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August 2012, Volume 8, Issue 8
- 1-15 Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics
by Reuben H Kraft & Phillip Justin Mckee & Amy M Dagro & Scott T Grafton
July 2012, Volume 8, Issue 7
- 1-10 Assessing Drug Target Association Using Semantic Linked Data
by Bin Chen & Ying Ding & David J Wild - 1-11 Why SIT Works: Normal Function Despite Typical Myofiber Pattern in Situs Inversus Totalis (SIT) Hearts Derived by Shear-induced Myofiber Reorientation
by Marieke Pluijmert & Wilco Kroon & Alessandro C Rossi & Peter H M Bovendeerd & Tammo Delhaas - 1-12 Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data
by Haipeng Xing & Yifan Mo & Will Liao & Michael Q Zhang
June 2012, Volume 8, Issue 6
- 1-2 A Report of the Curriculum Task Force of the ISCB Education Committee
by Lonnie R Welch & Russell Schwartz & Fran Lewitter - 1-12 A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts
by Arno Onken & Valentin Dragoi & Klaus Obermayer - 1-12 A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks
by Daniele De Martino & Matteo Figliuzzi & Andrea De Martino & Enzo Marinari - 1-12 The Role of Non-Native Interactions in the Folding of Knotted Proteins
by Tatjana Škrbić & Cristian Micheletti & Pietro Faccioli - 1-16 Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations
by Xin Wang & Mauro A Castro & Klaas W Mulder & Florian Markowetz - 1-17 Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees
by Eftychios A Pnevmatikakis & Keith Kelleher & Rebecca Chen & Petter Saggau & Krešimir Josić & Liam Paninski - 1-17 Modeling Boundary Vector Cell Firing Given Optic Flow as a Cue
by Florian Raudies & Michael E Hasselmo
May 2012, Volume 8, Issue 5
- 1-10 Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments
by Sepideh Bazazi & Frederic Bartumeus & Joseph J Hale & Iain D Couzin - 1-12 Crossing Over…Markov Meets Mendel
by Saad Mneimneh - 1-14 Measuring Granger Causality between Cortical Regions from Voxelwise fMRI BOLD Signals with LASSO
by Wei Tang & Steven L Bressler & Chad M Sylvester & Gordon L Shulman & Maurizio Corbetta - 1-17 Optimality of Human Contour Integration
by Udo A Ernst & Sunita Mandon & Nadja Schinkel–Bielefeld & Simon D Neitzel & Andreas K Kreiter & Klaus R Pawelzik - 1-18 Optimal Control of Saccades by Spatial-Temporal Activity Patterns in the Monkey Superior Colliculus
by H H L M Goossens & A J van Opstal
April 2012, Volume 8, Issue 4
- 1-7 Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat
by Yihwa Kim & Robert Sinclair & Nol Chindapol & Jaap A Kaandorp & Erik De Schutter - 1-12 Tension and Robustness in Multitasking Cellular Networks
by Jeffrey V Wong & Bochong Li & Lingchong You - 1-15 Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons
by Kyriaki Sidiropoulou & Panayiota Poirazi - 1-21 Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA
by Dina Zhabinskaya & Craig J Benham
March 2012, Volume 8, Issue 3
- 1-3 Ten Simple Rules for Starting a Company
by Anthony C Fletcher & Philip E Bourne - 1-10 Traffic Instabilities in Self-Organized Pedestrian Crowds
by Mehdi Moussaïd & Elsa G Guillot & Mathieu Moreau & Jérôme Fehrenbach & Olivier Chabiron & Samuel Lemercier & Julien Pettré & Cécile Appert-Rolland & Pierre Degond & Guy Theraulaz - 1-10 Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data
by Alexander R Macalalad & Michael C Zody & Patrick Charlebois & Niall J Lennon & Ruchi M Newman & Christine M Malboeuf & Elizabeth M Ryan & Christian L Boutwell & Karen A Power & Doug E Brackney & Kendra N Pesko & Joshua Z Levin & Gregory D Ebel & Todd M Allen & Bruce W Birren & Matthew R Henn - 1-14 Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery
by András Lörincz & Zsolt Palotai & Gábor Szirtes - 1-18 Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics
by Ruben Coen-Cagli & Peter Dayan & Odelia Schwartz
February 2012, Volume 8, Issue 2
- 1-11 Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1
by Xueyang Feng & You Xu & Yixin Chen & Yinjie J Tang - 1-13 Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina
by Pranidhi Sood & Robert J Johnston Jr. & Edo Kussell - 1-15 Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data
by Santiago Treviño III & Yudong Sun & Tim F Cooper & Kevin E Bassler
January 2012, Volume 8, Issue 1
- 1-9 Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies
by Nicoló Fusi & Oliver Stegle & Neil D Lawrence - 1-11 Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism
by Fiona Achcar & Eduard J Kerkhoven & The SilicoTryp Consortium & Barbara M Bakker & Michael P Barrett & Rainer Breitling - 1-12 Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress
by Patrick D McMullen & Erin Z Aprison & Peter B Winter & Luis A N Amaral & Richard I Morimoto & Ilya Ruvinsky - 1-13 Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding
by Iain H Moal & Paul A Bates - 1-14 Prediction by Promoter Logic in Bacterial Quorum Sensing
by Navneet Rai & Rajat Anand & Krishna Ramkumar & Varun Sreenivasan & Sugat Dabholkar & K V Venkatesh & Mukund Thattai - 1-15 Protein Design Using Continuous Rotamers
by Pablo Gainza & Kyle E Roberts & Bruce R Donald - 1-15 Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana
by Michael Seifert & André Gohr & Marc Strickert & Ivo Grosse
December 2011, Volume 7, Issue 12
- 1-8 Chemotaxis when Bacteria Remember: Drift versus Diffusion
by Sakuntala Chatterjee & Rava Azeredo da Silveira & Yariv Kafri - 1-10 Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes
by Amin R Mazloom & Ruth Dannenfelser & Neil R Clark & Arsen V Grigoryan & Kathryn M Linder & Timothy J Cardozo & Julia C Bond & Aislyn D W Boran & Ravi Iyengar & Anna Malovannaya & Rainer B Lanz & Avi Ma'ayan - 1-11 Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model
by Edward B Baskerville & Andy P Dobson & Trevor Bedford & Stefano Allesina & T Michael Anderson & Mercedes Pascual - 1-13 Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps)
by Zhichao Liu & Qiang Shi & Don Ding & Reagan Kelly & Hong Fang & Weida Tong - 1-15 Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers
by Andrew T Kwon & Alice Yi Chou & David J Arenillas & Wyeth W Wasserman - 1-16 Increased Vulnerability of Human Ventricle to Re-entrant Excitation in hERG-linked Variant 1 Short QT Syndrome
