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Table of Contents: December 2009

COVER

Bayesian surfing.

Image Credit: Daniel Flower (http://www.flickr.com/photos/danielflower/377500529/), adapted by Ian Stevenson.
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There is a growing body of work demonstrating that humans are close to statistically optimal in both their perception of the world and their actions on it. In this work, the authors introduce a full-body, goal-directed task similar to surfing where subjects steer an on-screen cursor with their center of pressure. They find that subjects respond to sensory uncertainty near-optimally in this task, but their behavior is highly non-linear (see Stevenson et al., doi:10.1371/journal.pcbi.1000629).

Education Articles

Research Articles

Bistability of Mitochondrial Respiration Underlies Paradoxical Reactive Oxygen Species Generation Induced by Anoxia

Vitaly A. Selivanov, Tatyana V. Votyakova, Jennifer A. Zeak, Massimo Trucco, Josep Roca, Marta Cascante

The Presence of VEGF Receptors on the Luminal Surface of Endothelial Cells Affects VEGF Distribution and VEGF Signaling

Marianne O. Stefanini, Florence T. H. Wu, Feilim Mac Gabhann, Aleksander S. Popel

A Stochastic Model for Microtubule Motors Describes the In Vivo Cytoplasmic Transport of Human Adenovirus

Mattia Gazzola, Christoph J. Burckhardt, Basil Bayati, Martin Engelke, Urs F. Greber, Petros Koumoutsakos

Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task

Ian H. Stevenson, Hugo L. Fernandes, Iris Vilares, Kunlin Wei, Konrad P. Körding

Emergent Patterns of Social Affiliation in Primates, a Model

Ivan Puga-Gonzalez, Hanno Hildenbrandt, Charlotte K. Hemelrijk

Transcriptome and Proteome Exploration to Model Translation Efficiency and Protein Stability in Lactococcus lactis

Clémentine Dressaire, Christophe Gitton, Pascal Loubière, Véronique Monnet, Isabelle Queinnec, Muriel Cocaign-Bousquet

Dissecting Early Differentially Expressed Genes in a Mixture of Differentiating Embryonic Stem Cells

Feng Hong, Fang Fang, Xuming He, Xiaoyi Cao, Hiram Chipperfield, Dan Xie, Wing H. Wong, Huck H. Ng, Sheng Zhong

Power-Law Scaling in the Brain Surface Electric Potential

Kai J. Miller, Larry B. Sorensen, Jeffrey G. Ojemann, Marcel den Nijs

Model of Transcriptional Activation by MarA in Escherichia coli

Michael E. Wall, David A. Markowitz, Judah L. Rosner, Robert G. Martin

Calculating Evolutionary Dynamics in Structured Populations

Charles G. Nathanson, Corina E. Tarnita, Martin A. Nowak

Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases

Kai Wang, Manikandan Narayanan, Hua Zhong, Martin Tompa, Eric E. Schadt, Jun Zhu

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

Florent E. Angly, Dana Willner, Alejandra Prieto-Davó, Robert A. Edwards, Robert Schmieder, Rebecca Vega-Thurber, Dionysios A. Antonopoulos, Katie Barott, Matthew T. Cottrell, Christelle Desnues, Elizabeth A. Dinsdale, Mike Furlan, Matthew Haynes, Matthew R. Henn, Yongfei Hu, David L. Kirchman, Tracey McDole, John D. McPherson, Folker Meyer, R. Michael Miller, Egbert Mundt, Robert K. Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, Forest Rohwer

Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR

Sean Ekins, Sandhya Kortagere, Manisha Iyer, Erica J. Reschly, Markus A. Lill, Matthew R. Redinbo, Matthew D. Krasowski

ON/OFF and Beyond - A Boolean Model of Apoptosis

Rebekka Schlatter, Kathrin Schmich, Ima Avalos Vizcarra, Peter Scheurich, Thomas Sauter, Christoph Borner, Michael Ederer, Irmgard Merfort, Oliver Sawodny

Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation

Jorge M. Pacheco, Flávio L. Pinheiro, Francisco C. Santos

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

Daniel Ramsköld, Eric T. Wang, Christopher B. Burge, Rickard Sandberg

Integrin Clustering Is Driven by Mechanical Resistance from the Glycocalyx and the Substrate

Matthew J. Paszek, David Boettiger, Valerie M. Weaver, Daniel A. Hammer

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt

Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis

Matthew D. Christensen, Wen Dun, Penelope A. Boyden, Mark E. Anderson, Peter J. Mohler, Thomas J. Hund

Defining an Essence of Structure Determining Residue Contacts in Proteins

R. Sathyapriya, Jose M. Duarte, Henning Stehr, Ioannis Filippis, Michael Lappe

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh, Thomas A. Funkhouser

Spike-Based Reinforcement Learning in Continuous State and Action Space: When Policy Gradient Methods Fail

Eleni Vasilaki, Nicolas Frémaux, Robert Urbanczik, Walter Senn, Wulfram Gerstner

Effective Reduced Diffusion-Models: A Data Driven Approach to the Analysis of Neuronal Dynamics

Gustavo Deco, Daniel Martí, Anders Ledberg, Ramon Reig, Maria V. Sanchez Vives

A Model Analysis of Arterial Oxygen Desaturation during Apnea in Preterm Infants

Scott A. Sands, Bradley A. Edwards, Vanessa J. Kelly, Malcolm R. Davidson, Malcolm H. Wilkinson, Philip J. Berger

Inferring Binding Energies from Selected Binding Sites

Yue Zhao, David Granas, Gary D. Stormo

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data

Alexander Mitsos, Ioannis N. Melas, Paraskeuas Siminelakis, Aikaterini D. Chairakaki, Julio Saez-Rodriguez, Leonidas G. Alexopoulos