Systems & Computational Biology
- A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2
Using relevant neuronal datasets and in vitro experiments, we show that MeCP2 function depends on methylated CAC (mCAC) sites regardless of their occurrence in CA repeats or elsewhere in the genome.
- Sibling rivalry among the ZBTB transcription factor family: homodimers versus heterodimers
BTB domains potentially can form homo- or heterodimers. The study examines the dimerization choice of several BTB domains and finds only one heterodimer, while all tested pairs can homodimerize.
- Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells
Single-cell RNA sequencing of porcine ileal lymphocytes reveals similarities to human cells and discovery of porcine intestinal innate lymphoid cells.
- 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.
- Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis
This work formulates a noise reduction method, RECODE, which resolves the curse of dimensionality in noisy high-dimensional data, including scRNA-seq data, for effective downstream analyses.
- Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usage
Paired 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 GPCRs
Evolutionary 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 sites
In 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 infection
A 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 drift
Analysis 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.