 Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation
by Daniele Linaro & Marco Storace & Michele Giugliano - 1-19 Causal Modeling Using Network Ensemble Simulations of Genetic and Gene Expression Data Predicts Genes Involved in Rheumatoid Arthritis
by Heming Xing & Paul D McDonagh & Jadwiga Bienkowska & Tanya Cashorali & Karl Runge & Robert E Miller & Dave DeCaprio & Bruce Church & Ronenn Roubenoff & Iya G Khalil & John Carulli - 1-19 A Compact Statistical Model of the Song Syntax in Bengalese Finch
by Dezhe Z Jin & Alexay A Kozhevnikov - 1-20 Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli
by Melody K Morris & Julio Saez-Rodriguez & David C Clarke & Peter K Sorger & Douglas A Lauffenburger - 1-21 Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
by Elijah Roberts & Andrew Magis & Julio O Ortiz & Wolfgang Baumeister & Zaida Luthey-Schulten
February 2011, Volume 7, Issue 2
- 1-3 ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature
by Richard H Lathrop & Burkhard Rost & ISCB Membership & ISCB Executive Committee & ISCB Board of Directors & ISCB Public Affairs Committee - 1-7 Application of Biomarkers in Cancer Risk Management: Evaluation from Stochastic Clonal Evolutionary and Dynamic System Optimization Points of View
by Xiaohong Li & Patricia L Blount & Thomas L Vaughan & Brian J Reid - 1-10 A Mathematical Framework for Protein Structure Comparison
by Wei Liu & Anuj Srivastava & Jinfeng Zhang - 1-10 A Hybrid Model of Mammalian Cell Cycle Regulation
by Rajat Singhania & R Michael Sramkoski & James W Jacobberger & John J Tyson - 1-10 Transition from Persistent to Anti-Persistent Correlations in Postural Sway Indicates Velocity-Based Control
by Didier Delignières & Kjerstin Torre & Pierre-Louis Bernard - 1-11 Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations
by Chikako Ragan & Michael Zuker & Mark A Ragan - 1-11 Mitigation Strategies for Pandemic Influenza A: Balancing Conflicting Policy Objectives
by T Déirdre Hollingsworth & Don Klinkenberg & Hans Heesterbeek & Roy M Anderson - 1-12 Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics
by Amber M Smith & Frederick R Adler & Julie L McAuley & Ryan N Gutenkunst & Ruy M Ribeiro & Jonathan A McCullers & Alan S Perelson - 1-13 Molecular Dynamics Simulations of Forced Unbending of Integrin αVβ3
by Wei Chen & Jizhong Lou & Jen Hsin & Klaus Schulten & Stephen C Harvey & Cheng Zhu - 1-13 Automatic Design of Digital Synthetic Gene Circuits
by Mario A Marchisio & Jörg Stelling - 1-13 De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference
by Jens Keilwagen & Jan Grau & Ivan A Paponov & Stefan Posch & Marc Strickert & Ivo Grosse - 1-14 First Principles Modeling of Nonlinear Incidence Rates in Seasonal Epidemics
by José M Ponciano & Marcos A Capistrán - 1-14 Pharmacodynamic Modeling of Anti-Cancer Activity of Tetraiodothyroacetic Acid in a Perfused Cell Culture System
by Hung-Yun Lin & Cornelia B Landersdorfer & David London & Ran Meng & Chang-Uk Lim & Cassie Lin & Sharon Lin & Heng-Yuan Tang & David Brown & Brian Van Scoy & Robert Kulawy & Lurdes Queimado & George L Drusano & Arnold Louie & Faith B Davis & Shaker A Mousa & Paul J Davis - 1-17 Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions
by John E Pearson & Paul Krapivsky & Alan S Perelson - 1-18 Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation
by David M Holloway & Francisco J P Lopes & Luciano da Fontoura Costa & Bruno A N Travençolo & Nina Golyandina & Konstantin Usevich & Alexander V Spirov - 1-21 Power-Law Input-Output Transfer Functions Explain the Contrast-Response and Tuning Properties of Neurons in Visual Cortex
by Erez Persi & David Hansel & Lionel Nowak & Pascal Barone & Carl van Vreeswijk
January 2011, Volume 7, Issue 1
- 1-2 Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia
by Philip E Bourne - 1-8 Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding
by Iain Melvin & Jason Weston & William Stafford Noble & Christina Leslie - 1-8 A Novel Approach to Pharmacodynamic Assessment of Antimicrobial Agents: New Insights to Dosing Regimen Design
