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Content
January 2010, Volume 6, Issue 1
- 1-8 FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model
by Dennis L Chao & M Elizabeth Halloran & Valerie J Obenchain & Ira M Longini Jr - 1-8 Network-Free Inference of Knockout Effects in Yeast
by Tal Peleg & Nir Yosef & Eytan Ruppin & Roded Sharan - 1-9 Associating Genes and Protein Complexes with Disease via Network Propagation
by Oron Vanunu & Oded Magger & Eytan Ruppin & Tomer Shlomi & Roded Sharan - 1-9 Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains
by Isabella Daidone & Hannes Neuweiler & Sören Doose & Markus Sauer & Jeremy C Smith - 1-9 How Synchronization Protects from Noise
by Nicolas Tabareau & Jean-Jacques Slotine & Quang-Cuong Pham - 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 - 1-14 Quantitative Modeling of GRK-Mediated β2AR Regulation
by Sharat J Vayttaden & Jacqueline Friedman & Tuan M Tran & Thomas C Rich & Carmen W Dessauer & Richard B Clark - 1-15 A Reaction-Diffusion Model of ROS-Induced ROS Release in a Mitochondrial Network
by Lufang Zhou & Miguel A Aon & Tabish Almas & Sonia Cortassa & Raimond L Winslow & Brian O'Rourke - 1-16 Modeling Mitochondrial Bioenergetics with Integrated Volume Dynamics
by Jason N Bazil & Gregery T Buzzard & Ann E Rundell - 1-18 Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments
by Lukas Burger & Erik van Nimwegen - 1-25 Axonal Velocity Distributions in Neural Field Equations
by Ingo Bojak & David T J Liley
December 2009, Volume 5, Issue 12
- 1-7 Calculating Evolutionary Dynamics in Structured Populations
by Charles G Nathanson & Corina E Tarnita & Martin A Nowak - 1-7 Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation
by Jorge M Pacheco & Flávio L Pinheiro & Francisco C Santos - 1-7 A Quick Guide for Developing Effective Bioinformatics Programming Skills
by Joel T Dudley & Atul J Butte - 1-8 Inferring Binding Energies from Selected Binding Sites
by Yue Zhao & David Granas & Gary D Stormo - 1-9 Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task
by Ian H Stevenson & Hugo L Fernandes & Iris Vilares & Kunlin Wei & Konrad P Körding - 1-10 Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening
by Vebjorn Ljosa & Anne E Carpenter - 1-10 Defining an Essence of Structure Determining Residue Contacts in Proteins
by R Sathyapriya & Jose M Duarte & Henning Stehr & Ioannis Filippis & Michael Lappe - 1-10 Effective Reduced Diffusion-Models: A Data Driven Approach to the Analysis of Neuronal Dynamics
by Gustavo Deco & Daniel Martí & Anders Ledberg & Ramon Reig & Maria V Sanchez Vives - 1-11 Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
by João F Matias Rodrigues & Andreas Wagner - 1-11 Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data
by Alexander Mitsos & Ioannis N Melas & Paraskeuas Siminelakis & Aikaterini D Chairakaki & Julio Saez-Rodriguez & Leonidas G Alexopoulos - 1-11 Distributed Dynamical Computation in Neural Circuits with Propagating Coherent Activity Patterns
by Pulin Gong & Cees van Leeuwen - 1-11 Model of Transcriptional Activation by MarA in Escherichia coli
by Michael E Wall & David A Markowitz & Judah L Rosner & Robert G Martin - 1-12 Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR
by Sean Ekins & Sandhya Kortagere & Manisha Iyer & Erica J Reschly & Markus A Lill & Matthew R Redinbo & Matthew D Krasowski - 1-13 Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
