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February 2013, Volume 9, Issue 2
- 1-14 Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model
by Thomas Stockner & Therese R Montgomery & Oliver Kudlacek & Rene Weissensteiner & Gerhard F Ecker & Michael Freissmuth & Harald H Sitte - 1-14 Biomolecular Events in Cancer Revealed by Attractor Metagenes
by Wei-Yi Cheng & Tai-Hsien Ou Yang & Dimitris Anastassiou - 1-14 Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila
by Andrea Censi & Andrew D Straw & Rosalyn W Sayaman & Richard M Murray & Michael H Dickinson - 1-15 Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions
by Romain Daniel Cazé & Mark Humphries & Boris Gutkin - 1-18 Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data
by Gerard J P van Westen & Alwin Hendriks & Jörg K Wegner & Adriaan P IJzerman & Herman W T van Vlijmen & Andreas Bender - 1-19 Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models
by Paul Michael Loriaux & Glenn Tesler & Alexander Hoffmann - 1-19 Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs
by Robert R Kerr & Anthony N Burkitt & Doreen A Thomas & Matthieu Gilson & David B Grayden
January 2013, Volume 9, Issue 1
- 1-3 Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator
by Jeroen de Ridder & Thomas Abeel & Magali Michaut & Venkata P Satagopam & Nils Gehlenborg - 1-6 Reward from Punishment Does Not Emerge at All Costs
by Jeromos Vukov & Flávio L Pinheiro & Francisco C Santos & Jorge M Pacheco - 1-9 Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation
by Linan Xu & Naushaba Hasin & Manli Shen & Jianwei He & Youlin Xue & Xiaohong Zhou & Sarah Perrett & Youtao Song & Gary W Jones - 1-9 The Effects of City Streets on an Urban Disease Vector
by Corentin M Barbu & Andrew Hong & Jennifer M Manne & Dylan S Small & Javier E Quintanilla Calderón & Karthik Sethuraman & Víctor Quispe-Machaca & Jenny Ancca-Juárez & Juan G Cornejo del Carpio & Fernando S Málaga Chavez & César Náquira & Michael Z Levy - 1-10 Approximate Bayesian Computation
by Mikael Sunnåker & Alberto Giovanni Busetto & Elina Numminen & Jukka Corander & Matthieu Foll & Christophe Dessimoz - 1-10 Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin
by Giovanni Settanni & David Serquera & Piotr E Marszalek & Emanuele Paci & Laura S Itzhaki - 1-11 Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations
by Thomas Lemmin & Cinque S Soto & Graham Clinthorne & William F DeGrado & Matteo Dal Peraro - 1-11 The Human Functional Brain Network Demonstrates Structural and Dynamical Resilience to Targeted Attack
by Karen E Joyce & Satoru Hayasaka & Paul J Laurienti - 1-12 The Effects of Temperature on the Stability of a Neuronal Oscillator
by Anatoly Rinberg & Adam L Taylor & Eve Marder - 1-13 Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images
by Fabian Sinz & Matthias Bethge - 1-13 Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy
by Niklas Wilming & Simon Harst & Nico Schmidt & Peter König - 1-13 Maximizing the Information Content of Experiments in Systems Biology
by Juliane Liepe & Sarah Filippi & Michał Komorowski & Michael P H Stumpf - 1-14 How Evolving Heterogeneity Distributions of Resource Allocation Strategies Shape Mortality Patterns
by Yann Le Cunff & Annette Baudisch & Khashayar Pakdaman - 1-14 Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships
by Nives Škunca & Matko Bošnjak & Anita Kriško & Panče Panov & Sašo Džeroski & Tomislav Šmuc & Fran Supek - 1-15 Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective
by Graham Rockwell & Nicholas J Guido & George M Church - 1-15 Refractoriness in Sustained Visuo-Manual Control: Is the Refractory Duration Intrinsic or Does It Depend on External System Properties?