by Vincent H Tam & Michael Nikolaou - 1-10 Decrypting the Sequence of Structural Events during the Gating Transition of Pentameric Ligand-Gated Ion Channels Based on an Interpolated Elastic Network Model
by Wenjun Zheng & Anthony Auerbach - 1-10 Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks
by Daniel M Cornforth & Timothy C Reluga & Eunha Shim & Chris T Bauch & Alison P Galvani & Lauren Ancel Meyers - 1-13 PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data
by Thomas J Sharpton & Samantha J Riesenfeld & Steven W Kembel & Joshua Ladau & James P O'Dwyer & Jessica L Green & Jonathan A Eisen & Katherine S Pollard - 1-13 A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt
by Peter Buske & Jörg Galle & Nick Barker & Gabriela Aust & Hans Clevers & Markus Loeffler - 1-14 Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings
by Elise Payzan-LeNestour & Peter Bossaerts - 1-14 Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA
by Dina Zhabinskaya & Craig J Benham - 1-14 Impact of Sarcoplasmic Reticulum Calcium Release on Calcium Dynamics and Action Potential Morphology in Human Atrial Myocytes: A Computational Study
by Jussi T Koivumäki & Topi Korhonen & Pasi Tavi - 1-15 Estimation of Parent Specific DNA Copy Number in Tumors using High-Density Genotyping Arrays
by Hao Chen & Haipeng Xing & Nancy R Zhang - 1-16 From Spiking Neuron Models to Linear-Nonlinear Models
by Srdjan Ostojic & Nicolas Brunel - 1-16 A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System
by Bing Liu & Jing Zhang & Pei Yi Tan & David Hsu & Anna M Blom & Benjamin Leong & Sunil Sethi & Bow Ho & Jeak Ling Ding & P S Thiagarajan - 1-18 Practical Measures of Integrated Information for Time-Series Data
by Adam B Barrett & Anil K Seth - 1-29 Is My Network Module Preserved and Reproducible?
by Peter Langfelder & Rui Luo & Michael C Oldham & Steve Horvath
December 2010, Volume 6, Issue 12
- 1-8 Phase-Locked Signals Elucidate Circuit Architecture of an Oscillatory Pathway
by Andreja Jovic & Bryan Howell & Michelle Cote & Susan M Wade & Khamir Mehta & Atsushi Miyawaki & Richard R Neubig & Jennifer J Linderman & Shuichi Takayama - 1-10 Axial and Radial Forces of Cross-Bridges Depend on Lattice Spacing
by C David Williams & Michael Regnier & Thomas L Daniel - 1-10 Little Italy: An Agent-Based Approach to the Estimation of Contact Patterns- Fitting Predicted Matrices to Serological Data
by Fabrizio Iozzi & Francesco Trusiano & Matteo Chinazzi & Francesco C Billari & Emilio Zagheni & Stefano Merler & Marco Ajelli & Emanuele Del Fava & Piero Manfredi - 1-11 Rhythmic Dynamics and Synchronization via Dimensionality Reduction: Application to Human Gait
by Jie Zhang & Kai Zhang & Jianfeng Feng & Michael Small - 1-12 Structure Learning in Human Sequential Decision-Making
by Daniel E Acuña & Paul Schrater - 1-12 Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs
by William H Majoros & Uwe Ohler - 1-13 Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW
by Faruck Morcos & Santanu Chatterjee & Christopher L McClendon & Paul R Brenner & Roberto López-Rendón & John Zintsmaster & Maria Ercsey-Ravasz & Christopher R Sweet & Matthew P Jacobson & Jeffrey W Peng & Jesús A Izaguirre - 1-13 Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations
by Benjamin A Logsdon & Jason Mezey - 1-13 Sequence-Based Prediction for Vaccine Strain Selection and Identification of Antigenic Variability in Foot-and-Mouth Disease Virus
by Richard Reeve & Belinda Blignaut & Jan J Esterhuysen & Pamela Opperman & Louise Matthews & Elizabeth E Fry & Tjaart A P de Beer & Jacques Theron & Elizabeth Rieder & Wilna Vosloo & Hester G O'Neill & Daniel T Haydon & Francois F Maree - 1-13 Determinants of Heterogeneity, Excitation and Conduction in the Sinoatrial Node: A Model Study
by Ronit V Oren & Colleen E Clancy - 1-18 A Scalable Approach for Discovering Conserved Active Subnetworks across Species
