PLoS Comput. Biol.

Keyphrases

Publications

volume 19, number 9, 2023

Zheng Jiang, Yue-Yue Shen, Rong Liu
Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches. PLoS Comput. Biol. 19 (9) (2023)
Nikhil Sharma, Sedigheh Yagoobi, Arne Traulsen
Self-loops in evolutionary graph theory: Friends or foes? PLoS Comput. Biol. 19 (9) (2023)
Shuming Liu, Cong Wang, Andrew P. Latham, Xinqiang Ding, Bin Zhang
OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates. PLoS Comput. Biol. 19 (9) (2023)
Christopher E. Overton, Sam Abbott, Rachel Christie, Fergus Cumming, Julie Day, Owen Jones, Rob Paton, Charlie Turner, Thomas Ward
Nowcasting the 2022 mpox outbreak in England. PLoS Comput. Biol. 19 (9) (2023)
Lucía Graña-Miraglia, Nadia Morales-Lizcano, Pauline W. Wang, David M. Hwang, Yvonne C. W. Yau, Valerie J. Waters, David S. Guttman
Predictive modeling of antibiotic eradication therapy success for new-onset Pseudomonas aeruginosa pulmonary infections in children with cystic fibrosis. PLoS Comput. Biol. 19 (9) (2023)
Joanna N. de Klerk, Erin E. Gorsich, John D. Grewar, Benjamin D. Atkins, Warren S. D. Tennant, Karien Labuschagne, Michael J. Tildesley
Modelling African horse sickness emergence and transmission in the South African control area using a deterministic metapopulation approach. PLoS Comput. Biol. 19 (9) (2023)
Peter Schuck, Samuel C. To, Huaying Zhao
An automated interface for sedimentation velocity analysis in SEDFIT. PLoS Comput. Biol. 19 (9) (2023)
Jay A. Hennig, Sandra A. Romero Pinto, Takahiro Yamaguchi, Scott W. Linderman, Naoshige Uchida, Samuel J. Gershman
Emergence of belief-like representations through reinforcement learning. PLoS Comput. Biol. 19 (9) (2023)
Charlie M. Sexton, Anthony N. Burkitt, Hinze Hogendoorn
Spike-timing dependent plasticity partially compensates for neural delays in a multi-layered network of motion-sensitive neurons. PLoS Comput. Biol. 19 (9) (2023)
Hola Adrakey, Gavin J. Gibson, Sandrine Eveillard, Sylvie Malembic-Maher, Frédéric Fabre
Bayesian inference for spatio-temporal stochastic transmission of plant disease in the presence of roguing: A case study to characterise the dispersal of Flavescence dorée. PLoS Comput. Biol. 19 (9) (2023)
Jonathan Vacher, Claire Launay, Pascal Mamassian, Ruben Coen Cagli
Measuring uncertainty in human visual segmentation. PLoS Comput. Biol. 19 (9) (2023)
Ruodan Liu, Naoki Masuda
Fixation dynamics on hypergraphs. PLoS Comput. Biol. 19 (9) (2023)
Neta Ravid Tannenbaum, Omer Gottesman, Azadeh Assadi, Mjaye Mazwi, Uri Shalit, Danny Eytan
iCVS - Inferring Cardio-Vascular hidden States from physiological signals available at the bedside. PLoS Comput. Biol. 19 (9) (2023)
Antoine De Comite, Philippe Lefèvre, Frédéric Crevecoeur
Continuous evaluation of cost-to-go for flexible reaching control and online decisions. PLoS Comput. Biol. 19 (9) (2023)
Jan Boelts, Philipp Harth, Richard Gao, Daniel Udvary, Felipe Yáñez, Daniel Baum, Hans-Christian Hege, Marcel Oberländer, Jakob H. Macke
Simulation-based inference for efficient identification of generative models in computational connectomics. PLoS Comput. Biol. 19 (9) (2023)
Casper de Visser, Lennart F. Johansson, Purva Kulkarni, Hailiang Mei, Pieter B. T. Neerincx, K. Joeri van der Velde, Peter Horvatovich, Alain J. van Gool, Morris A. Swertz, Peter A. C. 't Hoen, Anna Niehues
