October 2019

Fungi produce complex networks of filamentous structures that allow them to colonize different environments. The filamentous nature makes quantitative analyses of fungal growth dynamics and morphology challenging. Vidal-Diez de Ulzurrun et al. have developed a new method for capturing images of live fungi and a tool, Fungal Feature Tracker, to extract different morphological features from fungal images. FFT can quantitatively characterize fungal morphology, cell number and measure filamentous growth allowing objective and precise characterization of phenotypes which will advance our understanding of fungal growth and biology.

Image Credit: Guillermo Vidal-Diez de Ulzurrun, Institute of Molecular Biology, Academia Sinica, Taiwan

Editorials

Ten simple rules for providing optimal administrative support to research teams

Romina Garrido, Casandra A. Trowbridge, Nana Tamura

PLOS Computational Biology: published October 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007292

Ten simple rules to aid in achieving a vision

Philip E. Bourne

PLOS Computational Biology: published October 17, 2019 | https://doi.org/10.1371/journal.pcbi.1007395

Education

Ten quick tips for delivering programming lessons

Greg Wilson

PLOS Computational Biology: published October 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007433

Perspective

Patient Dossier: Healthcare queries over distributed resources

Miguel Vazquez, Alfonso Valencia

PLOS Computational Biology: published October 17, 2019 | https://doi.org/10.1371/journal.pcbi.1007291

Research Articles

Estimating influenza incidence using search query deceptiveness and generalized ridge regression

Reid Priedhorsky, Ashlynn R. Daughton, Martha Barnard, Fiona O’Connell, Dave Osthus

PLOS Computational Biology: published October 1, 2019 | https://doi.org/10.1371/journal.pcbi.1007165

Evolving generalists in switching rugged landscapes

Shenshen Wang, Lei Dai

PLOS Computational Biology: published October 1, 2019 | https://doi.org/10.1371/journal.pcbi.1007320

Using text-mined trait data to test for cooperate-and-radiate co-evolution between ants and plants

Katrina M. Kaur, Pierre-Jean G. Malé, Erik Spence, Crisanto Gomez, Megan E. Frederickson

PLOS Computational Biology: published October 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007323

A computational model of postprandial adipose tissue lipid metabolism derived using human arteriovenous stable isotope tracer data

Shauna D. O’Donovan, Michael Lenz, Roel G. Vink, Nadia J. T. Roumans, Theo M. C. M. de Kok, Edwin C. M. Mariman, Ralf L. M. Peeters, Natal A. W. van Riel, Marleen A. van Baak, Ilja C. W. Arts

PLOS Computational Biology: published October 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007400

Competition-driven evolution of organismal complexity

Iaroslav Ispolatov, Evgeniia Alekseeva, Michael Doebeli

PLOS Computational Biology: published October 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007388

Constrained inference in sparse coding reproduces contextual effects and predicts laminar neural dynamics

Federica Capparelli, Klaus Pawelzik, Udo Ernst

PLOS Computational Biology: published October 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007370

A simulation of the random and directed motion of dendritic cells in chemokine fields

Avery Parr, Nicholas R. Anderson, Daniel A. Hammer

PLOS Computational Biology: published October 7, 2019 | https://doi.org/10.1371/journal.pcbi.1007295

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations

Bogdan Barz, Jennifer Loschwitz, Birgit Strodel

PLOS Computational Biology: published October 7, 2019 | https://doi.org/10.1371/journal.pcbi.1007193

Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations

Carmichael F. Ong, Thomas Geijtenbeek, Jennifer L. Hicks, Scott L. Delp

PLOS Computational Biology: published October 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006993

Dimensional reduction in networks of non-Markovian spiking neurons: Equivalence of synaptic filtering and heterogeneous propagation delays

Maurizio Mattia, Matteo Biggio, Andrea Galluzzi, Marco Storace

PLOS Computational Biology: published October 8, 2019 | https://doi.org/10.1371/journal.pcbi.1007404

miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs

Jimmy Bell, Maureen Larson, Michelle Kutzler, Massimo Bionaz, Christiane V. Löhr, David Hendrix

PLOS Computational Biology: published October 9, 2019 | https://doi.org/10.1371/journal.pcbi.1007309

A computational account of threat-related attentional bias

Toby Wise, Jochen Michely, Peter Dayan, Raymond J. Dolan

PLOS Computational Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pcbi.1007341

Consensus and uncertainty in the geographic range of Aedes aegypti and Aedes albopictus in the contiguous United States: Multi-model assessment and synthesis

Andrew J. Monaghan, Rebecca J. Eisen, Lars Eisen, Janet McAllister, Harry M. Savage, John-Paul Mutebi, Michael A. Johansson

PLOS Computational Biology: published October 10, 2019 | https://doi.org/10.1371/journal.pcbi.1007369

Evaluation of linear and non-linear activation dynamics models for insect muscle

Nalin Harischandra, Anthony J. Clare, Jure Zakotnik, Laura M. L. Blackburn, Tom Matheson, Volker Dürr