by Raamesh Deshpande & Shikha Sharma & Catherine M Verfaillie & Wei-Shou Hu & Chad L Myers - 1-25 How Noisy Adaptation of Neurons Shapes Interspike Interval Histograms and Correlations
by Tilo Schwalger & Karin Fisch & Jan Benda & Benjamin Lindner
November 2010, Volume 6, Issue 11
- 1-4 PLoS Computational Biology Conference Postcards from ISMB 2010
by Guilhem Chalancon & Mickey Kosloff & Hatice Ulku Osmanbeyoglu & Saras Saraswathi - 1-8 Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification
by Cristina Marino Buslje & Elin Teppa & Tomas Di Doménico & José María Delfino & Morten Nielsen - 1-9 Untangling the Interplay between Epidemic Spread and Transmission Network Dynamics
by Christel Kamp - 1-10 Pattern Recognition Software and Techniques for Biological Image Analysis
by Lior Shamir & John D Delaney & Nikita Orlov & D Mark Eckley & Ilya G Goldberg - 1-11 Quantifying the Impact of Human Immunodeficiency Virus-1 Escape From Cytotoxic T-Lymphocytes
by Ulrich D Kadolsky & Becca Asquith - 1-11 Monte Carlo Analysis of Neck Linker Extension in Kinesin Molecular Motors
by Matthew L Kutys & John Fricks & William O Hancock - 1-11 Analysis of Stochastic Strategies in Bacterial Competence: A Master Equation Approach
by Sandra H Dandach & Mustafa Khammash - 1-11 A New Integrated Variable Based on Thermometry, Actimetry and Body Position (TAP) to Evaluate Circadian System Status in Humans
by Elisabet Ortiz-Tudela & Antonio Martinez-Nicolas & Manuel Campos & María Ángeles Rol & Juan Antonio Madrid - 1-12 On the Origins of the Weak Folding Cooperativity of a Designed ββα Ultrafast Protein FSD-1
by Chun Wu & Joan-Emma Shea - 1-13 A New Method to Reconstruct Recombination Events at a Genomic Scale
by Marta Melé & Asif Javed & Marc Pybus & Francesc Calafell & Laxmi Parida & Jaume Bertranpetit & The Genographic Consortium - 1-13 Genome-Wide Association between Branch Point Properties and Alternative Splicing
by André Corvelo & Martina Hallegger & Christopher W J Smith & Eduardo Eyras - 1-14 Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data
by Matthieu Wyart & David Botstein & Ned S Wingreen - 1-14 Compensation for Changing Motor Uncertainty
by Todd E Hudson & Hadley Tassinari & Michael S Landy - 1-17 Environments that Induce Synthetic Microbial Ecosystems
by Niels Klitgord & Daniel Segrè - 1-17 Modelling Vesicular Release at Hippocampal Synapses
by Suhita Nadkarni & Thomas M Bartol & Terrence J Sejnowski & Herbert Levine - 1-21 Lobe Specific Ca2+-Calmodulin Nano-Domain in Neuronal Spines: A Single Molecule Level Analysis
by Yoshihisa Kubota & M Neal Waxham
October 2010, Volume 6, Issue 10
- 1-3 In Memoriam: Rolf Kötter (1961–2010)
by Klaas Enno Stephan & Anthony Randal McIntosh & Claus C Hilgetag - 1-8 Individualization as Driving Force of Clustering Phenomena in Humans
by Michael Mäs & Andreas Flache & Dirk Helbing - 1-8 Critical Dynamics in the Evolution of Stochastic Strategies for the Iterated Prisoner's Dilemma
by Dimitris Iliopoulos & Arend Hintze & Christoph Adami - 1-9 Bistability in Apoptosis by Receptor Clustering
by Kenneth L Ho & Heather A Harrington - 1-10 Inherent High Correlation of Individual Motility Enhances Population Dispersal in a Heterotrophic, Planktonic Protist
by Susanne Menden-Deuer - 1-12 Biosensor Approach to Psychopathology Classification
by Misha Koshelev & Terry Lohrenz & Marina Vannucci & P Read Montague - 1-12 A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes
by Gaurav Bhatia & Vikas Bansal & Olivier Harismendy & Nicholas J Schork & Eric J Topol & Kelly Frazer & Vineet Bafna - 1-16 Non-Centered Spike-Triggered Covariance Analysis Reveals Neurotrophin-3 as a Developmental Regulator of Receptive Field Properties of ON-OFF Retinal Ganglion Cells
by Donald R Cantrell & Jianhua Cang & John B Troy & Xiaorong Liu
September 2010, Volume 6, Issue 9
- 1-3 Ten Simple Rules for Editing Wikipedia
by Darren W Logan & Massimo Sandal & Paul P Gardner & Magnus Manske & Alex Bateman - 1-9 Differences in Nutrient Requirements Imply a Non-Linear Emergence of Leaders in Animal Groups
