Table of Contents

August 2012

Whether an outgoing forager leaves the nest depends on its rate of interaction with foragers returning with seeds. This simple positive feedback links foraging activity to food availability: the more food is available, the more quickly foragers find it and return to the nest. See Prabhakar et al., doi:10.1371/journal.pcbi.1002670.

Image Credit: Katherine N. Dektar, Stanford University.

Message from ISCB

The Roots of Bioinformatics in ISMB

Todd A. Gibson


Design and Implementation of a Genomics Field Trip Program Aimed at Secondary School Students

Jennifer McQueen, Jody J. Wright, Joanne A. Fox


Research Articles

On Genetic Specificity in Symbiont-Mediated Host-Parasite Coevolution

Marek Kwiatkowski, Jan Engelstädter, Christoph Vorburger

Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries

Thomas R. Sokolowski, Thorsten Erdmann, Pieter Rein ten Wolde

Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability

Jie Zhang, Kewei Lu, Yang Xiang, Muhtadi Islam, Shweta Kotian, Zeina Kais, Cindy Lee, Mansi Arora, Hui-wen Liu, Jeffrey D. Parvin, Kun Huang

Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase

Daniel R. Ripoll, Ilja V. Khavrutskii, Sidhartha Chaudhury, Jin Liu, Robert A. Kuschner, Anders Wallqvist, Jaques Reifman

External Drive to Inhibitory Cells Induces Alternating Episodes of High- and Low-Amplitude Oscillations

Oscar J. Avella Gonzalez, Karlijn I. van Aerde, Ronald A. J. van Elburg, Simon-Shlomo Poil, Huibert D. Mansvelder, Klaus Linkenkaer-Hansen, Jaap van Pelt, Arjen van Ooyen

Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase

Andrei V. Pisliakov, Tomoya Hino, Yoshitsugu Shiro, Yuji Sugita

Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces

Jessica Andreani, Guilhem Faure, Raphaël Guerois

Coupling Mechanical Deformations and Planar Cell Polarity to Create Regular Patterns in the Zebrafish Retina

Guillaume Salbreux, Linda K. Barthel, Pamela A. Raymond, David K. Lubensky

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants

Konstantin Kozlov, Svetlana Surkova, Ekaterina Myasnikova, John Reinitz, Maria Samsonova

Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design

Elisabeth Humphris-Narayanan, Eyal Akiva, Rocco Varela, Shane Ó Conchúir, Tanja Kortemme

Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case

Rebeca García-Fandiño, Pau Bernadó, Sara Ayuso-Tejedor, Javier Sancho, Modesto Orozco

Diversity and Noise Effects in a Model of Homeostatic Regulation of the Sleep-Wake Cycle

Marco Patriarca, Svetlana Postnova, Hans A. Braun, Emilio Hernández-García, Raúl Toral

Evolutionary Dynamics of Strategic Behavior in a Collective-Risk Dilemma

Maria Abou Chakra, Arne Traulsen

Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals

Olav Stetter, Demian Battaglia, Jordi Soriano, Theo Geisel

Artificial Neural Networks Trained to Detect Viral and Phage Structural Proteins

Victor Seguritan, Nelson Alves Jr., Michael Arnoult, Amy Raymond, Don Lorimer, Alex B. Burgin Jr., Peter Salamon, Anca M. Segall

Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase

Elodie Laine, Christian Auclair, Luba Tchertanov

The Regulation of Ant Colony Foraging Activity without Spatial Information

Balaji Prabhakar, Katherine N. Dektar, Deborah M. Gordon

Activity Dependent Degeneration Explains Hub Vulnerability in Alzheimer's Disease

Willem de Haan, Katherine Mott, Elisabeth C. W. van Straaten, Philip Scheltens, Cornelis J. Stam

Unifying Time to Contact Estimation and Collision Avoidance across Species

Matthias S. Keil, Joan López-Moliner

Evolution of Stress Response in the Face of Unreliable Environmental Signals

Markus Arnoldini, Rafal Mostowy, Sebastian Bonhoeffer, Martin Ackermann

A Network-based Approach for Predicting Missing Pathway Interactions

Saket Navlakha, Anthony Gitter, Ziv Bar-Joseph

Locust Dynamics: Behavioral Phase Change and Swarming

Chad M. Topaz, Maria R. D'Orsogna, Leah Edelstein-Keshet, Andrew J. Bernoff

A Simple Histone Code Opens Many Paths to Epigenetics

Kim Sneppen, Ian B. Dodd

Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors

Jennifer M. Johnston, Hao Wang, Davide Provasi, Marta Filizola

Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration

Allen Cheung, David Ball, Michael Milford, Gordon Wyeth, Janet Wiles

A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology

Y. Dabaghian, F. Mémoli, L. Frank, G. Carlsson

Literature Based Drug Interaction Prediction with Clinical Assessment Using Electronic Medical Records: Novel Myopathy Associated Drug Interactions

Jon D. Duke, Xu Han, Zhiping Wang, Abhinita Subhadarshini, Shreyas D. Karnik, Xiaochun Li, Stephen D. Hall, Yan Jin, J. Thomas Callaghan, Marcus J. Overhage, David A. Flockhart, R. Matthew Strother, Sara K. Quinney, Lang Li

Performance Limitations of Relay Neurons

Rahul Agarwal, Sridevi V. Sarma

Hybrid Models and Biological Model Reduction with PyDSTool

Robert Clewley

A Canonical Model of Multistability and Scale-Invariance in Biological Systems

Frank Freyer, James A. Roberts, Petra Ritter, Michael Breakspear

Intrinsic Disorder in the Human Spliceosomal Proteome

Iga Korneta, Janusz M. Bujnicki

Decorrelation of Neural-Network Activity by Inhibitory Feedback

Tom Tetzlaff, Moritz Helias, Gaute T. Einevoll, Markus Diesmann

Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation

C. Scott Wylie, Eugene I. Shakhnovich

Molecular Constraints on Synaptic Tagging and Maintenance of Long-Term Potentiation: A Predictive Model

Paul Smolen, Douglas A. Baxter, John H. Byrne

Alternative Protein-Protein Interfaces Are Frequent Exceptions

Tobias Hamp, Burkhard Rost

Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems

Georg K. Gerber, Andrew B. Onderdonk, Lynn Bry

The Role of Local Backrub Motions in Evolved and Designed Mutations

Daniel A. Keedy, Ivelin Georgiev, Edward B. Triplett, Bruce R. Donald, David C. Richardson, Jane S. Richardson