Table of Contents: 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


The Roots of Bioinformatics in Theoretical Biology

Paulien Hogeweg

Research Articles

Inferring Visuomotor Priors for Sensorimotor Learning

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

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

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

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

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

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

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

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

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

Minimal Models of Multidimensional Computations

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

Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction

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

Mechanisms of Magnetic Stimulation of Central Nervous System Neurons

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

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

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

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

A Compact Statistical Model of the Song Syntax in Bengalese Finch

Dezhe Z. Jin, Alexay A. Kozhevnikov

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

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

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

Holk Cruse, Rüdiger Wehner

Frequency-Invariant Representation of Interaural Time Differences in Mammals

Hannes Lüling, Ida Siveke, Benedikt Grothe, Christian Leibold

Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies

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

Dynamic Phenotypic Clustering in Noisy Ecosystems

Morten Ernebjerg, Roy Kishony

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

Matteo Osella, Carla Bosia, Davide Corá, Michele Caselle

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

Daniele Linaro, Marco Storace, Michele Giugliano

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

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

Noise Driven Evolutionary Waves

Oskar Hallatschek

Crawling Cells Can Close Wounds without Purse Strings or Signaling

Pilhwa Lee, Charles W. Wolgemuth

Animal Interactions and the Emergence of Territoriality

Luca Giuggioli, Jonathan R. Potts, Stephen Harris

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study

Elijah Roberts, Andrew Magis, Julio O. Ortiz, Wolfgang Baumeister, Zaida Luthey-Schulten

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

Tomer Shlomi, Tomer Benyamini, Eyal Gottlieb, Roded Sharan, Eytan Ruppin

Natural Selection on Functional Modules, a Genome-Wide Analysis

François Serra, Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo

Informed Switching Strongly Decreases the Prevalence of Antibiotic Resistance in Hospital Wards

Roger D. Kouyos, Pia Abel zur Wiesch, Sebastian Bonhoeffer

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases

Yoo-Ah Kim, Stefan Wuchty, Teresa M. Przytycka

Flexible Cognitive Strategies during Motor Learning

Jordan A. Taylor, Richard B. Ivry

Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding

Dana Bar-On, Esther Nachliel, Menachem Gutman, Uri Ashery

Nucleotide Binding Switches the Information Flow in Ras GTPases

Francesco Raimondi, Guillem Portella, Modesto Orozco, Francesca Fanelli

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

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

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

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