PLOS Computational Biology

2005 - 2022

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Volume 4, issue 12, 2008

Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment pp. 1-12

Da-Wei Li, Sandipan Mohanty, Anders Irbäck and Shuanghong Huo

Identification of Mechanosensitive Genes during Embryonic Bone Formation pp. 1-10

Niamh C Nowlan, Patrick J Prendergast and Paula Murphy

Search Algorithms as a Framework for the Optimization of Drug Combinations pp. 1-14

Diego Calzolari, Stefania Bruschi, Laurence Coquin, Jennifer Schofield, Jacob D Feala, John C Reed, Andrew D McCulloch and Giovanni Paternostro

Game Theory of Mind pp. 1-14

Wako Yoshida, Ray J Dolan and Karl J Friston

Disordered Flanks Prevent Peptide Aggregation pp. 1-7

Sanne Abeln and Daan Frenkel

Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation pp. 1-7

Antonio Scialdone and Mario Nicodemi

The Morphological Identity of Insect Dendrites pp. 1-7

Hermann Cuntz, Friedrich Forstner, Juergen Haag and Alexander Borst

I Am Not a Scientist, I Am a Number pp. 1-3

Philip E Bourne and J Lynn Fink

Dependence of Bacterial Chemotaxis on Gradient Shape and Adaptation Rate pp. 1-17

Nikita Vladimirov, Linda Løvdok, Dirk Lebiedz and Victor Sourjik

Volume 4, issue 11, 2008

A Low Dimensional Description of Globally Coupled Heterogeneous Neural Networks of Excitatory and Inhibitory Neurons pp. 1-17

Roxana A Stefanescu and Viktor K Jirsa

Order-Based Representation in Random Networks of Cortical Neurons pp. 1-11

Goded Shahaf, Danny Eytan, Asaf Gal, Einat Kermany, Vladimir Lyakhov, Christoph Zrenner and Shimon Marom

A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates pp. 1-7

Stefan Auer, Filip Meersman, Christopher M Dobson and Michele Vendruscolo

Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks pp. 1-14

Sheila M Reynolds, Lukas Käll, Michael E Riffle, Jeff A Bilmes and William Stafford Noble

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag pp. 1-23

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 and David Heckerman

A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast pp. 1-21

Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang and Christina Leslie

A Hierarchy of Time-Scales and the Brain pp. 1-12

Stefan J Kiebel, Jean Daunizeau and Karl J Friston

Behavioral Sequence Analysis Reveals a Novel Role for ß2* Nicotinic Receptors in Exploration pp. 1-12

Nicolas Maubourguet, Annick Lesne, Jean-Pierre Changeux, Uwe Maskos and Philippe Faure

Hierarchical Models in the Brain pp. 1-24

Karl Friston

Volume 4, issue 10, 2008

Biophysical Basis for Three Distinct Dynamical Mechanisms of Action Potential Initiation pp. 1-18

Steven A Prescott, Yves De Koninck and Terrence J Sejnowski

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes pp. 1-12

Yang Shen, Ioannis Ch Paschalidis, Pirooz Vakili and Sandor Vajda

Noise during Rest Enables the Exploration of the Brain's Dynamic Repertoire pp. 1-12

Anandamohan Ghosh, Y Rho, A R McIntosh, R Kötter and V K Jirsa

Aggregation Propensity of the Human Proteome pp. 1-9

Elodie Monsellier, Matteo Ramazzotti, Niccolò Taddei and Fabrizio Chiti

Support Vector Machines and Kernels for Computational Biology pp. 1-10

Asa Ben-Hur, Cheng Soon Ong, Sören Sonnenburg, Bernhard Schölkopf and Gunnar Rätsch

Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs pp. 1-10

Ran Elkon and Reuven Agami

Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data pp. 1-10

Piers J Ingram, Michael P H Stumpf and Jaroslav Stark

Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web pp. 1-14

Duncan Hull, Steve R Pettifer and Douglas B Kell

Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development pp. 1-15

Szymon Stoma, Mikael Lucas, Jérôme Chopard, Marianne Schaedel, Jan Traas and Christophe Godin

Cell Groups Reveal Structure of Stimulus Space pp. 1-13

Carina Curto and Vladimir Itskov

The Effects of NR2 Subunit-Dependent NMDA Receptor Kinetics on Synaptic Transmission and CaMKII Activation pp. 1-16

David M Santucci and Sridhar Raghavachari

Volume 4, issue 9, 2008

Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo pp. 1-14

Francisco J P Lopes, Fernando M C Vieira, David M Holloway, Paulo M Bisch and Alexander V Spirov

Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information pp. 1-13

Kai Wang, Jeremy A Horst, Gong Cheng, David C Nickle and Ram Samudrala

A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction pp. 1-11

Patrick Flaherty, Mala L Radhakrishnan, Tuan Dinh, Robert A Rebres, Tamara I Roach, Michael I Jordan and Adam P Arkin

Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth pp. 1-16

Roeland M H Merks, Erica D Perryn, Abbas Shirinifard and James A Glazier

Adaptation and Selective Information Transmission in the Cricket Auditory Neuron AN2 pp. 1-18

Klaus Wimmer, K Jannis Hildebrandt, R Matthias Hennig and Klaus Obermayer

Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae pp. 1-10

Ji-Ping Wang, Yvonne Fondufe-Mittendorf, Liqun Xi, Guei-Feng Tsai, Eran Segal and Jonathan Widom

Probabilistic Phylogenetic Inference with Insertions and Deletions pp. 1-21

Elena Rivas and Sean R Eddy

Volume 4, issue 8, 2008

Retroviral Integration Process in the Human Genome: Is It Really Non-Random? A New Statistical Approach pp. 1-6

Alessandro Ambrosi, Claudia Cattoglio and Clelia Di Serio

Host Control of Malaria Infections: Constraints on Immune and Erythropoeitic Response Kinetics pp. 1-15

Philip G McQueen and F Ellis McKenzie

Network Inference Algorithms Elucidate Nrf2 Regulation of Mouse Lung Oxidative Stress pp. 1-15

Ronald C Taylor, George Acquaah-Mensah, Mudita Singhal, Deepti Malhotra and Shyam Biswal

A Novel Three-Phase Model of Brain Tissue Microstructure pp. 1-9

Jana L Gevertz and Salvatore Torquato

Modeling ChIP Sequencing In Silico with Applications pp. 1-10

Zhengdong D Zhang, Joel Rozowsky, Michael Snyder, Joseph Chang and Mark Gerstein

Combining Structural Connectivity and Response Latencies to Model the Structure of the Visual System pp. 1-14

Michael Capalbo, Eric Postma and Rainer Goebel

The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields pp. 1-35

Gustavo Deco, Viktor K Jirsa, Peter A Robinson, Michael Breakspear and Karl Friston

Cooperative Transition between Open and Closed Conformations in Potassium Channels pp. 1-11

Turkan Haliloglu and Nir Ben-Tal

Modeling the Violation of Reward Maximization and Invariance in Reinforcement Schedules pp. 1-17

Giancarlo La Camera and Barry J Richmond

A Feature-Based Approach to Modeling Protein–DNA Interactions pp. 1-17

Eilon Sharon, Shai Lubliner and Eran Segal

Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin pp. 1-13

V V Krishnan, Edmond Y Lau, Justin Yamada, Daniel P Denning, Samir S Patel, Michael E Colvin and Michael F Rexach

The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau pp. 1-12

Austin Huang and Collin M Stultz

Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways pp. 1-12

Sangjo Han and Dongsup Kim

Falling towards Forgetfulness: Synaptic Decay Prevents Spontaneous Recovery of Memory pp. 1-8

James V Stone and Peter E Jupp

Noise Reduction by Diffusional Dissipation in a Minimal Quorum Sensing Motif pp. 1-8

Yu Tanouchi, Dennis Tu, Jungsang Kim and Lingchong You

Volume 4, issue 7, 2008

Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology pp. 1-12

Karthik Devarajan

Increased Brain Signal Variability Accompanies Lower Behavioral Variability in Development pp. 1-9

Anthony Randal McIntosh, Natasa Kovacevic and Roxane J Itier

The Generation of Promoter-Mediated Transcriptional Noise in Bacteria pp. 1-9

Namiko Mitarai, Ian B Dodd, Michael T Crooks and Kim Sneppen

Memory Switches in Chemical Reaction Space pp. 1-9

Naren Ramakrishnan and Upinder S Bhalla

Optimal Compensation for Temporal Uncertainty in Movement Planning pp. 1-9

Todd E Hudson, Laurence T Maloney and Michael S Landy

Circadian Phase Resetting via Single and Multiple Control Targets pp. 1-10

Neda Bagheri, Jörg Stelling and Francis J Doyle

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan pp. 1-10

Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus and Ole Lund

Local Function Conservation in Sequence and Structure Space pp. 1-13

Nils Weinhold, Oliver Sander, Francisco S Domingues, Thomas Lengauer and Ingolf Sommer

Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions pp. 1-13

Denise G Teotico, Monica L Frazier, Feng Ding, Nikolay V Dokholyan, Brenda R S Temple and Matthew R Redinbo

Similarity Queries for Temporal Toxicogenomic Expression Profiles pp. 1-13

Adam A Smith, Aaron Vollrath, Christopher A Bradfield and Mark Craven

Computational Biology Resources Lack Persistence and Usability pp. 1-3

Stella Veretnik, J Lynn Fink and Philip E Bourne

Intrinsic Gain Modulation and Adaptive Neural Coding pp. 1-11

Sungho Hong, Brian Nils Lundstrom and Adrienne L Fairhall

Volume 4, issue 6, 2008

A Comparative Computer Simulation of Dendritic Morphology pp. 1-15

Duncan E Donohue and Giorgio A Ascoli

Ten Simple Rules for Organizing a Scientific Meeting pp. 1-3

Manuel Corpas, Nils Gehlenborg, Sarath Chandra Janga and Philip E Bourne

CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing pp. 1-20

Pradipta Ray, Suyash Shringarpure, Mladen Kolar and Eric P Xing

Model-Based Hypothesis Testing of Key Mechanisms in Initial Phase of Insulin Signaling pp. 1-10

Gunnar Cedersund, Jacob Roll, Erik Ulfhielm, Anna Danielsson, Henrik Tidefelt and Peter Strålfors

How To Advance Open International Scientific Exchange pp. 1-2

Barbara Bryant

ISMB 2008 Toronto pp. 1-5

Michal Linial, Jill P Mesirov, B J Morrison McKay and Burkhard Rost

Machine-Learning Approaches for Classifying Haplogroup from Y Chromosome STR Data pp. 1-12

Joseph Schlecht, Matthew E Kaplan, Kobus Barnard, Tatiana Karafet, Michael F Hammer and Nirav C Merchant

Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins pp. 1-12

Jason W Locasale and Arup K Chakraborty

Integrated Information in Discrete Dynamical Systems: Motivation and Theoretical Framework pp. 1-18

David Balduzzi and Giulio Tononi

Volume 4, issue 5, 2008

The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures pp. 1-13

Diego U Ferreiro, Aleksandra M Walczak, Elizabeth A Komives and Peter G Wolynes

Viral Population Estimation Using Pyrosequencing pp. 1-13

Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W Shafer and Niko Beerenwinkel

Why Are Computational Neuroscience and Systems Biology So Separate? pp. 1-6

Erik De Schutter

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation pp. 1-14

Sean R Eddy

An Allosteric Mechanism for Switching between Parallel Tracks in Mammalian Sulfur Metabolism pp. 1-10

Tatyana K Korendyaseva, Denis N Kuvatov, Vladimir A Volkov, Michael V Martinov, Victor M Vitvitsky, Ruma Banerjee and Fazoil I Ataullakhanov

Context-Specific Metabolic Networks Are Consistent with Experiments pp. 1-10

Scott A Becker and Bernhard O Palsson

Uncovering Interactions in the Frequency Domain pp. 1-10

Shuixia Guo, Jianhua Wu, Mingzhou Ding and Jianfeng Feng

Discovering Sequence Motifs with Arbitrary Insertions and Deletions pp. 1-12

Martin C Frith, Neil F W Saunders, Bostjan Kobe and Timothy L Bailey

Measuring Global Credibility with Application to Local Sequence Alignment pp. 1-12

Bobbie-Jo M Webb-Robertson, Lee Ann McCue and Charles E Lawrence

Transient Cognitive Dynamics, Metastability, and Decision Making pp. 1-9

Mikhail I Rabinovich, Ramón Huerta, Pablo Varona and Valentin S Afraimovich

Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing pp. 1-9

John Porrill and Paul Dean

Ten Simple Rules for Aspiring Scientists in a Low-Income Country pp. 1-2

Edgardo Moreno and José-María Gutiérrez

Volume 4, issue 4, 2008

The Statistical Neuroanatomy of Frontal Networks in the Macaque pp. 1-11

Bruno B Averbeck and Moonsang Seo

Efficient Olfactory Coding in the Pheromone Receptor Neuron of a Moth pp. 1-11

Lubomir Kostal, Petr Lansky and Jean-Pierre Rospars

Translational Systems Biology of Inflammation pp. 1-6

Yoram Vodovotz, Marie Csete, John Bartels, Steven Chang and Gary An

Dimensionality and Dynamics in the Behavior of C. elegans pp. 1-10

Greg J Stephens, Bethany Johnson-Kerner, William Bialek and William S Ryu

A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach pp. 1-10

Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette and Bjoern Peters

Predicting Co-Complexed Protein Pairs from Heterogeneous Data pp. 1-10

Jian Qiu and William Stafford Noble

Distinct Timing Mechanisms Produce Discrete and Continuous Movements pp. 1-8

Raoul Huys, Breanna E Studenka, Nicole L Rheaume, Howard N Zelaznik and Viktor K Jirsa

