April 2021

The illustration expresses that inhibitory neurons exert a higher level of control to the comparatively large number of excitatory neurons in the neocortex with the metaphor of babysitting many playing babies. The neurons can be largely categorized into excitatory and inhibitory. Exactly how the two interact in order to maintain balance of the brain is a fundamental question in neurobiology. The results demonstrated that not only is it the higher firing rate of inhibitory neurons that keep things in check, but it is also where these neurons are positioned to influence and control other neurons. Kajiwara et al. (2021)

Image Credit: Science Manga Studio (parsely918, noguchi.m, and Hayanon. 2021)

Research Articles

Constraints on the deformation of the vibrissa within the follicle

Yifu Luo, Chris S. Bresee, John W. Rudnicki, Mitra J. Z. Hartmann

PLOS Computational Biology: published April 1, 2021 | https://doi.org/10.1371/journal.pcbi.1007887

Dynamic decorrelation as a unifying principle for explaining a broad range of brightness phenomena

Alejandro Lerer, Hans Supèr, Matthias S. Keil

PLOS Computational Biology: published April 26, 2021 | https://doi.org/10.1371/journal.pcbi.1007907

Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data

David P. Shorten, Richard E. Spinney, Joseph T. Lizier

PLOS Computational Biology: published April 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008054

Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies

Lisette Meerstein-Kessel, Jeron Venhuizen, Daniel Garza, Nicholas I. Proellochs, Emma J. Vos, Joshua M. Obiero, Philip L. Felgner, Robert W. Sauerwein, Marynthe Peters, Annie S. P. Yang, Martijn A. Huynen

PLOS Computational Biology: published April 30, 2021 | https://doi.org/10.1371/journal.pcbi.1008067

Transmission delays and frequency detuning can regulate information flow between brain regions

Aref Pariz, Ingo Fischer, Alireza Valizadeh, Claudio Mirasso

PLOS Computational Biology: published April 15, 2021 | https://doi.org/10.1371/journal.pcbi.1008129

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion

Zhuliu Li, Tianci Song, Jeongsik Yong, Rui Kuang

PLOS Computational Biology: published April 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008218

Effect of synchronization of firings of different motor unit types on the force variability in a model of the rat medial gastrocnemius muscle

Rositsa Raikova, Vessela Krasteva, Piotr Krutki, Hanna Drzymała-Celichowska, Katarzyna Kryściak, Jan Celichowski

PLOS Computational Biology: published April 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008282

An extended catalogue of tandem alternative splice sites in human tissue transcriptomes

Aleksei Mironov, Stepan Denisov, Alexander Gress, Olga V. Kalinina, Dmitri D. Pervouchine

PLOS Computational Biology: published April 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008329

Hierarchical motor adaptations negotiate failures during force field learning

Tsuyoshi Ikegami, Gowrishankar Ganesh, Tricia L. Gibo, Toshinori Yoshioka, Rieko Osu, Mitsuo Kawato

PLOS Computational Biology: published April 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008481

Mistakes can stabilise the dynamics of rock-paper-scissors games

Maria Kleshnina, Sabrina S. Streipert, Jerzy A. Filar, Krishnendu Chatterjee

PLOS Computational Biology: published April 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008523

A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation

Diego Vidaurre

PLOS Computational Biology: published April 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008580

Efficient and robust coding in heterogeneous recurrent networks

Fleur Zeldenrust, Boris Gutkin, Sophie Denéve

PLOS Computational Biology: published April 30, 2021 | https://doi.org/10.1371/journal.pcbi.1008673

Differential contributions of synaptic and intrinsic inhibitory currents to speech segmentation via flexible phase-locking in neural oscillators

Benjamin R. Pittman-Polletta, Yangyang Wang, David A. Stanley, Charles E. Schroeder, Miles A. Whittington, Nancy J. Kopell

PLOS Computational Biology: published April 14, 2021 | https://doi.org/10.1371/journal.pcbi.1008783

Computational epitope map of SARS-CoV-2 spike protein

Mateusz Sikora, Sören von Bülow, Florian E. C. Blanc, Michael Gecht, Roberto Covino, Gerhard Hummer