by Cornelis van de Kamp & Peter J Gawthrop & Henrik Gollee & Ian D Loram - 1-15 Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics
by Nol Chindapol & Jaap A Kaandorp & Carolina Cronemberger & Tali Mass & Amatzia Genin - 1-15 Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations
by Hang Yu & Klaus Schulten - 1-17 Significance Analysis of Prognostic Signatures
by Andrew H Beck & Nicholas W Knoblauch & Marco M Hefti & Jennifer Kaplan & Stuart J Schnitt & Aedin C Culhane & Markus S Schroeder & Thomas Risch & John Quackenbush & Benjamin Haibe-Kains - 1-21 Dynamic Finite Size Effects in Spiking Neural Networks
by Michael A Buice & Carson C Chow
December 2012, Volume 8, Issue 12
- 1-3 Ten Simple Rules for the Open Development of Scientific Software
by Andreas Prlić & James B Procter - 1-8 Chapter 2: Data-Driven View of Disease Biology
by Casey S Greene & Olga G Troyanskaya - 1-9 Chapter 10: Mining Genome-Wide Genetic Markers
by Xiang Zhang & Shunping Huang & Zhaojun Zhang & Wei Wang - 1-9 Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought
by Ting Xiang & Debajyoti Ray & Terry Lohrenz & Peter Dayan & P Read Montague - 1-10 Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking
by Jens Vindahl Kringelum & Claus Lundegaard & Ole Lund & Morten Nielsen - 1-10 Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures
by Niels Röckendorf & Markus Borschbach & Andreas Frey - 1-12 Chapter 9: Analyses Using Disease Ontologies
by Nigam H Shah & Tyler Cole & Mark A Musen - 1-12 Chapter 8: Biological Knowledge Assembly and Interpretation
by Ju Han Kim - 1-13 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density
by Claudia Coronnello & Ryan Hartmaier & Arshi Arora & Luai Huleihel & Kusum V Pandit & Abha S Bais & Michael Butterworth & Naftali Kaminski & Gary D Stormo & Steffi Oesterreich & Panayiotis V Benos - 1-13 Mechanics of Undulatory Swimming in a Frictional Fluid
by Yang Ding & Sarah S Sharpe & Andrew Masse & Daniel I Goldman - 1-14 SnIPRE: Selection Inference Using a Poisson Random Effects Model
by Kirsten E Eilertson & James G Booth & Carlos D Bustamante - 1-14 ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes
by Kishore R Mosaliganti & Ramil R Noche & Fengzhu Xiong & Ian A Swinburne & Sean G Megason - 1-14 Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells
by Katja Rateitschak & Felix Winter & Falko Lange & Robert Jaster & Olaf Wolkenhauer - 1-14 Interconnected Cavernous Structure of Bacterial Fruiting Bodies
by Cameron W Harvey & Huijing Du & Zhiliang Xu & Dale Kaiser & Igor Aranson & Mark Alber - 1-14 Calcium Wave Propagation in Networks of Endothelial Cells: Model-based Theoretical and Experimental Study
by Juexuan Long & Michael Junkin & Pak Kin Wong & James Hoying & Pierre Deymier - 1-15 Chapter 13: Mining Electronic Health Records in the Genomics Era
by Joshua C Denny - 1-17 A Comparison of Computational Models for Eukaryotic Cell Shape and Motility
by William R Holmes & Leah Edelstein-Keshet - 1-18 Chapter 7: Pharmacogenomics
by Konrad J Karczewski & Roxana Daneshjou & Russ B Altman
November 2012, Volume 8, Issue 11
- 1-2 The PLOS Computational Biology Software Section
by Andreas Prlić & Hilmar Lapp - 1-4 Ten Simple Rules to Protect Your Intellectual Property
by Mark Jolly & Anthony C Fletcher & Philip E Bourne - 1-9 pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4
by Natali V Di Russo & Dario A Estrin & Marcelo A Martí & Adrian E Roitberg - 1-11 How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population
