September 2019

For undulatory swimming, fish form posteriorly traveling waves of body bending by activating their muscles sequentially along the body. However, experimental observations have shown that the muscle activation wave does not simply match the bending wave. Ming et al. use 3D computational fluid dynamics models to explain the muscle activation patterns by computing and analyzing the internal torque and power required for eel-like and mackerel-like swimming. They provide a mechanical picture in which the body shape, body movement, muscles, tendons, and body elasticity of a mackerel (or similar) orchestrate to make swimming efficient.

Image Credit: Bowen Jin, Beijing Computational Science Research Center (CSRC)

Editorial

Ten simple rules to create biological network figures for communication

G. Elisabeta Marai, Bruno Pinaud, Katja Bühler, Alexander Lex, John H. Morris

PLOS Computational Biology: published September 26, 2019 | https://doi.org/10.1371/journal.pcbi.1007244

Education

Ten simple rules for helping newcomers become contributors to open projects

Dan Sholler, Igor Steinmacher, Denae Ford, Mara Averick, Mike Hoye, Greg Wilson

PLOS Computational Biology: published September 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007296

Perspectives

Perspective: Dimensions of the scientific method

Eberhard O. Voit

PLOS Computational Biology: published September 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007279

Bioinformatics in Jordan: Status, challenges, and future directions

Qanita Bani Baker, Maryam S. Nuser

PLOS Computational Biology: published September 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007202

Research Articles

Estimating information in time-varying signals

Sarah Anhala Cepeda-Humerez, Jakob Ruess, Gašper Tkačik

PLOS Computational Biology: published September 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007290

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting

Alex X. Lu, Oren Z. Kraus, Sam Cooper, Alan M. Moses

PLOS Computational Biology: published September 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007348

The FACTS model of speech motor control: Fusing state estimation and task-based control

Benjamin Parrell, Vikram Ramanarayanan, Srikantan Nagarajan, John Houde

PLOS Computational Biology: published September 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007321

Benchmarking network propagation methods for disease gene identification

Sergio Picart-Armada, Steven J. Barrett, David R. Willé, Alexandre Perera-Lluna, Alex Gutteridge, Benoit H. Dessailly

PLOS Computational Biology: published September 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007276

Deconvolving multiplexed protease signatures with substrate reduction and activity clustering

Qinwei Zhuang, Brandon Alexander Holt, Gabriel A. Kwong, Peng Qiu

PLOS Computational Biology: published September 3, 2019 | https://doi.org/10.1371/journal.pcbi.1006909

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data

Allison L. Hicks, Nicole Wheeler, Leonor Sánchez-Busó, Jennifer L. Rakeman, Simon R. Harris, Yonatan H. Grad

PLOS Computational Biology: published September 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007349

Executable pathway analysis using ensemble discrete-state modeling for large-scale data

Rohith Palli, Mukta G. Palshikar, Juilee Thakar

PLOS Computational Biology: published September 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007317

Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction

Yufeng Su, Yunan Luo, Xiaoming Zhao, Yang Liu, Jian Peng

PLOS Computational Biology: published September 4, 2019 | https://doi.org/10.1371/journal.pcbi.1007283

3D computational models explain muscle activation patterns and energetic functions of internal structures in fish swimming

Tingyu Ming, Bowen Jin, Jialei Song, Haoxiang Luo, Ruxu Du, Yang Ding

PLOS Computational Biology: published September 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006883

Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making

Amir Dezfouli, Bernard W. Balleine

PLOS Computational Biology: published September 6, 2019 | https://doi.org/10.1371/journal.pcbi.1007334

Cost-benefit trade-offs in decision-making and learning

Nura Sidarus, Stefano Palminteri, Valérian Chambon

PLOS Computational Biology: published September 6, 2019 | https://doi.org/10.1371/journal.pcbi.1007326

p¹³CMFA: Parsimonious ¹³C metabolic flux analysis

Carles Foguet, Anusha Jayaraman, Silvia Marin, Vitaly A. Selivanov, Pablo Moreno, Ramon Messeguer, Pedro de Atauri, Marta Cascante

PLOS Computational Biology: published September 6, 2019 | https://doi.org/10.1371/journal.pcbi.1007310

