Hands-on training about data clustering with orange data mining toolbox

Janez Demšar, Blaž Zupan

PLOS Computational Biology: published December 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012574

Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper

Faye Orcales, Lucy Moctezuma Tan, Meris Johnson-Hagler, John Matthew Suntay, Jameel Ali, Kristiene Recto, Phelan Glenn, Pleuni Pennings

PLOS Computational Biology: published December 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012579

Stable developmental patterns of gene expression without morphogen gradients

Maciej Majka, Nils B. Becker, Pieter Rein ten Wolde, Marcin Zagorski, Thomas R. Sokolowski

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012555

Parallel development of object recognition in newborn chicks and deep neural networks

Lalit Pandey, Donsuk Lee, Samantha M. W. Wood, Justin N. Wood

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012600

Mapping genes for human face shape: Exploration of univariate phenotyping strategies

Meng Yuan, Seppe Goovaerts, Michiel Vanneste, Harold Matthews, Hanne Hoskens, Stephen Richmond, Ophir D. Klein, Richard A. Spritz, Benedikt Hallgrimsson, Susan Walsh, Mark D. Shriver, John R. Shaffer, Seth M. Weinberg, Hilde Peeters, Peter Claes

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012617

Theta oscillations optimize a speed-precision trade-off in phase coding neurons

Adrián F. Amil, Albert Albesa-González, Paul F. M. J. Verschure

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012628

Image-based force inference by biomechanical simulation

Michiel Vanslambrouck, Wim Thiels, Jef Vangheel, Casper van Bavel, Bart Smeets, Rob Jelier

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012629

Social conformity is a heuristic when individual risky decision-making is disrupted

Mark A. Orloff, Dongil Chung, Xiaosi Gu, Xingchao Wang, Zhixian Gao, Guiding Song, Chandana Tatineni, Shuai Xu, Brooks Casas, Pearl H. Chiu

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012602

Long distance calls: Negligible information loss of little auk social vocalisations due to high frequency propagation losses

Anna N. Osiecka, Przemysław Bryndza, Elodie F. Briefer, Katarzyna Wojczulanis-Jakubas

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1011961

scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum

Yuqian Liu, Yan Chen, Huanwen Wu, Xuanping Zhang, Yuqi Wang, Xin Yi, Zhiyong Liang, Jiayin Wang

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012608

Expansion of epileptogenic networks via neuroplasticity in neural mass models

Elif Köksal-Ersöz, Pascal Benquet, Fabrice Wendling

PLOS Computational Biology: published December 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012666

Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts

Ikram Mahmoudi, Chloé Quignot, Carla Martins, Jessica Andreani

PLOS Computational Biology: published December 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012650

Predicting proprioceptive cortical anatomy and neural coding with topographic autoencoders

Max Grogan, Kyle P. Blum, Yufei Wu, J. Alex Harston, Lee E. Miller, A. Aldo Faisal

PLOS Computational Biology: published December 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012614

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors

Henri Schmidt, Benjamin J. Raphael

PLOS Computational Biology: published December 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012631

Measuring genetic diversity across populations

Niloufar Abhari, Caroline Colijn, Arne Mooers, Paul Tupper

PLOS Computational Biology: published December 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012651

Public surface disinfection every 2 hours can reduce the infection risk of norovirus in airports up to 83%

Nan Zhang, Linan Zhuang, Marco-Felipe King, Hua Qian, Min Zhu

PLOS Computational Biology: published December 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012561

Whole brain functional connectivity: Insights from next generation neural mass modelling incorporating electrical synapses

Michael Forrester, Sammy Petros, Oliver Cattell, Yi Ming Lai, Reuben D. O’Dea, Stamatios Sotiropoulos, Stephen Coombes

PLOS Computational Biology: published December 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012647

Circuits and mechanisms for TMS-induced corticospinal waves: Connecting sensitivity analysis to the network graph

Gene J. Yu, Federico Ranieri, Vincenzo Di Lazzaro, Marc A. Sommer, Angel V. Peterchev, Warren M. Grill

PLOS Computational Biology: published December 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012640

Modelling the effectiveness of antiviral treatment strategies to prevent household transmission of acute respiratory viruses

Hind Zaaraoui, Clarisse Schumer, Xavier Duval, Bruno Hoen, Lulla Opatowski, Jérémie Guedj

PLOS Computational Biology: published December 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012573

OneNet—One network to rule them all: Consensus network inference from microbiome data