by Nicolas Perony & Claudio J Tessone & Barbara König & Frank Schweitzer - 1-12 Mesoscopic Model of Actin-Based Propulsion
by Jie Zhu & Alex Mogilner - 1-13 Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens
by Renske M A Vroomans & Athanasius F M Marée & Rob J de Boer & Joost B Beltman - 1-13 A Graphical Modelling Approach to the Dissection of Highly Correlated Transcription Factor Binding Site Profiles
by Robert Stojnic & Audrey Qiuyan Fu & Boris Adryan - 1-14 Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay
by Filippo Cacace & Paola Paci & Valerio Cusimano & Alfredo Germani & Lorenzo Farina - 1-14 A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data
by Marco J Morelli & Gaël Thébaud & Joël Chadœuf & Donald P King & Daniel T Haydon & Samuel Soubeyrand - 1-14 Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles
by Gergely Boza & Ádám Kun & István Scheuring & Ulf Dieckmann - 1-15 Efficient “Communication through Coherence” Requires Oscillations Structured to Minimize Interference between Signals
by Thomas E Akam & Dimitri M Kullmann - 1-15 Reconstructing Mammalian Sleep Dynamics with Data Assimilation
by Madineh Sedigh-Sarvestani & Steven J Schiff & Bruce J Gluckman - 1-16 The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains
by Márton Münz & Jotun Hein & Philip C Biggin - 1-17 Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation
by Anupam Saxena & Hod Lipson & Francisco J Valero-Cuevas - 1-19 Internal Representations of Temporal Statistics and Feedback Calibrate Motor-Sensory Interval Timing
by Luigi Acerbi & Daniel M Wolpert & Sethu Vijayakumar - 1-24 Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis
by Lars Reichl & Dominik Heide & Siegrid Löwel & Justin C Crowley & Matthias Kaschube & Fred Wolf - 1-26 Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies
by Lars Reichl & Dominik Heide & Siegrid Löwel & Justin C Crowley & Matthias Kaschube & Fred Wolf
October 2012, Volume 8, Issue 10
- 1-2 Seven Years; It's Time for a Change
by Philip E Bourne - 1-10 Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations
by Noah S Bieler & Tuomas P J Knowles & Daan Frenkel & Robert Vácha - 1-10 Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection
by Jan H Peters & Bert L de Groot - 1-10 Probability Fluxes and Transition Paths in a Markovian Model Describing Complex Subunit Cooperativity in HCN2 Channels
by Klaus Benndorf & Jana Kusch & Eckhard Schulz - 1-10 How Recent History Affects Perception: The Normative Approach and Its Heuristic Approximation
by Ofri Raviv & Merav Ahissar & Yonatan Loewenstein - 1-12 CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
by Eva Chovancova & Antonin Pavelka & Petr Benes & Ondrej Strnad & Jan Brezovsky & Barbora Kozlikova & Artur Gora & Vilem Sustr & Martin Klvana & Petr Medek & Lada Biedermannova & Jiri Sochor & Jiri Damborsky - 1-12 Predictive Dynamics of Human Pain Perception
by Guillermo A Cecchi & Lejian Huang & Javeria Ali Hashmi & Marwan Baliki & María V Centeno & Irina Rish & A Vania Apkarian - 1-12 Very Slow Search and Reach: Failure to Maximize Expected Gain in an Eye-Hand Coordination Task
by Hang Zhang & Camille Morvan & Louis-Alexandre Etezad-Heydari & Laurence T Maloney - 1-12 Evaluating the Adequacy of Gravity Models as a Description of Human Mobility for Epidemic Modelling
by James Truscott & Neil M Ferguson - 1-13 Emergence of the Mitochondrial Reticulum from Fission and Fusion Dynamics
by Valerii M Sukhorukov & Daniel Dikov & Andreas S Reichert & Michael Meyer-Hermann - 1-13 A Model of Reward- and Effort-Based Optimal Decision Making and Motor Control
