Table of Contents: May 2013

This image shows a prediction suffix tree for a single canary. In each branch, the number of links from the root node (center) to the outermost node represents the statistical depth required to accurately model the transition probabilities from a given phrase. A branch with 5 links indicates that one must look back at least 5 phrases, or roughly 5 seconds, in the song to accurately predict the next phrase. The nodes are scaled according to their frequency and contain pie charts that represent outgoing transition probabilities. See Markowitz et al.

Image Credit: Jeffrey E. Markowitz

Message from ISCB

Rocky Mountain Conference on Bioinformatics Celebrates 10 Years

Lawrence E. Hunter


Bioinformatics and Computational Biology in Poland

Janusz M. Bujnicki, Jerzy Tiuryn

Research Articles

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg

Coordination of Rapid Sphingolipid Responses to Heat Stress in Yeast

Po-Wei Chen, Luis L. Fonseca, Yusuf A. Hannun, Eberhard O. Voit

A Two-Stage Cascade Model of BOLD Responses in Human Visual Cortex

Kendrick N. Kay, Jonathan Winawer, Ariel Rokem, Aviv Mezer, Brian A. Wandell

A Mechanical Design Principle for Tissue Structure and Function in the Airway Tree

Adam S. LaPrad, Kenneth R. Lutchen, Béla Suki

Critical Role of Transient Activity of MT1-MMP for ECM Degradation in Invadopodia

Ayako Watanabe, Daisuke Hosino, Naohiko Koshikawa, Motoharu Seiki, Takashi Suzuki, Kazuhisa Ichikawa

Related Articles

  1. Correction: Critical Role of Transient Activity of MT1-MMP for ECM Degradation in Invadopodia

A Balance Equation Determines a Switch in Neuronal Excitability

Alessio Franci, Guillaume Drion, Vincent Seutin, Rodolphe Sepulchre

Simultaneous Identification of Multiple Driver Pathways in Cancer

Mark D. M. Leiserson, Dima Blokh, Roded Sharan, Benjamin J. Raphael

Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations

Xiaodong Cai, Juan Andrés Bazerque, Georgios B. Giannakis

Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task

Hang Zhang, Nathaniel D. Daw, Laurence T. Maloney

A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein

Anurag Sethi, Jianhui Tian, Cynthia A. Derdeyn, Bette Korber, S. Gnanakaran

The Emergence of Environmental Homeostasis in Complex Ecosystems

James G. Dyke, Iain S. Weaver

Connection between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels

Christoph A. Haselwandter, Rob Phillips

Two Misfolding Routes for the Prion Protein around pH 4.5

Julian Garrec, Ivano Tavernelli, Ursula Rothlisberger

Multiple Estimates of Transmissibility for the 2009 Influenza Pandemic Based on Influenza-like-Illness Data from Small US Military Populations

Pete Riley, Michal Ben-Nun, Richard Armenta, Jon A. Linker, Angela A. Eick, Jose L. Sanchez, Dylan George, David P. Bacon, Steven Riley

Interface-Resolved Network of Protein-Protein Interactions

Margaret E. Johnson, Gerhard Hummer

The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch

Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul-ela

Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions

Vincent Vagenende, Alvin X. Han, Han B. Pek, Bernard L. W. Loo

Sparse Coding Can Predict Primary Visual Cortex Receptive Field Changes Induced by Abnormal Visual Input

Jonathan J. Hunt, Peter Dayan, Geoffrey J. Goodhill

Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus

Fanny Gascuel, Marc Choisy, Jean-Marc Duplantier, Florence Débarre, Carine Brouat

Novel Developmental Analyses Identify Longitudinal Patterns of Early Gut Microbiota that Affect Infant Growth

Richard A. White, Jørgen V. Bjørnholt, Donna D. Baird, Tore Midtvedt, Jennifer R. Harris, Marcello Pagano, Winston Hide, Knut Rudi, Birgitte Moen, Nina Iszatt, Shyamal D. Peddada, Merete Eggesbø

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling

Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A. Logsdon, Gaurav Pandey, Benjamin A. Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H. Mecham, Oscar M. Rueda, Jorg Tost, Christina Curtis, Mariano J. Alvarez, Vessela N. Kristensen, Samuel Aparicio, Anne-Lise Børresen-Dale, Carlos Caldas, Andrea Califano, Stephen H. Friend, Trey Ideker, Eric E. Schadt, Gustavo A. Stolovitzky, Adam A. Margolin

Selection for Replicases in Protocells

Ginestra Bianconi, Kun Zhao, Irene A. Chen, Martin A. Nowak

Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability

Yunpeng Wang, Jon Olav Vik, Stig W. Omholt, Arne B. Gjuvsland

STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification

Szymon Stoma, Alexandre Donzé, François Bertaux, Oded Maler, Gregory Batt

Cell Patterns Emerge from Coupled Chemical and Physical Fields with Cell Proliferation Dynamics: The Arabidopsis thaliana Root as a Study System

Rafael A. Barrio, José Roberto Romero-Arias, Marco A. Noguez, Eugenio Azpeitia, Elizabeth Ortiz-Gutiérrez, Valeria Hernández-Hernández, Yuriria Cortes-Poza, Elena R. Álvarez-Buylla

Modeling and Measuring Signal Relay in Noisy Directed Migration of Cell Groups

Can Guven, Erin Rericha, Edward Ott, Wolfgang Losert

A Kinetic Platform to Determine the Fate of Nitric Oxide in Escherichia coli

Jonathan L. Robinson, Mark P. Brynildsen

Long-range Order in Canary Song

Jeffrey E. Markowitz, Elizabeth Ivie, Laura Kligler, Timothy J. Gardner

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA

Tobias Linder, Bert L. de Groot, Anna Stary-Weinzinger

Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission

David W. Eyre, Madeleine L. Cule, David Griffiths, Derrick W. Crook, Tim E. A. Peto, A. Sarah Walker, Daniel J. Wilson

Estimation of Vaccine Efficacy and Critical Vaccination Coverage in Partially Observed Outbreaks

Michiel van Boven, Wilhelmina L. M. Ruijs, Jacco Wallinga, Philip D. O'Neill, Susan Hahné