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Current Issue of PLoSBiology

Current Issue | PLOS Computational Biology
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Table of Contents

August 2024

Cover

Working model for START transition via SBF activation
Issue Image

The figure illustrates the core model of SBF activation and inactivation by Clns and Clbs, focusing on key interactions in the budding yeast start transition (START-BYCC). It highlights components such as Swi4, Swi6, Whi5, kinases (Cln3, Cln1,2, Clb5,6, Clb1,2), and the export protein Msn5, with color-coded elements representing various states of activity. Activating and inactivating phosphorylations are shown by white and black-filled circles, respectively. The nucleus and cytoplasm are distinguished by blue-gray and white backgrounds. Detailed descriptions of abundance, regulation, and localization are provided in the companion article and supplementary material. Ravi et al, 2024

Image Credit: Janani Ravi

Education Articles

Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure

Iratxe Puebla, Giorgio A. Ascoli, Jeffrey Blume, John Chodacki, Joshua Finnell, David N. Kennedy, Bernard Mair, Maryann E. Martone, Jamie Wittenberg, Jean-Baptiste Poline

PLOS Computational Biology: published August 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012296

Ten simple rules for successfully managing EU research grants

David G. Pina

PLOS Computational Biology: published August 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012335

Research Articles

Understanding patient-derived tumor organoid growth through an integrated imaging and mathematical modeling framework

Einar Bjarki Gunnarsson, Seungil Kim, Brandon Choi, J. Karl Schmid, Karn Kaura, Heinz-Josef Lenz, Shannon M. Mumenthaler, Jasmine Foo

PLOS Computational Biology: published August 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012256

Modeling the START transition in the budding yeast cell cycle

Janani Ravi, Kewalin Samart, Jason Zwolak

PLOS Computational Biology: published August 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012048

A general model unifying the adaptive, transient and sustained properties of ON and OFF auditory neural responses

Ulysse Rançon, Timothée Masquelier, Benoit R. Cottereau

PLOS Computational Biology: published August 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012288

Decoding dynamic visual scenes across the brain hierarchy

Ye Chen, Peter Beech, Ziwei Yin, Shanshan Jia, Jiayi Zhang, Zhaofei Yu, Jian K. Liu

PLOS Computational Biology: published August 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012297

Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy

Chadi M. Saad-Roy, Sinead E. Morris, Mike Boots, Rachel E. Baker, Bryan L. Lewis, Jeremy Farrar, Madhav V. Marathe, Andrea L. Graham, Simon A. Levin, Caroline E. Wagner, C. Jessica E. Metcalf, Bryan T. Grenfell

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012211

A transfer learning approach to identify Plasmodium in microscopic images

Jonathan da Silva Ramos, Ivo Henrique Provensi Vieira, Wan Song Rocha, Rosimar Pires Esquerdo, Carolina Yukari Veludo Watanabe, Fernando Berton Zanchi

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012327

A novel kinetic model to demonstrate the independent effects of ATP and ADP/Pi concentrations on sarcomere function

Andrew A. Schmidt, Alexander Y. Grosberg, Anna Grosberg

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012321

Reliable estimation of tree branch lengths using deep neural networks

Anton Suvorov, Daniel R. Schrider

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012337

Attentional selection and communication through coherence: Scope and limitations

Priscilla E. Greenwood, Lawrence M. Ward

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011431

A quantitative description of light-limited cyanobacterial growth using flux balance analysis

Rune Höper, Daria Komkova, Tomáš Zavřel, Ralf Steuer

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012280

COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms

Teemu J. Rintala, Vittorio Fortino

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012275

Diffusion model predicts the geometry of actin cytoskeleton from cell morphology

Honghan Li, Shiyou Liu, Shinji Deguchi, Daiki Matsunaga

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012312

Upper bounds for integrated information

Alireza Zaeemzadeh, Giulio Tononi

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012323

Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes

Seth Commichaux, Tu Luan, Harihara Subrahmaniam Muralidharan, Mihai Pop

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012343

Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning

The CRyPTIC consortium

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012260

Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel β-sheet topologies

Hiroto Murata, Kazuma Toko, George Chikenji

PLOS Computational Biology: published August 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012282

Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force

Vasyl V. Mykuliak, Rolle Rahikainen, Neil J. Ball, Giovanni Bussi, Benjamin T. Goult, Vesa P. Hytönen

PLOS Computational Biology: published August 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012341