by Lionel Rigoux & Emmanuel Guigon - 1-13 Analysis of Slow (Theta) Oscillations as a Potential Temporal Reference Frame for Information Coding in Sensory Cortices
by Christoph Kayser & Robin A A Ince & Stefano Panzeri - 1-14 Estimating the Hidden Burden of Bovine Tuberculosis in Great Britain
by Andrew J K Conlan & Trevelyan J McKinley & Katerina Karolemeas & Ellen Brooks Pollock & Anthony V Goodchild & Andrew P Mitchell & Colin P D Birch & Richard S Clifton-Hadley & James L N Wood - 1-14 Coding and Decoding with Adapting Neurons: A Population Approach to the Peri-Stimulus Time Histogram
by Richard Naud & Wulfram Gerstner - 1-16 Spatially Pooled Contrast Responses Predict Neural and Perceptual Similarity of Naturalistic Image Categories
by Iris I A Groen & Sennay Ghebreab & Victor A F Lamme & H Steven Scholte - 1-17 Modeling Dynamic Regulatory Processes in Stroke
by Jason E McDermott & Kenneth Jarman & Ronald Taylor & Mary Lancaster & Harish Shankaran & Keri B Vartanian & Susan L Stevens & Mary P Stenzel-Poore & Antonio Sanfilippo - 1-31 How Entorhinal Grid Cells May Learn Multiple Spatial Scales from a Dorsoventral Gradient of Cell Response Rates in a Self-organizing Map
by Stephen Grossberg & Praveen K Pilly
September 2012, Volume 8, Issue 9
- 1-3 Ten Simple Rules To Commercialize Scientific Research
by Anthony C Fletcher & Philip E Bourne - 1-3 Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models
by Antony J Williams & John Wilbanks & Sean Ekins - 1-7 Risk-Sensitivity in Bayesian Sensorimotor Integration
by Jordi Grau-Moya & Pedro A Ortega & Daniel A Braun - 1-8 Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function
by Michael A Jamros & Leandro C Oliveira & Paul C Whitford & José N Onuchic & Joseph A Adams & Patricia A Jennings - 1-9 Speeded Reaching Movements around Invisible Obstacles
by Todd E Hudson & Uta Wolfe & Laurence T Maloney - 1-9 Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study
by Iskra Staneva & Yongqi Huang & Zhirong Liu & Stefan Wallin - 1-9 Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles
by Benjamin A Hall & Judith P Armitage & Mark S P Sansom - 1-10 Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks
by Oded Magger & Yedael Y Waldman & Eytan Ruppin & Roded Sharan - 1-10 Analysis of Surface Protein Expression Reveals the Growth Pattern of the Gram-Negative Outer Membrane
by Tristan S Ursell & Eliane H Trepagnier & Kerwyn Casey Huang & Julie A Theriot - 1-10 The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels
by Danielle E Chandler & François Penin & Klaus Schulten & Christophe Chipot - 1-10 Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease
by Omar Haq & Michael Andrec & Alexandre V Morozov & Ronald M Levy - 1-11 Confidence-based Somatic Mutation Evaluation and Prioritization
by Martin Löwer & Bernhard Y Renard & Jos de Graaf & Meike Wagner & Claudia Paret & Christoph Kneip & Özlem Türeci & Mustafa Diken & Cedrik Britten & Sebastian Kreiter & Michael Koslowski & John C Castle & Ugur Sahin - 1-12 Spike-based Decision Learning of Nash Equilibria in Two-Player Games
by Johannes Friedrich & Walter Senn - 1-12 High-throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications
by Ping-Chang Lee & Chao-Chun Chuang & Ann-Shyn Chiang & Yu-Tai Ching - 1-13 Spike-Timing Dependence of Structural Plasticity Explains Cooperative Synapse Formation in the Neocortex