PLOS Computational Biology: published April 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008790

ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network

Lifan Liang, Kunju Zhu, Junyan Tao, Songjian Lu

PLOS Computational Biology: published April 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008792

Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families

Claudio Bassot, Arne Elofsson

PLOS Computational Biology: published April 15, 2021 | https://doi.org/10.1371/journal.pcbi.1008798

VolPy: Automated and scalable analysis pipelines for voltage imaging datasets

Changjia Cai, Johannes Friedrich, Amrita Singh, M. Hossein Eybposh, Eftychios A. Pnevmatikakis, Kaspar Podgorski, Andrea Giovannucci

PLOS Computational Biology: published April 14, 2021 | https://doi.org/10.1371/journal.pcbi.1008806

Behavioral discrimination and time-series phenotyping of birdsong performance

Avishek Paul, Helen McLendon, Veronica Rally, Jon T. Sakata, Sarah C. Woolley

PLOS Computational Biology: published April 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008820

Sperm chemotaxis in marine species is optimal at physiological flow rates according theory of filament surfing

Steffen Lange, Benjamin M. Friedrich

PLOS Computational Biology: published April 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008826

Using Hawkes Processes to model imported and local malaria cases in near-elimination settings

H. Juliette T. Unwin, Isobel Routledge, Seth Flaxman, Marian-Andrei Rizoiu, Shengjie Lai, Justin Cohen, Daniel J. Weiss, Swapnil Mishra, Samir Bhatt

PLOS Computational Biology: published April 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008830

Computational modelling of muscle fibre operating ranges in the hindlimb of a small ground bird (Eudromia elegans), with implications for modelling locomotion in extinct species

Peter J. Bishop, Krijn B. Michel, Antoine Falisse, Andrew R. Cuff, Vivian R. Allen, Friedl De Groote, John R. Hutchinson

PLOS Computational Biology: published April 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008843

Inhibitory neurons exhibit high controlling ability in the cortical microconnectome

Motoki Kajiwara, Ritsuki Nomura, Felix Goetze, Masanori Kawabata, Yoshikazu Isomura, Tatsuya Akutsu, Masanori Shimono

PLOS Computational Biology: published April 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008846

Avoiding the bullies: The resilience of cooperation among unequals

Michael Foley, Rory Smead, Patrick Forber, Christoph Riedl

PLOS Computational Biology: published April 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008847

Linking statistical shape models and simulated function in the healthy adult human heart

Cristobal Rodero, Marina Strocchi, Maciej Marciniak, Stefano Longobardi, John Whitaker, Mark D. O’Neill, Karli Gillette, Christoph Augustin, Gernot Plank, Edward J. Vigmond, Pablo Lamata, Steven A. Niederer

PLOS Computational Biology: published April 15, 2021 | https://doi.org/10.1371/journal.pcbi.1008851

Interactions between all pairs of neighboring trees in 16 forests worldwide reveal details of unique ecological processes in each forest, and provide windows into their evolutionary histories

Christopher Wills, Bin Wang, Shuai Fang, Yunquan Wang, Yi Jin, James Lutz, Jill Thompson, Kyle E. Harms, Sandeep Pulla, Bonifacio Pasion, Sara Germain, Heming Liu, Joseph Smokey, Sheng-Hsin Su, Nathalie Butt, Chengjin Chu, George Chuyong, Chia-Hao Chang-Yang, H. S. Dattaraja, Stuart Davies, Sisira Ediriweera, Shameema Esufali, Christine Dawn Fletcher, Nimal Gunatilleke, Savi Gunatilleke, Chang-Fu Hsieh, Fangliang He, Stephen Hubbell, Zhanqing Hao, Akira Itoh, David Kenfack, Buhang Li, Xiankun Li, Keping Ma, Michael Morecroft, Xiangcheng Mi, Yadvinder Malhi, Perry Ong, Lillian Jennifer Rodriguez, H. S. Suresh, I Fang Sun, Raman Sukumar, Sylvester Tan, Duncan Thomas, Maria Uriarte, Xihua Wang, Xugao Wang, T. L. Yao, Jess Zimmermann