Ten quick tips for building FAIR workflows. PLoS Comput. Biol. 19 (9) (2023)
Claire Ecotière, Sylvain Billiard, Jean-Baptiste André, Pierre Collet, Régis Ferrière, Sylvie Méléard
Human-environment feedback and the consistency of proenvironmental behavior. PLoS Comput. Biol. 19 (9) (2023)
Georgi K. Kanev, Yaran Zhang, Albert J. Kooistra, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J. P. de Esch, Bart A. Westerman
Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks. PLoS Comput. Biol. 19 (9) (2023)
Erik B. Nordquist, Guohui Zhang, Shrishti Barethiya, Nathan Ji, Kelli M. White, Lu Han, Zhiguang Jia, Jingyi Shi, Jianmin Cui, Jianhan Chen
Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels. PLoS Comput. Biol. 19 (9) (2023)
Roberta Maria Lorenzi, Alice Geminiani, Yann Zerlaut, Marialaura De Grazia, Alain Destexhe, Claudia A. M. Gandini Wheeler-Kingshott, Fulvia Palesi, Claudia Casellato, Egidio D'Angelo
A multi-layer mean-field model of the cerebellum embedding microstructure and population-specific dynamics. PLoS Comput. Biol. 19 (9) (2023)
Matthew J. Simpson, Oliver J. Maclaren
Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models. PLoS Comput. Biol. 19 (9) (2023)
Nhat Minh Le, Murat Yildirim, Yizhi Wang, Hiroki Sugihara, Mehrdad Jazayeri, Mriganka Sur
Mixtures of strategies underlie rodent behavior during reversal learning. PLoS Comput. Biol. 19 (9) (2023)
Bo Yuan, Shulei Wang
RSim: A reference-based normalization method via rank similarity. PLoS Comput. Biol. 19 (9) (2023)
James D. Munday, Sam Abbott, Sophie Meakin, Sebastian Funk
Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England. PLoS Comput. Biol. 19 (9) (2023)
Yolanda Larriba, Ivy C. Mason, Richa Saxena, Frank A. J. L. Scheer, Cristina Rueda
CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans. PLoS Comput. Biol. 19 (9) (2023)
Simon Boutry, Raphaël Helaers, Tom Lenaerts, Miikka Vikkula
Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data. PLoS Comput. Biol. 19 (9) (2023)
Jelmer P. Borst, Sean Aubin, Terrence C. Stewart
A whole-task brain model of associative recognition that accounts for human behavior and neuroimaging data. PLoS Comput. Biol. 19 (9) (2023)
Emanuel Cunha, Miguel Silva, Inês Chaves, Hüseyin Demirci, Davide Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Días
The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS Comput. Biol. 19 (9) (2023)
Thao Vu, Souvik Seal, Tusharkanti Ghosh, Mansooreh Ahmadian, Julia Wrobel, Debashis Ghosh
FunSpace: A functional and spatial analytic approach to cell imaging data using entropy measures. PLoS Comput. Biol. 19 (9) (2023)
Zhaohong Huang, Xinyue Cui, Yuhao Xia, Kailong Zhao, Guijun Zhang
Pathfinder: Protein folding pathway prediction based on conformational sampling. PLoS Comput. Biol. 19 (9) (2023)
Yiming Zhang, Ran Zhou, Lunxu Liu, Lu Chen, Yuan Wang
Trackplot: A flexible toolkit for combinatorial analysis of genomic data. PLoS Comput. Biol. 19 (9) (2023)
Adrian L. Hauber, Marcus Rosenblatt, Jens Timmer
Uncovering specific mechanisms across cell types in dynamical models. PLoS Comput. Biol. 19 (9) (2023)
Ilias Rentzeperis, Luca Calatroni, Laurent U. Perrinet, Dario Prandi
Beyond ℓ1 sparse coding in V1. PLoS Comput. Biol. 19 (9) (2023)
Ziheng Duan, Yi Dai, Ahyeon Hwang, Cheyu Lee, Kaichi Xie, Chutong Xiao, Min Xu, Matthew J. Girgenti, Jing Zhang
iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease. PLoS Comput. Biol. 19 (9) (2023)
Sofia Farina, Valérie Voorsluijs, Sonja Fixemer, David S. Bouvier, Susanne Claus, Mark H. Ellisman, Stéphane P. A. Bordas, Alexander Skupin
Mechanistic multiscale modelling of energy metabolism in human astrocytes reveals the impact of morphology changes in Alzheimer's Disease. PLoS Comput. Biol. 19 (9) (2023)
Bayarbaatar Amgalan, Chi-Ping Day, Teresa M. Przytycka
Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression. PLoS Comput. Biol. 19 (9) (2023)
Bryan C. Daniels, Ying Wang, Robert E. Page Jr., Gro V. Amdam
Identifying a developmental transition in honey bees using gene expression data. PLoS Comput. Biol. 19 (9) (2023)
Joshua Atienza, Anjalee Benedict, Lincoln D. Stein, Kashif Pirzada, Cheryl White, Shraddha Pai
Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy. PLoS Comput. Biol. 19 (9) (2023)
Christian Tönsing, Bernhard Steiert, Jens Timmer, Clemens Kreutz
Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models. PLoS Comput. Biol. 19 (9) (2023)
Francis Banville, Dominique Gravel, Timothée Poisot
What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases. PLoS Comput. Biol. 19 (9) (2023)
Tom Arthur, Samuel J. Vine, Gavin Buckingham, Mark Brosnan, Mark R. Wilson, David J. Harris
Testing predictive coding theories of autism spectrum disorder using models of active inference. PLoS Comput. Biol. 19 (9) (2023)
Serena Aneli, Piero Fariselli, Elena Chierto, Carla Bini, Carlo Robino, Giovanni Birolo
Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics. PLoS Comput. Biol. 19 (9) (2023)
Mansooreh Ahmadian, Christian Rickert, Angela Minic, Julia Wrobel, Benjamin G. Bitler, Fuyong Xing, Michael Angelo, Elena W. Y. Hsieh, Debashis Ghosh, Kimberly R. Jordan
A platform-independent framework for phenotyping of multiplex tissue imaging data. PLoS Comput. Biol. 19 (9) (2023)
Shuaijie Zhang, Fan Yang, Lijie Wang, Shucheng Si, Jianmei Zhang, Fuzhong Xue
Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model. PLoS Comput. Biol. 19 (9) (2023)
Ronan F. Arthur, May Levin, Alexandre Labrogere, Marcus W. Feldman
Age-differentiated incentives for adaptive behavior during epidemics produce oscillatory and chaotic dynamics. PLoS Comput. Biol. 19 (9) (2023)
Leijun Ye, Jianfeng Feng, Chunhe Li
Controlling brain dynamics: Landscape and transition path for working memory. PLoS Comput. Biol. 19 (9) (2023)
Seirana Hashemi, Zahra Razaghi-Moghadam, Zoran Nikoloski
Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony. PLoS Comput. Biol. 19 (9) (2023)
Tomohiro Otani, Nozomi Nishimura, Hiroshi Yamashita, Satoshi Ii, Shigeki Yamada, Yoshiyuki Watanabe, Marie Oshima, Shigeo Wada
Computational modeling of multiscale collateral blood supply in a whole-brain-scale arterial network. PLoS Comput. Biol. 19 (9) (2023)
Christopher L. Hewitson, David M. Kaplan, Matthew J. Crossley
Error-independent effect of sensory uncertainty on motor learning when both feedforward and feedback control processes are engaged. PLoS Comput. Biol. 19 (9) (2023)
Kun Zhang, Zhichu Xia, Shudong Huang, Gui-Quan Sun, Jiancheng Lv, Marco Ajelli, Keisuke Ejima, Quan-Hui Liu
Evaluating the impact of test-trace-isolate for COVID-19 management and alternative strategies. PLoS Comput. Biol. 19 (9) (2023)