BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
Gene prediction has remained an active area of bioinformatics research for a long time. Still,
gene prediction in large eukaryotic genomes presents a challenge that must be addressed …
gene prediction in large eukaryotic genomes presents a challenge that must be addressed …
Northern light reviews–Application of orthology and network biology to infer gene functions in non‐model plants
K Vandepoele, S Thierens, M Van Bel - Physiologia Plantarum, 2024 - Wiley Online Library
Approximately 60% of the genes and gene products in the model species Arabidopsis
thaliana have been functionally characterized. In non‐model plant species, the functional …
thaliana have been functionally characterized. In non‐model plant species, the functional …
Tiberius: end-to-end deep learning with an HMM for gene prediction
Motivation For more than 25 years, learning-based eukaryotic gene predictors were driven
by hidden Markov models (HMMs), which were directly inputted a DNA sequence. Recently …
by hidden Markov models (HMMs), which were directly inputted a DNA sequence. Recently …
Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
Interspecies hybridization is prevalent in various eukaryotic lineages and plays important
roles in phenotypic diversification, adaptation, and speciation. To better understand the …
roles in phenotypic diversification, adaptation, and speciation. To better understand the …
New insights into the phylogeny of Neogastropoda aided by draft genome sequencing of a volutid snail
Neogastropoda is a large order of predominantly marine gastropod molluscs, typically
predatory or parasitic on other animals. It includes over 16,000 species representing a large …
predatory or parasitic on other animals. It includes over 16,000 species representing a large …
Chromosome-level subgenome-aware de novo assembly of Saccharomyces bayanus provides insight into genome divergence after hybridization
Interspecies hybridization is prevalent in various eukaryotic lineages and plays important
roles in phenotypic diversification, adaptation, and speciation. To better understand the …
roles in phenotypic diversification, adaptation, and speciation. To better understand the …
Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)
L Männer, T Schell, J Spies, C Galià-Camps… - BMC genomics, 2024 - Springer
Background Sequencing and annotating genomes of non-model organisms helps to
understand genome architecture, the genetic processes underlying species traits, and how …
understand genome architecture, the genetic processes underlying species traits, and how …
Newly sequenced genomes reveal patterns of gene family expansion in select Dragonflies (Odonata: Anisoptera)
As in many other lineages, the dragonflies, or anisoptera (Insecta: Odonata), contain a
myriad of life history and diversification patterns. Two families within anisoptera highlight the …
myriad of life history and diversification patterns. Two families within anisoptera highlight the …
The genomes of Dahlia pinnata, Cosmos bipinnatus, and Bidens alba in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis
H Wang, D Xu, F Jiang, S Wang, A Wang, H Liu… - …, 2024 - academic.oup.com
Abstract Background The Coreopsideae tribe, a subset of the Asteraceae family,
encompasses economically vital genera like Dahlia, Cosmos, and Bidens, which are widely …
encompasses economically vital genera like Dahlia, Cosmos, and Bidens, which are widely …
A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation
C Liu, J Zhang, R Xu, J Lv, Z Qiao, M Bai, S Zhao… - …, 2025 - academic.oup.com
Background Drought is a major limiting factor for plant survival and crop productivity.
Stylosanthes angustifolia, a pioneer plant, exhibits remarkable drought tolerance, yet the …
Stylosanthes angustifolia, a pioneer plant, exhibits remarkable drought tolerance, yet the …