PLOS Computational Biology: published April 29, 2021 | https://doi.org/10.1371/journal.pcbi.1008853

Temporal dynamics of a CSF1R signaling gene regulatory network involved in epilepsy

Claude Gérard, Laurane De Mot, Sabine Cordi, Jonathan van Eyll, Frédéric P. Lemaigre

PLOS Computational Biology: published April 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008854

Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment

Benjamin Deneu, Maximilien Servajean, Pierre Bonnet, Christophe Botella, François Munoz, Alexis Joly

PLOS Computational Biology: published April 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008856

Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection

Piyush Nanda, Amit Ghosh

PLOS Computational Biology: published April 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008860

Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex

Jean-Charles Walter, Thibaut Lepage, Jérôme Dorignac, Frédéric Geniet, Andrea Parmeggiani, John Palmeri, Jean-Yves Bouet, Ivan Junier

PLOS Computational Biology: published April 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008869

Individual differences in the perception of probability

Mel W. Khaw, Luminita Stevens, Michael Woodford

PLOS Computational Biology: published April 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008871

Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge

Vladislav Uzunangelov, Christopher K. Wong, Joshua M. Stuart

PLOS Computational Biology: published April 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008878

MAUI (MBI Analysis User Interface)—An image processing pipeline for Multiplexed Mass Based Imaging

Alex Baranski, Idan Milo, Shirley Greenbaum, John-Paul Oliveria, Dunja Mrdjen, Michael Angelo, Leeat Keren

PLOS Computational Biology: published April 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008887

Building blocks and blueprints for bacterial autolysins

Spencer J. Mitchell, Deeptak Verma, Karl E. Griswold, Chris Bailey-Kellogg

PLOS Computational Biology: published April 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008889

Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor

Valeria Velásquez-Zapata, J. Mitch Elmore, Sagnik Banerjee, Karin S. Dorman, Roger P. Wise

PLOS Computational Biology: published April 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008890

A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

Linnea Österberg, Iván Domenzain, Julia Münch, Jens Nielsen, Stefan Hohmann, Marija Cvijovic

PLOS Computational Biology: published April 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008891

Computation of the electroencephalogram (EEG) from network models of point neurons

Pablo Martínez-Cañada, Torbjørn V. Ness, Gaute T. Einevoll, Tommaso Fellin, Stefano Panzeri

PLOS Computational Biology: published April 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008893

Efficient population coding depends on stimulus convergence and source of noise

Kai Röth, Shuai Shao, Julijana Gjorgjieva

PLOS Computational Biology: published April 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008897

Machine learning-based investigation of the cancer protein secretory pathway

Rasool Saghaleyni, Azam Sheikh Muhammad, Pramod Bangalore, Jens Nielsen, Jonathan L. Robinson

PLOS Computational Biology: published April 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008898

Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes

Christophe Menichelli, Vincent Guitard, Rafael M. Martins, Sophie Lèbre, Jose-Juan Lopez-Rubio, Charles-Henri Lecellier, Laurent Bréhélin

PLOS Computational Biology: published April 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008909

WormPose: Image synthesis and convolutional networks for pose estimation in C. elegans

Laetitia Hebert, Tosif Ahamed, Antonio C. Costa, Liam O’Shaughnessy, Greg J. Stephens

PLOS Computational Biology: published April 27, 2021 | https://doi.org/10.1371/journal.pcbi.1008914

Unraveling the mechanisms of surround suppression in early visual processing

Yao Li, Lai-Sang Young

PLOS Computational Biology: published April 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008916

Genome-wide analysis of lncRNA stability in human

Kaiwen Shi, Tao Liu, Hanjiang Fu, Wuju Li, Xiaofei Zheng

PLOS Computational Biology: published April 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008918

Detecting adherence to the recommended childhood vaccination schedule from user-generated content in a US parenting forum

Lorenzo Betti, Gianmarco De Francisci Morales, Laetitia Gauvin, Kyriaki Kalimeri, Yelena Mejova, Daniela Paolotti, Michele Starnini

PLOS Computational Biology: published April 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008919

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