by Moritz Deger & Moritz Helias & Stefan Rotter & Markus Diesmann - 1-13 The Mechanistic Basis of Myxococcus xanthus Rippling Behavior and Its Physiological Role during Predation
by Haiyang Zhang & Zalman Vaksman & Douglas B Litwin & Peng Shi & Heidi B Kaplan & Oleg A Igoshin - 1-13 Dependencies among Editing Sites in Serotonin 2C Receptor mRNA
by Liran Carmel & Eugene V Koonin & Stella Dracheva - 1-15 The Spatial Structure of Stimuli Shapes the Timescale of Correlations in Population Spiking Activity
by Ashok Litwin-Kumar & Maurice J Chacron & Brent Doiron - 1-15 Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations
by Evelyne Deplazes & Martti Louhivuori & Dylan Jayatilaka & Siewert J Marrink & Ben Corry - 1-16 Multistationary and Oscillatory Modes of Free Radicals Generation by the Mitochondrial Respiratory Chain Revealed by a Bifurcation Analysis
by Vitaly A Selivanov & Marta Cascante & Mark Friedman & Mark F Schumaker & Massimo Trucco & Tatyana V Votyakova - 1-16 Predicting the Extension of Biomedical Ontologies
by Catia Pesquita & Francisco M Couto - 1-17 Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts
by Tobias Sikosek & Erich Bornberg-Bauer & Hue Sun Chan - 1-20 Spontaneous Excitation Patterns Computed for Axons with Injury-like Impairments of Sodium Channels and Na/K Pumps
by Na Yu & Catherine E Morris & Béla Joós & André Longtin - 1-20 An Online Bioinformatics Curriculum
by David B Searls
August 2012, Volume 8, Issue 8
- 1-1 Design and Implementation of a Genomics Field Trip Program Aimed at Secondary School Students
by Jennifer McQueen & Jody J Wright & Joanne A Fox - 1-1 Unifying Time to Contact Estimation and Collision Avoidance across Species
by Matthias S Keil & Joan López-Moliner - 1-7 Evolutionary Dynamics of Strategic Behavior in a Collective-Risk Dilemma
by Maria Abou Chakra & Arne Traulsen - 1-8 Hybrid Models and Biological Model Reduction with PyDSTool
by Robert Clewley - 1-10 The Roots of Bioinformatics in ISMB
by Todd A Gibson - 1-11 Locust Dynamics: Behavioral Phase Change and Swarming
by Chad M Topaz & Maria R D'Orsogna & Leah Edelstein-Keshet & Andrew J Bernoff - 1-13 A Network-based Approach for Predicting Missing Pathway Interactions
by Saket Navlakha & Anthony Gitter & Ziv Bar-Joseph - 1-14 The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles
by Deena M A Gendoo & Paul M Harrison - 1-14 A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology
by Y Dabaghian & F Mémoli & L Frank & G Carlsson - 1-14 Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems
by Georg K Gerber & Andrew B Onderdonk & Lynn Bry - 1-15 Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case
by Rebeca García-Fandiño & Pau Bernadó & Sara Ayuso-Tejedor & Javier Sancho & Modesto Orozco - 1-15 A Canonical Model of Multistability and Scale-Invariance in Biological Systems
by Frank Freyer & James A Roberts & Petra Ritter & Michael Breakspear - 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 - 1-19 Performance Limitations of Relay Neurons
by Rahul Agarwal & Sridevi V Sarma - 1-22 Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration
by Allen Cheung & David Ball & Michael Milford & Gordon Wyeth & Janet Wiles - 1-29 Decorrelation of Neural-Network Activity by Inhibitory Feedback
by Tom Tetzlaff & Moritz Helias & Gaute T Einevoll & Markus Diesmann
July 2012, Volume 8, Issue 7
- 1-4 Bioinformatics Meets User-Centred Design: A Perspective
by Katrina Pavelin & Jennifer A Cham & Paula de Matos & Cath Brooksbank & Graham Cameron & Christoph Steinbeck - 1-5 Which of Our Modeling Predictions Are Robust?
