Systems & Computational Biology
Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencingSingle-cell RNA-seq is an important technology for capturing gene expression in individual cells. It has limitations as spatial context and accurate representation of cell types in the tissue are lost. Here, we show that MERFISH is comparable to scRNA-seq.
Identifying novel regulators of placental development using time-series transcriptome dataNetwork analysis of RNA-seq data generated from mouse placenta at embryonic days 7.5, 8.5, and 9.5 identifies novel regulators of placental development.
Synergistic activation of RARβ and RARγ nuclear receptors restores cell specialization during stem cell differentiation by hijacking RARα-controlled programsSynergistic activation of RARβ and RARγ nuclear receptors in mouse stem cells restores cell specialization during neuronal differentiation by hijacking RARα-controlled programs.
Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolutionThe human genome, unlike the genomes of other primates, contains tandemly organized higher order NBPF structures that represent a link to the development of their cognitive abilities.
A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2Using 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 heterodimersBTB 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 cellsSingle-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 tissuesWe 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 analysisThis 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 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.