DNA & RNA research

Phylogenomic approach uncovers the hybrid origin and biogeographic diversification of the plum genus doi.org/10.1101/2023.0… Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in Cucurbitaceae doi.org/10.1101/2025.1…

A New Cost Effective, Simplified Workflow for Transposon Insertion Sequencing (TIS) doi.org/10.64898/2026.… Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis doi.org/10.1101/2021.0… #Genomics #Bioinformatics

MAVISp: A Modular Structure-Based Framework for Protein Variant Effects doi.org/10.1101/2022.1… NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction doi.org/10.1101/596718

Distribution of Gene Tree Topologies with Duplication, Loss, and Coalescence doi.org/10.64898/2026.… DupyliCate - mining, classifying, and characterizing gene duplications doi.org/10.1101/2025.1…

LoFi: 4 haplotype-resolved Cannabis genomes enable characterization of large structural variants doi.org/10.64898/2026.… Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis doi.org/10.1101/2021.0…

orthogene: a Bioconductor package to easily map genes within and across hundreds of species doi.org/10.64898/2026.… DupyliCate - mining, classifying, and characterizing gene duplications doi.org/10.1101/2025.1… #Evolution #Bioinformatics

NEMO: Improved and accurate models for identification of 6mA using Nanopore sequencing doi.org/10.1101/2024.0… Large scale genomic rearrangements in selected A. thaliana T-DNA lines are caused by T-DNA insertion mutagenesis doi.org/10.1101/2021.0… #Genomics #Bioinformatics

This never gets old although it is actually about the language used in publications 😂

Ubiquitous functional synergy partially explains why most transcription factor binding is non-functional doi.org/10.64898/2026.… Automatic identification and annotation of MYB gene family members in plants doi.org/10.1101/2021.1… #Genomics #Bioinformatics

Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation doi.org/10.1101/2024.1… Cookbook for Plant Genome Sequences doi.org/10.20944/prepr… #Genomics #Bioinformatics #PlantSciences

Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis doi.org/10.1101/2025.0… DupyliCate - mining, classifying, and characterizing gene duplications doi.org/10.1101/2025.1… #Genomics #Bioinformatics #Evolution

Evolutionary dynamics of the proanthocyanidin biosynthesis gene LAR doi.org/10.1186/s12864… #Evolution #FlavonoidBiosynthesis #PlantSciences #Bioinformatics #Genomics #SciComm #OpenScience

ProteoCast: a web server to predict, validate, and interpret missense variant effects doi.org/10.1101/2025.1… NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction doi.org/10.1101/596718 #Protein #Diversity #Variation

Explaining how mutations affect AlphaFold predictions doi.org/10.64898/2025.… NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction doi.org/10.1101/596718 #Bioinformatics #Genomics

AdaGenes: A streaming processor for high-throughput annotation and filtering of sequence variant data doi.org/10.1101/2025.0… NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction doi.org/10.1101/596718

In light of the launch of Cell Press Blue cell.com/cell-press-blu…, I want to let everyone know about @biorxivpreprint Blue

Evolutionary dynamics of the proanthocyanidin biosynthesis gene LAR doi.org/10.1186/s12864…

The grain amaranth pangenome reveals domestication-associated changes in diversity and function of structural variation doi.org/10.64898/2026.… Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet doi.org/10.1101/2023.0…

LORA: a polymorphic multi-sample LOng Read Assembly pipeline doi.org/10.64898/2026.… Cookbook for Plant Genome Sequences doi.org/10.20944/prepr…