The rate of genome sequencing and availability has rapidly increased. It is anticipated that conventional de novo phylogenetic inference may no longer be efficient for such an increasing number of sequences. By integrating parsimony analysis with pre-computed ancestral sequences, we developed TIPars, which allows rapid and memory-efficient insertion of sequences into a reference phylogeny at high accuracy. This enables real-time monitoring of pathogen transmission during a pandemic using large-scale global phylogenetic analysis such as those demonstrated in COVID-19 pandemic. Ye et al 2024
Image Credit: Ningqi Zhao (jeaning7@d24h.hk), Yongtao Ye (yytao@connect.hku.hk), Marcus H. Shum (hohin2@d24h.hk) and Tommy Tsan-Yuk Lam (ttylam@hku.hk) should be credited with the creation of the image.
Education
Studentsourcing—Aggregating and reusing data from a practical cell biology course
PLOS Computational Biology: published February 15, 2024 | https://doi.org/10.1371/journal.pcbi.1011836
Perspective
Ten simple rules for designing graphical abstracts
PLOS Computational Biology: published February 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011789
Research Articles
The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion
PLOS Computational Biology: published February 2, 2024 | https://doi.org/10.1371/journal.pcbi.1011825
The geometric evolution of aortic dissections: Predicting surgical success using fluctuations in integrated Gaussian curvature
PLOS Computational Biology: published February 2, 2024 | https://doi.org/10.1371/journal.pcbi.1011815
Foldy: An open-source web application for interactive protein structure analysis
PLOS Computational Biology: published February 2, 2024 | https://doi.org/10.1371/journal.pcbi.1011171
Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae)
PLOS Computational Biology: published February 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011845
Trained recurrent neural networks develop phase-locked limit cycles in a working memory task
PLOS Computational Biology: published February 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011852
Index analysis: An approach to understand signal transduction with application to the EGFR signalling pathway
PLOS Computational Biology: published February 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011777
Sleep deprivation detected by voice analysis
PLOS Computational Biology: published February 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011849
Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells
PLOS Computational Biology: published February 7, 2024 | https://doi.org/10.1371/journal.pcbi.1011798
Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production
PLOS Computational Biology: published February 7, 2024 | https://doi.org/10.1371/journal.pcbi.1011373
Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data
PLOS Computational Biology: published February 7, 2024 | https://doi.org/10.1371/journal.pcbi.1011519
Attractor neural networks with double well synapses
PLOS Computational Biology: published February 7, 2024 | https://doi.org/10.1371/journal.pcbi.1011354
Multiscale networks in multiple sclerosis
PLOS Computational Biology: published February 8, 2024 | https://doi.org/10.1371/journal.pcbi.1010980
Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems
PLOS Computational Biology: published February 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011675
A beta-Poisson model for infectious disease transmission
PLOS Computational Biology: published February 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011856
Compressive stress gradients direct mechanoregulation of anisotropic growth in the zebrafish jaw joint
PLOS Computational Biology: published February 8, 2024 | https://doi.org/10.1371/journal.pcbi.1010940
Dynamic predictive coding: A model of hierarchical sequence learning and prediction in the neocortex
PLOS Computational Biology: published February 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011801
An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level
PLOS Computational Biology: published February 9, 2024 | https://doi.org/10.1371/journal.pcbi.1011873
Mathematical model of oxygen, nutrient, and drug transport in tuberculosis granulomas
PLOS Computational Biology: published February 9, 2024 | https://doi.org/10.1371/journal.pcbi.1011847
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis
PLOS Computational Biology: published February 9, 2024 | https://doi.org/10.1371/journal.pcbi.1011860
Accounting for isoform expression increases power to identify genetic regulation of gene expression
PLOS Computational Biology: published February 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011857
Generating synthetic population for simulating the spatiotemporal dynamics of epidemics
PLOS Computational Biology: published February 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011810
Learning what matters: Synaptic plasticity with invariance to second-order input correlations
PLOS Computational Biology: published February 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011844
magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing
PLOS Computational Biology: published February 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011875
Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis
PLOS Computational Biology: published February 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011868
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses
PLOS Computational Biology: published February 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011865
Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians
PLOS Computational Biology: published February 14, 2024 | https://doi.org/10.1371/journal.pcbi.1011876
Enhanced perfusion following exposure to radiotherapy: A theoretical investigation
PLOS Computational Biology: published February 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011252
Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents
PLOS Computational Biology: published February 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011902
Fast adaptation to rule switching using neuronal surprise
PLOS Computational Biology: published February 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011839
The successor representation subserves hierarchical abstraction for goal-directed behavior
PLOS Computational Biology: published February 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011312
Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus
PLOS Computational Biology: published February 20, 2024 | https://doi.org/10.1371/journal.pcbi.1010706
Ecological and evolutionary dynamics of cell-virus-virophage systems
PLOS Computational Biology: published February 20, 2024 | https://doi.org/10.1371/journal.pcbi.1010925
Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations
PLOS Computational Biology: published February 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011886
EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks
PLOS Computational Biology: published February 21, 2024 | https://doi.org/10.1371/journal.pcbi.1011375
Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis
PLOS Computational Biology: published February 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011113
Genome scale metabolic network modelling for metabolic profile predictions
PLOS Computational Biology: published February 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011381
Diverse mutant selection windows shape spatial heterogeneity in evolving populations
PLOS Computational Biology: published February 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011878
A simulation framework to determine optimal strength training and musculoskeletal geometry for sprinting and distance running
PLOS Computational Biology: published February 23, 2024 | https://doi.org/10.1371/journal.pcbi.1011410
Shared input and recurrency in neural networks for metabolically efficient information transmission
PLOS Computational Biology: published February 23, 2024 | https://doi.org/10.1371/journal.pcbi.1011896
A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites
PLOS Computational Biology: published February 23, 2024 | https://doi.org/10.1371/journal.pcbi.1011267
Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference
PLOS Computational Biology: published February 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011108
Disentangled deep generative models reveal coding principles of the human face processing network
PLOS Computational Biology: published February 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011887
Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity
PLOS Computational Biology: published February 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011907
Bidirectional de novo peptide sequencing using a transformer model
PLOS Computational Biology: published February 28, 2024 | https://doi.org/10.1371/journal.pcbi.1011892
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2
PLOS Computational Biology: published February 28, 2024 | https://doi.org/10.1371/journal.pcbi.1011586
STGIC: A graph and image convolution-based method for spatial transcriptomic clustering
PLOS Computational Biology: published February 28, 2024 | https://doi.org/10.1371/journal.pcbi.1011935
Dissecting the roles of calcium cycling and its coupling with voltage in the genesis of early afterdepolarizations in cardiac myocyte models
PLOS Computational Biology: published February 28, 2024 | https://doi.org/10.1371/journal.pcbi.1011930
Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory
PLOS Computational Biology: published February 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011867
TimeTeller: A tool to probe the circadian clock as a multigene dynamical system
PLOS Computational Biology: published February 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011779
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism
PLOS Computational Biology: published February 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011919
Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0
PLOS Computational Biology: published February 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011303
HormoneBayes: A novel Bayesian framework for the analysis of pulsatile hormone dynamics
PLOS Computational Biology: published February 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011928
Methods
Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology
PLOS Computational Biology: published February 2, 2024 | https://doi.org/10.1371/journal.pcbi.1011299
Robust expansion of phylogeny for fast-growing genome sequence data
PLOS Computational Biology: published February 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011871
CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data
PLOS Computational Biology: published February 9, 2024 | https://doi.org/10.1371/journal.pcbi.1011870
Inference of annealed protein fitness landscapes with AnnealDCA
PLOS Computational Biology: published February 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011812
Connectivity Matrix Seriation via Relaxation
PLOS Computational Biology: published February 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011904
Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets
PLOS Computational Biology: published February 20, 2024 | https://doi.org/10.1371/journal.pcbi.1011890
A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization
PLOS Computational Biology: published February 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011880
DeepD3, an open framework for automated quantification of dendritic spines
PLOS Computational Biology: published February 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011774
Software
CyVerse: Cyberinfrastructure for open science
PLOS Computational Biology: published February 7, 2024 | https://doi.org/10.1371/journal.pcbi.1011270
Quantifying the clusterness and trajectoriness of single-cell RNA-seq data
PLOS Computational Biology: published February 28, 2024 | https://doi.org/10.1371/journal.pcbi.1011866