Table of Contents: December 2009

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).

Image Credit: Daniel Flower (, adapted by Ian Stevenson.

Education Articles

A Quick Guide for Developing Effective Bioinformatics Programming Skills

Joel T. Dudley, Atul J. Butte

Biomedical Text Mining and Its Applications

Raul Rodriguez-Esteban

Research Articles

Burst-Time-Dependent Plasticity Robustly Guides ON/OFF Segregation in the Lateral Geniculate Nucleus

Julijana Gjorgjieva, Taro Toyoizumi, Stephen J. Eglen

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

Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes

Xi Chen, Andrew D. Ellington

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

Rational Mutational Analysis of a Multidrug MFS Transporter CaMdr1p of Candida albicans by Employing a Membrane Environment Based Computational Approach

Khyati Kapoor, Mohd Rehan, Ajeeta Kaushiki, Ritu Pasrija, Andrew M. Lynn, Rajendra Prasad

Hyperbolic Planforms in Relation to Visual Edges and Textures Perception

Pascal Chossat, Olivier Faugeras

Decomposition of Gene Expression State Space Trajectories

Jessica C. Mar, John Quackenbush

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins

Menachem Fromer, Julia M. Shifman

Order and Stochastic Dynamics in Drosophila Planar Cell Polarity

Yoram Burak, Boris I. Shraiman

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

Predicting Functional Alternative Splicing by Measuring RNA Selection Pressure from Multigenome Alignments

Hongchao Lu, Lan Lin, Seiko Sato, Yi Xing, Christopher J. Lee

Power-Law Scaling in the Brain Surface Electric Potential

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

Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation

Brian J. Schmidt, Jason A. Papin, Michael B. Lawrence

Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks

João F. Matias Rodrigues, Andreas Wagner

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

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What Do Transitive Inference and Class Inclusion Have in Common? Categorical (Co)Products and Cognitive Development

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Human Cancer Protein-Protein Interaction Network: A Structural Perspective

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

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

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

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Defining an Essence of Structure Determining Residue Contacts in Proteins

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

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

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

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Inferring Binding Energies from Selected Binding Sites

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

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