by Alexandra M Schnoes & Shoshana D Brown & Igor Dodevski & Patricia C Babbitt - 1-16 Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases
by Kai Wang & Manikandan Narayanan & Hua Zhong & Martin Tompa & Eric E Schadt & Jun Zhu - 1-16 Hyperbolic Planforms in Relation to Visual Edges and Textures Perception
by Pascal Chossat & Olivier Faugeras - 1-18 Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
by John A Capra & Roman A Laskowski & Janet M Thornton & Mona Singh & Thomas A Funkhouser - 1-19 Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation
by Brian J Schmidt & Jason A Papin & Michael B Lawrence - 1-19 Burst-Time-Dependent Plasticity Robustly Guides ON/OFF Segregation in the Lateral Geniculate Nucleus
by Julijana Gjorgjieva & Taro Toyoizumi & Stephen J Eglen
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 - 1-10 Quantification of Circadian Rhythms in Single Cells
by Pål O Westermark & David K Welsh & Hitoshi Okamura & Hanspeter Herzel - 1-11 Interactions between Connected Half-Sarcomeres Produce Emergent Mechanical Behavior in a Mathematical Model of Muscle
by Kenneth S Campbell - 1-12 A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen
by Omer Dushek & Raibatak Das & Daniel Coombs - 1-12 Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model
by Samuel Bandara & Johannes P Schlöder & Roland Eils & Hans Georg Bock & Tobias Meyer - 1-13 Attention Increases the Temporal Precision of Conscious Perception: Verifying the Neural-ST2 Model
by Srivas Chennu & Patrick Craston & Brad Wyble & Howard Bowman - 1-13 Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation
by Arno Onken & Steffen Grünewälder & Matthias H J Munk & Klaus Obermayer - 1-13 A Novel Extended Granger Causal Model Approach Demonstrates Brain Hemispheric Differences during Face Recognition Learning
by Tian Ge & Keith M Kendrick & Jianfeng Feng - 1-16 A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton
by Raibatak Das & Christopher W Cairo & Daniel Coombs - 1-16 Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary
by Dominik M Wittmann & Florian Blöchl & Dietrich Trümbach & Wolfgang Wurst & Nilima Prakash & Fabian J Theis - 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 - 1-13 High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
by Noriaki Okimoto & Noriyuki Futatsugi & Hideyoshi Fuji & Atsushi Suenaga & Gentaro Morimoto & Ryoko Yanai & Yousuke Ohno & Tetsu Narumi & Makoto Taiji - 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 - 1-19 Specific Entrainment of Mitral Cells during Gamma Oscillation in the Rat Olfactory Bulb
by François O David & Etienne Hugues & Tristan Cenier & Nicolas Fourcaud-Trocmé & Nathalie Buonviso - 1-26 Towards a Mathematical Theory of Cortical Micro-circuits
by Dileep George & Jeff Hawkins
September 2009, Volume 5, Issue 9
- 1-6 Chemically Based Mathematical Model for Development of Cerebral Cortical Folding Patterns
by Deborah A Striegel & Monica K Hurdal - 1-6 Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?
by Stefano Allesina & Mercedes Pascual - 1-9 A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels
by Steven H Wu & Michael A Black & Robyn A North & Kelly R Atkinson & Allen G Rodrigo - 1-10 Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models
by Timothy R Lezon & Andrej Sali & Ivet Bahar - 1-11 Noise Management by Molecular Networks