Designing combination therapies with modeling chaperoned machine learning

Yin Zhang, Julie M. Huynh, Guan-Sheng Liu, Richard Ballweg, Kayenat S. Aryeh, Andrew L. Paek, Tongli Zhang

PLOS Computational Biology: published September 9, 2019 | https://doi.org/10.1371/journal.pcbi.1007158

MHC binding affects the dynamics of different T-cell receptors in different ways

Bernhard Knapp, P. Anton van der Merwe, Omer Dushek, Charlotte M. Deane

PLOS Computational Biology: published September 9, 2019 | https://doi.org/10.1371/journal.pcbi.1007338

Prepaid parameter estimation without likelihoods

Merijn Mestdagh, Stijn Verdonck, Kristof Meers, Tim Loossens, Francis Tuerlinckx

PLOS Computational Biology: published September 9, 2019 | https://doi.org/10.1371/journal.pcbi.1007181

Systematically understanding the immunity leading to CRPC progression

Zhiwei Ji, Weiling Zhao, Hui-Kuan Lin, Xiaobo Zhou

PLOS Computational Biology: published September 10, 2019 | https://doi.org/10.1371/journal.pcbi.1007344

From Escherichia coli mutant ¹³C labeling data to a core kinetic model: A kinetic model parameterization pipeline

Charles J. Foster, Saratram Gopalakrishnan, Maciek R. Antoniewicz, Costas D. Maranas

PLOS Computational Biology: published September 10, 2019 | https://doi.org/10.1371/journal.pcbi.1007319

Role of dynamic nuclear deformation on genomic architecture reorganization

Sungrim Seirin-Lee, Fumitaka Osakada, Junichi Takeda, Satoshi Tashiro, Ryo Kobayashi, Takashi Yamamoto, Hiroshi Ochiai

PLOS Computational Biology: published September 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007289

Network trade-offs and homeostasis in Arabidopsis shoot architectures

Adam Conn, Arjun Chandrasekhar, Martin van Rongen, Ottoline Leyser, Joanne Chory, Saket Navlakha

PLOS Computational Biology: published September 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007325

Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features

David F. Read, Kate Cook, Yang Y. Lu, Karine G. Le Roch, William Stafford Noble

PLOS Computational Biology: published September 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007329

Generation of Binary Tree-Child phylogenetic networks

Gabriel Cardona, Joan Carles Pons, Celine Scornavacca

PLOS Computational Biology: published September 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007347

Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination

Alexander D. Becker, Amy Wesolowski, Ottar N. Bjørnstad, Bryan T. Grenfell

PLOS Computational Biology: published September 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007305

Characterizing and dissociating multiple time-varying modulatory computations influencing neuronal activity

Kaiser Niknam, Amir Akbarian, Kelsey Clark, Yasin Zamani, Behrad Noudoost, Neda Nategh

PLOS Computational Biology: published September 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007275

Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics

Christoph Schmal, Daisuke Ono, Jihwan Myung, J. Patrick Pett, Sato Honma, Ken-Ichi Honma, Hanspeter Herzel, Isao T. Tokuda

PLOS Computational Biology: published September 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007330

Loop analysis of blood pressure/volume homeostasis

Bruno Burlando, Franco Blanchini, Giulia Giordano

PLOS Computational Biology: published September 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007346

Deep attention networks reveal the rules of collective motion in zebrafish

Francisco J. H. Heras, Francisco Romero-Ferrero, Robert C. Hinz, Gonzalo G. de Polavieja

PLOS Computational Biology: published September 13, 2019 | https://doi.org/10.1371/journal.pcbi.1007354

EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology

Sébastien Picault, Yu-Lin Huang, Vianney Sicard, Sandie Arnoux, Gaël Beaunée, Pauline Ezanno

PLOS Computational Biology: published September 13, 2019 | https://doi.org/10.1371/journal.pcbi.1007342

Close spatial arrangement of mutants favors and disfavors fixation

Yunming Xiao, Bin Wu

PLOS Computational Biology: published September 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007212

A flexible and generalizable model of online latent-state learning

Amy L. Cochran, Josh M. Cisler

PLOS Computational Biology: published September 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007331

Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints

Srinivasan Venkatramanan, Jiangzhuo Chen, Arindam Fadikar, Sandeep Gupta, Dave Higdon, Bryan Lewis, Madhav Marathe, Henning Mortveit, Anil Vullikanti

