- CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
- DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
- Dissecting indirect genetic effects from peers in laboratory mice
- Enabling reproducible re-analysis of single-cell data
- STRONG: metagenomics strain resolution on assembly graphs
- A neural network-based method for polypharmacy side effects prediction
- Uncovering the effects of heterogeneity and parameter sensitivity on within-host dynamics of disease: malaria as a case study
- MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits
- PDBeCIF: an open-source mmCIF/CIF parsing and processing package
- neoDL: a novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival
- Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses
- Feature selection for RNA cleavage efficiency at specific sites using the LASSO regression model in Arabidopsis thaliana
- GAT-LI: a graph attention network based learning and interpreting method for functional brain network classification
- Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing
- Haploflow: strain-resolved de novo assembly of viral genomes
- HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
- Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks
- MSCFS: inferring circRNA functional similarity based on multiple data sources
- The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime
- Publisher Correction: Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
Whats new in Bioinformatics
Genome Biology
- MARS: leveraging allelic heterogeneity to increase power of association testing
- Genetic impacts on DNA methylation: research findings and future perspectives
- PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data
- Next-generation microbiology: from comparative genomics to gene function
- The impact of cell type and context-dependent regulatory variants on human immune traits
- Best practices on the differential expression analysis of multi-species RNA-seq
- Complete vertebrate mitogenomes reveal widespread repeats and gene duplications
- Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
- Drosophila primary microRNA-8 encodes a microRNA-encoded peptide acting in parallel of miR-8
- G-quadruplexes are transcription factor binding hubs in human chromatin