by Cédric Sueur & Jean-Louis Deneubourg & Odile Petit & Iain D Couzin - 1-9 The Distinct Conformational Dynamics of K-Ras and H-Ras A59G
by Suryani Lukman & Barry J Grant & Alemayehu A Gorfe & Guy H Grant & J Andrew McCammon - 1-10 Wide-Field Motion Integration in Fly VS Cells: Insights from an Inverse Approach
by Benjamin Torben-Nielsen & Klaus M Stiefel - 1-10 Instantaneous Non-Linear Processing by Pulse-Coupled Threshold Units
by Moritz Helias & Moritz Deger & Stefan Rotter & Markus Diesmann - 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 - 1-13 Forcing Versus Feedback: Epidemic Malaria and Monsoon Rains in Northwest India
by Karina Laneri & Anindya Bhadra & Edward L Ionides & Menno Bouma & Ramesh C Dhiman & Rajpal S Yadav & Mercedes Pascual - 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 - 1-16 Rescuing Loading Induced Bone Formation at Senescence
by Sundar Srinivasan & Brandon J Ausk & Jitendra Prasad & Dewayne Threet & Steven D Bain & Thomas S Richardson & Ted S Gross
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 - 1-12 Linking Changes in Epithelial Morphogenesis to Cancer Mutations Using Computational Modeling
by Katarzyna A Rejniak & Shizhen E Wang & Nicole S Bryce & Hang Chang & Bahram Parvin & Jerome Jourquin & Lourdes Estrada & Joe W Gray & Carlos L Arteaga & Alissa M Weaver & Vito Quaranta & Alexander R A Anderson - 1-13 Reinforcement Learning on Slow Features of High-Dimensional Input Streams
by Robert Legenstein & Niko Wilbert & Laurenz Wiskott - 1-14 Nonlinear Gap Junctions Enable Long-Distance Propagation of Pulsating Calcium Waves in Astrocyte Networks
by Mati Goldberg & Maurizio De Pittà & Vladislav Volman & Hugues Berry & Eshel Ben-Jacob - 1-14 Modeling and Dynamics of the Inward-Facing State of a Na+/Cl− Dependent Neurotransmitter Transporter Homologue
by Saher Afshan Shaikh & Emad Tajkhorshid - 1-17 CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences
by Wayne Delport & Konrad Scheffler & Gordon Botha & Mike B Gravenor & Spencer V Muse & Sergei L Kosakovsky Pond - 1-18 Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes
by Robert C Cannon & Cian O'Donnell & Matthew F Nolan - 1-19 Continuous Attractors with Morphed/Correlated Maps
by Sandro Romani & Misha Tsodyks - 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 - 1-24 Dendritic Spikes Amplify the Synaptic Signal to Enhance Detection of Motion in a Simulation of the Direction-Selective Ganglion Cell
by Michael J Schachter & Nicholas Oesch & Robert G Smith & W Rowland Taylor
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 Large-Scale Analysis of Network Bistability for Human Cancers
by Tetsuya Shiraishi & Shinako Matsuyama & Hiroaki Kitano - 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 Computer Simulation of Cellular Patterning Within the Drosophila Pupal Eye
by David E Larson & Ruth I Johnson & Maciej Swat & Julia B Cordero & James A Glazier & Ross L Cagan - 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
- 1-2 2010 ISCB Overton Prize Awarded to Steven E. Brenner
by BJ Morrison McKay & Clare Sansom - 1-7 The Roots of Bioinformatics
by David B Searls - 1-8 Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails
by Peter M Kasson & Erik Lindahl & Vijay S Pande - 1-8 Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks
by Javier De Las Rivas & Celia Fontanillo - 1-9 Nonlinearity of Mechanochemical Motions in Motor Proteins
by Yuichi Togashi & Toshio Yanagida & Alexander S Mikhailov - 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 - 1-12 Multiscale Coarse-Graining of the Protein Energy Landscape
by Ronald D Hills Jr & Lanyuan Lu & Gregory A Voth - 1-13 Rule-Based Cell Systems Model of Aging using Feedback Loop Motifs Mediated by Stress Responses
by Andres Kriete & William J Bosl & Glenn Booker - 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
- 1-3 What Do I Want from the Publisher of the Future?
