Genomics & Functional Genomics
- Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs
Published predictions of 5-methylcytosine at GCU sites inferred from direct RNA sequencing and the Tombo Alternative Model should be reconsidered unless further validated with orthogonal methods.
- Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells
The study shows that estrogen activates transcription within pre-established chromosomal 3D architectures, strengthening enhancer interactions through local accumulation of the estrogen receptor α.
- Suppressed transcript diversity and immune response in COVID-19 ICU patients: a longitudinal study
This integrative longitudinal clinico-genomic study delves deep into the gene and transcript expression pattern dynamics in severe COVID-19 patients with ARDS admitted to the ICU.
- The highly improved genome of Ixodes scapularis with X and Y pseudochromosomes
Ixodes scapularis Gulia-Nuss (IscGN) genome assembly and gene set were obtained using DNA from eggs and male and female adult ticks. By combining Hi-C, PacBio HiFi, and Illumina sequencing technologies, we assembled 13 pseudoautosomes and sex chromosomes: X and Y.
- Causal links of α-thalassemia indices and cardiometabolic traits and diabetes: MR study
Causal MR study links α-thalassemia-related erythrocyte traits to cardiometabolic risks and diabetes susceptibility in Taiwan.
- Cost-effective DNA methylation profiling by FML-seq
A low-cost, high-throughput method for genome-wide DNA methylation profiling based on methylation-specific restriction digestion and sequencing.
- Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs
This study compares the performances of three different software in the identification of canonical and noncanonical sgRNAs in amplicon data sequenced with Illumina MiSeq in 250-bp paired ends.
- KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomas
KCNQ3, 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 transplantation
Cell-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 transcriptomics
We describe the targeted sequencing extension and provide two proof-of-concept examples of how it can assist with understanding the impact of genetic variants.