by Frank J Bruggeman & Nils Blüthgen & Hans V Westerhoff - 1-12 Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities
by Rui-Ru Ji & Heshani de Silva & Yisheng Jin & Robert E Bruccoleri & Jian Cao & Aiqing He & Wenjun Huang & Paul S Kayne & Isaac M Neuhaus & Karl-Heinz Ott & Becky Penhallow & Mark I Cockett & Michael G Neubauer & Nathan O Siemers & Petra Ross-Macdonald - 1-12 Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning
by Samuel A Danziger & Roberta Baronio & Lydia Ho & Linda Hall & Kirsty Salmon & G Wesley Hatfield & Peter Kaiser & Richard H Lathrop - 1-12 Species Tree Inference by Minimizing Deep Coalescences
by Cuong Than & Luay Nakhleh - 1-15 Interrogating and Predicting Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein
by Jennifer L Lahti & Adam P Silverman & Jennifer R Cochran - 1-15 The Role of Ongoing Dendritic Oscillations in Single-Neuron Dynamics
by Michiel W H Remme & Máté Lengyel & Boris S Gutkin - 1-15 Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification
by Stephen A Stanhope & Srikumar Sengupta & Johan den Boon & Paul Ahlquist & Michael A Newton - 1-16 Parallel Computational Subunits in Dentate Granule Cells Generate Multiple Place Fields
by Balázs Ujfalussy & Tamás Kiss & Péter Érdi - 1-16 A Structured Model of Video Reproduces Primary Visual Cortical Organisation
by Pietro Berkes & Richard E Turner & Maneesh Sahani - 1-17 Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine
by Jiyong Park & Byungnam Kahng & Wonmuk Hwang
August 2009, Volume 5, Issue 8
- 1-4 A Quick Guide to Teaching R Programming to Computational Biology Students
by Stephen J Eglen - 1-7 A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation
by Stefan Auer & Antonio Trovato & Michele Vendruscolo - 1-8 Nash Equilibria in Multi-Agent Motor Interactions
by Daniel A Braun & Pedro A Ortega & Daniel M Wolpert - 1-9 Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data
by Joost Van Durme & Sebastian Maurer-Stroh & Rodrigo Gallardo & Hannah Wilkinson & Frederic Rousseau & Joost Schymkowitz - 1-10 Strong Inference for Systems Biology
by Daniel A Beard & Martin J Kushmerick - 1-10 A Generalized Framework for Quantifying the Dynamics of EEG Event-Related Desynchronization
by Steven Lemm & Klaus-Robert Müller & Gabriel Curio - 1-10 Computation of Conformational Coupling in Allosteric Proteins
by Brian A Kidd & David Baker & Wendy E Thomas - 1-10 Geometric De-noising of Protein-Protein Interaction Networks
by Oleksii Kuchaiev & Marija Rašajski & Desmond J Higham & Nataša Pržulj - 1-11 A Self-Organizing Algorithm for Modeling Protein Loops
by Pu Liu & Fangqiang Zhu & Dmitrii N Rassokhin & Dimitris K Agrafiotis - 1-12 FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies
by Oliver C Redfern & Benoît H Dessailly & Timothy J Dallman & Ian Sillitoe & Christine A Orengo - 1-12 Investigating CTL Mediated Killing with a 3D Cellular Automaton
by Frederik Graw & Roland R Regoes - 1-13 Recognizing Sequences of Sequences
by Stefan J Kiebel & Katharina von Kriegstein & Jean Daunizeau & Karl J Friston - 1-13 The Origins of Lactase Persistence in Europe
by Yuval Itan & Adam Powell & Mark A Beaumont & Joachim Burger & Mark G Thomas - 1-13 Detection of Functional Modes in Protein Dynamics
by Jochen S Hub & Bert L de Groot - 1-14 Can Molecular Motors Drive Distance Measurements in Injured Neurons?
