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Table of Contents: September 2013

COVER

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

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

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.

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

Messages from ISCB

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

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

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

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

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

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

Adaptation Dynamics in Densely Clustered Chemoreceptors

William Pontius, Michael W. Sneddon, Thierry Emonet

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

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

Learning Contrast-Invariant Cancellation of Redundant Signals in Neural Systems

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

Predicting Odor Perceptual Similarity from Odor Structure

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

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

Trial-Type Dependent Frames of Reference for Value Comparison

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

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

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

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

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

Spike Triggered Covariance in Strongly Correlated Gaussian Stimuli

Johnatan Aljadeff, Ronen Segev, Michael J. Berry II, Tatyana O. Sharpee

Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum

Eddy J. Bautista, Joseph Zinski, Steven M. Szczepanek, Erik L. Johnson, Edan R. Tulman, Wei-Mei Ching, Steven J. Geary, Ranjan Srivastava

Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization

Giuseppe Maccari, Mariagrazia Di Luca, Riccardo Nifosí, Francesco Cardarelli, Giovanni Signore, Claudia Boccardi, Angelo Bifone

Mammalian Rest/Activity Patterns Explained by Physiologically Based Modeling

A. J. K. Phillips, B. D. Fulcher, P. A. Robinson, E. B. Klerman

From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells

Julián Candia, Ryan Maunu, Meghan Driscoll, Angélique Biancotto, Pradeep Dagur, J. Philip McCoy Jr, H. Nida Sen, Lai Wei, Amos Maritan, Kan Cao, Robert B. Nussenblatt, Jayanth R. Banavar, Wolfgang Losert