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October 2011, Volume 7, Issue 10
- 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 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 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 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
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 - 1-11 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 - 1-12 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 - 1-14 Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations
by Lipi Thukral & Isabella Daidone & Jeremy C Smith - 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
August 2011, Volume 7, Issue 8
- 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 - 1-11 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 - 1-15 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 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 - 1-13 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 - 1-15 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 Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models
by Iulian Pruteanu-Malinici & Daniel L Mace & Uwe Ohler - 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 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 - 1-13 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
- 1-6 Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases
by Frank Emmert-Streib & Galina V Glazko - 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 Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability
by Alistair N Boettiger & Peter L Ralph & Steven N Evans - 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
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 In Silico Elucidation of the Recognition Dynamics of Ubiquitin
by Dong Long & Rafael Brüschweiler - 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
- 1-9 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 - 1-12 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 - 1-13 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 - 1-17 Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation
by Daniele Linaro & Marco Storace & Michele Giugliano - 1-19 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 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 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 - 1-18 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 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 - 1-14 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 - 1-15 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 - 1-12 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 - 1-18 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
- 1-8 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 - 1-10 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 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 - 1-13 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 - 1-21 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 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 - 1-16 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 - 1-14 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