Systems & Computational Biology
Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usagePaired scRNA-seq and scTCR-seq reveals that diabetogenic CD8 T cells in the islets and spleens of NOD mice exhibit phenotypic and clonal heterogeneity despite restricted TCR gene usage. Expression of certain TCR genes correlates with clonal proliferation and effector phenotype.
Evolutionary association of receptor-wide amino acids with G protein–coupling selectivity in aminergic GPCRsEvolutionary analyses of aminergic G protein–coupled receptors reveal receptor-wide potential determinants of G protein–coupling selectivity.
Expression regulation of genes is linked to their CpG density distributions around transcription start sitesIn this work, we performed a gene classification which revealed that different gene clusters harbor distinct gene regulatory mechanisms as well as epigenetic mark and expression variations in tumorigenesis.
Genome-scale metabolic models for natural and long-term drug-induced viral control in HIV infectionA system-level up-regulation of OXPHOS and glycolysis could play a role in latent reservoir dynamics and immunosenescence in HIV-1–infected individuals with long-term successful therapy.
Reduced adhesion of aged intestinal stem cells contributes to an accelerated clonal driftAnalysis of clonal dynamics of intestinal stem cells supports an accelerated clonal drift upon aging, likely because of reduced adhesion of aged ISCs because of reduced canonical Wnt signaling.
Subgenomic RNA profiling suggests novel mechanism in coronavirus gene regulation and host adaptionCORONATATOR, developed to analyze the subgenomic RNA of coronavirus, was applied on large number of sequencing data sets from coronaviruses, and shed light on viral gene regulation.
The value of genotype-specific reference for transcriptome analyses in barleyWe demonstrate in this study that using a common reference genome may lead to loss of genotype-specific information in the assembled Reference Transcript Dataset (RTD) and the generation of erroneous, incomplete, or misleading transcriptomics analysis results in barley.
Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in HymenopteransA 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.
Conserved exchange of paralog proteins during neuronal differentiationParalog proteins promote fine tuning of protein complexes. The author identified a specific paralog signature conserved across vertebrate neuronal differentiation. Altering the ratio of SEC23 paralogs in the COPII complex influences neuronal differentiation in a opposite way.
Proteomic landscape of SARS-CoV-2– and MERS-CoV–infected primary human renal epithelial cellsTranslatome and proteome analyses of human proximal and distal tubular cells during coronavirus infection reveal distinctive host cell response patterns important for viral replication and renal pathology.