PLoS computational biology

Keyphrases

Publications

volume 20, number 9, 2024

Katharina Duecker, Marco Idiart, Marcel van Gerven, Ole Jensen
Oscillations in an artificial neural network convert competing inputs into a temporal code. PLoS computational biology 20 (9) (2024)
Artemy Bakulin, Noam B Teyssier, Martin Kampmann, Matvei Khoroshkin, Hani Goodarzi
pyPAGE: A framework for Addressing biases in gene-set enrichment analysis-A case study on Alzheimer's disease. PLoS computational biology 20 (9) (2024)
Aakash Agrawal, Stanislas Dehaene
Cracking the neural code for word recognition in convolutional neural networks. PLoS computational biology 20 (9) (2024)
Israel Luis, Maarten Afschrift, Friedl De Groote, Elena M Gutierrez-Farewik
Insights into muscle metabolic energetics: Modelling muscle-tendon mechanics and metabolic rates during walking across speeds. PLoS computational biology 20 (9) (2024)
Zhichao Zhu, Yang Qi, Wenlian Lu, Jianfeng Feng
Learning to integrate parts for whole through correlated neural variability. PLoS computational biology 20 (9) (2024)
Justin Lin, Julia Fukuyama
Calibrating dimension reduction hyperparameters in the presence of noise. PLoS computational biology 20 (9) (2024)
Maansi Desai, Alyssa M Field, Liberty S Hamilton
A comparison of EEG encoding models using audiovisual stimuli and their unimodal counterparts. PLoS computational biology 20 (9) (2024)
Breanne Sparta, Timothy Hamilton, Gunalan Natesan, Samuel D Aragones, Eric J Deeds
Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing. PLoS computational biology 20 (9) (2024)
Olav N L Aga, Morten Brun, Kazeem A Dauda, Ramon Diaz-Uriarte, Konstantinos Giannakis, Iain G Johnston
HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures. PLoS computational biology 20 (9) (2024)
Clémence Bergerot, Wolfram Barfuss, Pawel Romanczuk
Moderate confirmation bias enhances decision-making in groups of reinforcement-learning agents. PLoS computational biology 20 (9) (2024)
Silja Tammi, Satu Koskela, Blood Service Biobank, Kati Hyvärinen, Jukka Partanen, Jarmo Ritari
Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data. PLoS computational biology 20 (9) (2024)
Annika Schmidt, Marion Forano, Arne Sachtler, Davide Calzolari, Bernhard M Weber, David W Franklin, Alin Albu-Schäffer
Finding the rhythm: Humans exploit nonlinear intrinsic dynamics of compliant systems in periodic interaction tasks. PLoS computational biology 20 (9) (2024)
Monica Golumbeanu, Olivier Briët, Clara Champagne, Jeanne Lemant, Munir Winkel, Barnabas Zogo, Maximilian Gerhards, Marianne Sinka, Nakul Chitnis, Melissa Penny, Emilie Pothin, Thomas A Smith
AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact. PLoS computational biology 20 (9) (2024)
Tobias Pfennig, Elena Kullmann, Tomáš Zavřel, Andreas Nakielski, Oliver Ebenhöh, Jan Červený, Gábor Bernát, Anna Barbara Matuszyńska
Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803. PLoS computational biology 20 (9) (2024)
Kit Gallagher, Richard Creswell, Ben Lambert, Martin Robinson, Chon Lok Lei, Gary R Mirams, David J Gavaghan
Ten simple rules for training scientists to make better software. PLoS computational biology 20 (9) (2024)
Adrian J Green, Lisa Truong, Preethi Thunga, Connor Leong, Melody Hancock, Robyn L Tanguay, David M Reif
Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies. PLoS computational biology 20 (9) (2024)
Hamza Giaffar, Sergey Shuvaev, Dmitry Rinberg, Alexei A Koulakov
The primacy model and the structure of olfactory space. PLoS computational biology 20 (9) (2024)
Alia Abbara, Lisa Pagani, Celia García-Pareja, Anne-Florence Bitbol
Mutant fate in spatially structured populations on graphs: Connecting models to experiments. PLoS computational biology 20 (9) (2024)
Janice Yang, Neil J Daily, Taylor K Pullinger, Tetsuro Wakatsuki, Eric A Sobie
Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. PLoS computational biology 20 (9) (2024)
Israel Luis, Maarten Afschrift, Elena M Gutierrez-Farewik
Springs vs. motors: Ideal assistance in the lower limbs during walking at different speeds. PLoS computational biology 20 (9) (2024)
Yann Le Cunff, Laurent Chesneau, Sylvain Pastezeur, Xavier Pinson, Nina Soler, Danielle Fairbrass, Benjamin Mercat, Ruddi Rodriguez-Garcia, Zahraa Alayan, Ahmed Abdouni, Gary de Neidhardt, Valentin Costes, Mélodie Anjubault, Hélène Bouvrais, Christophe Héligon, Jacques Pécréaux
Unveiling inter-embryo variability in spindle length over time: Towards quantitative phenotype analysis. PLoS computational biology 20 (9) (2024)
Anis Ur Rahman, Gleb Tikhonov, Jari Oksanen, Tuomas P Rossi, Otso Ovaskainen
Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting. PLoS computational biology 20 (9) (2024)
Gustavo Menesse, Joaquin J Torres
Information dynamics of in silico EEG Brain Waves: Insights into oscillations and functions. PLoS computational biology 20 (9) (2024)
Yujin Goto, Keiichi Kitajo
Selective consistency of recurrent neural networks induced by plasticity as a mechanism of unsupervised perceptual learning. PLoS computational biology 20 (9) (2024)
Kath Nicholls, Chris Wallace
Bayesian clustering with uncertain data. PLoS computational biology 20 (9) (2024)
Travis M Blimkie, Andy An, Robert E W Hancock
Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR. PLoS computational biology 20 (9) (2024)
Dong Yu, Tianyu Li, Qianming Ding, Yong Wu, Ziying Fu, Xuan Zhan, Lijian Yang, Ya Jia
Maintenance of delay-period activity in working memory task is modulated by local network structure. PLoS computational biology 20 (9) (2024)
Anibal S Amaral, Damien Paul Devos
The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes. PLoS computational biology 20 (9) (2024)
Brian C O'Meara, Jeremy M Beaulieu
Noise leads to the perceived increase in evolutionary rates over short time scales. PLoS computational biology 20 (9) (2024)
Hannah Zoller, Carlos Garcia Perez, Javier Betel Geijo Fernández, Wolfgang Zu Castell
Measuring and understanding information storage and transfer in a simulated human gut microbiome. PLoS computational biology 20 (9) (2024)
Daniel Steiert, Corey Wittig, Priyanka Banerjee, Robert Preissner, Robert Szulcek
An exploration into CTEPH medications: Combining natural language processing, embedding learning, in vitro models, and real-world evidence for drug repurposing. PLoS computational biology 20 (9) (2024)
Constance Creux, Farida Zehraoui, François Radvanyi, Fariza Tahi
Comparison and benchmark of deep learning methods for non-coding RNA classification. PLoS computational biology 20 (9) (2024)
Seema B Plaisier, Danielle O Alarid, Joelle A Denning, Sara E Brownell, Kenneth H Buetow, Katelyn M Cooper, Melissa A Wilson
Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics. PLoS computational biology 20 (9) (2024)
Ke Li, Chrispin Chaguza, Julian Stamp, Yi Ting Chew, Nicholas F G Chen, David Ferguson, Sameer Pandya, Nick Kerantzas, Wade Schulz, null null, Anne M Hahn, C Brandon Ogbunugafor, Virginia E Pitzer, Lorin Crawford, Daniel M Weinberger, Nathan D Grubaugh
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. PLoS computational biology 20 (9) (2024)
Shuo Wang, ShanJin Wang, Wei Pan, YuYang Yi, JunYan Lu
Construct prognostic models of multiple myeloma with pathway information incorporated. PLoS computational biology 20 (9) (2024)
Bharadwaj Vemparala, Vincent Madelain, Caroline Passaes, Antoine Millet, Veronique Avettand-Fenoel, Ramsès Djidjou-Demasse, Nathalie Dereuddre-Bosquet, Roger Le Grand, Christine Rouzioux, Bruno Vaslin, Asier Sáez-Cirión, Jérémie Guedj, Narendra M Dixit
Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection: Learning in vivo dynamics using ex vivo data. PLoS computational biology 20 (9) (2024)
Ahmadou Sylla, Christine Chevillon, Ramsès Djidjiou-Demasse, Ousmane Seydi, Carlos A Vargas Campos, Magdalene Dogbe, Kayla M Fast, Jennifer L Pechal, Alex Rakestraw, Matthew E Scott, Michael W Sandel, Heather Jordan, Mark Eric Benbow, Jean-François Guégan
Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model. PLoS computational biology 20 (9) (2024)
Mario Grassi, Barbara Tarantino
SEMbap: Bow-free covariance search and data de-correlation. PLoS computational biology 20 (9) (2024)
Joseph W Shingleton, David Mustard, Steven Dyke, Hannah Williams, Emma Bennett, Thomas J R Finnie
Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases. PLoS computational biology 20 (9) (2024)
Eslam Abousamra, Marlin Figgins, Trevor Bedford
Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency. PLoS computational biology 20 (9) (2024)
Ariel Rokem
Ten simple rules for scientific code review. PLoS computational biology 20 (9) (2024)
G Eric Bastien, Rachel N Cable, Cecelia Batterbee, A J Wing, Luis Zaman, Melissa B Duhaime
Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks. PLoS computational biology 20 (9) (2024)
Hao Duan, Qingchen Zhang, Feifei Cui, Guishen Wang, Zilong Zhang
MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks. PLoS computational biology 20 (9) (2024)
Caterina Millevoi, Damiano Pasetto, Massimiliano Ferronato
A Physics-Informed Neural Network approach for compartmental epidemiological models. PLoS computational biology 20 (9) (2024)
Wilson Wen Bin Goh, Mohammad Neamul Kabir, Sehwan Yoo, Limsoon Wong
Ten quick tips for ensuring machine learning model validity. PLoS computational biology 20 (9) (2024)
Kiesha Prem, Kevin van Zandvoort, Petra Klepac, Rosalind M Eggo, Nicholas G Davies, null null
Correction: Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era. PLoS computational biology 20 (9) (2024)
Kirstin I Oliveira Roster, Stephen M Kissler, Enoma Omoregie, Jade C Wang, Helly Amin, Steve Di Lonardo, Scott Hughes, Yonatan Hagai Grad
Surveillance strategies for the detection of new pathogen variants across epidemiological contexts. PLoS computational biology 20 (9) (2024)
Steffen Krüppel, Mohammad Hossein Khani, Helene M Schreyer, Shashwat Sridhar, Varsha Ramakrishna, Sören J Zapp, Matthias Mietsch, Dimokratis Karamanlis, Tim Gollisch
Applying Super-Resolution and Tomography Concepts to Identify Receptive Field Subunits in the Retina. PLoS computational biology 20 (9) (2024)
Laura Collesano, Marta Łuksza, Michael Lässig
Energy landscapes of peptide-MHC binding. PLoS computational biology 20 (9) (2024)
Yanpeng Yang, Yanyi Zheng, Quan Zou, Jian Li, Hailin Feng
Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model. PLoS computational biology 20 (9) (2024)