Table of Contents

November 2018

Sensory neural systems of living organisms encode the representation of their environment with remarkable efficiency. This is manifested, e.g., in the way how male moths perform long-distance searches of their females by tracking the pheromone plumes. In the study "Moth olfactory receptor neurons adjust their encoding efficiency to temporal statistics of pheromone fluctuations" Levakova et al. analyzed responses of pheromone-specific antennal neurons to naturalistic stimulation. It was shown that the coding accuracy and the stimulus distribution are in the optimal relationship as predicted by both information theory and statistical estimation theory.

Image Credit: Marie Levakova


Putting benchmarks in their rightful place: The heart of computational biology

Bjoern Peters, Steven E. Brenner, Edwin Wang, Donna Slonim, Maricel G. Kann

Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars

Denise Carvalho-Silva, Leyla Garcia, Sarah L. Morgan, Cath Brooksbank, Ian Dunham

Ten simple rules for collaboratively writing a multi-authored paper

Marieke A. Frassl, David P. Hamilton, Blaize A. Denfeld, Elvira de Eyto, Stephanie E. Hampton, Philipp S. Keller, Sapna Sharma, Abigail S. L. Lewis, Gesa A. Weyhenmeyer, Catherine M. O’Reilly, Mary E. Lofton, Núria Catalán


Strategies and opportunities for promoting bioinformatics in Zimbabwe

Ryman Shoko, Justen Manasa, Mcebisi Maphosa, Joshua Mbanga, Reagan Mudziwapasi, Victoria Nembaware, Walter T. Sanyika, Tawanda Tinago, Zedias Chikwambi, Cephas Mawere, Alice Matimba, Grace Mugumbate, Jonathan Mufandaedza, Nicola Mulder, Hugh Patterton

Research Articles

Active dendrites regulate the spatiotemporal spread of signaling microdomains

Reshma Basak, Rishikesh Narayanan

Motif-Aware PRALINE: Improving the alignment of motif regions

Maurits Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan Fokkink, Jaap Heringa

Efficient pedigree recording for fast population genetics simulation

Jerome Kelleher, Kevin R. Thornton, Jaime Ashander, Peter L. Ralph

Modeling driver cells in developing neuronal networks

Stefano Luccioli, David Angulo-Garcia, Rosa Cossart, Arnaud Malvache, Laura Módol, Vitor Hugo Sousa, Paolo Bonifazi, Alessandro Torcini

Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction

Susann Vorberg, Stefan Seemayer, Johannes Söding

Prediction and classification in equation-free collective motion dynamics

Keisuke Fujii, Takeshi Kawasaki, Yuki Inaba, Yoshinobu Kawahara

Modulation of voltage-dependent K+ conductances in photoreceptors trades off investment in contrast gain for bandwidth

Francisco J. H. Heras, Mikko Vähäsöyrinki, Jeremy E. Niven

A computational analysis of dynamic, multi-organ inflammatory crosstalk induced by endotoxin in mice

Ruben Zamora, Sebastian Korff, Qi Mi, Derek Barclay, Lukas Schimunek, Riccardo Zucca, Xerxes D. Arsiwalla, Richard L. Simmons, Paul Verschure, Timothy R. Billiar, Yoram Vodovotz

The Cultural Brain Hypothesis: How culture drives brain expansion, sociality, and life history

Michael Muthukrishna, Michael Doebeli, Maciej Chudek, Joseph Henrich

Comparative structural dynamic analysis of GTPases

Hongyang Li, Xin-Qiu Yao, Barry J. Grant

Oscillations in working memory and neural binding: A mechanism for multiple memories and their interactions

Jason E. Pina, Mark Bodner, Bard Ermentrout

Visual physiology of the layer 4 cortical circuit in silico

Anton Arkhipov, Nathan W. Gouwens, Yazan N. Billeh, Sergey Gratiy, Ramakrishnan Iyer, Ziqiang Wei, Zihao Xu, Reza Abbasi-Asl, Jim Berg, Michael Buice, Nicholas Cain, Nuno da Costa, Saskia de Vries, Daniel Denman, Severine Durand, David Feng, Tim Jarsky, Jérôme Lecoq, Brian Lee, Lu Li, Stefan Mihalas, Gabriel K. Ocker, Shawn R. Olsen, R. Clay Reid, Gilberto Soler-Llavina, Staci A. Sorensen, Quanxin Wang, Jack Waters, Massimo Scanziani, Christof Koch

