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Table of Contents: June 2011

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Pictured are two biomolecular networks from budding yeast, composed of different basic architectures. The generalized time-frequency analysis framework developed by Ratushny et al. enables the systematic exploration of the dynamical properties of biomolecular networks. Using this framework, the authors reveal remarkably distinct network behaviors in terms of trade-offs between responsiveness and noise suppression that are appropriately tuned to each biological response. (See Ratushny et al., doi: 10.1371/journal.pcbi.1002091)

Editorial

Message from ISCB

Perspectives

The Development of Computational Biology in Pakistan: Still a Long Way to Go

Muhammad Ilyas, Samrene Sadique, Kahlid Masood, Raheel Qamar, Shahid Nadeem Chohan

Eurekometrics: Analyzing the Nature of Discovery

Samuel Arbesman, Nicholas A. Christakis

Research Articles

Activated Membrane Patches Guide Chemotactic Cell Motility

Inbal Hecht, Monica L. Skoge, Pascale G. Charest, Eshel Ben-Jacob, Richard A. Firtel, William F. Loomis, Herbert Levine, Wouter-Jan Rappel

Learning, Memory, and the Role of Neural Network Architecture

Ann M. Hermundstad, Kevin S. Brown, Danielle S. Bassett, Jean M. Carlson

Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line

Velia Siciliano, Filippo Menolascina, Lucia Marucci, Chiara Fracassi, Immacolata Garzilli, Maria Nicoletta Moretti, Diego di Bernardo

How Haptic Size Sensations Improve Distance Perception

Peter W. Battaglia, Daniel Kersten, Paul R. Schrater

Colocalization of Protein Kinase A with Adenylyl Cyclase Enhances Protein Kinase A Activity during Induction of Long-Lasting Long-Term-Potentiation

Myungsook Kim, Alan Jung Park, Robbert Havekes, Andrew Chay, Leonardo Antonio Guercio, Rodrigo Freire Oliveira, Ted Abel, Kim T. Blackwell

Spatio-Temporal Credit Assignment in Neuronal Population Learning

Johannes Friedrich, Robert Urbanczik, Walter Senn

Network Clustering Revealed the Systemic Alterations of Mitochondrial Protein Expression

Jouhyun Jeon, Jae Hoon Jeong, Je-Hyun Baek, Hyun-Jung Koo, Wook-Ha Park, Jae-Seong Yang, Myeong-Hee Yu, Sanguk Kim, Youngmi Kim Pak

The Binding of Learning to Action in Motor Adaptation

Luis Nicolas Gonzalez Castro, Craig Bryant Monsen, Maurice A. Smith

Dynamic Structure Formation of Peripheral Membrane Proteins

Diana Morozova, Gernot Guigas, Matthias Weiss

The Origin of Behavioral Bursts in Decision-Making Circuitry

Amanda Sorribes, Beatriz G. Armendariz, Diego Lopez-Pigozzi, Cristina Murga, Gonzalo G. de Polavieja

Generative Embedding for Model-Based Classification of fMRI Data

Kay H. Brodersen, Thomas M. Schofield, Alexander P. Leff, Cheng Soon Ong, Ekaterina I. Lomakina, Joachim M. Buhmann, Klaas E. Stephan

Predicting Binding to P-Glycoprotein by Flexible Receptor Docking

Elena Dolghih, Clifford Bryant, Adam R. Renslo, Matthew P. Jacobson

An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins

Greet De Baets, Joke Reumers, Javier Delgado Blanco, Joaquin Dopazo, Joost Schymkowitz, Frederic Rousseau

Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation

Wenyuan Li, Chun-Chi Liu, Tong Zhang, Haifeng Li, Michael S. Waterman, Xianghong Jasmine Zhou

Impact of Microscopic Motility on the Swimming Behavior of Parasites: Straighter Trypanosomes are More Directional

Sravanti Uppaluri, Jan Nagler, Eric Stellamanns, Niko Heddergott, Stephan Herminghaus, Markus Engstler, Thomas Pfohl

Bayesian Comparison of Neurovascular Coupling Models Using EEG-fMRI

Maria J. Rosa, James M. Kilner, Will D. Penny

Towards an Evolutionary Model of Transcription Networks

Dan Xie, Chieh-Chun Chen, Xin He, Xiaoyi Cao, Sheng Zhong

A New View of the Bacterial Cytosol Environment

Benjamin P. Cossins, Matthew P. Jacobson, Victor Guallar

Mutual Inactivation of Notch Receptors and Ligands Facilitates Developmental Patterning

David Sprinzak, Amit Lakhanpal, Lauren LeBon, Jordi Garcia-Ojalvo, Michael B. Elowitz

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

Nathan L. Nehrt, Wyatt T. Clark, Predrag Radivojac, Matthew W. Hahn

Neurobiologically Realistic Determinants of Self-Organized Criticality in Networks of Spiking Neurons

Mikail Rubinov, Olaf Sporns, Jean-Philippe Thivierge, Michael Breakspear

Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics

Erik M. Volz, Joel C. Miller, Alison Galvani, Lauren Ancel Meyers

Extracting Message Inter-Departure Time Distributions from the Human Electroencephalogram

Bratislav Mišić, Vasily A. Vakorin, Nataša Kovačević, Tomáš Paus, Anthony R. McIntosh