David Sims

TL;DR: The issue of sequencing depth in the design of next-generation sequencing experiments is discussed and current guidelines and precedents on the issue of coverage are reviewed for four major study designs, including de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses.

TL;DR: It is discovered that KDM2B (FBXL10) specifically recognizes non-methylated DNA in CGIs and recruits the polycomb repressive complex 1 (PRC1), which contributes to histone H2A lysine 119 ubiquitylation (H2AK119ub1) and gene repression.

TL;DR: This paper presents a new probabilistic method for estimating the planktonic resolution of the response of the immune system to EMTs, which has shown promise in both the low and high-resolution models.

TL;DR: Deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence and indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering.

TL;DR: In models of high-grade serous ovarian cancer (HGS-OVCa), CDK12 attenuation was sufficient to confer sensitivity to PARP1/2 inhibition, suppression of DNA repair via homologous recombination, and reduced expression of BRCA1.