Invasion and effective size of graph-structured populations

Stefano Giaimo, Jordi Arranz, Arne Traulsen

Functional mechanisms underlie the emergence of a diverse range of plasticity phenomena

James A. Henderson, Pulin Gong

A regularity index for dendrites - local statistics of a neuron's input space

Laura Anton-Sanchez, Felix Effenberger, Concha Bielza, Pedro Larrañaga, Hermann Cuntz

Bayesian phylodynamic inference with complex models

Erik M. Volz, Igor Siveroni

Comparing Bayesian and non-Bayesian accounts of human confidence reports

William T. Adler, Wei Ji Ma

Moth olfactory receptor neurons adjust their encoding efficiency to temporal statistics of pheromone fluctuations

Marie Levakova, Lubomir Kostal, Christelle Monsempès, Vincent Jacob, Philippe Lucas

Patterning the insect eye: From stochastic to deterministic mechanisms

Haleh Ebadi, Michael Perry, Keith Short, Konstantin Klemm, Claude Desplan, Peter F. Stadler, Anita Mehta

Cytoplasmic flows in starfish oocytes are fully determined by cortical contractions

Nils Klughammer, Johanna Bischof, Nikolas D. Schnellbächer, Andrea Callegari, Péter Lénárt, Ulrich S. Schwarz

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers

Andrej Berg, Oleksandra Kukharenko, Martin Scheffner, Christine Peter

Simulations of blood as a suspension predicts a depth dependent hematocrit in the circulation throughout the cerebral cortex

Grant Hartung, Claudia Vesel, Ryan Morley, Ali Alaraj, John Sled, David Kleinfeld, Andreas Linninger

Rosetta FunFolDes – A general framework for the computational design of functional proteins

Jaume Bonet, Sarah Wehrle, Karen Schriever, Che Yang, Anne Billet, Fabian Sesterhenn, Andreas Scheck, Freyr Sverrisson, Barbora Veselkova, Sabrina Vollers, Roxanne Lourman, Mélanie Villard, Stéphane Rosset, Thomas Krey, Bruno E. Correia

Adaptive feature detection from differential processing in parallel retinal pathways

Yusuf Ozuysal, David B. Kastner, Stephen A. Baccus

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

Ryan R. Wick, Louise M. Judd, Kathryn E. Holt

Determinants of early afterdepolarization properties in ventricular myocyte models

Xiaodong Huang, Zhen Song, Zhilin Qu

Binding of the general anesthetic sevoflurane to ion channels

Letícia Stock, Juliana Hosoume, Leonardo Cirqueira, Werner Treptow

RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks

Jun Li, Wei Zhu, Jun Wang, Wenfei Li, Sheng Gong, Jian Zhang, Wei Wang

A Bayesian mixture modelling approach for spatial proteomics

Oliver M. Crook, Claire M. Mulvey, Paul D. W. Kirk, Kathryn S. Lilley, Laurent Gatto

Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch

Lina Meinecke, Praveer P. Sharma, Huijing Du, Lei Zhang, Qing Nie, Thomas F. Schilling

powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire

Hillary Koch, Dmytro Starenki, Sara J. Cooper, Richard M. Myers, Qunhua Li

Atlases of cognition with large-scale human brain mapping

Gaël Varoquaux, Yannick Schwartz, Russell A. Poldrack, Baptiste Gauthier, Danilo Bzdok, Jean-Baptiste Poline, Bertrand Thirion

Deterministic response strategies in a trial-and-error learning task

Holger Mohr, Katharina Zwosta, Dimitrije Markovic, Sebastian Bitzer, Uta Wolfensteller, Hannes Ruge

Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs

Brandon M. Butler, I. Can Kazan, Avishek Kumar, S. Banu Ozkan

Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening

Daniel Jimenez-Carretero, Vahid Abrishami, Laura Fernández-de-Manuel, Irene Palacios, Antonio Quílez-Álvarez, Alberto Díez-Sánchez, Miguel A. del Pozo, María C. Montoya

Mechanistic insight into spontaneous transition from cellular alternans to arrhythmia—A simulation study

Wei Wang, Shanzhuo Zhang, Haibo Ni, Clifford J. Garratt, Mark R. Boyett, Jules C. Hancox, Henggui Zhang