Table of Contents

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


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

Research Articles

Developmental trajectory of Caenorhabditis elegans nervous system governs its structural organization

Anand Pathak, Nivedita Chatterjee, Sitabhra Sinha

Interpreting neural decoding models using grouped model reliance

Simon Valentin, Maximilian Harkotte, Tzvetan Popov

Computational optimization of associative learning experiments

Filip Melinscak, Dominik R. Bach

Increasing growth rate slows adaptation when genotypes compete for diffusing resources

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

The origin of biological homochirality along with the origin of life

Yong Chen, Wentao Ma

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

Jaideep Joshi, Åke Brännström, Ulf Dieckmann

Learning from animals: How to Navigate Complex Terrains

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

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

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

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

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

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

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

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

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

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

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

Maria Bargués-Ribera, Chaitanya S. Gokhale

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

Related Articles

Limits on amplifiers of natural selection under death-Birth updating

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

Related Articles

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

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

Collaboration leads to cooperation on sparse networks

Simon D. Angus, Jonathan Newton

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

Learning spatiotemporal signals using a recurrent spiking network that discretizes time

Amadeus Maes, Mauricio Barahona, Claudia Clopath

Between-tumor and within-tumor heterogeneity in invasive potential

Veena Padmanaban, Yohannes Tsehay, Kevin J. Cheung, Andrew J. Ewald, Joel S. Bader

Tissue-guided LASSO for prediction of clinical drug response using preclinical samples

Edward W. Huang, Ameya Bhope, Jing Lim, Saurabh Sinha, Amin Emad

ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets

Christopher A. Lavender, Andrew J. Shapiro, Frank S. Day, David C. Fargo

A system for tracking whisker kinematics and whisker shape in three dimensions

Rasmus S. Petersen, Andrea Colins Rodriguez, Mathew H. Evans, Dario Campagner, Michaela S. E. Loft

Nucleosome positioning sequence patterns as packing or regulatory

Erinija Pranckeviciene, Sergey Hosid, Nathan Liang, Ilya Ioshikhes

Elementary Growth Modes provide a molecular description of cellular self-fabrication

Daan H. de Groot, Josephus Hulshof, Bas Teusink, Frank J. Bruggeman, Robert Planqué

Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome

Sean M. Cascarina, Mikaela R. Elder, Eric D. Ross

Notch signaling and taxis mechanisms regulate early stage angiogenesis: A mathematical and computational model

Rocío Vega, Manuel Carretero, Rui D. M. Travasso, Luis L. Bonilla

Incremental data integration for tracking genotype-disease associations

Tomasz Konopka, Damian Smedley

Optimizing circadian drug infusion schedules towards personalized cancer chronotherapy

Roger J. W. Hill, Pasquale F. Innominato, Francis Lévi, Annabelle Ballesta

Recurrent interactions can explain the variance in single trial responses

Subhodh Kotekal, Jason N. MacLean

Heterogeneity coordinates bacterial multi-gene expression in single cells

Yichao Han, Fuzhong Zhang

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