January 2020

Rats and mice explore their environment by 3D whisker movements. However, most previous efforts to measure whisker movement have imaged whiskers only in the horizontal plane. Petersen et al developed a non-invasive whisker tracker that automatically reconstructs 3D whisker information directly from ‘stereo’ video data. The algorithm is able to track multiple whiskers in parallel with low error rate, and produces a 3D description of each tracked whisker, including its 3D orientation, 3D shape and bending-related mechanical force.

Image Credit: Andrea Colins Rodriguez, University of Manchester

Education

An educational guide for nanopore sequencing in the classroom

Alex N. Salazar, Franklin L. Nobrega, Christine Anyansi, Cristian Aparicio-Maldonado, Ana Rita Costa, Anna C. Haagsma, Anwar Hiralal, Ahmed Mahfouz, Rebecca E. McKenzie, Teunke van Rossum, Stan J. J. Brouns, Thomas Abeel

PLOS Computational Biology: published January 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007314

Research Articles

Developmental trajectory of Caenorhabditis elegans nervous system governs its structural organization

Anand Pathak, Nivedita Chatterjee, Sitabhra Sinha

PLOS Computational Biology: published January 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007602

Interpreting neural decoding models using grouped model reliance

Simon Valentin, Maximilian Harkotte, Tzvetan Popov

PLOS Computational Biology: published January 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007148

Computational optimization of associative learning experiments

Filip Melinscak, Dominik R. Bach

PLOS Computational Biology: published January 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007593

Increasing growth rate slows adaptation when genotypes compete for diffusing resources

Jeremy M. Chacón, Allison K. Shaw, William R. Harcombe

PLOS Computational Biology: published January 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007585

The origin of biological homochirality along with the origin of life

Yong Chen, Wentao Ma

PLOS Computational Biology: published January 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007592

Emergence of social inequality in the spatial harvesting of renewable public goods

Jaideep Joshi, Åke Brännström, Ulf Dieckmann

PLOS Computational Biology: published January 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007483

Learning from animals: How to Navigate Complex Terrains

Henghui Zhu, Hao Liu, Armin Ataei, Yonatan Munk, Thomas Daniel, Ioannis Ch. Paschalidis

PLOS Computational Biology: published January 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007452

Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power

Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam, Thomas Simonson

PLOS Computational Biology: published January 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007600

Emergence and suppression of cooperation by action visibility in transparent games

Anton M. Unakafov, Thomas Schultze, Alexander Gail, Sebastian Moeller, Igor Kagan, Stephan Eule, Fred Wolf

PLOS Computational Biology: published January 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007588

Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming

Jake P. Taylor-King, Asbjørn N. Riseth, Will Macnair, Manfred Claassen

PLOS Computational Biology: published January 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007491

DetEdit: A graphical user interface for annotating and editing events detected in long-term acoustic monitoring data

Alba Solsona-Berga, Kaitlin E. Frasier, Simone Baumann-Pickering, Sean M. Wiggins, John A. Hildebrand

PLOS Computational Biology: published January 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007598

VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning

Jiwoong Kim, David E. Greenberg, Reed Pifer, Shuang Jiang, Guanghua Xiao, Samuel A. Shelburne, Andrew Koh, Yang Xie, Xiaowei Zhan

PLOS Computational Biology: published January 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007511

The role of actin protrusion dynamics in cell migration through a degradable viscoelastic extracellular matrix: Insights from a computational model

Tommy Heck, Diego A. Vargas, Bart Smeets, Herman Ramon, Paul Van Liedekerke, Hans Van Oosterwyck

PLOS Computational Biology: published January 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007250

BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis

Manoj Kumar, Cameron T. Ellis, Qihong Lu, Hejia Zhang, Mihai Capotă, Theodore L. Willke, Peter J. Ramadge, Nicholas B. Turk-Browne, Kenneth A. Norman

PLOS Computational Biology: published January 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007549

A single reaction-diffusion equation for the multifarious eruptions of urticaria

Sungrim Seirin-Lee, Yuhki Yanase, Shunsuke Takahagi, Michihiro Hide

PLOS Computational Biology: published January 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007590

The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations

Christie A. Bahlai, Elise F. Zipkin

PLOS Computational Biology: published January 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007542

Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations

Maria Bargués-Ribera, Chaitanya S. Gokhale

PLOS Computational Biology: published January 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007546

Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs

Benjamin Allen, Christine Sample, Robert Jencks, James Withers, Patricia Steinhagen, Lori Brizuela, Joshua Kolodny, Darren Parke, Gabor Lippner, Yulia A. Dementieva

PLOS Computational Biology: published January 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007529

Limits on amplifiers of natural selection under death-Birth updating

Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee, Martin A. Nowak

PLOS Computational Biology: published January 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007494

A new method for inferring timetrees from temporally sampled molecular sequences

Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A. Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar

PLOS Computational Biology: published January 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007046

Computational simulation of the reactive oxygen species and redox network in the regulation of chloroplast metabolism

Melanie Gerken, Sergej Kakorin, Kamel Chibani, Karl-Josef Dietz

PLOS Computational Biology: published January 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007102

Collaboration leads to cooperation on sparse networks

Simon D. Angus, Jonathan Newton

PLOS Computational Biology: published January 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007557

Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma

Jennifer Hannig, Hendrik Schäfer, Jörg Ackermann, Marie Hebel, Tim Schäfer, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch

PLOS Computational Biology: published January 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007516

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data

Jordan A. Berg, Jonathan R. Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter

PLOS Computational Biology: published January 31, 2020 | https://doi.org/10.1371/journal.pcbi.1007625

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Tracking whisker kinematics and whisker shape in three dimensions

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