by Naaman Kam & Yitzhak Pilpel & Mike Fainzilber - 1-17 Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens
by Leighton Pritchard & Hui Liu & Clare Booth & Emma Douglas & Patrice François & Jacques Schrenzel & Peter E Hedley & Paul R J Birch & Ian K Toth - 1-18 A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations
by Fabrizio Marinelli & Fabio Pietrucci & Alessandro Laio & Stefano Piana - 1-18 Towards Reproducible Descriptions of Neuronal Network Models
by Eilen Nordlie & Marc-Oliver Gewaltig & Hans Ekkehard Plesser - 1-20 Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo
by Yurie Okabe-Oho & Hiroki Murakami & Suguru Oho & Masaki Sasai - 1-20 Evolutionary Triplet Models of Structured RNA
by Robert K Bradley & Ian Holmes - 1-24 Qualia: The Geometry of Integrated Information
by David Balduzzi & Giulio Tononi
July 2009, Volume 5, Issue 7
- 1-5 A Quick Guide to Organizing Computational Biology Projects
by William Stafford Noble - 1-9 Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels
by Guido Gigante & Maurizio Mattia & Jochen Braun & Paolo Del Giudice - 1-10 Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation
by Daniel Geberth & Marc-Thorsten Hütt - 1-10 Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations
by Lucy R Allen & Sergei V Krivov & Emanuele Paci - 1-10 Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors
by Andrew J Olaharski & Nina Gonzaludo & Hans Bitter & David Goldstein & Stephan Kirchner & Hirdesh Uppal & Kyle Kolaja - 1-10 Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs
by Flávio Codeço Coelho & Claudia T Codeço - 1-10 Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation
by Olgun Guvench & Alexander D MacKerell Jr - 1-11 Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View
by Yongping Pan & Ruth Nussinov - 1-12 Semantic Similarity in Biomedical Ontologies
by Catia Pesquita & Daniel Faria & André O Falcão & Phillip Lord & Francisco M Couto - 1-14 An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility
by Susanne M Rafelski & Jonathan B Alberts & Garrett M Odell - 1-15 Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants
by Jiang Du & Robert D Bjornson & Zhengdong D Zhang & Yong Kong & Michael Snyder & Mark B Gerstein
June 2009, Volume 5, Issue 6
- 1-2 The Need for Centralization of Computational Biology Resources
by Fran Lewitter & Michael Rebhan & Brent Richter & David Sexton - 1-3 Establishing a Successful Bioinformatics Core Facility Team
by Fran Lewitter & Michael Rebhan - 1-4 Ten Simple Rules for Choosing between Industry and Academia
by David B Searls - 1-8 Modeling and Inferring Cleavage Patterns in Proliferating Epithelia
by Ankit B Patel & William T Gibson & Matthew C Gibson & Radhika Nagpal - 1-9 Exploring the Free Energy Landscape: From Dynamics to Networks and Back
by Diego Prada-Gracia & Jesús Gómez-Gardeñes & Pablo Echenique & Fernando Falo - 1-10 The Voice of Bats: How Greater Mouse-eared Bats Recognize Individuals Based on Their Echolocation Calls
by Yossi Yovel & Mariana Laura Melcon & Matthias O Franz & Annette Denzinger & Hans-Ulrich Schnitzler - 1-11 A Probabilistic Model of RNA Conformational Space
by Jes Frellsen & Ida Moltke & Martin Thiim & Kanti V Mardia & Jesper Ferkinghoff-Borg & Thomas Hamelryck - 1-11 Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening
by Nobuyoshi Nagamine & Takayuki Shirakawa & Yusuke Minato & Kentaro Torii & Hiroki Kobayashi & Masaya Imoto & Yasubumi Sakakibara - 1-12 Active Dendrites Enhance Neuronal Dynamic Range
by Leonardo L Gollo & Osame Kinouchi & Mauro Copelli - 1-12 The Effect of Ongoing Exposure Dynamics in Dose Response Relationships
by Josep M Pujol & Joseph E Eisenberg & Charles N Haas & James S Koopman - 1-14 Taking the Lag out of Jet Lag through Model-Based Schedule Design
by Dennis A Dean , II & Daniel B Forger & Elizabeth B Klerman - 1-14 Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences
by Zhang Zhang & Jeffrey P Townsend - 1-15 Optimal Control Predicts Human Performance on Objects with Internal Degrees of Freedom
by Arne J Nagengast & Daniel A Braun & Daniel M Wolpert
May 2009, Volume 5, Issue 5
- 1-2 BioLINK Special Interest Group Session on the Future of Scientific Publishing
by Scott Markel - 1-4 Getting Started in Computational Mass Spectrometry–Based Proteomics
by Olga Vitek - 1-6 Hypergraphs and Cellular Networks
by Steffen Klamt & Utz-Uwe Haus & Fabian Theis - 1-11 SHRiMP: Accurate Mapping of Short Color-space Reads
by Stephen M Rumble & Phil Lacroute & Adrian V Dalca & Marc Fiume & Arend Sidow & Michael Brudno - 1-13 How to Get the Most out of Your Curation Effort
by Andrey Rzhetsky & Hagit Shatkay & W John Wilbur - 1-14 Functional Brain Networks Develop from a “Local to Distributed” Organization
by Damien A Fair & Alexander L Cohen & Jonathan D Power & Nico U F Dosenbach & Jessica A Church & Francis M Miezin & Bradley L Schlaggar & Steven E Petersen - 1-14 Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling
by Smita Agrawal & Colin Archer & David V Schaffer - 1-15 Fast Statistical Alignment
by Robert K Bradley & Adam Roberts & Michael Smoot & Sudeep Juvekar & Jaeyoung Do & Colin Dewey & Ian Holmes & Lior Pachter - 1-15 A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation
by Nicholas J Hudson & Antonio Reverter & Brian P Dalrymple - 1-16 Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings
by Quentin J M Huys & Liam Paninski - 1-16 A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family
by Gregory D Friedland & Nils-Alexander Lakomek & Christian Griesinger & Jens Meiler & Tanja Kortemme - 1-18 Prediction of Protein Binding Regions in Disordered Proteins
by Bálint Mészáros & István Simon & Zsuzsanna Dosztányi - 1-18 Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't
by Yasser Roudi & Sheila Nirenberg & Peter E Latham
April 2009, Volume 5, Issue 4
- 1-2 Ten Simple Rules To Combine Teaching and Research
by Quentin Vicens & Philip E Bourne - 1-4 Webb Miller and Trey Ideker To Receive Top International Bioinformatics Awards for 2009 from the International Society for Computational Biology
by B J Morrison McKay & Clare Sansom - 1-6 Polymorphism Data Can Reveal the Origin of Species Abundance Statistics
by Yosef E Maruvka & Nadav M Shnerb - 1-10 A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)
by Srinivas Ramachandran & Adrian W R Serohijos & Le Xu & Gerhard Meissner & Nikolay V Dokholyan - 1-11 Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
by James Robert White & Niranjan Nagarajan & Mihai Pop - 1-12 Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons
by Cheng Ly & Brent Doiron - 1-13 Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling
by Bree B Aldridge & Julio Saez-Rodriguez & Jeremy L Muhlich & Peter K Sorger & Douglas A Lauffenburger - 1-14 An Analytically Solvable Model for Rapid Evolution of Modular Structure
by Nadav Kashtan & Avi E Mayo & Tomer Kalisky & Uri Alon - 1-14 Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis
by Gitanjali Yadav & Rajesh S Gokhale & Debasisa Mohanty - 1-16 Natural Image Coding in V1: How Much Use Is Orientation Selectivity?
by Jan Eichhorn & Fabian Sinz & Matthias Bethge - 1-17 Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article
by David Shotton & Katie Portwin & Graham Klyne & Alistair Miles - 1-18 The Role of the Frank–Starling Law in the Transduction of Cellular Work to Whole Organ Pump Function: A Computational Modeling Analysis
by Steven A Niederer & Nicolas P Smith - 1-21 Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
by Zheng Yang & Peter Májek & Ivet Bahar
March 2009, Volume 5, Issue 3
- 1-7 T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules
by Aidan MacNamara & Ulrich Kadolsky & Charles R M Bangham & Becca Asquith - 1-9 Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior
by Jeremy E Purvis & Ravi Radhakrishnan & Scott L Diamond - 1-10 Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter
