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Table of Contents: November 2010

COVER

Biology of the microtubule-associated protein tau.

Image Credit: Peter Allen
Issue Image

The phosphoprotein tau is normally bound to microtubules. However, tau that is abnormally phosphorylated dissociates from microtubules. Accumulated soluble tau molecules then misfold and aggregate. These aggregations are a hallmark of the tauopathies responsible for cognitive dysfunction and neuropathies such as Alzheimer's disease (see Yuraszeck et al. doi:10.1371/journal.pcbi.1000997).

Education

Pattern Recognition Software and Techniques for Biological Image Analysis

Lior Shamir, John D. Delaney, Nikita Orlov, D. Mark Eckley, Ilya G. Goldberg

Perspective

PLoS Computational Biology Conference Postcards from ISMB 2010

Guilhem Chalancon, Mickey Kosloff, Hatice Ulku Osmanbeyoglu, Saras Saraswathi

Research Articles

Deciphering the Code for Retroviral Integration Target Site Selection

Federico Andrea Santoni, Oliver Hartley, Jeremy Luban

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components

Christopher Y. Park, David C. Hess, Curtis Huttenhower, Olga G. Troyanskaya

A New Method to Reconstruct Recombination Events at a Genomic Scale

Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit , The Genographic Consortium

Treatment-Mediated Alterations in HIV Fitness Preserve CD4+ T Cell Counts but Have Minimal Effects on Viral Load

Naveen K. Vaidya, Libin Rong, Vincent C. Marconi, Daniel R. Kuritzkes, Steven G. Deeks, Alan S. Perelson

Genome-Wide Association between Branch Point Properties and Alternative Splicing

André Corvelo, Martina Hallegger, Christopher W. J. Smith, Eduardo Eyras

Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction

Aalt D. J. van Dijk, Giuseppa Morabito, Martijn Fiers, Roeland C. H. J. van Ham, Gerco C. Angenent, Richard G. H. Immink

How Cations Can Assist DNase I in DNA Binding and Hydrolysis

Marc Guéroult, Daniel Picot, Joséphine Abi-Ghanem, Brigitte Hartmann, Marc Baaden

A Computational Approach to Analyze the Mechanism of Action of the Kinase Inhibitor Bafetinib

Thomas R. Burkard, Uwe Rix, Florian P. Breitwieser, Giulio Superti-Furga, Jacques Colinge

Network Analysis of Global Influenza Spread

Joseph Chan, Antony Holmes, Raul Rabadan

Abnormal Cortical Networks in Mild Cognitive Impairment and Alzheimer's Disease

Zhijun Yao, Yuanchao Zhang, Lei Lin, Yuan Zhou, Cunlu Xu, Tianzi Jiang , the Alzheimer's Disease Neuroimaging Initiative

Modelling Vesicular Release at Hippocampal Synapses

Suhita Nadkarni, Thomas M. Bartol, Terrence J. Sejnowski, Herbert Levine

Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity

Sebastian M. Waszak, Yehudit Hasin, Thomas Zichner, Tsviya Olender, Ifat Keydar, Miriam Khen, Adrian M. Stütz, Andreas Schlattl, Doron Lancet, Jan O. Korbel

Robustness of Circadian Clocks to Daylight Fluctuations: Hints from the Picoeucaryote Ostreococcus tauri

Quentin Thommen, Benjamin Pfeuty, Pierre-Emmanuel Morant, Florence Corellou, François-Yves Bouget, Marc Lefranc

Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations

Yuanfang Guan, Cheryl L. Ackert-Bicknell, Braden Kell, Olga G. Troyanskaya, Matthew A. Hibbs

Finding the Way with a Noisy Brain

Allen Cheung, Robert Vickerstaff

Solving Navigational Uncertainty Using Grid Cells on Robots

Michael J. Milford, Janet Wiles, Gordon F. Wyeth

A New Integrated Variable Based on Thermometry, Actimetry and Body Position (TAP) to Evaluate Circadian System Status in Humans

Elisabet Ortiz-Tudela, Antonio Martinez-Nicolas, Manuel Campos, María Ángeles Rol, Juan Antonio Madrid

Vulnerabilities in the Tau Network and the Role of Ultrasensitive Points in Tau Pathophysiology

Theresa M. Yuraszeck, Pierre Neveu, Maria Rodriguez-Fernandez, Anne Robinson, Kenneth S. Kosik, Francis J. Doyle III

Exploring the Universe of Protein Structures beyond the Protein Data Bank

Pilar Cossio, Antonio Trovato, Fabio Pietrucci, Flavio Seno, Amos Maritan, Alessandro Laio

Infectious Disease Modeling of Social Contagion in Networks

Alison L. Hill, David G. Rand, Martin A. Nowak, Nicholas A. Christakis

Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks

Julien F. Ollivier, Vahid Shahrezaei, Peter S. Swain

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne

Coding “What” and “When” in the Archer Fish Retina

Genadiy Vasserman, Maoz Shamir, Avi Ben Simon, Ronen Segev

Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

Cristina Marino Buslje, Elin Teppa, Tomas Di Doménico, José María Delfino, Morten Nielsen

Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data

Matthieu Wyart, David Botstein, Ned S. Wingreen

Monte Carlo Analysis of Neck Linker Extension in Kinesin Molecular Motors

Matthew L. Kutys, John Fricks, William O. Hancock

Compensation for Changing Motor Uncertainty

Todd E. Hudson, Hadley Tassinari, Michael S. Landy