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Table of Contents: November 2009

This image shows a hoverfly, Eristalis tenax, face to face with a VLSI vision chip that mimics neurons involved in real-time motion processing. The fly is a superb model for biologically inspired vision, since many key image processing stages have been studied in depth physiologically. Computational models that take full account of the adaptive properties of fly vision provide robust and efficient processing of motion in natural scenes independent of their structure. Such models are well suited to VLSI implementation or other low-power approaches to real-time artificial image processing (see Brinkworth and O'Carroll, doi:10.1371/journal.pcbi.1000555).

Image Credit: David C O'Carroll (The University of Adelaide)

Perspectives

The Rat Genome Database Curators: Who, What, Where, Why

Mary Shimoyama, G. Thomas Hayman, Stanley J. F. Laulederkind, Rajni Nigam, Timothy F. Lowry, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob, the RGD Team

Live Coverage of Scientific Conferences Using Web Technologies

Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider

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  1. Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009

Reviews

Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

Albert A. de Graaf, Andreas P. Freidig, Baukje De Roos, Neema Jamshidi, Matthias Heinemann, Johan A.C. Rullmann, Kevin D. Hall, Martin Adiels, Ben van Ommen

Research Articles

Attention Increases the Temporal Precision of Conscious Perception: Verifying the Neural-ST2 Model

Srivas Chennu, Patrick Craston, Brad Wyble, Howard Bowman

Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation

Arno Onken, Steffen Grünewälder, Matthias H. J. Munk, Klaus Obermayer

A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen

Omer Dushek, Raibatak Das, Daniel Coombs

A High-Throughput Screening Approach to Discovering Good Forms of Biologically Inspired Visual Representation

Nicolas Pinto, David Doukhan, James J. DiCarlo, David D. Cox

Quantification of Circadian Rhythms in Single Cells

Pål O. Westermark, David K. Welsh, Hitoshi Okamura, Hanspeter Herzel

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

Sergei L. Kosakovsky Pond, David Posada, Eric Stawiski, Colombe Chappey, Art F.Y. Poon, Gareth Hughes, Esther Fearnhill, Mike B. Gravenor, Andrew J. Leigh Brown, Simon D.W. Frost

Circadian KaiC Phosphorylation: A Multi-Layer Network

Congxin Li, Xiaofang Chen, Pengye Wang, Weichi Wang

Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary

Dominik M. Wittmann, Florian Blöchl, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash, Fabian J. Theis

Exon Array Analysis of Head and Neck Cancers Identifies a Hypoxia Related Splice Variant of LAMA3 Associated with a Poor Prognosis

Carla S. Moller-Levet, Guy N. J. Betts, Adrian L. Harris, Jarrod J. Homer, Catharine M. L. West, Crispin J. Miller

Stochastic Drift in Mitochondrial DNA Point Mutations: A Novel Perspective Ex Silico

Suresh Kumar Poovathingal, Jan Gruber, Barry Halliwell, Rudiyanto Gunawan

Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators

Eric A. Zilli, Motoharu Yoshida, Babak Tahvildari, Lisa M. Giocomo, Michael E. Hasselmo

Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis

Wolfram Stacklies, Fei Xia, Frauke Gräter

Computational Model of Membrane Fission Catalyzed by ESCRT-III

Gur Fabrikant, Suman Lata, James D. Riches, John A. G. Briggs, Winfried Weissenhorn, Michael M. Kozlov

Dynamics of Trimming the Content of Face Representations for Categorization in the Brain

Nicola J. van Rijsbergen, Philippe G. Schyns

Discovery of Regulatory Elements is Improved by a Discriminatory Approach

Eivind Valen, Albin Sandelin, Ole Winther, Anders Krogh

Identifying Changes in Selective Constraints: Host Shifts in Influenza

Asif U. Tamuri, Mario dos Reis, Alan J. Hay, Richard A. Goldstein

Discovery and Annotation of Functional Chromatin Signatures in the Human Genome

Gary Hon, Wei Wang, Bing Ren

Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors

Nathan Salomonis, Brandon Nelson, Karen Vranizan, Alexander R. Pico, Kristina Hanspers, Allan Kuchinsky, Linda Ta, Mark Mercola, Bruce R. Conklin

Robust Models for Optic Flow Coding in Natural Scenes Inspired by Insect Biology

Russell S. A. Brinkworth, David C. O'Carroll

Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model

Samuel Bandara, Johannes P. Schlöder, Roland Eils, Hans Georg Bock, Tobias Meyer

Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans

Ivan Iossifov, Raul Rodriguez-Esteban, Ilya Mayzus, Kathleen J. Millen, Andrey Rzhetsky