by Rob J De Boer - 1-5 Data Sharing in the Post-Genomic World: The Experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO)
by Yann Joly & Edward S Dove & Bartha M Knoppers & Martin Bobrow & Don Chalmers - 1-7 A Quick Guide to Software Licensing for the Scientist-Programmer
by Andrew Morin & Jennifer Urban & Piotr Sliz - 1-8 Automated Tracking of Whiskers in Videos of Head Fixed Rodents
by Nathan G Clack & Daniel H O'Connor & Daniel Huber & Leopoldo Petreanu & Andrew Hires & Simon Peron & Karel Svoboda & Eugene W Myers - 1-9 Predicting Signatures of “Synthetic Associations” and “Natural Associations” from Empirical Patterns of Human Genetic Variation
by Diana Chang & Alon Keinan - 1-10 A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations
by Michael Knott & Robert B Best - 1-10 Assessing Drug Target Association Using Semantic Linked Data
by Bin Chen & Ying Ding & David J Wild - 1-11 Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia
by Peilin Jia & Lily Wang & Ayman H Fanous & Carlos N Pato & Todd L Edwards & The International Schizophrenia Consortium & Zhongming Zhao - 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 Individual Rules for Trail Pattern Formation in Argentine Ants (Linepithema humile)
by Andrea Perna & Boris Granovskiy & Simon Garnier & Stamatios C Nicolis & Marjorie Labédan & Guy Theraulaz & Vincent Fourcassié & David J T Sumpter - 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 - 1-12 Adaptive Temperature Compensation in Circadian Oscillations
by Paul François & Nicolas Despierre & Eric D Siggia - 1-13 Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation
by Jason Flannick & Joshua M Korn & Pierre Fontanillas & George B Grant & Eric Banks & Mark A Depristo & David Altshuler - 1-15 Shaping the Dynamics of a Bidirectional Neural Interface
by Alessandro Vato & Marianna Semprini & Emma Maggiolini & Francois D Szymanski & Luciano Fadiga & Stefano Panzeri & Ferdinando A Mussa-Ivaldi - 1-15 A Range-Normalization Model of Context-Dependent Choice: A New Model and Evidence
by Alireza Soltani & Benedetto De Martino & Colin Camerer - 1-16 Coding Conspecific Identity and Motion in the Electric Sense
by Na Yu & Ginette Hupé & Charles Garfinkle & John E Lewis & André Longtin - 1-18 Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity
by Miles Miller & Marc Hafner & Eduardo Sontag & Noah Davidsohn & Sairam Subramanian & Priscilla E M Purnick & Douglas Lauffenburger & Ron Weiss - 1-22 Spectral Analysis of Input Spike Trains by Spike-Timing-Dependent Plasticity
by Matthieu Gilson & Tomoki Fukai & Anthony N Burkitt
June 2012, Volume 8, Issue 6
- 1-1 Complementarity of Spike- and Rate-Based Dynamics of Neural Systems
by M T Wilson & P A Robinson & B O'Neill & D A Steyn-Ross - 1-2 What Can Systems Theory of Networks Offer to Biology?
