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Table of Contents

September 2010

This mosquito species is an important vector of urban and rural malaria in Western India. (See Laneri et al., 10.1371/journal.pcbi.1000898).

Image Credit: Mr. Kedar Bhide


Ten Simple Rules for Editing Wikipedia

Darren W. Logan, Massimo Sandal, Paul P. Gardner, Magnus Manske, Alex Bateman

Research Articles

Quantitative Analysis of Immune Response and Erythropoiesis during Rodent Malarial Infection

Martin R. Miller, Lars Råberg, Andrew F. Read, Nicholas J. Savill

Insights into the Evolution and Emergence of a Novel Infectious Disease

Ruben J. Kubiak, Nimalan Arinaminpathy, Angela R. McLean

Systems Biology of Coagulation Initiation: Kinetics of Thrombin Generation in Resting and Activated Human Blood

Manash S. Chatterjee, William S. Denney, Huiyan Jing, Scott L. Diamond

Synchronization of Firing in Cortical Fast-Spiking Interneurons at Gamma Frequencies: A Phase-Resetting Analysis

Nathan W. Gouwens, Hugo Zeberg, Kunichika Tsumoto, Takashi Tateno, Kazuyuki Aihara, Hugh P. C. Robinson

HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency

Ron Skupsky, John C. Burnett, Jonathan E. Foley, David V. Schaffer, Adam P. Arkin

Semantic Similarity for Automatic Classification of Chemical Compounds

João D. Ferreira, Francisco M. Couto

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson

Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases

Ly Le, Eric H. Lee, David J. Hardy, Thanh N. Truong, Klaus Schulten

Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions

Rong Chen, Tara K. Sigdel, Li Li, Neeraja Kambham, Joel T. Dudley, Szu-chuan Hsieh, R. Bryan Klassen, Amery Chen, Tuyen Caohuu, Alexander A. Morgan, Hannah A. Valantine, Kiran K. Khush, Minnie M. Sarwal, Atul J. Butte

Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases

Raoul Frijters, Marianne van Vugt, Ruben Smeets, René van Schaik, Jacob de Vlieg, Wynand Alkema

Experimental and Computational Analysis of Polyglutamine-Mediated Cytotoxicity

Matthew Y. Tang, Carole J. Proctor, John Woulfe, Douglas A. Gray

Finding the “Dark Matter” in Human and Yeast Protein Network Prediction and Modelling

Juan A. G. Ranea, Ian Morilla, Jon G. Lees, Adam J. Reid, Corin Yeats, Andrew B. Clegg, Francisca Sanchez-Jimenez, Christine Orengo

Is Protein Folding Sub-Diffusive?

Sergei V. Krivov

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

Andreas Kowarsch, Angelika Fuchs, Dmitrij Frishman, Philipp Pagel

Wide-Field Motion Integration in Fly VS Cells: Insights from an Inverse Approach

Benjamin Torben-Nielsen, Klaus M. Stiefel

Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer

Thomas S. Rask, Daniel A. Hansen, Thor G. Theander, Anders Gorm Pedersen, Thomas Lavstsen

Optimal Information Transfer in the Cortex through Synchronization

Andres Buehlmann, Gustavo Deco

A Boolean Model of the Gene Regulatory Network Underlying Mammalian Cortical Area Development

Clare E. Giacomantonio, Geoffrey J. Goodhill

Pavlovian-Instrumental Interaction in ‘Observing Behavior’

Ulrik R. Beierholm, Peter Dayan

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions

Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble, Christina Leslie

A Dynamic Neural Field Model of Mesoscopic Cortical Activity Captured with Voltage-Sensitive Dye Imaging

Valentin Markounikau, Christian Igel, Amiram Grinvald, Dirk Jancke

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G

Suryani Lukman, Barry J. Grant, Alemayehu A. Gorfe, Guy H. Grant, J. Andrew McCammon

Rescuing Loading Induced Bone Formation at Senescence

Sundar Srinivasan, Brandon J. Ausk, Jitendra Prasad, Dewayne Threet, Steven D. Bain, Thomas S. Richardson, Ted S. Gross

Drug-Induced Regulation of Target Expression

Murat Iskar, Monica Campillos, Michael Kuhn, Lars Juhl Jensen, Vera van Noort, Peer Bork

Minimal Mesoscale Model for Protein-Mediated Vesiculation in Clathrin-Dependent Endocytosis

Neeraj J. Agrawal, Jonathan Nukpezah, Ravi Radhakrishnan

An Integrative Multi-Network and Multi-Classifier Approach to Predict Genetic Interactions

Gaurav Pandey, Bin Zhang, Aaron N. Chang, Chad L. Myers, Jun Zhu, Vipin Kumar, Eric E. Schadt

Instantaneous Non-Linear Processing by Pulse-Coupled Threshold Units

Moritz Helias, Moritz Deger, Stefan Rotter, Markus Diesmann

Forcing Versus Feedback: Epidemic Malaria and Monsoon Rains in Northwest India

Karina Laneri, Anindya Bhadra, Edward L. Ionides, Menno Bouma, Ramesh C. Dhiman, Rajpal S. Yadav, Mercedes Pascual

Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata

Ludovic Cottret, Paulo Vieira Milreu, Vicente Acuña, Alberto Marchetti-Spaccamela, Leen Stougie, Hubert Charles, Marie-France Sagot

Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues

Rob J. De Boer, Ruy M. Ribeiro, Alan S. Perelson

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling

Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, Denis Thieffry

Occurrence and Treatment of Bone Atrophic Non-Unions Investigated by an Integrative Approach

Liesbet Geris, Anita A. C. Reed, Jos Vander Sloten, A. Hamish R. W. Simpson, Hans Van Oosterwyck

Differences in Nutrient Requirements Imply a Non-Linear Emergence of Leaders in Animal Groups

Cédric Sueur, Jean-Louis Deneubourg, Odile Petit, Iain D. Couzin

Latent Factor Analysis to Discover Pathway-Associated Putative Segmental Aneuploidies in Human Cancers

Joseph E. Lucas, Hsiu-Ni Kung, Jen-Tsan A. Chi