Nucleotide dependency analysis of genomic language models detects functional elements
SpeciesLM training For SpeciesLM metazoa, we obtained metazoan genomes comprising 494 different species from the Ensembl 110 database36.…
A novel gene expression stability metric to unveil homeostasis and regulation | Genome Biology
K-proportion and gene homeostasis Z-Index identify regulatory genes As cells of the same type and in the same…
The genetic influence of sex on gene expression for blood in pigs | BMC Genomics
Data summary We collected 386 blood samples with matched genotype and gene expression data from the PigGTEx project…
Genomic predictions for growth and feed efficiency traits in a duck breeding population | BMC Genomics
Animal population and phenotype data This study used a breeding population of Zhongxin white duck (a commercial breed…
A genetic map of human metabolism across the allele frequency spectrum
Study design The UKB is a prospective cohort study from the UK that contains more than 500,000 volunteers…
Incorporating additive genetic effects and linkage disequilibrium information to discover gene-environment interactions using BV-LDER-GE | Genome Biology
Model overview We consider the following model to incorporate both additive and interaction effects: $${Y}_{i}={\sum }_{j=1}^{M}{G}_{ji}{\beta }_{j}+{\sum }_{j=1}^{M}{S}_{ji}{\gamma…
Exploring the genetic basis of heterosis in eucalypt growth based on transcriptome analysis | BMC Genomics
Preparation of preliminary data In all samples, the proportion of clean reads was higher than 99.5% (Table S2),…
Spatial architecture of development and disease
Bressan, D., Battistoni, G. & Hannon, G. J. The dawn of spatial omics. Science 381, eabq4964 (2023). Article …
Limited overlap between genetic effects on disease susceptibility and disease survival
Ethics statement This study was conducted in compliance with the relevant ethical guidelines and approved by the appropriate…
TrueSpot: a robust automated tool for quantifying signal puncta in fluorescent imaging | Genome Biology
TrueSpot uses an automated threshold selection algorithm that utilizes multiple approaches TrueSpot accepts either a 2D image or…
Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage | BMC Genomics
Wang K, Zhang SH, Wang DQ, Wu JM, Wang CY, Wei QW. Conservation genetics assessment and phylogenetic relationships…
Advances in haplotype phasing and genotype imputation
Voight, B. F., Kudaravalli, S., Wen, X. & Pritchard, J. K. A map of recent positive selection in…