Genomics & Functional Genomics
KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomasKCNQ3, a potassium channel, is frequently genetically altered in gastro-oesophageal adenocarcinomas and found to be significantly associated with WNT and MYC activity, and cellular proliferation.
Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantationCell-free DNA chromatin immunoprecipitation detects molecular pathways and profiles the sources of tissue injury in heart transplant patients.
A targeted sequencing extension for transcript genotyping in single-cell transcriptomicsWe describe the targeted sequencing extension and provide two proof-of-concept examples of how it can assist with understanding the impact of genetic variants.
Unique activities of two overlapping PAX6 retinal enhancersA unique combination of high-resolution imaging and single-cell RNA sequencing in zebrafish reveals cell type-specific activities of developmental eye enhancers.
De novo network analysis reveals autism causal genes and developmental links to co-occurring traitsIn this study, we provide a biological argument for looking at an autistic individual’s phenotype as being related to their combined genetic risk for different clusters of traits.
Refining the genetic risk of breast cancer with rare haplotypes and pattern miningA closed-pattern mining algorithm helps identify rare, noncontiguous haplotypes underlying breast cancer risk in British women in the UK Biobank.
Gene-regulation modules in nonalcoholic fatty liver disease revealed by single-nucleus ATAC-seqThis study uncovers cell-type-specific global gene regulation in NAFLD progression, identifying core genes and shedding light on the disease’s molecular mechanisms.
Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20This work characterizes the transcriptional and epigenetic control of memory CD8 T cell differentiation by the BTB-ZF family transcription factor Zbtb20 using single cell RNA and ATAC sequencing and identifies direct genomic targets of Zbtb20 using CUT&RUN.
Missense variant interaction scanning reveals a critical role of the FERM domain for tumor suppressor protein NF2 conformation and functionDeep mutational interaction perturbation scanning of NF2 with conformation-dependent interaction partners KDM1A, EMILIN, and PIK3R3 revealed two regions critical for NF2 tumor suppressor function.
Z-flipon variants reveal the many roles of Z-DNA and Z-RNA in health and diseaseZ-DNABERT uses the transformer algorithm to map genomic Z-DNA. We validate the approach using chemical footprinting data from live cells. We show the utility of the approach by mapping the Z-flipons discovered to Mendelian disease variants and various quantitative traits.