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

PLOS Computational Biology: published May 30, 2013 | https://doi.org/10.1371/journal.pcbi.1003076

Perspective

Bioinformatics and Computational Biology in Poland

Janusz M. Bujnicki, Jerzy Tiuryn

PLOS Computational Biology: published May 2, 2013 | https://doi.org/10.1371/journal.pcbi.1003048

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

PLOS Computational Biology: published May 30, 2013 | https://doi.org/10.1371/journal.pcbi.1003063

Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay

Peng Jiang, Mona Singh, Hilary A. Coller

PLOS Computational Biology: published May 30, 2013 | https://doi.org/10.1371/journal.pcbi.1003075

Coordination of Rapid Sphingolipid Responses to Heat Stress in Yeast

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

PLOS Computational Biology: published May 30, 2013 | https://doi.org/10.1371/journal.pcbi.1003078

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

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

PLOS Computational Biology: published May 30, 2013 | https://doi.org/10.1371/journal.pcbi.1003079

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

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

PLOS Computational Biology: published May 30, 2013 | https://doi.org/10.1371/journal.pcbi.1003083

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

PLOS Computational Biology: published May 30, 2013 | https://doi.org/10.1371/journal.pcbi.1003086

A Balance Equation Determines a Switch in Neuronal Excitability

Alessio Franci, Guillaume Drion, Vincent Seutin, Rodolphe Sepulchre

PLOS Computational Biology: published May 23, 2013 | https://doi.org/10.1371/journal.pcbi.1003040

Simultaneous Identification of Multiple Driver Pathways in Cancer

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

PLOS Computational Biology: published May 23, 2013 | https://doi.org/10.1371/journal.pcbi.1003054

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

Xiaodong Cai, Juan Andrés Bazerque, Georgios B. Giannakis

PLOS Computational Biology: published May 23, 2013 | https://doi.org/10.1371/journal.pcbi.1003068

“Gate-keeper” Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides

Yunlang Li, Tamar Schlick

PLOS Computational Biology: published May 23, 2013 | https://doi.org/10.1371/journal.pcbi.1003074

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

PLOS Computational Biology: published May 23, 2013 | https://doi.org/10.1371/journal.pcbi.1003080

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

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003046

The Emergence of Environmental Homeostasis in Complex Ecosystems

James G. Dyke, Iain S. Weaver

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003050

Connection between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels

Christoph A. Haselwandter, Rob Phillips

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003055

Two Misfolding Routes for the Prion Protein around pH 4.5

Julian Garrec, Ivano Tavernelli, Ursula Rothlisberger

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003057

Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation

Haipeng Li, Thomas Wiehe

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003060

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

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003064

Interface-Resolved Network of Protein-Protein Interactions

Margaret E. Johnson, Gerhard Hummer

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003065

Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment

Gouri Shankar Pandey, Chen Yanover, Tom E. Howard, Zuben E. Sauna

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003066

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

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

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003069

Hybrid Equation/Agent-Based Model of Ischemia-Induced Hyperemia and Pressure Ulcer Formation Predicts Greater Propensity to Ulcerate in Subjects with Spinal Cord Injury

Alexey Solovyev, Qi Mi, Yi-Ting Tzen, David Brienza, Yoram Vodovotz

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003070

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

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

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003072

Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs

Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork

PLOS Computational Biology: published May 16, 2013 | https://doi.org/10.1371/journal.pcbi.1003073

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

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

PLOS Computational Biology: published May 9, 2013 | https://doi.org/10.1371/journal.pcbi.1003005

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

PLOS Computational Biology: published May 9, 2013 | https://doi.org/10.1371/journal.pcbi.1003039

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

PLOS Computational Biology: published May 9, 2013 | https://doi.org/10.1371/journal.pcbi.1003042

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

PLOS Computational Biology: published May 9, 2013 | https://doi.org/10.1371/journal.pcbi.1003047

Selection for Replicases in Protocells

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

PLOS Computational Biology: published May 9, 2013 | https://doi.org/10.1371/journal.pcbi.1003051

Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability

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

PLOS Computational Biology: published May 9, 2013 | https://doi.org/10.1371/journal.pcbi.1003053

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

PLOS Computational Biology: published May 9, 2013 | https://doi.org/10.1371/journal.pcbi.1003056

Inference of R₀ and Transmission Heterogeneity from the Size Distribution of Stuttering Chains

Seth Blumberg, James O. Lloyd-Smith

PLOS Computational Biology: published May 2, 2013 | https://doi.org/10.1371/journal.pcbi.1002993

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

PLOS Computational Biology: published May 2, 2013 | https://doi.org/10.1371/journal.pcbi.1003026

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

PLOS Computational Biology: published May 2, 2013 | https://doi.org/10.1371/journal.pcbi.1003059

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

PLOS Computational Biology: published May 2, 2013 | https://doi.org/10.1371/journal.pcbi.1003061

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Prediction suffix trees pinpoint the long-range structure in canary song

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