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

Related Articles

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

Adaptive Gain Modulation in V1 Explains Contextual Modifications during Bisection Learning

Roland Schäfer, Eleni Vasilaki, Walter Senn

Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins

Orly Noivirt-Brik, Amnon Horovitz, Ron Unger

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

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

Steven Phillips, William H. Wilson, Graeme S. Halford

A Multi-Component Model of the Developing Retinocollicular Pathway Incorporating Axonal and Synaptic Growth

Keith B. Godfrey, Stephen J. Eglen, Nicholas V. Swindale

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

Gozde Kar, Attila Gursoy, Ozlem Keskin

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

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