Bird song comparison using deep learning trained from avian perceptual judgments

Lies Zandberg, Veronica Morfi, Julia M. George, David F. Clayton, Dan Stowell, Robert F. Lachlan

PLOS Computational Biology: published August 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012329

Bacteria face trade-offs in the decomposition of complex biopolymers

Ksenia Guseva, Moritz Mohrlok, Lauren Alteio, Hannes Schmidt, Shaul Pollak, Christina Kaiser

PLOS Computational Biology: published August 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012320

Credibility assessment of in silico clinical trials for medical devices

Pras Pathmanathan, Kenneth Aycock, Andreu Badal, Ramin Bighamian, Jeff Bodner, Brent A. Craven, Steven Niederer

PLOS Computational Biology: published August 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012289

Prioritising older individuals for COVID-19 booster vaccination leads to optimal public health outcomes in a range of socio-economic settings

Ioana Bouros, Edward M. Hill, Matt J. Keeling, Sam Moore, Robin N. Thompson

PLOS Computational Biology: published August 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012309

Convolutional neural networks can identify brain interactions involved in decoding spatial auditory attention

Keyvan Mahjoory, Andreas Bahmer, Molly J. Henry

PLOS Computational Biology: published August 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012376

Interacting particle models on the impact of spatially heterogeneous human behavioral factors on dynamics of infectious diseases

Yunfeng Xiong, Chuntian Wang, Yuan Zhang

PLOS Computational Biology: published August 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012345

scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization

Yuqing Qian, Quan Zou, Mengyuan Zhao, Yi Liu, Fei Guo, Yijie Ding

PLOS Computational Biology: published August 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012339

Evolution of phenotypic plasticity leads to tumor heterogeneity with implications for therapy

Simon Syga, Harish P. Jain, Marcus Krellner, Haralampos Hatzikirou, Andreas Deutsch

PLOS Computational Biology: published August 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012003

The Na+/K+-ATPase generically enables deterministic bursting in class I neurons by shearing the spike-onset bifurcation structure

Mahraz Behbood, Louisiane Lemaire, Jan-Hendrik Schleimer, Susanne Schreiber

PLOS Computational Biology: published August 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011751

Impact of oxygen and glucose availability on the viability and connectivity of islet cells: A computational study of reconstructed avascular human islets

Gerardo J. Félix-Martínez, Diana Osorio-Londoño, J. Rafael Godínez-Fernández

PLOS Computational Biology: published August 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012357

A proactive/reactive mass screening approach with uncertain symptomatic cases

Jiayi Lin, Hrayer Aprahamian, George Golovko

PLOS Computational Biology: published August 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012308

Influence of surprise on reinforcement learning in younger and older adults

Christoph Koch, Ondrej Zika, Rasmus Bruckner, Nicolas W. Schuck

PLOS Computational Biology: published August 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012331

Alternate conformational trajectories in ribosome translocation

Jose L. Alejo, Dylan Girodat, Michael J. Hammerling, Jessica A. Willi, Michael C. Jewett, Aaron E. Engelhart, Katarzyna P. Adamala

PLOS Computational Biology: published August 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012319

Quantifying the risk of spillover reduction programs for human health

Scott L. Nuismer, Andrew J. Basinski, Courtney L. Schreiner, Evan A. Eskew, Elisabeth Fichet-Calvet, Christopher H. Remien

PLOS Computational Biology: published August 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012358

Estimating orientation in natural scenes: A spiking neural network model of the insect central complex

Rachael Stentiford, James C. Knight, Thomas Nowotny, Andrew Philippides, Paul Graham

PLOS Computational Biology: published August 15, 2024 | https://doi.org/10.1371/journal.pcbi.1011913

Spatial kinetics and immune control of murine cytomegalovirus infection in the salivary glands

Catherine M Byrne, Ana Citlali Márquez, Bing Cai, Daniel Coombs, Soren Gantt

PLOS Computational Biology: published August 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011940

The rules of multiplayer cooperation in networks of communities

Diogo L. Pires, Mark Broom

PLOS Computational Biology: published August 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012388

In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences

Ayooluwa J. Bolaji, Ana T. Duggan

PLOS Computational Biology: published August 19, 2024 | https://doi.org/10.1371/journal.pcbi.1011539

A comprehensive data-driven model of cat primary visual cortex

Ján Antolík, Rémy Cagnol, Tibor Rózsa, Cyril Monier, Yves Frégnac, Andrew P. Davison

