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

Editorials

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

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

PLOS Computational Biology: published November 8, 2018 | https://doi.org/10.1371/journal.pcbi.1006494

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

PLOS Computational Biology: published November 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006419

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

PLOS Computational Biology: published November 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006508

Perspective

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

PLOS Computational Biology: published November 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006480

Research Articles

Active dendrites regulate the spatiotemporal spread of signaling microdomains

Reshma Basak, Rishikesh Narayanan

PLOS Computational Biology: published November 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006485

Motif-Aware PRALINE: Improving the alignment of motif regions

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

PLOS Computational Biology: published November 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006547

Efficient pedigree recording for fast population genetics simulation

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

PLOS Computational Biology: published November 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006581

Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter

Yarden Golan, Raphael Alhadeff, Fabian Glaser, Assaf Ganoth, Arieh Warshel, Yehuda G. Assaraf

PLOS Computational Biology: published November 2, 2018 | https://doi.org/10.1371/journal.pcbi.1006503

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

PLOS Computational Biology: published November 2, 2018 | https://doi.org/10.1371/journal.pcbi.1006551

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

Giovanni B. Brandani, Shoji Takada

PLOS Computational Biology: published November 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006512

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

Susann Vorberg, Stefan Seemayer, Johannes Söding

PLOS Computational Biology: published November 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006526

Prediction and classification in equation-free collective motion dynamics

Keisuke Fujii, Takeshi Kawasaki, Yuki Inaba, Yoshinobu Kawahara

PLOS Computational Biology: published November 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006545

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

PLOS Computational Biology: published November 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006566

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

PLOS Computational Biology: published November 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006582

Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes

Weilong Zhao, Xinwei Sher

PLOS Computational Biology: published November 8, 2018 | https://doi.org/10.1371/journal.pcbi.1006457

A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

Christiane Ehrt, Tobias Brinkjost, Oliver Koch

PLOS Computational Biology: published November 8, 2018 | https://doi.org/10.1371/journal.pcbi.1006483

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

Michael Muthukrishna, Michael Doebeli, Maciej Chudek, Joseph Henrich

PLOS Computational Biology: published November 8, 2018 | https://doi.org/10.1371/journal.pcbi.1006504

Comparative structural dynamic analysis of GTPases

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

PLOS Computational Biology: published November 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006364

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

Jason E. Pina, Mark Bodner, Bard Ermentrout

PLOS Computational Biology: published November 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006517

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

PLOS Computational Biology: published November 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006535

Invasion and effective size of graph-structured populations

Stefano Giaimo, Jordi Arranz, Arne Traulsen

PLOS Computational Biology: published November 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006559

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

James A. Henderson, Pulin Gong

PLOS Computational Biology: published November 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006590

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

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

PLOS Computational Biology: published November 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006593

Inferring interaction partners from protein sequences using mutual information

Anne-Florence Bitbol

PLOS Computational Biology: published November 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006401

Bayesian phylodynamic inference with complex models

Erik M. Volz, Igor Siveroni

PLOS Computational Biology: published November 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006546

Comparing Bayesian and non-Bayesian accounts of human confidence reports

William T. Adler, Wei Ji Ma

PLOS Computational Biology: published November 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006572

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

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

PLOS Computational Biology: published November 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006586

Patterning the insect eye: From stochastic to deterministic mechanisms

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

PLOS Computational Biology: published November 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006363

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

PLOS Computational Biology: published November 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006588

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

Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha

PLOS Computational Biology: published November 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006556

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

Andrej Berg, Oleksandra Kukharenko, Martin Scheffner, Christine Peter

PLOS Computational Biology: published November 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006589

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

PLOS Computational Biology: published November 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006549

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

PLOS Computational Biology: published November 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006623

Adaptive feature detection from differential processing in parallel retinal pathways

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

PLOS Computational Biology: published November 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006560

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

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

PLOS Computational Biology: published November 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006583

Determinants of early afterdepolarization properties in ventricular myocyte models

Xiaodong Huang, Zhen Song, Zhilin Qu

PLOS Computational Biology: published November 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006382

Comprehensive computational modelling of the development of mammalian cortical connectivity underlying an architectonic type principle

Sarah F. Beul, Alexandros Goulas, Claus C. Hilgetag

PLOS Computational Biology: published November 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006550

Binding of the general anesthetic sevoflurane to ion channels

Letícia Stock, Juliana Hosoume, Leonardo Cirqueira, Werner Treptow

PLOS Computational Biology: published November 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006605

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

PLOS Computational Biology: published November 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006514

A Bayesian mixture modelling approach for spatial proteomics

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

PLOS Computational Biology: published November 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006516

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

PLOS Computational Biology: published November 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006569

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

PLOS Computational Biology: published November 28, 2018 | https://doi.org/10.1371/journal.pcbi.1006571

Correction

Correction: Assessment of ab initio models of protein complexes by molecular dynamics

The PLOS Computational Biology Staff

PLOS Computational Biology: published November 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006598

Cover

Moth antennal neurons adjust their encoding optimally with respect to pheromone fluctuations

Editorials

Perspective

Research Articles

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Correction

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