PLOS Computational Biology: published September 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007111

Deep learning as a tool for neural data analysis: Speech classification and cross-frequency coupling in human sensorimotor cortex

Jesse A. Livezey, Kristofer E. Bouchard, Edward F. Chang

PLOS Computational Biology: published September 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007091

Fast and near-optimal monitoring for healthcare acquired infection outbreaks

Bijaya Adhikari, Bryan Lewis, Anil Vullikanti, José Mauricio Jiménez, B. Aditya Prakash

PLOS Computational Biology: published September 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007284

Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics

Sanggeun Song, Gil-Suk Yang, Seong Jun Park, Sungguan Hong, Ji-Hyun Kim, Jaeyoung Sung

PLOS Computational Biology: published September 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007356

Unified feature association networks through integration of transcriptomic and proteomic data

Ryan S. McClure, Jason P. Wendler, Joshua N. Adkins, Jesica Swanstrom, Ralph Baric, Brooke L. Deatherage Kaiser, Kristie L. Oxford, Katrina M. Waters, Jason E. McDermott

PLOS Computational Biology: published September 17, 2019 | https://doi.org/10.1371/journal.pcbi.1007241

3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients

Cansu Dincer, Tugba Kaya, Ozlem Keskin, Attila Gursoy, Nurcan Tuncbag

PLOS Computational Biology: published September 17, 2019 | https://doi.org/10.1371/journal.pcbi.1006789

Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program

Mónica Chagoyen, Juan F. Poyatos

PLOS Computational Biology: published September 17, 2019 | https://doi.org/10.1371/journal.pcbi.1007353

Predicting gene regulatory interactions based on spatial gene expression data and deep learning

Yang Yang, Qingwei Fang, Hong-Bin Shen

PLOS Computational Biology: published September 17, 2019 | https://doi.org/10.1371/journal.pcbi.1007324

Multi-cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space

Michaëlle N. Mayalu, Min-Cheol Kim, H. Harry Asada

PLOS Computational Biology: published September 20, 2019 | https://doi.org/10.1371/journal.pcbi.1006798

Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail

Mateusz Kogut, Cyprian Kleist, Jacek Czub

PLOS Computational Biology: published September 20, 2019 | https://doi.org/10.1371/journal.pcbi.1007383

Time scales and wave formation in non-linear spatial public goods games

Gregory J. Kimmel, Philip Gerlee, Philipp M. Altrock

PLOS Computational Biology: published September 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007361

Quantifying model evidence for yellow fever transmission routes in Africa

Katy A. M. Gaythorpe, Kévin Jean, Laurence Cibrelus, Tini Garske

PLOS Computational Biology: published September 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007355

A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance

Jordan P. Skittrall, Carin K. Ingemarsdotter, Julia R. Gog, Andrew M. L. Lever

PLOS Computational Biology: published September 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007345

Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons

Timothy Rumbell, James Kozloski

PLOS Computational Biology: published September 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007375

Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform

Anna Matveeva, Michael Fichtner, Katherine McAllister, Christopher McCann, Marc Sturrock, Daniel B. Longley, Jochen H. M. Prehn

PLOS Computational Biology: published September 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007374

Computational modelling predicts substantial carbon assimilation gains for C₃ plants with a single-celled C₄ biochemical pump

Ivan Jurić, Julian M. Hibberd, Mike Blatt, Nigel J. Burroughs

PLOS Computational Biology: published September 30, 2019 | https://doi.org/10.1371/journal.pcbi.1007373

Corrections

Correction: Minimal model of interictal and ictal discharges “Epileptor-2”

Anton V. Chizhov, Artyom V. Zefirov, Dmitry V. Amakhin, Elena Yu. Smirnova, Aleksey V. Zaitsev

PLOS Computational Biology: published September 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007359

Correction: Comprehensively benchmarking applications for detecting copy number variation

Le Zhang, Wanyu Bai, Na Yuan, Zhenglin Du

PLOS Computational Biology: published September 20, 2019 | https://doi.org/10.1371/journal.pcbi.1007367

Cover

3D computational models explain how fish power swimming

Editorial

Education

Perspectives

Research Articles

Related Articles

Corrections

Related Articles

Related Articles