by Boian S Alexandrov & Vladimir Gelev & Sang Wook Yoo & Alan R Bishop & Kim Ø Rasmussen & Anny Usheva - 1-10 Accurate Prediction of Peptide Binding Sites on Protein Surfaces
by Evangelia Petsalaki & Alexander Stark & Eduardo García-Urdiales & Robert B Russell - 1-10 Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
by Barry J Grant & Alemayehu A Gorfe & J Andrew McCammon - 1-11 BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis
by Allen W Bryan Jr. & Matthew Menke & Lenore J Cowen & Susan L Lindquist & Bonnie Berger - 1-12 A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis
by Gabriel Krouk & Daniel Tranchina & Laurence Lejay & Alexis A Cruikshank & Dennis Shasha & Gloria M Coruzzi & Rodrigo A Gutiérrez - 1-12 Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis
by Matthew A Hibbs & Chad L Myers & Curtis Huttenhower & David C Hess & Kai Li & Amy A Caudy & Olga G Troyanskaya - 1-13 Broadband Criticality of Human Brain Network Synchronization
by Manfred G Kitzbichler & Marie L Smith & Søren R Christensen & Ed Bullmore - 1-13 “I Look in Your Eyes, Honey”: Internal Face Features Induce Spatial Frequency Preference for Human Face Processing
by Matthias S Keil - 1-13 Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments
by Oscar Westesson & Ian Holmes - 1-14 Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution
by Xin He & Xu Ling & Saurabh Sinha - 1-15 Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation
by Emili Balaguer-Ballester & Nicholas R Clark & Martin Coath & Katrin Krumbholz & Susan L Denham - 1-15 Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors
by Manu & Svetlana Surkova & Alexander V Spirov & Vitaly V Gursky & Hilde Janssens & Ah-Ram Kim & Ovidiu Radulescu & Carlos E Vanario-Alonso & David H Sharp & Maria Samsonova & John Reinitz - 1-15 Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy
by Arash Bahrami & Amir H Assadi & John L Markley & Hamid R Eghbalnia - 1-16 Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer
by Giulia Morra & Gennady Verkhivker & Giorgio Colombo - 1-20 Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures
by Alberto Pascual-García & David Abia & Ángel R Ortiz & Ugo Bastolla - 1-24 Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System
by Patrick Blomquist & Anna Devor & Ulf G Indahl & Istvan Ulbert & Gaute T Einevoll & Anders M Dale
February 2009, Volume 5, Issue 2
- 1-10 Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing
by John M Higgins & David T Eddington & Sangeeta N Bhatia & L Mahadevan - 1-12 Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments
by Vincent A Voelz & M Scott Shell & Ken A Dill - 1-13 The Temporal Winner-Take-All Readout
by Maoz Shamir - 1-14 Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins
by Michael D Daily & Jeffrey J Gray - 1-17 Rapid Sampling of Molecular Motions with Prior Information Constraints
by Barak Raveh & Angela Enosh & Ora Schueler-Furman & Dan Halperin - 1-20 Stochastically Gating Ion Channels Enable Patterned Spike Firing through Activity-Dependent Modulation of Spike Probability
by Joshua T Dudman & Matthew F Nolan
April 2009, Volume 5, Issue 1
- 1-9 Estimating the Location and Spatial Extent of a Covert Anthrax Release
by Judith Legrand & Joseph R Egan & Ian M Hall & Simon Cauchemez & Steve Leach & Neil M Ferguson
January 2009, Volume 5, Issue 1
- 1-1 A Review of 2008 for PLoS Computational Biology
by Evie Browne & Rosemary Dickin & Philip E Bourne - 1-5 Microblogging the ISMB: A New Approach to Conference Reporting
by Neil Saunders & Pedro Beltrão & Lars Jensen & Daniel Jurczak & Roland Krause & Michael Kuhn & Shirley Wu - 1-7 Action Potential Initiation in the Hodgkin-Huxley Model
by Lucy J Colwell & Michael P Brenner - 1-12 Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures
by Dirk Müller & Jörg Stelling - 1-12 State Based Model of Long-Term Potentiation and Synaptic Tagging and Capture
by Adam B Barrett & Guy O Billings & Richard G M Morris & Mark C W van Rossum - 1-12 Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks
by Adel Dayarian & Madalena Chaves & Eduardo D Sontag & Anirvan M Sengupta - 1-12 Evolutionary Sequence Modeling for Discovery of Peptide Hormones
by Kemal Sonmez & Naunihal T Zaveri & Ilan A Kerman & Sharon Burke & Charles R Neal & Xinmin Xie & Stanley J Watson & Lawrence Toll - 1-15 Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties
by Wenxu Tong & Ying Wei & Leonel F Murga & Mary Jo Ondrechen & Ronald J Williams - 1-20 Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches
by Sinisa Pajevic & Dietmar Plenz
December 2008, Volume 4, Issue 12
- 1-3 I Am Not a Scientist, I Am a Number
by Philip E Bourne & J Lynn Fink - 1-7 Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation
by Antonio Scialdone & Mario Nicodemi - 1-7 The Morphological Identity of Insect Dendrites
by Hermann Cuntz & Friedrich Forstner & Juergen Haag & Alexander Borst - 1-7 Disordered Flanks Prevent Peptide Aggregation
by Sanne Abeln & Daan Frenkel - 1-10 Identification of Mechanosensitive Genes during Embryonic Bone Formation
by Niamh C Nowlan & Patrick J Prendergast & Paula Murphy - 1-12 Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment
by Da-Wei Li & Sandipan Mohanty & Anders Irbäck & Shuanghong Huo - 1-14 Game Theory of Mind
by Wako Yoshida & Ray J Dolan & Karl J Friston - 1-14 Search Algorithms as a Framework for the Optimization of Drug Combinations
by Diego Calzolari & Stefania Bruschi & Laurence Coquin & Jennifer Schofield & Jacob D Feala & John C Reed & Andrew D McCulloch & Giovanni Paternostro - 1-17 Dependence of Bacterial Chemotaxis on Gradient Shape and Adaptation Rate
by Nikita Vladimirov & Linda Løvdok & Dirk Lebiedz & Victor Sourjik
November 2008, Volume 4, Issue 11
- 1-7 A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates
by Stefan Auer & Filip Meersman & Christopher M Dobson & Michele Vendruscolo - 1-11 Order-Based Representation in Random Networks of Cortical Neurons
by Goded Shahaf & Danny Eytan & Asaf Gal & Einat Kermany & Vladimir Lyakhov & Christoph Zrenner & Shimon Marom - 1-12 Behavioral Sequence Analysis Reveals a Novel Role for ß2* Nicotinic Receptors in Exploration
by Nicolas Maubourguet & Annick Lesne & Jean-Pierre Changeux & Uwe Maskos & Philippe Faure - 1-12 A Hierarchy of Time-Scales and the Brain
by Stefan J Kiebel & Jean Daunizeau & Karl J Friston - 1-14 Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks
by Sheila M Reynolds & Lukas Käll & Michael E Riffle & Jeff A Bilmes & William Stafford Noble - 1-17 A Low Dimensional Description of Globally Coupled Heterogeneous Neural Networks of Excitatory and Inhibitory Neurons
by Roxana A Stefanescu & Viktor K Jirsa - 1-21 A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast
by Anshul Kundaje & Xiantong Xin & Changgui Lan & Steve Lianoglou & Mei Zhou & Li Zhang & Christina Leslie - 1-23 Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
by Jonathan M Carlson & Zabrina L Brumme & Christine M Rousseau & Chanson J Brumme & Philippa Matthews & Carl Kadie & James I Mullins & Bruce D Walker & P Richard Harrigan & Philip J R Goulder & David Heckerman - 1-24 Hierarchical Models in the Brain
by Karl Friston
October 2008, Volume 4, Issue 10
- 1-9 Aggregation Propensity of the Human Proteome
by Elodie Monsellier & Matteo Ramazzotti & Niccolò Taddei & Fabrizio Chiti - 1-10 Support Vector Machines and Kernels for Computational Biology
by Asa Ben-Hur & Cheng Soon Ong & Sören Sonnenburg & Bernhard Schölkopf & Gunnar Rätsch - 1-10 Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs
by Ran Elkon & Reuven Agami - 1-10 Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data
by Piers J Ingram & Michael P H Stumpf & Jaroslav Stark - 1-12 Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
by Yang Shen & Ioannis Ch Paschalidis & Pirooz Vakili & Sandor Vajda - 1-12 Noise during Rest Enables the Exploration of the Brain's Dynamic Repertoire
by Anandamohan Ghosh & Y Rho & A R McIntosh & R Kötter & V K Jirsa