PLOS Computational Biology: published October 14, 2019 | https://doi.org/10.1371/journal.pcbi.1007437

Categorical encoding of decision variables in orbitofrontal cortex

Arno Onken, Jue Xie, Stefano Panzeri, Camillo Padoa-Schioppa

PLOS Computational Biology: published October 14, 2019 | https://doi.org/10.1371/journal.pcbi.1006667

Combinations of low-level and high-level neural processes account for distinct patterns of context-dependent choice

Mehran Spitmaan, Oihane Horno, Emily Chu, Alireza Soltani

PLOS Computational Biology: published October 14, 2019 | https://doi.org/10.1371/journal.pcbi.1007427

Phylogenetic correlations can suffice to infer protein partners from sequences

Guillaume Marmier, Martin Weigt, Anne-Florence Bitbol

PLOS Computational Biology: published October 14, 2019 | https://doi.org/10.1371/journal.pcbi.1007179

Key residues in TLR4-MD2 tetramer formation identified by free energy simulations

Alireza Tafazzol, Yong Duan

PLOS Computational Biology: published October 14, 2019 | https://doi.org/10.1371/journal.pcbi.1007228

Transitions in information processing dynamics at the whole-brain network level are driven by alterations in neural gain

Mike Li, Yinuo Han, Matthew J. Aburn, Michael Breakspear, Russell A. Poldrack, James M. Shine, Joseph T. Lizier

PLOS Computational Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006957

TAPES: A tool for assessment and prioritisation in exome studies

Alexandre Xavier, Rodney J. Scott, Bente A. Talseth-Palmer

PLOS Computational Biology: published October 15, 2019 | https://doi.org/10.1371/journal.pcbi.1007453

A Kuramoto model of self-other integration across interpersonal synchronization strategies

Ole Adrian Heggli, Joana Cabral, Ivana Konvalinka, Peter Vuust, Morten L. Kringelbach

PLOS Computational Biology: published October 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007422

Computational design and interpretation of single-RNA translation experiments

Luis U. Aguilera, William Raymond, Zachary R. Fox, Michael May, Elliot Djokic, Tatsuya Morisaki, Timothy J. Stasevich, Brian Munsky

PLOS Computational Biology: published October 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007425

Detecting distant-homology protein structures by aligning deep neural-network based contact maps

Wei Zheng, Qiqige Wuyun, Yang Li, S. M. Mortuza, Chengxin Zhang, Robin Pearce, Jishou Ruan, Yang Zhang

PLOS Computational Biology: published October 17, 2019 | https://doi.org/10.1371/journal.pcbi.1007411

Surfactant delivery in rat lungs: Comparing 3D geometrical simulation model with experimental instillation

Alireza Kazemi, Bruno Louis, Daniel Isabey, Gary F. Nieman, Louis A. Gatto, Joshua Satalin, Sarah Baker, James B. Grotberg, Marcel Filoche

PLOS Computational Biology: published October 17, 2019 | https://doi.org/10.1371/journal.pcbi.1007408

Action potential propagation and synchronisation in myelinated axons

Helmut Schmidt, Thomas R. Knösche

PLOS Computational Biology: published October 17, 2019 | https://doi.org/10.1371/journal.pcbi.1007004

Color improves edge classification in human vision

Camille Breuil, Ben J. Jennings, Simon Barthelmé, Nathalie Guyader, Frederick A. A. Kingdom

PLOS Computational Biology: published October 18, 2019 | https://doi.org/10.1371/journal.pcbi.1007398

Spectral tuning of adaptation supports coding of sensory context in auditory cortex

Mateo Lopez Espejo, Zachary P. Schwartz, Stephen V. David

PLOS Computational Biology: published October 18, 2019 | https://doi.org/10.1371/journal.pcbi.1007430

Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein

Ruchi Lohia, Reza Salari, Grace Brannigan

PLOS Computational Biology: published October 18, 2019 | https://doi.org/10.1371/journal.pcbi.1007390

The folded X-pattern is not necessarily a statistical signature of decision confidence

Manuel Rausch, Michael Zehetleitner

PLOS Computational Biology: published October 21, 2019 | https://doi.org/10.1371/journal.pcbi.1007456

A multi-scale coevolutionary approach to predict interactions between protein domains

Giancarlo Croce, Thomas Gueudré, Maria Virginia Ruiz Cuevas, Victoria Keidel, Matteo Figliuzzi, Hendrik Szurmant, Martin Weigt

PLOS Computational Biology: published October 21, 2019 | https://doi.org/10.1371/journal.pcbi.1006891

LASSI: A lattice model for simulating phase transitions of multivalent proteins

Jeong-Mo Choi, Furqan Dar, Rohit V. Pappu

PLOS Computational Biology: published October 21, 2019 | https://doi.org/10.1371/journal.pcbi.1007028

Hypergraph-based connectivity measures for signaling pathway topologies

Nicholas Franzese, Adam Groce, T. M. Murali, Anna Ritz

PLOS Computational Biology: published October 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007384

SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways

Elisa Salviato, Vera Djordjilović, Monica Chiogna, Chiara Romualdi

PLOS Computational Biology: published October 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007357

From space to time: Spatial inhomogeneities lead to the emergence of spatiotemporal sequences in spiking neuronal networks

Sebastian Spreizer, Ad Aertsen, Arvind Kumar

PLOS Computational Biology: published October 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007432

Matrigel patterning reflects multicellular contractility

Előd Méhes, Beáta Biri-Kovács, Dona G. Isai, Márton Gulyás, László Nyitray, András Czirók

PLOS Computational Biology: published October 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007431

Uncovering and characterizing splice variants associated with survival in lung cancer patients

Sean West, Sushil Kumar, Surinder K. Batra, Hesham Ali, Dario Ghersi

PLOS Computational Biology: published October 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007469

Matrix feedback enables diverse higher-order patterning of the extracellular matrix

Esther Wershof, Danielle Park, Robert P. Jenkins, David J. Barry, Erik Sahai, Paul A. Bates

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007251

Coding Locations Relative to One or Many Landmarks in Childhood

James Negen, Linda Bou Ali, Brittney Chere, Hannah E. Roome, Yeachan Park, Marko Nardini

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007380

Evolution of the nonsense-mediated decay pathway is associated with decreased cytolytic immune infiltration

Boyang Zhao, Justin R. Pritchard

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007467

Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature

Qiao Liu, Di He, Lei Xie

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007480

SCMarker: Ab initio marker selection for single cell transcriptome profiling

Fang Wang, Shaoheng Liang, Tapsi Kumar, Nicholas Navin, Ken Chen

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007445

Ancestral reconstruction of protein interaction networks

Benjamin J. Liebeskind, Richard W. Aldrich, Edward M. Marcotte

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007396

Seasonal influenza: Modelling approaches to capture immunity propagation

Edward M. Hill, Stavros Petrou, Simon de Lusignan, Ivelina Yonova, Matt J. Keeling

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007096

Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort

Gabriel Balaban, Brian P. Halliday, Wenjia Bai, Bradley Porter, Carlotta Malvuccio, Pablo Lamata, Christopher A. Rinaldi, Gernot Plank, Daniel Rueckert, Sanjay K. Prasad, Martin J. Bishop

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007421

Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise

Mariana Gómez-Schiavon, Nicolas E. Buchler

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007364

Simple models of quantitative firing phenotypes in hippocampal neurons: Comprehensive coverage of intrinsic diversity

Siva Venkadesh, Alexander O. Komendantov, Diek W. Wheeler, David J. Hamilton, Giorgio A. Ascoli

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007462

Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling

Parul Maheshwari, Hao Du, Jen Sheen, Sarah M. Assmann, Reka Albert

PLOS Computational Biology: published October 28, 2019 | https://doi.org/10.1371/journal.pcbi.1007429

EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions

Tianshun Gao, Jiang Qian

PLOS Computational Biology: published October 30, 2019 | https://doi.org/10.1371/journal.pcbi.1007436

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

Neil J. Bruce, Daniele Narzi, Daniel Trpevski, Siri C. van Keulen, Anu G. Nair, Ursula Röthlisberger, Rebecca C. Wade, Paolo Carloni, Jeanette Hellgren Kotaleski

PLOS Computational Biology: published October 30, 2019 | https://doi.org/10.1371/journal.pcbi.1007382

Energetics of optimal undulatory swimming organisms

Grgur Tokić, Dick K. P. Yue

PLOS Computational Biology: published October 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007387

Delayed feedback embedded in perception-action coordination cycles results in anticipation behavior during synchronized rhythmic action: A dynamical systems approach

Iran R. Roman, Auriel Washburn, Edward W. Large, Chris Chafe, Takako Fujioka

PLOS Computational Biology: published October 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007371

Fungal feature tracker (FFT): A tool for quantitatively characterizing the morphology and growth of filamentous fungi

Guillermo Vidal-Diez de Ulzurrun, Tsung-Yu Huang, Ching-Wen Chang, Hung-Che Lin, Yen-Ping Hsueh

PLOS Computational Biology: published October 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007428

Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers

David J. Wooten, Sarah M. Groves, Darren R. Tyson, Qi Liu, Jing S. Lim, Réka Albert, Carlos F. Lopez, Julien Sage, Vito Quaranta

PLOS Computational Biology: published October 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007343

Bayesian inference of neuronal assemblies

Giovanni Diana, Thomas T. J. Sainsbury, Martin P. Meyer

PLOS Computational Biology: published October 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007481

Corrections

Correction: A unifying Bayesian account of contextual effects in value-based choice

Francesco Rigoli, Christoph Mathys, Karl J. Friston, Raymond J. Dolan

PLOS Computational Biology: published October 2, 2019 | https://doi.org/10.1371/journal.pcbi.1007366

Correction: Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism

The PLOS Computational Biology Staff

PLOS Computational Biology: published October 7, 2019 | https://doi.org/10.1371/journal.pcbi.1007420

Cover

Image analysis to characterize fungal growth and morphology

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