Modeling heterogeneity in single-cell perturbation states enhances detection of response eQTLs
Cohorts We used published data (GEO accession no. GSE162632) to study the effect of 12 h of ex vivo…
Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes
Overview of the genotyping method We represent variation as haplotype segments that are short enough to minimize disruption…
Redefining cellular reprogramming with advanced genomic technologies
Briggs, R. & King, T. J. Transplantation of living nuclei from blastula cells into enucleated Frogs’ eggs. Proc.…
Meta-analysis reveals differences in somatic alterations by genetic ancestry across common cancers
Genetic ancestry is a quantitative measure of inherited genetic variation and correlates with human migration patterns1. It contributes…
SPAmix: a scalable, accurate, and universal analysis framework for large-scale genetic association studies in admixed populations | Genome Biology
Model residuals of linear regression and logistic regression Linear regression and logistic regression are regular models to fit…
Genetic variation and genome-enabled selection of white lupin for key seed quality traits | BMC Genomics
Foyer CH, Lam H-M, Nguyen HT, Siddique KHM, Varshney RK, Colmer TD, et al. Neglecting legumes has compromised…
Population-scale gene-based analysis of whole-genome sequencing provides insights into metabolic health
Ethics Our research complies with all relevant ethical regulations. All studies included in this research were approved by…
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…
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq
Constructing the scTF-seq library and single-cell atlas To establish scTF-seq, we built a dox-inducible lentiviral open reading frame…
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…
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),…