Camille Champion, Raphaëlle Momal, Emmanuelle Le Chatelier, Mathilde Sola, Mahendra Mariadassou, Magali Berland

PLOS Computational Biology: published December 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012627

Large scale paired antibody language models

Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane

PLOS Computational Biology: published December 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012646

Dose-dependent interaction of parasites with tiers of host defense predicts “wormholes” that prolong infection at intermediate inoculum sizes

Andrea L. Graham, Roland R. Regoes

PLOS Computational Biology: published December 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012652

Oscillatory dynamics of Rac1 activity in Dictyostelium discoideum amoebae

Marko Šoštar, Maja Marinović, Vedrana Filić, Nenad Pavin, Igor Weber

PLOS Computational Biology: published December 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012025

Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform

Xavier Escriba-Montagut, Yannick Marcon, Augusto Anguita-Ruiz, Demetris Avraam, Jose Urquiza, Andrei S. Morgan, Rebecca C. Wilson, Paul Burton, Juan R. Gonzalez

PLOS Computational Biology: published December 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012626

Preserving friendships in school contacts: An algorithm to construct synthetic temporal networks for epidemic modelling

Lucille Calmon, Elisabetta Colosi, Giulia Bassignana, Alain Barrat, Vittoria Colizza

PLOS Computational Biology: published December 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012661

Bacterial clustering amplifies the reshaping of eutrophic plumes around marine particles: A hybrid data-driven model

George E. Kapellos, Hermann J. Eberl, Nicolas Kalogerakis, Patrick S. Doyle, Christakis A. Paraskeva

PLOS Computational Biology: published December 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012660

Quantitative and Kinetic Proteomics Reveal ApoE Isoform-dependent Proteostasis Adaptations in Mouse Brain

Nathan R. Zuniga, Noah E. Earls, Ariel E. A. Denos, Jared M. Elison, Benjamin S. Jones, Ethan G. Smith, Noah G. Moran, Katie L. Broce, Gerome M. Romero, Chad D. Hyer, Kimberly B. Wagstaff, Haifa M. Almughamsi, Mark K. Transtrum, John C. Price

PLOS Computational Biology: published December 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012407

Uncovering population contributions to the extracellular potential in the mouse visual system using Laminar Population Analysis

Atle E. Rimehaug, Anders M. Dale, Anton Arkhipov, Gaute T. Einevoll

PLOS Computational Biology: published December 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011830

Hierarchical marker genes selection in scRNA-seq analysis

Yutong Sun, Peng Qiu

PLOS Computational Biology: published December 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012643

Mechanical network equivalence between the katydid and mammalian inner ears

Emine Celiker, Charlie Woodrow, Òscar Guadayol, Leonidas-Romanos Davranoglou, Christian M. Schlepütz, Beth Mortimer, Graham K. Taylor, Stuart Humphries, Fernando Montealegre-Z

PLOS Computational Biology: published December 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012641

Adapting to time: Why nature may have evolved a diverse set of neurons

Karim G. Habashy, Benjamin D. Evans, Dan F. M. Goodman, Jeffrey S. Bowers

PLOS Computational Biology: published December 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012673

Neural networks with optimized single-neuron adaptation uncover biologically plausible regularization

Victor Geadah, Stefan Horoi, Giancarlo Kerg, Guy Wolf, Guillaume Lajoie

PLOS Computational Biology: published December 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012567

Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding

Pengyu Liu, Jacob Lusk, Nataša Jonoska, Mariel Vázquez

PLOS Computational Biology: published December 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012669

Advanced vision transformers and open-set learning for robust mosquito classification: A novel approach to entomological studies

Ahmed Akib Jawad Karim, Muhammad Zawad Mahmud, Riasat Khan

PLOS Computational Biology: published December 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012654

A multi-scale study of thalamic state-dependent responsiveness

Jorin Overwiening, Federico Tesler, Domenico Guarino, Alain Destexhe

PLOS Computational Biology: published December 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012262

Dopamine facilitates the response to glutamatergic inputs in astrocyte cell models

Thiago Ohno Bezerra, Antonio C. Roque

PLOS Computational Biology: published December 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012688

Novel travel time aware metapopulation models and multi-layer waning immunity for late-phase epidemic and endemic scenarios

Henrik Zunker, René Schmieding, David Kerkmann, Alain Schengen, Sophie Diexer, Rafael Mikolajczyk, Michael Meyer-Hermann, Martin J. Kühn

PLOS Computational Biology: published December 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012630

