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Table of Contents

November 2010

Cover

Biology of the microtubule-associated protein tau.
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).

Image Credit: Peter Allen

Education

Pattern Recognition Software and Techniques for Biological Image Analysis

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

PLOS Computational Biology: published November 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000974

Perspective

PLoS Computational Biology Conference Postcards from ISMB 2010

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

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1002000

Research Articles

Deciphering the Code for Retroviral Integration Target Site Selection

Federico Andrea Santoni, Oliver Hartley, Jeremy Luban

PLOS Computational Biology: published November 24, 2010 | https://doi.org/10.1371/journal.pcbi.1001008

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

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

PLOS Computational Biology: published November 24, 2010 | https://doi.org/10.1371/journal.pcbi.1001009

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

PLOS Computational Biology: published November 24, 2010 | https://doi.org/10.1371/journal.pcbi.1001010

Reconstructing the Three-Dimensional GABAergic Microcircuit of the Striatum

Mark D. Humphries, Ric Wood, Kevin Gurney

PLOS Computational Biology: published November 24, 2010 | https://doi.org/10.1371/journal.pcbi.1001011

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

PLOS Computational Biology: published November 24, 2010 | https://doi.org/10.1371/journal.pcbi.1001012

Genome-Wide Association between Branch Point Properties and Alternative Splicing

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

PLOS Computational Biology: published November 24, 2010 | https://doi.org/10.1371/journal.pcbi.1001016

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

PLOS Computational Biology: published November 24, 2010 | https://doi.org/10.1371/journal.pcbi.1001017

Untangling the Interplay between Epidemic Spread and Transmission Network Dynamics

Christel Kamp

PLOS Computational Biology: published November 18, 2010 | https://doi.org/10.1371/journal.pcbi.1000984

On the Origins of the Weak Folding Cooperativity of a Designed ββα Ultrafast Protein FSD-1

Chun Wu, Joan-Emma Shea

PLOS Computational Biology: published November 18, 2010 | https://doi.org/10.1371/journal.pcbi.1000998

On the Inverse Problem of Binocular 3D Motion Perception

Martin Lages, Suzanne Heron

PLOS Computational Biology: published November 18, 2010 | https://doi.org/10.1371/journal.pcbi.1000999

How Cations Can Assist DNase I in DNA Binding and Hydrolysis

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

PLOS Computational Biology: published November 18, 2010 | https://doi.org/10.1371/journal.pcbi.1001000

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

PLOS Computational Biology: published November 18, 2010 | https://doi.org/10.1371/journal.pcbi.1001001

Environments that Induce Synthetic Microbial Ecosystems

Niels Klitgord, Daniel Segrè

PLOS Computational Biology: published November 18, 2010 | https://doi.org/10.1371/journal.pcbi.1001002

Network Analysis of Global Influenza Spread

Joseph Chan, Antony Holmes, Raul Rabadan

PLOS Computational Biology: published November 18, 2010 | https://doi.org/10.1371/journal.pcbi.1001005

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

PLOS Computational Biology: published November 18, 2010 | https://doi.org/10.1371/journal.pcbi.1001006

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

PLOS Computational Biology: published November 18, 2010 | https://doi.org/10.1371/journal.pcbi.1001007

Modelling Vesicular Release at Hippocampal Synapses

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

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000983

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

Sandra H. Dandach, Mustafa Khammash

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000985

Chromosome Driven Spatial Patterning of Proteins in Bacteria

Saeed Saberi, Eldon Emberly

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000986

Lobe Specific Ca2+-Calmodulin Nano-Domain in Neuronal Spines: A Single Molecule Level Analysis

Yoshihisa Kubota, M. Neal Waxham

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000987

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

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000988

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

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

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000989

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

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000990

Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations

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

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000991

Finding the Way with a Noisy Brain

Allen Cheung, Robert Vickerstaff

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000992

Spike-Timing-Based Computation in Sound Localization

Dan F. M. Goodman, Romain Brette

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000993

The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase

M. Qaiser Fatmi, Chia-en A. Chang

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000994

Solving Navigational Uncertainty Using Grid Cells on Robots

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

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000995

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

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000996

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

PLOS Computational Biology: published November 11, 2010 | https://doi.org/10.1371/journal.pcbi.1000997

Exploring the Universe of Protein Structures beyond the Protein Data Bank

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

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000957

Intrinsic Stability of Temporally Shifted Spike-Timing Dependent Plasticity

Baktash Babadi, L. F. Abbott

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000961

Infectious Disease Modeling of Social Contagion in Networks

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

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000968

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

Vladislav Volman, Herbert Levine, Terrence J. Sejnowski

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000973

Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks

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

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000975

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

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

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000976

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

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

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000977

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

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000978

Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data

Matthieu Wyart, David Botstein, Ned S. Wingreen

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000979

Monte Carlo Analysis of Neck Linker Extension in Kinesin Molecular Motors

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

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000980

Quantifying the Impact of Human Immunodeficiency Virus-1 Escape From Cytotoxic T-Lymphocytes

Ulrich D. Kadolsky, Becca Asquith

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000981

Compensation for Changing Motor Uncertainty

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

PLOS Computational Biology: published November 4, 2010 | https://doi.org/10.1371/journal.pcbi.1000982