Evolution
- Telescoping bimodal latent Dirichlet allocation to identify expression QTLs across tissues
We present telescoping bimodal LDA, a method to identify complex associations across high-dimensional count data, and we show TBLDA’s behavior for expression QTL mapping for bulk RNA-seq data from 10 tissues in the GTEx data.
- Comprehensive evolutionary analysis and nomenclature of plant G3BPs
A thorough phylogenetic analysis of eukaryotic G3BPs (Rasputins) with a focus on plant G3BP proteins, classification into two subfamilies and a proposed systematic nomenclature.
- Evolutionary association of receptor-wide amino acids with G protein–coupling selectivity in aminergic GPCRs
Evolutionary analyses of aminergic G protein–coupled receptors reveal receptor-wide potential determinants of G protein–coupling selectivity.
- Phylogenetic profiling resolves early emergence of PRC2 and illuminates its functional core
This study strengthens the support for PRC2 emergence before the diversification of eukaryotes, detects a common presence of E(z) and ESC, indicating a conserved core, identifies diverse VEFS-Box Su(z)12 candidate proteins, and proposes a substrate specificity shift during E(z) evolution.
- Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in Hymenopterans
A bioinformatic pipeline for telomeric repeat motif detection was applied to 129 insect species and identified diverse forms of telomeric motifs in Hymenopterans, including canonical 5-bp, novel 8- and 9-bp forms, suggesting extraordinary evolutionary fluidity of telomeric repeat in Hymenopterans.
- LINE-1 and SINE-B1 mapping and genome diversification in Proechimys species (Rodentia: Echimyidae)
Signal distribution of L1 and B1 among chromosomes in five species of Proechimys may represent a strong indication of their role in karyotype diversity of this speciose Neotropical rodent.
- Human BRCA pathogenic variants were originated during recent human history
Evolutionary origin of pathogenic variants in human BRCA1 and BRCA2.
- Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law
This study globally investigates the allelic splicing pattern in multiple tissues of an F1 hybrid mouse and reveals the underlying driving forces shaping such tissue-dependent splicing divergence.
- CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly
Next-generation sequencing of three caribou ecotypes aligned to a new annotated genome assembly revealed divergent CNVs, including genes with annotations in line with adaptation.
- Distinct mechanisms mediate X chromosome dosage compensation in Anopheles and Drosophila
CRISPR knockout of msl-2 and epigenome analyses in Anopheles reveal that X chromosome dosage compensation in mosquitos and Drosophila is achieved by two different molecular mechanisms.