Neuro-cognitive multilevel causal modeling: A framework that bridges the explanatory gap between neuronal activity and cognition

Moritz Grosse-Wentrup, Akshey Kumar, Anja Meunier, Manuel Zimmer

PLOS Computational Biology: published December 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012674

Randomness as a driver of inactivity in social groups

Abel Bernadou, Raphaël Jeanson

PLOS Computational Biology: published December 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012668

In–silico simultaneous respiratory and circulatory measurement during voluntary breathing, exercise, and mental stress: A computational approach

Masami Iwamoto, Satoko Hirabayashi, Noritoshi Atsumi

PLOS Computational Biology: published December 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012645

Model supports asymmetric regulation across the intercellular junction for collective cell polarization

Katherine Levandosky, Calina Copos

PLOS Computational Biology: published December 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012216

scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis

Wei Lan, Tongsheng Ling, Qingfeng Chen, Ruiqing Zheng, Min Li, Yi Pan

PLOS Computational Biology: published December 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012679

A framework for modelling desert locust population dynamics and large-scale dispersal

Renata Retkute, William Thurston, Keith Cressman, Christopher A. Gilligan

PLOS Computational Biology: published December 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012562

Optimisation strategies for directed evolution without sequencing

Jessica James, Sebastian Towers, Jakob Foerster, Harrison Steel

PLOS Computational Biology: published December 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012695

Predicting lung aging using scRNA-Seq data

Qi Song, Alex Singh, John E. McDonough, Taylor S. Adams, Robin Vos, Ruben De Man, Greg Myers, Laurens J. Ceulemans, Bart M. Vanaudenaerde, Wim A. Wuyts, Xiting Yan, Jonas Schupp, James S. Hagood, Naftali Kaminski, Ziv Bar-Joseph

PLOS Computational Biology: published December 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012632

Evolution of cooperation in multichannel games on multiplex networks

Amit Basak, Supratim Sengupta

PLOS Computational Biology: published December 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012678

A computational model for angular velocity integration in a locust heading circuit

Kathrin Pabst, Evripidis Gkanias, Barbara Webb, Uwe Homberg, Dominik Endres

PLOS Computational Biology: published December 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012155

A mathematical model of plasmin-mediated fibrinolysis of single fibrin fibers

Roukayatou R. Ouedraogo, Hannah K. Sowers, Spencer R. Lynch, Nathan E. Hudson, Brittany E. Bannish

PLOS Computational Biology: published December 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012684

Sensitivity analysis of closed-loop one-chamber and four-chamber models with baroreflex

Karolina Tlałka, Harry Saxton, Ian Halliday, Xu Xu, Andrew Narracott, Daniel Taylor, Maciej Malawski

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012377

Adolescent and adult mice use both incremental reinforcement learning and short term memory when learning concurrent stimulus-action associations

Juliana Chase, Liyu Xia, Lung-Hao Tai, Wan Chen Lin, Anne G. E. Collins, Linda Wilbrecht

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012667

Machine learning mathematical models for incidence estimation during pandemics

Oscar Fajardo-Fontiveros, Mattia Mattei, Giulio Burgio, Clara Granell, Sergio Gómez, Alex Arenas, Marta Sales-Pardo, Roger Guimerà

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012687

A multivalent binding model infers antibody Fc species from systems serology

Armaan A. Abraham, Zhixin Cyrillus Tan, Priyanka Shrestha, Emily R. Bozich, Aaron S. Meyer

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012663

Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software framework

Máté Mohácsi, Márk Patrik Török, Sára Sáray, Luca Tar, Gábor Farkas, Szabolcs Káli

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012039

Integration of partially observed multimodal and multiscale neural signals for estimating a neural circuit using dynamic causal modeling

Jiyoung Kang, Hae-Jeong Park

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012655

Extracting interpretable signatures of whole-brain dynamics through systematic comparison

Annie G. Bryant, Kevin Aquino, Linden Parkes, Alex Fornito, Ben D. Fulcher

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012692

Estimating the distribution of parameters in differential equations with repeated cross-sectional data

Hyeontae Jo, Sung Woong Cho, Hyung Ju Hwang

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012696

Predicting the infecting dengue serotype from antibody titre data using machine learning

Bethan Cracknell Daniels, Darunee Buddhari, Taweewun Hunsawong, Sopon Iamsirithaworn, Aaron R. Farmer, Derek A. T. Cummings, Kathryn B. Anderson, Ilaria Dorigatti

