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Table of Contents

August 2018

Epileptic seizures are hypersynchronous states disrupting normal brain function unfolding across brain networks. We can now image the network wide changes in brain dynamics using light sheet imaging in the larval zebrafish brain. Combined with computational modelling, this gives us a powerful tool to investigate the connectivity changes that allow these abnormal seizure states to emerge.

Image Credit: Richard Ewald Rosch

Research Articles

Irrelevance by inhibition: Learning, computation, and implications for schizophrenia

Nathan Insel, Jordan Guerguiev, Blake A. Richards

Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015

Valentina Marziano, Piero Poletti, Guillaume Béraud, Pierre-Yves Boëlle, Stefano Merler, Vittoria Colizza

The permeation mechanism of organic cations through a CNG mimic channel

Luisa M. R. Napolitano, Arin Marchesi, Alex Rodriguez, Matteo De March, Silvia Onesti, Alessandro Laio, Vincent Torre

Profiling cellular morphodynamics by spatiotemporal spectrum decomposition

Xiao Ma, Onur Dagliyan, Klaus M. Hahn, Gaudenz Danuser

Rare-event sampling of epigenetic landscapes and phenotype transitions

Margaret J. Tse, Brian K. Chu, Cameron P. Gallivan, Elizabeth L. Read

A mechanism for bistability in glycosylation

Andrew G. McDonald, Keith F. Tipton, Gavin P. Davey

Network supporting contextual fear learning after dorsal hippocampal damage has increased dependence on retrosplenial cortex

Cesar A. O. Coelho, Tatiana L. Ferreira, Juliana C. Kramer-Soares, João R. Sato, Maria Gabriela M. Oliveira

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials

James T. Yurkovich, Miguel A. Alcantar, Zachary B. Haiman, Bernhard O. Palsson

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization

Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard

Flexible resonance in prefrontal networks with strong feedback inhibition

Jason S. Sherfey, Salva Ardid, Joachim Hass, Michael E. Hasselmo, Nancy J. Kopell

Modeling subjective relevance in schizophrenia and its relation to aberrant salience

Teresa Katthagen, Christoph Mathys, Lorenz Deserno, Henrik Walter, Norbert Kathmann, Andreas Heinz, Florian Schlagenhauf

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

Luyi Tian, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Fabio Lauria, Toma Tebaldi, Paola Bernabò, Ewout J. N. Groen, Thomas H. Gillingwater, Gabriella Viero

Regulation of Pom cluster dynamics in Myxococcus xanthus

Silke Bergeler, Erwin Frey

Scaling up data curation using deep learning: An application to literature triage in genomic variation resources

Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline Ann Langdon MacArthur, Sylvain Poux, Lionel Breuza, Alan Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu

Interplay of multiple pathways and activity-dependent rules in STDP

Gaëtan Vignoud, Laurent Venance, Jonathan D. Touboul

Integration and multiplexing of positional and contextual information by the hippocampal network

Lorenzo Posani, Simona Cocco, Rémi Monasson

Characterising seasonal influenza epidemiology using primary care surveillance data

Robert C. Cope, Joshua V. Ross, Monique Chilver, Nigel P. Stocks, Lewis Mitchell

MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies

Christos Vlachos, Robert Kofler

Exploring of the feature space of de novo developed post-transcriptional riboregulators

Gert Peters, Jo Maertens, Jeroen Lammertyn, Marjan De Mey

The role of curvature feedback in the energetics and dynamics of lamprey swimming: A closed-loop model

Christina L. Hamlet, Kathleen A. Hoffman, Eric D. Tytell, Lisa J. Fauci

ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization

Diego Garrido-Martín, Emilio Palumbo, Roderic Guigó, Alessandra Breschi

How ecological feedbacks between human population and land cover influence sustainability

Kirsten Henderson, Michel Loreau

Unraveling the mechanism of the cadherin-catenin-actin catch bond

Shishir Adhikari, Jacob Moran, Christopher Weddle, Michael Hinczewski

Domes and cones: Adhesion-induced fission of membranes by ESCRT proteins

Jaime Agudo-Canalejo, Reinhard Lipowsky

Lineage space and the propensity of bacterial cells to undergo growth transitions

Arnab Bandyopadhyay, Huijing Wang, J. Christian J. Ray

NFTsim: Theory and Simulation of Multiscale Neural Field Dynamics

Paula Sanz-Leon, Peter A. Robinson, Stuart A. Knock, Peter M. Drysdale, Romesh G. Abeysuriya, Felix K. Fung, Chris J. Rennie, Xuelong Zhao

Inferring hidden structure in multilayered neural circuits

Niru Maheswaranathan, David B. Kastner, Stephen A. Baccus, Surya Ganguli

Calcium imaging and dynamic causal modelling reveal brain-wide changes in effective connectivity and synaptic dynamics during epileptic seizures

Richard E. Rosch, Paul R. Hunter, Torsten Baldeweg, Karl J. Friston, Martin P. Meyer

Dorsal anterior cingulate-brainstem ensemble as a reinforcement meta-learner

Massimo Silvetti, Eliana Vassena, Elger Abrahamse, Tom Verguts

coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers

Alena van Bömmel, Michael I. Love, Ho-Ryun Chung, Martin Vingron

Identification of excitatory-inhibitory links and network topology in large-scale neuronal assemblies from multi-electrode recordings

Vito Paolo Pastore, Paolo Massobrio, Aleksandar Godjoski, Sergio Martinoia

General differential Hebbian learning: Capturing temporal relations between events in neural networks and the brain

Stefano Zappacosta, Francesco Mannella, Marco Mirolli, Gianluca Baldassarre

New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images

Ilya Patrushev, Christina James-Zorn, Aldo Ciau-Uitz, Roger Patient, Michael J. Gilchrist

Corrections

Correction: Subgraphs of functional brain networks identify dynamical constraints of cognitive control

Ankit N. Khambhati, John D. Medaglia, Elisabeth A. Karuza, Sharon L. Thompson-Schill, Danielle S. Bassett

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