December 2016

During their development, many plants display a revolving movement, the circumnutation. In spite of its ubiquity, plant nutation has not received as much attention as other plant movements, and its underlying mechanism remains unclear. Here we show that a simple relation between curvature and differential growth can be revealed. This sheds a new light on classical measurements where only the movement of the apical tip was measured. The relation between the observed pattern and the growth dynamics is not unique, and the full kinematics of the organ in 3 dimensions should be acquired. See See Bastien, Meroz.

Image Credit: Renaud Bastien & Yasmine Meroz

Message from ISCB

The 5th ISCB Wikipedia Competition: Coming to a Classroom Near You?

Alastair M. Kilpatrick

PLOS Computational Biology: published December 29, 2016 | https://doi.org/10.1371/journal.pcbi.1005235

Research Articles

Detecting Mild Traumatic Brain Injury Using Resting State Magnetoencephalographic Connectivity

Vasily A. Vakorin, Sam M. Doesburg, Leodante da Costa, Rakesh Jetly, Elizabeth W. Pang, Margot J. Taylor

PLOS Computational Biology: published December 1, 2016 | https://doi.org/10.1371/journal.pcbi.1004914

Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms

Thomas LaBar, Christoph Adami

PLOS Computational Biology: published December 6, 2016 | https://doi.org/10.1371/journal.pcbi.1005066

Zipf’s Law Arises Naturally When There Are Underlying, Unobserved Variables

Laurence Aitchison, Nicola Corradi, Peter E. Latham

PLOS Computational Biology: published December 20, 2016 | https://doi.org/10.1371/journal.pcbi.1005110

Temporal Dynamics and Developmental Maturation of Salience, Default and Central-Executive Network Interactions Revealed by Variational Bayes Hidden Markov Modeling

Srikanth Ryali, Kaustubh Supekar, Tianwen Chen, John Kochalka, Weidong Cai, Jonathan Nicholas, Aarthi Padmanabhan, Vinod Menon

PLOS Computational Biology: published December 13, 2016 | https://doi.org/10.1371/journal.pcbi.1005138

Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models

Ryan C. Williamson, Benjamin R. Cowley, Ashok Litwin-Kumar, Brent Doiron, Adam Kohn, Matthew A. Smith, Byron M. Yu

PLOS Computational Biology: published December 7, 2016 | https://doi.org/10.1371/journal.pcbi.1005141

Fused Regression for Multi-source Gene Regulatory Network Inference

Kari Y. Lam, Zachary M. Westrick, Christian L. Müller, Lionel Christiaen, Richard Bonneau

PLOS Computational Biology: published December 6, 2016 | https://doi.org/10.1371/journal.pcbi.1005157

Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex

Benjamin R. Cowley, Matthew A. Smith, Adam Kohn, Byron M. Yu

PLOS Computational Biology: published December 9, 2016 | https://doi.org/10.1371/journal.pcbi.1005185

The Hamiltonian Brain: Efficient Probabilistic Inference with Excitatory-Inhibitory Neural Circuit Dynamics

Laurence Aitchison, Máté Lengyel

PLOS Computational Biology: published December 27, 2016 | https://doi.org/10.1371/journal.pcbi.1005186

When Optimal Feedback Control Is Not Enough: Feedforward Strategies Are Required for Optimal Control with Active Sensing

Sang-Hoon Yeo, David W. Franklin, Daniel M. Wolpert

PLOS Computational Biology: published December 14, 2016 | https://doi.org/10.1371/journal.pcbi.1005190

Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites

Angela Re, Levi Waldron, Alessandro Quattrone

PLOS Computational Biology: published December 6, 2016 | https://doi.org/10.1371/journal.pcbi.1005198

In Silico Knockout Studies of Xenophagic Capturing of Salmonella

Jennifer Scheidel, Leonie Amstein, Jörg Ackermann, Ivan Dikic, Ina Koch

PLOS Computational Biology: published December 1, 2016 | https://doi.org/10.1371/journal.pcbi.1005200

Universal or Specific? A Modeling-Based Comparison of Broad-Spectrum Influenza Vaccines against Conventional, Strain-Matched Vaccines

Rahul Subramanian, Andrea L. Graham, Bryan T. Grenfell, Nimalan Arinaminpathy

PLOS Computational Biology: published December 15, 2016 | https://doi.org/10.1371/journal.pcbi.1005204

Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa

Jantien A. Backer, Jacco Wallinga

PLOS Computational Biology: published December 8, 2016 | https://doi.org/10.1371/journal.pcbi.1005210

Beyond the Hypercube: Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks

Marcin Zagorski, Zdzislaw Burda, Bartlomiej Waclaw

PLOS Computational Biology: published December 9, 2016 | https://doi.org/10.1371/journal.pcbi.1005218

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

Brian Drawert, Andreas Hellander, Ben Bales, Debjani Banerjee, Giovanni Bellesia, Bernie J. Daigle Jr., Geoffrey Douglas, Mengyuan Gu, Anand Gupta, Stefan Hellander, Chris Horuk, Dibyendu Nath, Aviral Takkar, Sheng Wu, Per Lötstedt, Chandra Krintz, Linda R. Petzold

PLOS Computational Biology: published December 8, 2016 | https://doi.org/10.1371/journal.pcbi.1005220

A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics

Haixu Tang, Sujun Li, Yuzhen Ye

PLOS Computational Biology: published December 5, 2016 | https://doi.org/10.1371/journal.pcbi.1005224

An Extended Normalization Model of Attention Accounts for Feature-Based Attentional Enhancement of Both Response and Coherence Gain

Philipp Schwedhelm, B. Suresh Krishna, Stefan Treue

PLOS Computational Biology: published December 15, 2016 | https://doi.org/10.1371/journal.pcbi.1005225

The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems

Andrew White, Malachi Tolman, Howard D. Thames, Hubert Rodney Withers, Kathy A. Mason, Mark K. Transtrum

PLOS Computational Biology: published December 6, 2016 | https://doi.org/10.1371/journal.pcbi.1005227

A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability

Debashis Barik, David A. Ball, Jean Peccoud, John J. Tyson

PLOS Computational Biology: published December 9, 2016 | https://doi.org/10.1371/journal.pcbi.1005230

Synchronization and Random Triggering of Lymphatic Vessel Contractions

James W. Baish, Christian Kunert, Timothy P. Padera, Lance L. Munn

PLOS Computational Biology: published December 9, 2016 | https://doi.org/10.1371/journal.pcbi.1005231

Dopamine Neurons Change the Type of Excitability in Response to Stimuli

Ekaterina O. Morozova, Denis Zakharov, Boris S. Gutkin, Christopher C. Lapish, Alexey Kuznetsov

PLOS Computational Biology: published December 8, 2016 | https://doi.org/10.1371/journal.pcbi.1005233

Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series

Anna Klimovskaia, Stefan Ganscha, Manfred Claassen

PLOS Computational Biology: published December 6, 2016 | https://doi.org/10.1371/journal.pcbi.1005234

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology

James C. Schaff, Fei Gao, Ye Li, Igor L. Novak, Boris M. Slepchenko

PLOS Computational Biology: published December 13, 2016 | https://doi.org/10.1371/journal.pcbi.1005236

The Kinematics of Plant Nutation Reveals a Simple Relation between Curvature and the Orientation of Differential Growth

Renaud Bastien, Yasmine Meroz

PLOS Computational Biology: published December 6, 2016 | https://doi.org/10.1371/journal.pcbi.1005238

Modeling Contact Inhibition of Locomotion of Colliding Cells Migrating on Micropatterned Substrates

Dirk Alexander Kulawiak, Brian A. Camley, Wouter-Jan Rappel

PLOS Computational Biology: published December 16, 2016 | https://doi.org/10.1371/journal.pcbi.1005239

Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model

Kristen A. Marino, Diego Prada-Gracia, Davide Provasi, Marta Filizola

PLOS Computational Biology: published December 13, 2016 | https://doi.org/10.1371/journal.pcbi.1005240

Alpha Helices Are More Robust to Mutations than Beta Strands

György Abrusán, Joseph A. Marsh

PLOS Computational Biology: published December 9, 2016 | https://doi.org/10.1371/journal.pcbi.1005242

Hierarchical Post-transcriptional Regulation of Colicin E2 Expression in Escherichia coli

Matthias Lechner, Mathias Schwarz, Madeleine Opitz, Erwin Frey

PLOS Computational Biology: published December 15, 2016 | https://doi.org/10.1371/journal.pcbi.1005243

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations

Sahra Uygun, Cheng Peng, Melissa D. Lehti-Shiu, Robert L. Last, Shin-Han Shiu

PLOS Computational Biology: published December 9, 2016 | https://doi.org/10.1371/journal.pcbi.1005244

Atrial Heterogeneity Generates Re-entrant Substrate during Atrial Fibrillation and Anti-arrhythmic Drug Action: Mechanistic Insights from Canine Atrial Models

Marta Varela, Michael A. Colman, Jules C. Hancox, Oleg V. Aslanidi

PLOS Computational Biology: published December 16, 2016 | https://doi.org/10.1371/journal.pcbi.1005245

Lack of Ecological and Life History Context Can Create the Illusion of Social Interactions in Dictyostelium discoideum

Ricardo Martínez-García, Corina E. Tarnita

PLOS Computational Biology: published December 15, 2016 | https://doi.org/10.1371/journal.pcbi.1005246

Evolution at ‘Sutures’ and ‘Centers’: Recombination Can Aid Adaptation of Spatially Structured Populations on Rugged Fitness Landscapes

Jacob D. Cooper, Benjamin Kerr

PLOS Computational Biology: published December 14, 2016 | https://doi.org/10.1371/journal.pcbi.1005247

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns

Matthew Huska, Martin Vingron

PLOS Computational Biology: published December 16, 2016 | https://doi.org/10.1371/journal.pcbi.1005249

Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1

Russell Gould, David M. Bassen, Anirikh Chakrabarti, Jeffrey D. Varner, Jonathan Butcher

PLOS Computational Biology: published December 27, 2016 | https://doi.org/10.1371/journal.pcbi.1005251

Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota

Sébastien Raguideau, Sandra Plancade, Nicolas Pons, Marion Leclerc, Béatrice Laroche

PLOS Computational Biology: published December 16, 2016 | https://doi.org/10.1371/journal.pcbi.1005252

The Effect of Gap Junctional Coupling on the Spatiotemporal Patterns of Ca²⁺ Signals and the Harmonization of Ca²⁺-Related Cellular Responses

Michaël Dougoud, Laura Vinckenbosch, Christian Mazza, Beat Schwaller, László Pecze

PLOS Computational Biology: published December 27, 2016 | https://doi.org/10.1371/journal.pcbi.1005295

Cover

Kinematics of Plant Nutation

Message from ISCB

Research Articles

Related Articles

Related Articles

Related Articles