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012188

Surveillance for TB drug resistance using routine rapid diagnostic testing data: Methodological development and application in Brazil

Sarah E. Baum, Daniele M. Pelissari, Fernanda Dockhorn Costa, Luiza O. Harada, Mauro Sanchez, Patricia Bartholomay, Ted Cohen, Marcia C. Castro, Nicolas A. Menzies

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012662

Multicellular model of neuroblastoma proposes unconventional therapy based on multiple roles of p53

Kenneth Y. Wertheim, Robert Chisholm, Paul Richmond, Dawn Walker

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012648

Estimating the time-varying effective reproduction number via Cycle Threshold-based Transformer

Xin-Yu Zhang, Lan-Lan Yu, Wei-Yi Wang, Gui-Quan Sun, Jian-Cheng Lv, Tao Zhou, Quan-Hui Liu

PLOS Computational Biology: published December 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012694

Properties of winning Iterated Prisoner’s Dilemma strategies

Nikoleta E. Glynatsi, Vincent Knight, Marc Harper

PLOS Computational Biology: published December 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012644

Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns

Rosalind Wenshan Pan, Tom Röschinger, Kian Faizi, Hernan G. Garcia, Rob Phillips

PLOS Computational Biology: published December 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012697

Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding

Tal Gutman, Tamir Tuller

PLOS Computational Biology: published December 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012685

Cancer molecular subtyping using limited multi-omics data with missingness

Yongqi Bu, Jiaxuan Liang, Zhen Li, Jianbo Wang, Jun Wang, Guoxian Yu

PLOS Computational Biology: published December 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012710

Therapeutic dose prediction of α5-GABA receptor modulation from simulated EEG of depression severity

Alexandre Guet-McCreight, Frank Mazza, Thomas D. Prevot, Etienne Sibille, Etay Hay

PLOS Computational Biology: published December 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012693

The Burr distribution as a model for the delay between key events in an individual’s infection history

Nyall Jamieson, Christiana Charalambous, David M. Schultz, Ian Hall

PLOS Computational Biology: published December 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012041

Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction

Akash Bahai, Chee Keong Kwoh, Yuguang Mu, Yinghui Li

PLOS Computational Biology: published December 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012715

Response to comment on: Toward an optimal contraception dosing strategy

Brenda Lyn A. Gavina, Aurelio A. de los Reyes V, Mette S. Olufsen, Suzanne Lenhart, Johnny T. Ottesen

PLOS Computational Biology: published December 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012649

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Nisha Ann Viswan, Alexandre Tribut, Manvel Gasparyan, Ovidiu Radulescu, Upinder S. Bhalla

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012624

Homeodynamic feedback inhibition control in whole-brain simulations

Jan Stasinski, Halgurd Taher, Jil Mona Meier, Michael Schirner, Dionysios Perdikis, Petra Ritter

PLOS Computational Biology: published December 2, 2024 | https://doi.org/10.1371/journal.pcbi.1012595

Differential quantification of alternative splicing events on spliced pangenome graphs

Simone Ciccolella, Davide Cozzi, Gianluca Della Vedova, Stephen Njuguna Kuria, Paola Bonizzoni, Luca Denti

PLOS Computational Biology: published December 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012665

Orchard: Building large cancer phylogenies using stochastic combinatorial search

Ethan Kulman, Rui Kuang, Quaid Morris

PLOS Computational Biology: published December 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012653

Marked point process variational autoencoder with applications to unsorted spiking activities

Ryohei Shibue, Tomoharu Iwata

PLOS Computational Biology: published December 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012620

ClustAll: An R package for patient stratification in complex diseases

Asier Ortega-Legarreta, Sara Palomino-Echeverria, Estefania Huergo, Vincenzo Lagani, Narsis A. Kiani, Pierre-Emmanuel Rautou, Nuria Planell Picola, Jesper Tegner, David Gomez-Cabrero

PLOS Computational Biology: published December 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012656

BharatSim: An agent-based modelling framework for India

Philip Cherian, Jayanta Kshirsagar, Bhavesh Neekhra, Gaurav Deshkar, Harshal Hayatnagarkar, Kshitij Kapoor, Chandrakant Kaski, Ganesh Kathar, Swapnil Khandekar, Saurabh Mookherjee, Praveen Ninawe, Riz Fernando Noronha, Pranjal Ranka, Vaibhhav Sinha, Tina Vinod, Chhaya Yadav, Debayan Gupta, Gautam I. Menon

PLOS Computational Biology: published December 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012682