by Philip E Bourne - 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 - 1-11 Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks
by Karine Audouze & Agnieszka Sierakowska Juncker & Francisco J S S A Roque & Konrad Krysiak-Baltyn & Nils Weinhold & Olivier Taboureau & Thomas Skøt Jensen & Søren Brunak - 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 - 1-14 A Differentiation-Based Phylogeny of Cancer Subtypes
by Markus Riester & Camille Stephan-Otto Attolini & Robert J Downey & Samuel Singer & Franziska Michor - 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
- 1-6 A Stevedore's Protein Knot
by Daniel Bölinger & Joanna I Sułkowska & Hsiao-Ping Hsu & Leonid A Mirny & Mehran Kardar & José N Onuchic & Peter Virnau - 1-9 Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences
by Vinal V Lakhani & Feng Ding & Nikolay V Dokholyan - 1-9 Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions
by Dirk Helbing & Attila Szolnoki & Matjaž Perc & György Szabó - 1-10 Asymmetric Switching in a Homodimeric ABC Transporter: A Simulation Study
by Jussi Aittoniemi & Heidi de Wet & Frances M Ashcroft & Mark S P Sansom - 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 How Informative Are Spatial CA3 Representations Established by the Dentate Gyrus?
by Erika Cerasti & Alessandro Treves - 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 - 1-17 A Critical Quantity for Noise Attenuation in Feedback Systems
by Liming Wang & Jack Xin & Qing Nie - 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 - 1-26 Global Entrainment of Transcriptional Systems to Periodic Inputs
by Giovanni Russo & Mario di Bernardo & Eduardo D Sontag
March 2010, Volume 6, Issue 3
- 1-9 The Impact of Contact Tracing in Clustered Populations
by Thomas House & Matt J Keeling - 1-9 Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation
by Carey D Nadell & Kevin R Foster & João B Xavier - 1-10 Within- and Cross-Modal Distance Information Disambiguate Visual Size-Change Perception
by Peter W Battaglia & Massimiliano Di Luca & Marc O Ernst & Paul R Schrater & Tonja Machulla & Daniel Kersten - 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 - 1-12 Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ9-40 Peptide: A Comparison to Agitated Fibrils
by Chun Wu & Michael T Bowers & Joan-Emma Shea - 1-13 Systematic Planning of Genome-Scale Experiments in Poorly Studied Species
by Yuanfang Guan & Maitreya Dunham & Amy Caudy & Olga Troyanskaya - 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 - 1-15 Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement
by Laurence Calzone & Laurent Tournier & Simon Fourquet & Denis Thieffry & Boris Zhivotovsky & Emmanuel Barillot & Andrei Zinovyev - 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 - 1-18 Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
by Sean R McGuffee & Adrian H Elcock - 1-22 Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction
by Hiroyuki Kuwahara & Chris J Myers & Michael S Samoilov - 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
- 1-2 A Review of 2009 for PLoS Computational Biology
by Rosemary Dickin & Cecy Marden & Catherine Nancarrow & Philip E Bourne - 1-9 A Bayesian Approach to Quantifying the Effects of Mass Poultry Vaccination upon the Spatial and Temporal Dynamics of H5N1 in Northern Vietnam
by Patrick G T Walker & Simon Cauchemez & Raphaëlle Métras & Do Huu Dung & Dirk Pfeiffer & Azra C Ghani - 1-10 Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species
by Shiri Freilich & Anat Kreimer & Elhanan Borenstein & Uri Gophna & Roded Sharan & Eytan Ruppin - 1-11 Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks
by Sashi Marella & Bard Ermentrout - 1-11 Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells
by Murat Cirit & Matej Krajcovic & Colin K Choi & Erik S Welf & Alan F Horwitz & Jason M Haugh - 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 Numerical Modelling Of The V-J Combinations Of The T Cell Receptor TRA/TRD Locus
by Florence Thuderoz & Maria-Ana Simonet & Olivier Hansen & Nicolas Pasqual & Aurélie Dariz & Thierry Pascal Baum & Vivien Hierle & Jacques Demongeot & Patrice Noël Marche & Evelyne Jouvin-Marche - 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 - 1-15 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II
by Shirley Pepke & Tamara Kinzer-Ursem & Stefan Mihalas & Mary B Kennedy - 1-15 Identifying the Rules of Engagement Enabling Leukocyte Rolling, Activation, and Adhesion
by Jonathan Tang & C Anthony Hunt - 1-18 Predicted Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage
by Sohyoung Kim & Mirit I Aladjem & Geoffrey B McFadden & Kurt W Kohn