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data pp. 1-8

Sourav Bandyopadhyay, Ryan Kelley, Nevan J Krogan and Trey Ideker

Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes pp. 1-9

Jon Bohlin, Eystein Skjerve and David W Ussery

Volume 4, issue 3, 2008

Open Access: Taking Full Advantage of the Content pp. 1-3

Philip E Bourne, J Lynn Fink and Mark Gerstein

Neurobiological Models of Two-Choice Decision Making Can Be Reduced to a One-Dimensional Nonlinear Diffusion Equation pp. 1-13

Alex Roxin and Anders Ledberg

Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation pp. 1-11

Bin Kang, Yuan-Yuan Li, Xiao Chang, Lei Liu and Yi-Xue Li

The Dynamics of Human Body Weight Change pp. 1-11

Carson C Chow and Kevin D Hall

Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms pp. 1-14

Sichun Yang and Benoît Roux

Robustness of Learning That Is Based on Covariance-Driven Synaptic Plasticity pp. 1-10

Yonatan Loewenstein

Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions pp. 1-10

Thomas Manke, Helge G Roider and Martin Vingron

Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution pp. 1-12

Ilya Nemenman, Geoffrey D Lewen, William Bialek and Rob R de Ruyter van Steveninck

Volume 4, issue 2, 2008

Computational Methods for Protein Identification from Mass Spectrometry Data pp. 1-12

Leo McHugh and Jonathan W Arthur

Stimulus Design for Model Selection and Validation in Cell Signaling pp. 1-10

Joshua F Apgar, Jared E Toettcher, Drew Endy, Forest M White and Bruce Tidor

Predicting the Receptive Range of Olfactory Receptors pp. 1-8

Rafi Haddad, Liran Carmel, Noam Sobel and David Harel

Accurate Structural Correlations from Maximum Likelihood Superpositions pp. 1-8

Douglas L Theobald and Deborah S Wuttke

Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding pp. 1-8

Adrian W R Serohijos, Tamás Hegedűs, John R Riordan and Nikolay V Dokholyan

Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes pp. 1-7

Ivan Coluzza, Alfonso De Simone, Franca Fraternali and Daan Frenkel

Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability pp. 1-11

Antti Saarinen, Marja-Leena Linne and Olli Yli-Harja

Selective Adaptation in Networks of Heterogeneous Populations: Model, Simulation, and Experiment pp. 1-16

Avner Wallach, Danny Eytan, Shimon Marom and Ron Meir

A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval pp. 1-16

Naomi Habib, Tommy Kaplan, Hanah Margalit and Nir Friedman

Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures pp. 1-6

Dennis Kostka and Rainer Spang

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks pp. 1-15

Derek Ruths, Melissa Muller, Jen-Te Tseng, Luay Nakhleh and Prahlad T Ram

Statistical Resolution of Ambiguous HLA Typing Data pp. 1-15

Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Philip Goulder and David Heckerman

Filling-In and Suppression of Visual Perception from Context: A Bayesian Account of Perceptual Biases by Contextual Influences pp. 1-13

Li Zhaoping and Li Jingling

On the Process of Becoming a Great Scientist pp. 1-3

Morgan C Giddings

Volume 4, issue 1, 2008

Why is Real-World Visual Object Recognition Hard? pp. 1-6

Nicolas Pinto, David D Cox and James J DiCarlo

Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion pp. 1-11

Guo-Cheng Yuan and Jun S Liu

Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor pp. 1-11

Xinli Liu, Yechun Xu, Honglin Li, Xicheng Wang, Hualiang Jiang and Francisco J Barrantes

Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation pp. 1-1

Clinton H Hansen, Robert G Endres and Ned S Wingreen

Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback pp. 1-7

Gil Hornung and Naama Barkai

Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al pp. 1-2

David C Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei Kosakovsky Pond and James I Mullins

Matt: Local Flexibility Aids Protein Multiple Structure Alignment pp. 1-12

Matthew Menke, Bonnie Berger and Lenore Cowen