by Indika Rajapakse & Mark Groudine & Mehran Mesbahi - 1-2 A Report of the Curriculum Task Force of the ISCB Education Committee
by Lonnie R Welch & Russell Schwartz & Fran Lewitter - 1-9 Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems
by Carlo Chan & Xinfeng Liu & Liming Wang & Lee Bardwell & Qing Nie & Germán Enciso - 1-9 A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis
by R Zachariah Aandahl & Josephine F Reyes & Scott A Sisson & Mark M Tanaka - 1-10 MC EMiNEM Maps the Interaction Landscape of the Mediator
by Theresa Niederberger & Stefanie Etzold & Michael Lidschreiber & Kerstin C Maier & Dietmar E Martin & Holger Fröhlich & Patrick Cramer & Achim Tresch - 1-11 Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation
by Crina-Maria Ionescu & Radka Svobodová Vařeková & Jochen H M Prehn & Heinrich J Huber & Jaroslav Koča - 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 Structural Drift: The Population Dynamics of Sequential Learning
by James P Crutchfield & Sean Whalen - 1-12 The Role of Non-Native Interactions in the Folding of Knotted Proteins
by Tatjana Škrbić & Cristian Micheletti & Pietro Faccioli - 1-15 Complex Spatial Dynamics of Oncolytic Viruses In Vitro: Mathematical and Experimental Approaches
by Dominik Wodarz & Andrew Hofacre & John W Lau & Zhiying Sun & Hung Fan & Natalia L Komarova - 1-15 Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach
by Hector Garcia-Seisdedos & Beatriz Ibarra-Molero & Jose M Sanchez-Ruiz - 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 - 1-16 Fast Coding of Orientation in Primary Visual Cortex
by Oren Shriki & Adam Kohn & Maoz Shamir - 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 - 1-18 Short Term Synaptic Depression Imposes a Frequency Dependent Filter on Synaptic Information Transfer
by Robert Rosenbaum & Jonathan Rubin & Brent Doiron - 1-18 Deceleration of Fusion–Fission Cycles Improves Mitochondrial Quality Control during Aging
by Marc Thilo Figge & Andreas S Reichert & Michael Meyer-Hermann & Heinz D Osiewacz
May 2012, Volume 8, Issue 5
- 1-8 Simulation of Molecular Data under Diverse Evolutionary Scenarios
by Miguel Arenas - 1-10 Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments
by Sepideh Bazazi & Frederic Bartumeus & Joseph J Hale & Iain D Couzin - 1-10 Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs
by Adrian M Altenhoff & Romain A Studer & Marc Robinson-Rechavi & Christophe Dessimoz - 1-11 Quality of Computationally Inferred Gene Ontology Annotations
by Nives Škunca & Adrian Altenhoff & Christophe Dessimoz - 1-12 Exploring Massive, Genome Scale Datasets with the GenometriCorr Package
by Alexander Favorov & Loris Mularoni & Leslie M Cope & Yulia Medvedeva & Andrey A Mironov & Vsevolod J Makeev & Sarah J Wheelan - 1-12 Crossing Over…Markov Meets Mendel
by Saad Mneimneh - 1-12 Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference
by Feixiong Cheng & Chuang Liu & Jing Jiang & Weiqiang Lu & Weihua Li & Guixia Liu & Weixing Zhou & Jin Huang & Yun Tang - 1-13 A Spatial Model of Mosquito Host-Seeking Behavior
by Bree Cummins & Ricardo Cortez & Ivo M Foppa & Justin Walbeck & James M Hyman - 1-13 Termination of Ca2+ Release for Clustered IP3R Channels
by Sten Rüdiger & Peter Jung & Jian-Wei Shuai - 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 - 1-14 Identification of Molecular Pathologies Sufficient to Cause Neuropathic Excitability in Primary Somatosensory Afferents Using Dynamical Systems Theory
by Young-Ah Rho & Steven A Prescott - 1-16 Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes
by Christof Winter & Glen Kristiansen & Stephan Kersting & Janine Roy & Daniela Aust & Thomas Knösel & Petra Rümmele & Beatrix Jahnke & Vera Hentrich & Felix Rückert & Marco Niedergethmann & Wilko Weichert & Marcus Bahra & Hans J Schlitt & Utz Settmacher & Helmut Friess & Markus Büchler & Hans-Detlev Saeger & Michael Schroeder & Christian Pilarsky & Robert Grützmann - 1-16 Conformational Spread in the Flagellar Motor Switch: A Model Study
by Qi Ma & Dan V Nicolau Jr & Philip K Maini & Richard M Berry & Fan Bai - 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 - 1-17 Emergence of a Small-World Functional Network in Cultured Neurons
by Julia H Downes & Mark W Hammond & Dimitris Xydas & Matthew C Spencer & Victor M Becerra & Kevin Warwick & Ben J Whalley & Slawomir J Nasuto - 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 - 1-21 The Layer-Oriented Approach to Declarative Languages for Biological Modeling
by Ivan Raikov & Erik De Schutter
April 2012, Volume 8, Issue 4
- 1-1 Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?
