MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

Manifold Alignment without Correspondence

Manifold alignment has been found to be useful in many areas of machine learning and data mining. In this paper we introduce a novel manifold alignment approach, which differs from “semisupervised alignment” and “Procrustes alignment” in that it does not require predetermining correspondences. Our approach learns a projection that maps data instances (from two different spaces) to a lower dimen...

I-13: Transcriptome Dynamics of Human and Mouse Preimplantation Embryos Revealed by Single Cell RNA-Sequencing

Background: Mammalian preimplantation development is a complex process involving dramatic changes in the transcriptional architecture. However, it is still unclear about the crucial transcriptional network and key hub genes that regulate the proceeding of preimplantation embryos. Materials and Methods: Through single-cell RNAsequencing (RNA-seq) of both human and mouse preimplantation embryos, ...

Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data

An increasing number of single cell transcriptome and epigenome technologies, including single cell ATAC-seq (scATAC-seq), have been recently developed as powerful tools to analyze the features of many individual cells simultaneously. However, the methods and software were designed for one certain data type and only for single cell transcriptome data. A systematic approach for epigenome data an...

Manifold Alignment

An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions.

Epstein-Barr virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly...