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Table of Contents: 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

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

Alastair M. Kilpatrick

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

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

Laurence Aitchison, Nicola Corradi, Peter E. Latham

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

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

Fused Regression for Multi-source Gene Regulatory Network Inference

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

Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex

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

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

Angela Re, Levi Waldron, Alessandro Quattrone

In Silico Knockout Studies of Xenophagic Capturing of Salmonella

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

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

Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa

Jantien A. Backer, Jacco Wallinga

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

Marcin Zagorski, Zdzislaw Burda, Bartlomiej Waclaw

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

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

Synchronization and Random Triggering of Lymphatic Vessel Contractions

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

Dopamine Neurons Change the Type of Excitability in Response to Stimuli

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

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

Anna Klimovskaia, Stefan Ganscha, Manfred Claassen

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

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

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

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

Alpha Helices Are More Robust to Mutations than Beta Strands

György Abrusán, Joseph A. Marsh

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

Matthias Lechner, Mathias Schwarz, Madeleine Opitz, Erwin Frey

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

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

Competing Mechanistic Hypotheses of Acetaminophen-Induced Hepatotoxicity Challenged by Virtual Experiments

Andrew K. Smith, Brenden K. Petersen, Glen E. P. Ropella, Ryan C. Kennedy, Neil Kaplowitz, Murad Ookhtens, C. Anthony Hunt

Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos

Jonathan Desponds, Huy Tran, Teresa Ferraro, Tanguy Lucas, Carmina Perez Romero, Aurelien Guillou, Cecile Fradin, Mathieu Coppey, Nathalie Dostatni, Aleksandra M. Walczak

Encoding in Balanced Networks: Revisiting Spike Patterns and Chaos in Stimulus-Driven Systems

Guillaume Lajoie, Kevin K. Lin, Jean-Philippe Thivierge, Eric Shea-Brown

Human Inferences about Sequences: A Minimal Transition Probability Model

Florent Meyniel, Maxime Maheu, Stanislas Dehaene

Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level

Kawai Leung, Aylia Mohammadi, William S. Ryu, Ilya Nemenman

Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator

J. Patrick Pett, Anja Korenčič, Felix Wesener, Achim Kramer, Hanspeter Herzel

Role of Autoregulation and Relative Synthesis of Operon Partners in Alternative Sigma Factor Networks

Jatin Narula, Abhinav Tiwari, Oleg A. Igoshin

Stability of Cross-Feeding Polymorphisms in Microbial Communities

Ivana Gudelj, Margie Kinnersley, Peter Rashkov, Karen Schmidt, Frank Rosenzweig

Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets

Aitor Blanco-Míguez, Jan P. Meier-Kolthoff, Alberto Gutiérrez-Jácome, Markus Göker, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço

Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs

Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi

The Multilayer Connectome of Caenorhabditis elegans

Barry Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew, Eviatar Yemini, Edward T. Bullmore, Petra E. Vértes, William R. Schafer

Decoding Single Molecule Time Traces with Dynamic Disorder

Wonseok Hwang, Il-Buem Lee, Seok-Cheol Hong, Changbong Hyeon

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks

Song-Yao Zhang, Shao-Wu Zhang, Lian Liu, Jia Meng, Yufei Huang

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

Simeon Carstens, Michael Nilges, Michael Habeck

Normal Modes Expose Active Sites in Enzymes

Yitav Glantz-Gashai, Tomer Meirson, Abraham O. Samson

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations

Andrew F. Neuwald, Stephen F. Altschul

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

Systematic Approximations to Susceptible-Infectious-Susceptible Dynamics on Networks

Matt J. Keeling, Thomas House, Alison J. Cooper, Lorenzo Pellis

Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations

Katharina Baum, Antonio Z. Politi, Bente Kofahl, Ralf Steuer, Jana Wolf

Glycoside Hydrolases across Environmental Microbial Communities

Renaud Berlemont, Adam C. Martiny

Novel Models of Visual Topographic Map Alignment in the Superior Colliculus

Ruben A. Tikidji-Hamburyan, Tarek A. El-Ghazawi, Jason W. Triplett