by Mahmoud Moradi & Volodymyr Babin & Christopher Roland & Celeste Sagui - 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 - 1-9 Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability
by Yunpeng Wang & Arne B Gjuvsland & Jon Olav Vik & Nicolas P Smith & Peter J Hunter & Stig W Omholt - 1-9 Non-Additive Coupling Enables Propagation of Synchronous Spiking Activity in Purely Random Networks
by Raoul-Martin Memmesheimer & Marc Timme - 1-10 Storage of Correlated Patterns in Standard and Bistable Purkinje Cell Models
by Claudia Clopath & Jean-Pierre Nadal & Nicolas Brunel - 1-10 The Impact of Imitation on Vaccination Behavior in Social Contact Networks
by Martial L Ndeffo Mbah & Jingzhou Liu & Chris T Bauch & Yonas I Tekel & Jan Medlock & Lauren Ancel Meyers & Alison P Galvani - 1-11 Determinants of Sexual Network Structure and Their Impact on Cumulative Network Measures
by Boris V Schmid & Mirjam Kretzschmar - 1-11 Power-Law Inter-Spike Interval Distributions Infer a Conditional Maximization of Entropy in Cortical Neurons
by Yasuhiro Tsubo & Yoshikazu Isomura & Tomoki Fukai - 1-12 Tension and Robustness in Multitasking Cellular Networks
by Jeffrey V Wong & Bochong Li & Lingchong You - 1-12 Evolutionary Game Theory and Social Learning Can Determine How Vaccine Scares Unfold
by Chris T Bauch & Samit Bhattacharyya - 1-12 Deconvolution of the Cellular Force-Generating Subsystems that Govern Cytokinesis Furrow Ingression
by Christopher C Poirier & Win Pin Ng & Douglas N Robinson & Pablo A Iglesias - 1-12 Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity
by Kyle E Roberts & Patrick R Cushing & Prisca Boisguerin & Dean R Madden & Bruce R Donald - 1-12 Optimizing Provider Recruitment for Influenza Surveillance Networks
by Samuel V Scarpino & Nedialko B Dimitrov & Lauren Ancel Meyers - 1-12 What Can Causal Networks Tell Us about Metabolic Pathways?
by Rachael Hageman Blair & Daniel J Kliebenstein & Gary A Churchill - 1-15 Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons
by Kyriaki Sidiropoulou & Panayiota Poirazi - 1-15 Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis
by Suzanne Gaudet & Sabrina L Spencer & William W Chen & Peter K Sorger - 1-15 Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein
by Yong Wang & Chun Tang & Erkang Wang & Jin Wang - 1-17 Optimization of Muscle Activity for Task-Level Goals Predicts Complex Changes in Limb Forces across Biomechanical Contexts
by J Lucas McKay & Lena H Ting - 1-21 Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA
by Dina Zhabinskaya & Craig J Benham
March 2012, Volume 8, Issue 3
- 1-1 A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons
by Dimitrios V Vavoulis & Volko A Straub & John A D Aston & Jianfeng Feng - 1-3 Ten Simple Rules for Starting a Company
by Anthony C Fletcher & Philip E Bourne - 1-8 Beyond the Binding Site: The Role of the β2 – β3 Loop and Extra-Domain Structures in PDZ Domains
by Stefano Mostarda & David Gfeller & Francesco Rao - 1-8 Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza
by Ken T D Eames & Natasha L Tilston & Ellen Brooks-Pollock & W John Edmunds