by Ismail Adeniran & Mark J McPate & Harry J Witchel & Jules C Hancox & Henggui Zhang - 1-25 Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons
by Dejan Pecevski & Lars Buesing & Wolfgang Maass
November 2011, Volume 7, Issue 11
- 1-8 How Landscape Heterogeneity Frames Optimal Diffusivity in Searching Processes
by E P Raposo & F Bartumeus & M G E da Luz & P J Ribeiro-Neto & T A Souza & G M Viswanathan - 1-9 The What and Where of Adding Channel Noise to the Hodgkin-Huxley Equations
by Joshua H Goldwyn & Eric Shea-Brown - 1-9 Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits
by Rutger Hermsen & David W Erickson & Terence Hwa - 1-13 Trade-Offs and Constraints in Allosteric Sensing
by Bruno MC Martins & Peter S Swain - 1-14 Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy
by Seyed Yahya Anvar & Allan Tucker & Veronica Vinciotti & Andrea Venema & Gert-Jan B van Ommen & Silvere M van der Maarel & Vered Raz & Peter A C ‘t Hoen - 1-18 Optimizing Experimental Design for Comparing Models of Brain Function
by Jean Daunizeau & Kerstin Preuschoff & Karl Friston & Klaas Stephan - 1-22 Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons
by Lars Buesing & Johannes Bill & Bernhard Nessler & Wolfgang Maass
October 2011, Volume 7, Issue 10
- 1-9 Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models
by Jeffrey D Fitzgerald & Ryan J Rowekamp & Lawrence C Sincich & Tatyana O Sharpee - 1-10 The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers
by Sean A Rands - 1-10 Coupled Information Diffusion–Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs
by François Rebaudo & Olivier Dangles - 1-10 Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer
by Anup Dewanji & Jihyoun Jeon & Rafael Meza & E Georg Luebeck - 1-12 Estimating the Relevance of World Disturbances to Explain Savings, Interference and Long-Term Motor Adaptation Effects
by Max Berniker & Konrad P Kording - 1-12 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 - 1-14 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 - 1-15 Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis
by Anna Divoli & Eneida A Mendonça & James A Evans & Andrey Rzhetsky - 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 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 - 1-15 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
July 2011, Volume 7, Issue 7
- 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
- 1-4 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 - 1-14 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 - 1-22 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 - 1-21 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 - 1-15 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 - 1-13 Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding
by Dana Bar-On & Esther Nachliel & Menachem Gutman & Uri Ashery - 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 - 1-20 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
February 2011, Volume 7, Issue 2
- 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 Transition from Persistent to Anti-Persistent Correlations in Postural Sway Indicates Velocity-Based Control
by Didier Delignières & Kjerstin Torre & Pierre-Louis Bernard - 1-11 Mitigation Strategies for Pandemic Influenza A: Balancing Conflicting Policy Objectives
by T Déirdre Hollingsworth & Don Klinkenberg & Hans Heesterbeek & Roy M Anderson - 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
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 - 1-10 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 - 1-14 Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings
by Elise Payzan-LeNestour & Peter Bossaerts - 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 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
December 2010, Volume 6, Issue 12
- 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 - 1-18 A Scalable Approach for Discovering Conserved Active Subnetworks across Species
by Raamesh Deshpande & Shikha Sharma & Catherine M Verfaillie & Wei-Shou Hu & Chad L Myers
November 2010, Volume 6, Issue 11
- 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 - 1-13 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 - 1-14 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
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 - 1-10 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 - 1-10 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 - 1-12 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 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 - 1-11 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 - 1-17 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
June 2010, Volume 6, Issue 6
- 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 Combinatorial Gene Regulation Using Auto-Regulation
by Rutger Hermsen & Bas Ursem & Pieter Rein ten Wolde
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 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 - 1-12 Assimilating Seizure Dynamics
by Ghanim Ullah & Steven J Schiff - 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 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 - 1-13 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 Coordinate Dependence of Variability Analysis
by Dagmar Sternad & Se-Woong Park & Hermann Müller & Neville Hogan
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 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 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 - 1-25 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 - 1-13 Spatial Simulations of Myxobacterial Development
by Antony B Holmes & Sara Kalvala & David E Whitworth
January 2010, Volume 6, Issue 1
- 1-9 Associating Genes and Protein Complexes with Disease via Network Propagation
by Oron Vanunu & Oded Magger & Eytan Ruppin & Tomer Shlomi & Roded Sharan - 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 - 1-25 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 - 1-11 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 - 1-18 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 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 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 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 Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?
by Stefano Allesina & Mercedes Pascual