We present SCENIC, a computational method for simultaneous gene regulatory network
reconstruction and cell-state identification from single-cell RNA-seq data (http://scenic. aertslab. …

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary
among human genomes, but are still relatively under-ascertained. Here we use tiling …

To understand the biology and evolution of ruminants, the cattle genome was sequenced to
about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a …

The imprints of domestication and breed development on the genomes of livestock likely differ
from those of companion animals. A deep draft sequence assembly of shotgun reads from …

Understanding complex systems often requires a bottom-up analysis towards a systems
biology approach. The need to investigate a system, not only as individual components but as a …

The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims
to foster the coordinated development of minimum-information checklists and provide a …

Inferring a Gene Regulatory Network (GRN) from gene expression data is a computationally
expensive task, exacerbated by increasing data sizes due to advances in high-throughput …

Background Bovine whole genome linkage disequilibrium maps were constructed for eight
breeds of cattle. These data provide fundamental information concerning bovine genome …

Functional impairment of DNA damage response pathways leads to increased genomic
instability. Here we describe the centrosomal protein CEP152 as a new regulator of genomic …

Strategies for assembling large, complex genomes have evolved to include a combination of
whole-genome shotgun sequencing and hierarchal map-assisted sequencing 1 , 2 . Whole-…