PLoS computational biology

Keyphrases

Publications

volume 19, number 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 computational biology 19 (9) (2023)
Joanna N de Klerk, Erin E Gorsich, John Duncan 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 computational biology 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 computational biology 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 computational biology 19 (9) (2023)
Georgi K Kanev, Yaran Zhang, Albert Jelke 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 computational biology 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 computational biology 19 (9) (2023)
Billy Tchounke, Leopoldo Sanchez, Joseph Martin Bell, David Cros
Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding. PLoS computational biology 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 computational biology 19 (9) (2023)
Grishma Palkar, Jian-Young Wu, G Bard Ermentrout
The inhibitory control of traveling waves in cortical networks. PLoS computational biology 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 computational biology 19 (9) (2023)
Emanuel Cunha, Miguel Silva, Inês Chaves, Huseyin Demirci, Davide Rafael Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Óscar Dias
The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS computational biology 19 (9) (2023)
Hola Kwame Adrakey, Gavin J Gibson, Sandrine Eveillard, Sylvie Malembic-Maher, Frederic 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 computational biology 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 computational biology 19 (9) (2023)
Elias Vera-Siguenza, Cristina Escribano-Gonzalez, Irene Serrano-Gonzalo, Kattri-Liis Eskla, Fabian Spill, Daniel A Tennant
Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model. PLoS computational biology 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 computational biology 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 computational biology 19 (9) (2023)
Tom Arthur, Sam Vine, Gavin Buckingham, Mark Brosnan, Mark Wilson, David J Harris
Testing predictive coding theories of autism spectrum disorder using models of active inference. PLoS computational biology 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 computational biology 19 (9) (2023)
Adrian L Hauber, Marcus Rosenblatt, Jens Timmer
Uncovering specific mechanisms across cell types in dynamical models. PLoS computational biology 19 (9) (2023)
Peter W Schuck, Samuel C To, Huaying Zhao
An automated interface for sedimentation velocity analysis in SEDFIT. PLoS computational biology 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 computational biology 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 computational biology 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 computational biology 19 (9) (2023)
Zhengqing Zhou, Dianjie Li, Ziheng Zhao, Shuyu Shi, Jianghua Wu, Jianwei Li, Jingpeng Zhang, Ke Gui, Yu Zhang, Qi Ouyang, Heng Mei, Yu Hu, Fangting Li
Dynamical modelling of viral infection and cooperative immune protection in COVID-19 patients. PLoS computational biology 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 computational biology 19 (9) (2023)
Sofia Farina, Valérie Voorsluijs, Sonja Fixemer, David Bouvier, Susanne Claus, Mark 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 computational biology 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 computational biology 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 computational biology 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 computational biology 19 (9) (2023)
Mansooreh Ahmadian, Christian Rickert, Angela Minic, Julia Wrobel, Benjamin G Bitler, Fuyong Xing, Michael Angelo, Elena W Y Hsieh, Debashis Ghosh, Kimberley R Jordan
A platform-independent framework for phenotyping of multiplex tissue imaging data. PLoS computational biology 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 computational biology 19 (9) (2023)
Zengmiao Wang, Peiyi Wu, Lin Wang, Bingying Li, Yonghong Liu, Yuxi Ge, Ruixue Wang, Ligui Wang, Hua Tan, Chieh-Hsi Wu, Marko Laine, Henrik Salje, Hongbin Song
Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study. PLoS computational biology 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 computational biology 19 (9) (2023)
Bryan C Daniels, Ying Wang, Robert E Page, Gro V Amdam
Identifying a developmental transition in honey bees using gene expression data. PLoS computational biology 19 (9) (2023)
Yves Carpentier Solorio, Florent Lemaître, Bassam Jabbour, Olivier Tastet, Nathalie Arbour, Elie Bou Assi
Classification of T lymphocyte motility behaviors using a machine learning approach. PLoS computational biology 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 computational biology 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 computational biology 19 (9) (2023)
Ilias Rentzeperis, Luca Calatroni, Laurent Udo Perrinet, Dario Prandi
Beyond ℓ1 sparse coding in V1. PLoS computational biology 19 (9) (2023)
Zhaohong Huang, Xinyue Cui, Yuhao Xia, Kailong Zhao, Gui-Jun Zhang
Pathfinder: Protein folding pathway prediction based on conformational sampling. PLoS computational biology 19 (9) (2023)
Luca Mantovanelli, Dmitrii S Linnik, Michiel Punter, Hildeberto Jardón Kojakhmetov, Wojciech M Śmigiel, Bert Poolman
Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli. PLoS computational biology 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 computational biology 19 (9) (2023)
Shuaijie Zhang, Fan Yang, Lijie Wang, Shucheng Si, Jianmei Zhang, Xiaokang Ji
Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model. PLoS computational biology 19 (9) (2023)
Leijun Ye, Jianfeng Feng, Chunhe Li
Controlling brain dynamics: Landscape and transition path for working memory. PLoS computational biology 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 computational biology 19 (9) (2023)
Xu Pan, Annie DeForge, Odelia Schwartz
Generalizing biological surround suppression based on center surround similarity via deep neural network models. PLoS computational biology 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 computational biology 19 (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 computational biology 19 (9) (2023)
Yiming Zhang, Ran Zhou, Lunxu Liu, Lu Chen, Zhongwang Wang
Trackplot: A flexible toolkit for combinatorial analysis of genomic data. PLoS computational biology 19 (9) (2023)
Nikhil Sharma, Sedigheh Yagoobi, Arne Traulsen
Self-loops in evolutionary graph theory: Friends or foes? PLoS computational biology 19 (9) (2023)
Bo Yuan, Shulei Wang
RSim: A reference-based normalization method via rank similarity. PLoS computational biology 19 (9) (2023)