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Table of Contents: November 2010

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).

Image Credit: Peter Allen

Education Articles

Pattern Recognition Software and Techniques for Biological Image Analysis

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

Perspectives

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

Reconstructing the Three-Dimensional GABAergic Microcircuit of the Striatum

Mark D. Humphries, Ric Wood, Kevin Gurney

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

On the Inverse Problem of Binocular 3D Motion Perception

Martin Lages, Suzanne Heron

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

Environments that Induce Synthetic Microbial Ecosystems

Niels Klitgord, Daniel Segrè

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

Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites

Amy L. Bauer, William S. Hlavacek, Pat J. Unkefer, Fangping Mu

Modelling Vesicular Release at Hippocampal Synapses

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

Analysis of Stochastic Strategies in Bacterial Competence: A Master Equation Approach

Sandra H. Dandach, Mustafa Khammash

Chromosome Driven Spatial Patterning of Proteins in Bacteria

Saeed Saberi, Eldon Emberly

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

Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family

Francisco M. Camas, Eric J. Alm, Juan F. Poyatos

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

Spike-Timing-Based Computation in Sound Localization

Dan F. M. Goodman, Romain Brette

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

Intrinsic Stability of Temporally Shifted Spike-Timing Dependent Plasticity

Baktash Babadi, L. F. Abbott

Infectious Disease Modeling of Social Contagion in Networks

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

Shunting Inhibition Controls the Gain Modulation Mediated by Asynchronous Neurotransmitter Release in Early Development

Vladislav Volman, Herbert Levine, Terrence J. Sejnowski

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