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Table of Contents

June 2011

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)

Image Credit: Alexander V. Ratushny, Institute for Systems Biology, USA.


Ten Simple Rules for Building and Maintaining a Scientific Reputation

Philip E. Bourne, Virginia Barbour


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

Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis

Bhushan K. Bonde, Dany J. V. Beste, Emma Laing, Andrzej M. Kierzek, Johnjoe McFadden

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

Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues

Alexander V. Ratushny, Ilya Shmulevich, John D. Aitchison

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

Partially Glycosylated Dendrimers Block MD-2 and Prevent TLR4-MD-2-LPS Complex Mediated Cytokine Responses

Teresa S. Barata, Ian Teo, Steve Brocchini, Mire Zloh, Sunil Shaunak

Heterogeneous Host Susceptibility Enhances Prevalence of Mixed-Genotype Micro-Parasite Infections

Wopke van der Werf, Lia Hemerik, Just M. Vlak, Mark P. Zwart

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

Robust Network Topologies for Generating Switch-Like Cellular Responses

Najaf A. Shah, Casim A. Sarkar

Changes of Mind in an Attractor Network of Decision-Making

Larissa Albantakis, Gustavo Deco

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

Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms

Elodie Laine, Isaure Chauvot de Beauchêne, David Perahia, Christian Auclair, Luba Tchertanov

Bayesian Comparison of Neurovascular Coupling Models Using EEG-fMRI

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

Generation of Diverse Biological Forms through Combinatorial Interactions between Tissue Polarity and Growth

Richard Kennaway, Enrico Coen, Amelia Green, Andrew Bangham

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

Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex

Ruhollah Moussavi-Baygi, Yousef Jamali, Reza Karimi, Mohammad R. K. Mofrad

Extracting Message Inter-Departure Time Distributions from the Human Electroencephalogram

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