September 2013

The image shows cyanobacterial cells on a moist surface, moving towards a directed light source. This phototactic behavior results in striking and regularly ordered "fingers" of cell groups. We model this behavior as a biased random walk, which, in combination with cell-mediated surface modification, recapitulates many experimentally observed features. By tuning cellular concentration and light intensity, we show that this behavior follows robust scaling laws and only emerges under certain conditions, and may be a general mechanism for cells to change their group behavior in response to external cues. See Ursell et al.

Image Credit: photo/image attributed to Devaki Bhaya and image overlay to Rosanna Chau and Tristan Ursell.

Editorial

Ten Simple Rules for Cultivating Open Science and Collaborative R&D

Hassan Masum, Aarthi Rao, Benjamin M. Good, Matthew H. Todd, Aled M. Edwards, Leslie Chan, Barry A. Bunin, Andrew I. Su, Zakir Thomas, Philip E. Bourne

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003244

Messages from ISCB

The Regional Student Group Program of the ISCB Student Council: Stories from the Road

Geoff Macintyre, Magali Michaut, Thomas Abeel

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003241

ISCB Computational Biology Wikipedia Competition

Alex Bateman, Janet Kelso, Daniel Mietchen, Geoff Macintyre, Tomás Di Domenico, Thomas Abeel, Darren W. Logan, Predrag Radivojac, Burkhard Rost

PLOS Computational Biology: published September 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003242

Research Articles

Task-Based Core-Periphery Organization of Human Brain Dynamics

Danielle S. Bassett, Nicholas F. Wymbs, M. Puck Rombach, Mason A. Porter, Peter J. Mucha, Scott T. Grafton

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003171

Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells

Dipak Barua, William S. Hlavacek

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003217

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

Stephen A. Smith, Joseph W. Brown, Cody E. Hinchliff

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003223

Tunable Stochastic Pulsing in the Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops

Javier Garcia-Bernardo, Mary J. Dunlop

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003229

Whisker Movements Reveal Spatial Attention: A Unified Computational Model of Active Sensing Control in the Rat

Ben Mitchinson, Tony J. Prescott

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003236

Frequency Response of a Protein to Local Conformational Perturbations

Dilek Eren, Burak Alakent

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003238

Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family

Jianhui Song, Sheung Chun Ng, Peter Tompa, Kevin A. W. Lee, Hue Sun Chan

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003239

Barcoding T Cell Calcium Response Diversity with Methods for Automated and Accurate Analysis of Cell Signals (MAAACS)

Audrey Salles, Cyrille Billaudeau, Arnauld Sergé, Anne-Marie Bernard, Marie-Claire Phélipot, Nicolas Bertaux, Mathieu Fallet, Pierre Grenot, Didier Marguet, Hai-Tao He, Yannick Hamon

PLOS Computational Biology: published September 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003245

Specialization of Gene Expression during Mouse Brain Development

Noa Liscovitch, Gal Chechik

PLOS Computational Biology: published September 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003185

Using Biological Pathway Data with Paxtools

Emek Demir, Özgün Babur, Igor Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin Gross, Onur Selçuk Sümer, Gary D. Bader, Chris Sander

PLOS Computational Biology: published September 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003194

Adaptation Dynamics in Densely Clustered Chemoreceptors

William Pontius, Michael W. Sneddon, Thierry Emonet

PLOS Computational Biology: published September 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003230

Predictive Modeling of In Vivo Response to Gemcitabine in Pancreatic Cancer

James J. Lee, Justin Huang, Christopher G. England, Lacey R. McNally, Hermann B. Frieboes

PLOS Computational Biology: published September 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003231

Collective Dynamics Underlying Allosteric Transitions in Hemoglobin

Martin D. Vesper, Bert L. de Groot

PLOS Computational Biology: published September 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003232

Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors

Linhui Hao, Qiuling He, Zhishi Wang, Mark Craven, Michael A. Newton, Paul Ahlquist

PLOS Computational Biology: published September 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003235

Network Signatures of Survival in Glioblastoma Multiforme

Vishal N. Patel, Giridharan Gokulrangan, Salim A. Chowdhury, Yanwen Chen, Andrew E. Sloan, Mehmet Koyutürk, Jill Barnholtz-Sloan, Mark R. Chance

PLOS Computational Biology: published September 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003237

Learning Contrast-Invariant Cancellation of Redundant Signals in Neural Systems

Jorge F. Mejias, Gary Marsat, Kieran Bol, Leonard Maler, André Longtin

PLOS Computational Biology: published September 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003180

Predicting Odor Perceptual Similarity from Odor Structure

Kobi Snitz, Adi Yablonka, Tali Weiss, Idan Frumin, Rehan M. Khan, Noam Sobel

PLOS Computational Biology: published September 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003184

From Birdsong to Human Speech Recognition: Bayesian Inference on a Hierarchy of Nonlinear Dynamical Systems

Izzet B. Yildiz, Katharina von Kriegstein, Stefan J. Kiebel

PLOS Computational Biology: published September 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003219

Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model

John C. Williams, Jianjin Xu, Zhongju Lu, Aleksandra Klimas, Xuxin Chen, Christina M. Ambrosi, Ira S. Cohen, Emilia Entcheva

PLOS Computational Biology: published September 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003220

Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of Caulobacter crescentus

Kartik Subramanian, Mark R. Paul, John J. Tyson

PLOS Computational Biology: published September 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003221

Mechanistic Model of Natural Killer Cell Proliferative Response to IL-15 Receptor Stimulation

Yun M. Zhao, Anthony R. French

PLOS Computational Biology: published September 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003222

Trial-Type Dependent Frames of Reference for Value Comparison

Laurence T. Hunt, Mark W. Woolrich, Matthew F. S. Rushworth, Timothy E. J. Behrens

PLOS Computational Biology: published September 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003225

Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways

Jing Tang, Leena Karhinen, Tao Xu, Agnieszka Szwajda, Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio

PLOS Computational Biology: published September 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003226

Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks

Julia Lasserre, Ho-Ryun Chung, Martin Vingron

PLOS Computational Biology: published September 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003168

Distal Loop Flexibility of a Regulatory Domain Modulates Dynamics and Activity of C-Terminal Src Kinase (Csk)

Sulyman Barkho, Levi C. T. Pierce, Maria L. McGlone, Sheng Li, Virgil L. Woods Jr, Ross C. Walker, Joseph A. Adams, Patricia A. Jennings

PLOS Computational Biology: published September 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003188

Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules

Jing Chen, Zhen Hu, Mukta Phatak, John Reichard, Johannes M. Freudenberg, Siva Sivaganesan, Mario Medvedovic

PLOS Computational Biology: published September 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003198

Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs

Ioannis N. Melas, Regina Samaga, Leonidas G. Alexopoulos, Steffen Klamt

PLOS Computational Biology: published September 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003204

Motility Enhancement through Surface Modification Is Sufficient for Cyanobacterial Community Organization during Phototaxis

Tristan Ursell, Rosanna Man Wah Chau, Susanne Wisen, Devaki Bhaya, Kerwyn Casey Huang

PLOS Computational Biology: published September 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003205

Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization

Rudi Agius, Mieczyslaw Torchala, Iain H. Moal, Juan Fernández-Recio, Paul A. Bates

PLOS Computational Biology: published September 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003216

Cover

A population of photosynthetic cyanobacteria move towards a light source, splitting into groups that exhibit a distinct fingering morphology.

Editorial

Messages from ISCB

Research Articles

Related Articles

Related Articles

Related Articles