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Khabre desk
Recent reporting, analysis and explainers from the Genomics desk.
science
A bioRxiv preprint introduces hEVO, a genomic model trained on 4.784 billion haplotype sequences reconstructed from whole-genome data. Its authors report strong results across variant-interpretation benchmarks, including tests that required no task-specific training.
science
A bioRxiv preprint reports more than 200 newly identified transposable-element families in Arabidopsis thaliana, based on long-read genome assemblies from 91 strains. The authors say these families contribute to genetic variants with large effects, even though full-length copies are often found in only a few strains.
science
A bioRxiv preprint describes RaMN-Seq, a roughly two-hour method for purifying micronuclei and sequencing their DNA. The researchers report tests in induced chromosome-missegregation experiments and cancer cell lines and tumour samples.
science
A bioRxiv preprint benchmarked 16 tools using 30× Illumina whole-genome sequencing and found that only five reliably produced exact deletion, insertion and duplication calls against truth sets. It also reported accuracy losses in ensemble pipelines compared with their strongest component tools.
science
A bioRxiv preprint analysing a PLP1-mutant Jimpy brain dataset finds that normalization choices and shared controls can affect which genes appear to move toward healthy levels after a rescue. The authors say such transcriptomic patterns can indicate broad state restoration without identifying which downstream gene mediates it.
science
A bioRxiv preprint analysing 231 haplotype-resolved human pangenomes reports that variable transposable elements can gain, change or lose regulatory effects before they become fixed. Their effects depend on DNA methylation and transcript context.
science
A bioRxiv preprint finds that the reproducibility of functional assays can cap measured performance for variant-effect predictors. Correcting for assay reliability shifts the apparent prediction gap from canonical splice sites toward intronic regions 11–50 base pairs from the splice boundary.
science
A bioRxiv preprint uses electronic genome mapping to measure CRISPR-Cas9 target and off-target binding across the human genome in vitro. The study also examines how guide-RNA mismatches and binding-site spacing affect the system.
science
A bioRxiv preprint from Queen Mary University of London presents a genome-wide framework that uses native Oxford Nanopore reads to measure molecule-level DNA methylation variation and co-methylation. In human lymphoblastoid cell data, the analysis found patterns hidden by site-level averages.