March 2011

Fear is a basic survival mechanism shaped during evolution to protect us from dangerous situations. We learn to fear threats, but also to forget them. However, forgetting fear is not mere unlearning, but is in fact masking of fear memories. In this computational study Vlachos et al. (doi:10.1371/journal.pcbi.1000038) propose a mechanism that explains how different neural populations in the basal amygdala may evoke or suppress fear responses depending on the particular environment in which fear-related stimuli appear.

Image Credit: Carlos Toledo and Gunnar Grah, Bernstein Center Freiburg, Germany

Perspectives

PLoS Computational Biology Conference Postcard from PSB 2011

A. Murat Eren

PLOS Computational Biology: published March 31, 2011 | https://doi.org/10.1371/journal.pcbi.1002019

The Roots of Bioinformatics in Theoretical Biology

Paulien Hogeweg

PLOS Computational Biology: published March 31, 2011 | https://doi.org/10.1371/journal.pcbi.1002021

Research Articles

Inferring Visuomotor Priors for Sensorimotor Learning

Edward J. A. Turnham, Daniel A. Braun, Daniel M. Wolpert

PLOS Computational Biology: published March 31, 2011 | https://doi.org/10.1371/journal.pcbi.1001112

Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells

Rachel Cavill, Atanas Kamburov, James K. Ellis, Toby J. Athersuch, Marcus S. C. Blagrove, Ralf Herwig, Timothy M. D. Ebbels, Hector C. Keun

PLOS Computational Biology: published March 31, 2011 | https://doi.org/10.1371/journal.pcbi.1001113

CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data

Kelvin Xi Zhang, B. F. Francis Ouellette

PLOS Computational Biology: published March 31, 2011 | https://doi.org/10.1371/journal.pcbi.1001114

Reactive Oxygen Species Production by Forward and Reverse Electron Fluxes in the Mitochondrial Respiratory Chain

Vitaly A. Selivanov, Tatyana V. Votyakova, Violetta N. Pivtoraiko, Jennifer Zeak, Tatiana Sukhomlin, Massimo Trucco, Josep Roca, Marta Cascante

PLOS Computational Biology: published March 31, 2011 | https://doi.org/10.1371/journal.pcbi.1001115

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

Matthew A. Oberhardt, Jacek Puchałka, Vítor A. P. Martins dos Santos, Jason A. Papin

PLOS Computational Biology: published March 31, 2011 | https://doi.org/10.1371/journal.pcbi.1001116

Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study

Lun Yang, Kejian Wang, Jian Chen, Anil G. Jegga, Heng Luo, Leming Shi, Chunling Wan, Xizhi Guo, Shengying Qin, Guang He, Guoyin Feng, Lin He

PLOS Computational Biology: published March 31, 2011 | https://doi.org/10.1371/journal.pcbi.1002016

A Bayesian Approach to Analyse Genetic Variation within RNA Viral Populations

Trevelyan J. McKinley, Pablo R. Murcia, Julia R. Gog, Mariana Varela, James L. N. Wood

PLOS Computational Biology: published March 31, 2011 | https://doi.org/10.1371/journal.pcbi.1002027

A Granger Causality Measure for Point Process Models of Ensemble Neural Spiking Activity

Sanggyun Kim, David Putrino, Soumya Ghosh, Emery N. Brown

PLOS Computational Biology: published March 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001110

Minimal Models of Multidimensional Computations

Jeffrey D. Fitzgerald, Lawrence C. Sincich, Tatyana O. Sharpee

PLOS Computational Biology: published March 24, 2011 | https://doi.org/10.1371/journal.pcbi.1001111

Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction

Cesar A. López, Alex H. de Vries, Siewert J. Marrink

PLOS Computational Biology: published March 24, 2011 | https://doi.org/10.1371/journal.pcbi.1002020

Mechanisms of Magnetic Stimulation of Central Nervous System Neurons

Tamar Pashut, Shuki Wolfus, Alex Friedman, Michal Lavidor, Izhar Bar-Gad, Yosef Yeshurun, Alon Korngreen

PLOS Computational Biology: published March 24, 2011 | https://doi.org/10.1371/journal.pcbi.1002022

