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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

Messages from ISCB

Perspectives

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

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Simultaneous Identification of Multiple Driver Pathways in Cancer

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

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

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

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The Emergence of Environmental Homeostasis in Complex Ecosystems

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Two Misfolding Routes for the Prion Protein around pH 4.5

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

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Interface-Resolved Network of Protein-Protein Interactions

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

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

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

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Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling

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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

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