PLOS Computational Biology: published August 21, 2024 | https://doi.org/10.1371/journal.pcbi.1012342

iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites

Lin Yuan, Ling Zhao, Jinling Lai, Yufeng Jiang, Qinhu Zhang, Zhen Shen, Chun-Hou Zheng, De-Shuang Huang

PLOS Computational Biology: published August 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012399

Signatures of hierarchical temporal processing in the mouse visual system

Lucas Rudelt, Daniel González Marx, F. Paul Spitzner, Benjamin Cramer, Johannes Zierenberg, Viola Priesemann

PLOS Computational Biology: published August 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012355

MAGICAL: A multi-class classifier to predict synthetic lethal and viable interactions using protein-protein interaction network

Anubha Dey, Suresh Mudunuri, Manjari Kiran

PLOS Computational Biology: published August 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012336

Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions

Efrat Cohen-Davidi, Isana Veksler-Lublinsky

PLOS Computational Biology: published August 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012385

Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer’s disease

Easwaran Ramamurthy, Snigdha Agarwal, Noelle Toong, Heather Sestili, Irene M. Kaplow, Ziheng Chen, BaDoi Phan, Andreas R. Pfenning

PLOS Computational Biology: published August 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012356

Identification of a serum proteomic biomarker panel using diagnosis specific ensemble learning and symptoms for early pancreatic cancer detection

Alexander Ney, Nuno R. Nené, Eva Sedlak, Pilar Acedo, Oleg Blyuss, Harry J. Whitwell, Eithne Costello, Aleksandra Gentry-Maharaj, Norman R. Williams, Usha Menon, Giuseppe K. Fusai, Alexey Zaikin, Stephen P. Pereira

PLOS Computational Biology: published August 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012408

Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos

Daniel Seeler, Nastasja Grdseloff, Claudia Jasmin Rödel, Charlotte Kloft, Salim Abdelilah-Seyfried, Wilhelm Huisinga

PLOS Computational Biology: published August 30, 2024 | https://doi.org/10.1371/journal.pcbi.1011924

ECD-CDGI: An efficient energy-constrained diffusion model for cancer driver gene identification

Tao Wang, Linlin Zhuo, Yifan Chen, Xiangzheng Fu, Xiangxiang Zeng, Quan Zou

PLOS Computational Biology: published August 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012400

Methods

scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data

Fengdi Zhao, Xin Ma, Bing Yao, Qing Lu, Li Chen

PLOS Computational Biology: published August 2, 2024 | https://doi.org/10.1371/journal.pcbi.1011854

An optimal normalization method for high sparse compositional microbiome data

Michael B. Sohn, Cynthia Monaco, Steven R. Gill

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012338

rtestim: Time-varying reproduction number estimation with trend filtering

Jiaping Liu, Zhenglun Cai, Paul Gustafson, Daniel J. McDonald

PLOS Computational Biology: published August 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012324

aiSEGcell: User-friendly deep learning-based segmentation of nuclei in transmitted light images

Daniel Schirmacher, Ümmünur Armagan, Yang Zhang, Tobias Kull, Markus Auler, Timm Schroeder

PLOS Computational Biology: published August 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012361

IMI-driver: Integrating multi-level gene networks and multi-omics for cancer driver gene identification

Peiting Shi, Junmin Han, Yinghao Zhang, Guanpu Li, Xionghui Zhou

PLOS Computational Biology: published August 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012389

CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images

Yicheng Tao, Fan Feng, Xin Luo, Conrad V. Reihsmann, Alexander L. Hopkirk, Jean-Philippe Cartailler, Marcela Brissova, Stephen C. J. Parker, Diane C. Saunders, Jie Liu

PLOS Computational Biology: published August 28, 2024 | https://doi.org/10.1371/journal.pcbi.1012344

Software

Rhythmidia: A modern tool for circadian period analysis of filamentous fungi

Alex T. Keeley, Jeffrey M. Lotthammer, Jacqueline F. Pelham

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012167

DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models

Robby Concha-Eloko, Michiel Stock, Bernard De Baets, Yves Briers, Rafael Sanjuán, Pilar Domingo-Calap, Dimitri Boeckaerts

PLOS Computational Biology: published August 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011831

OOPS: Object-Oriented Polarization Software for analysis of fluorescence polarization microscopy images

William F. Dean, Tomasz J. Nawara, Rose M. Albert, Alexa L. Mattheyses

PLOS Computational Biology: published August 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011723