February 2013

The electrostatic field forms three distinctive funnels leading to the vicinity of the active sites. These funnels serve as electrostatic guide for the positively charged spermidine substrate. Coloring scale data range: -1; 1 (blue, positive; red, negative). Calculated with DelPhi and visualized with VMD. See Zhang, et al.

Image Credit: Marharyta Petukh, Zhe Zhang, Emil Alexov, Clemson University

Editorial

Let's Make Those Book Chapters Open Too!

Philip E. Bourne

PLOS Computational Biology: published February 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002941

Research Articles

Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions

Romain Daniel Cazé, Mark Humphries, Boris Gutkin

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002867

Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila

Andrea Censi, Andrew D. Straw, Rosalyn W. Sayaman, Richard M. Murray, Michael H. Dickinson

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002891

Virus Neutralisation: New Insights from Kinetic Neutralisation Curves

Carsten Magnus

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002900

Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models

Paul Michael Loriaux, Glenn Tesler, Alexander Hoffmann

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002901

The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions

Lizhe Zhu, Peter G. Bolhuis, Jocelyne Vreede

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002913

An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules

Michael Thomas, Dylan Jayatilaka, Ben Corry

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002914

Collective States, Multistability and Transitional Behavior in Schooling Fish

Kolbjørn Tunstrøm, Yael Katz, Christos C. Ioannou, Cristián Huepe, Matthew J. Lutz, Iain D. Couzin

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002915

Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems

Kieran Alden, Mark Read, Jon Timmis, Paul S. Andrews, Henrique Veiga-Fernandes, Mark Coles

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002916

The Vast, Conserved Mammalian lincRNome

David Managadze, Alexander E. Lobkovsky, Yuri I. Wolf, Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002917

Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package

David C. Sterratt, Daniel Lyngholm, David J. Willshaw, Ian D. Thompson

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002921

Functional Connectivity in Islets of Langerhans from Mouse Pancreas Tissue Slices

Andraž Stožer, Marko Gosak, Jurij Dolenšek, Matjaž Perc, Marko Marhl, Marjan Slak Rupnik, Dean Korošak

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002923

Enhancing Human Spermine Synthase Activity by Engineered Mutations

Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002924

Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries

Min-Cheol Kim, Devin M. Neal, Roger D. Kamm, H. Harry Asada

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002926

No Evidence for an Item Limit in Change Detection

Shaiyan Keshvari, Ronald van den Berg, Wei Ji Ma

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002927

Extraction of Sub-microscopic Ca Fluxes from Blurred and Noisy Fluorescent Indicator Images with a Detailed Model Fitting Approach

Cherrie H. T. Kong, Derek R. Laver, Mark B. Cannell

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002931

A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways

Paul Michael Loriaux, Alexander Hoffmann

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002932

Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish

Ying Li, Guang Li, Haifang Wang, Jiulin Du, Jun Yan

PLOS Computational Biology: published February 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002940

Cost and Effects of Different Admission Screening Strategies to Control the Spread of Methicillin-resistant Staphylococcus aureus

Tanya Gurieva, Martin C. J. Bootsma, Marc J. M. Bonten

PLOS Computational Biology: published February 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002874

Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data

Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender

PLOS Computational Biology: published February 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002899

Pairwise Analysis Can Account for Network Structures Arising from Spike-Timing Dependent Plasticity

Baktash Babadi, L. F. Abbott

PLOS Computational Biology: published February 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002906

Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model

Thomas Stockner, Therese R. Montgomery, Oliver Kudlacek, Rene Weissensteiner, Gerhard F. Ecker, Michael Freissmuth, Harald H. Sitte

PLOS Computational Biology: published February 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002909

From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization

Jimin Song, Mona Singh

PLOS Computational Biology: published February 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002910

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

Shao-shan Carol Huang, David C. Clarke, Sara J. C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel

PLOS Computational Biology: published February 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002887

Connecting a Connectome to Behavior: An Ensemble of Neuroanatomical Models of C. elegans Klinotaxis

Eduardo J. Izquierdo, Randall D. Beer

PLOS Computational Biology: published February 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002890

Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs

Robert R. Kerr, Anthony N. Burkitt, Doreen A. Thomas, Matthieu Gilson, David B. Grayden

PLOS Computational Biology: published February 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002897

Viral Capsid Proteins Are Segregated in Structural Fold Space

Shanshan Cheng, Charles L. Brooks III

PLOS Computational Biology: published February 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002905

The Timing and Targeting of Treatment in Influenza Pandemics Influences the Emergence of Resistance in Structured Populations

Benjamin M. Althouse, Oscar Patterson-Lomba, Georg M. Goerg, Laurent Hébert-Dufresne

PLOS Computational Biology: published February 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002912

Cover

Electrostatic field lines generated by the atomic charges of human spermine synthase dimer.

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