“Fluctuograms” Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution

Jordi Silvestre-Ryan, Yuchun Lin, Jhih-Wei Chu

PLOS Computational Biology: published March 24, 2011 | https://doi.org/10.1371/journal.pcbi.1002023

On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems

Nobuto Takeuchi, Paulien Hogeweg, Eugene V. Koonin

PLOS Computational Biology: published March 24, 2011 | https://doi.org/10.1371/journal.pcbi.1002024

Context-Dependent Encoding of Fear and Extinction Memories in a Large-Scale Network Model of the Basal Amygdala

Ioannis Vlachos, Cyril Herry, Andreas Lüthi, Ad Aertsen, Arvind Kumar

PLOS Computational Biology: published March 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001104

Human Leg Model Predicts Ankle Muscle-Tendon Morphology, State, Roles and Energetics in Walking

Pavitra Krishnaswamy, Emery N. Brown, Hugh M. Herr

PLOS Computational Biology: published March 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001107

A Compact Statistical Model of the Song Syntax in Bengalese Finch

Dezhe Z. Jin, Alexay A. Kozhevnikov

PLOS Computational Biology: published March 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001108

Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts

Luis E. C. Rocha, Fredrik Liljeros, Petter Holme

PLOS Computational Biology: published March 17, 2011 | https://doi.org/10.1371/journal.pcbi.1001109

No Need for a Cognitive Map: Decentralized Memory for Insect Navigation

Holk Cruse, Rüdiger Wehner

PLOS Computational Biology: published March 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002009

Frequency-Invariant Representation of Interaural Time Differences in Mammals

Hannes Lüling, Ida Siveke, Benedikt Grothe, Christian Leibold

PLOS Computational Biology: published March 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002013

Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies

Vincent T. Metzger, James O. Lloyd-Smith, Leor S. Weinberger

PLOS Computational Biology: published March 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002015

Dynamic Phenotypic Clustering in Noisy Ecosystems

Morten Ernebjerg, Roy Kishony

PLOS Computational Biology: published March 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002017

The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering

Matteo Osella, Carla Bosia, Davide Corá, Michele Caselle

PLOS Computational Biology: published March 10, 2011 | https://doi.org/10.1371/journal.pcbi.1001101

Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation

Daniele Linaro, Marco Storace, Michele Giugliano

PLOS Computational Biology: published March 10, 2011 | https://doi.org/10.1371/journal.pcbi.1001102

Causal Modeling Using Network Ensemble Simulations of Genetic and Gene Expression Data Predicts Genes Involved in Rheumatoid Arthritis

Heming Xing, Paul D. McDonagh, Jadwiga Bienkowska, Tanya Cashorali, Karl Runge, Robert E. Miller, Dave DeCaprio, Bruce Church, Ronenn Roubenoff, Iya G. Khalil, John Carulli

PLOS Computational Biology: published March 10, 2011 | https://doi.org/10.1371/journal.pcbi.1001105

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations

Lars Skjaerven, Barry Grant, Arturo Muga, Knut Teigen, J. Andrew McCammon, Nathalie Reuter, Aurora Martinez

PLOS Computational Biology: published March 10, 2011 | https://doi.org/10.1371/journal.pcbi.1002004

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

Melody K. Morris, Julio Saez-Rodriguez, David C. Clarke, Peter K. Sorger, Douglas A. Lauffenburger

PLOS Computational Biology: published March 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001099

Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression

Alvaro Sanchez, Hernan G. Garcia, Daniel Jones, Rob Phillips, Jané Kondev

PLOS Computational Biology: published March 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001100

Quantification of the Relative Importance of CTL, B Cell, NK Cell, and Target Cell Limitation in the Control of Primary SIV-Infection

Marjet Elemans, Rodolphe Thiébaut, Amitinder Kaur, Becca Asquith

PLOS Computational Biology: published March 3, 2011 | https://doi.org/10.1371/journal.pcbi.1001103

Blockade of Neuronal α7-nAChR by α-Conotoxin ImI Explained by Computational Scanning and Energy Calculations

Rilei Yu, David J. Craik, Quentin Kaas

PLOS Computational Biology: published March 3, 2011 | https://doi.org/10.1371/journal.pcbi.1002011

Cover

Fear (not)!

Perspectives

Research Articles