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Khabre desk
Recent reporting, analysis and explainers from the Genetics desk.
science
A bioRxiv preprint reports that nonsense-mediated decay suppresses many RNA isoforms created when transposable-element sequences become part of genes. The findings suggest this cellular quality-control system helps regulate a pool of potential evolutionary novelty.
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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.
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A bioRxiv preprint describes LongVerse, a system that uses AI agents to configure a fixed pipeline for haplotype-resolved DNA methylation analysis from Nanopore or PacBio reads. In tests on the HG002 reference genome, the authors report calls identical to a human expert’s and comparisons with bisulfite sequencing.
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A bioRxiv preprint describes a prime-editing method that creates genomic deletions while adding molecular tags, letting researchers identify edited cells and measure gene-expression effects. In K562 cells, the team reports intronic enhancer deletions associated with 20–30% lower host-gene expression.
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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.
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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.
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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.
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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.
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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.
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A bioRxiv preprint introduces Tau, a mathematical method for reconstructing and timing copy-number gains in cancer genomes. Its authors report that abrupt amplification bursts, including at oncogenes, cluster around whole-genome duplication.
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A bioRxiv preprint introduces EpiZoo, a 2.6-billion-parameter model trained on about 20.9 million single cells from multiple species. Its authors report performance on several single-cell analysis tasks and describe applications in comparing regulatory patterns and prioritising cancer mutations.
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A bioRxiv preprint reports that TabICL and TabPFN prediction performance declines as genetic ancestry dispersion increases in evaluation data. The authors also report that instruction-tuning TabICL on synthetic tasks designed to model ancestry-dependent effects improves performance stability across ancestry-distance groups.
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A bioRxiv preprint reports that UHRF1 reads ubiquitin marks it places on histone H3, promoting further marking and supporting DNA methylation maintenance in CpG-sparse regions.
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A bioRxiv preprint reports nine high-confidence hybrids between invasive Bursaphelenchus xylophilus and native B. mucronatus in Japanese field samples. Genome-wide analyses identified both F1-like and advanced backcross-like individuals, including some missed by a single-locus test.
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A bioRxiv preprint profiles RISC-bound small interfering RNAs produced after insecticidal double-stranded RNA was injected into Tribolium castaneum larvae. The study links strand representation and terminal RNA modifications with sequence and structural features that could improve future pest-control design.
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A bioRxiv preprint introduces SPECTRA, a graph-based model that predicts gene-expression responses to CRISPR perturbations by propagating signals through gene regulatory networks. The authors report improved recovery of sparse perturbation-related changes in a large-scale single-cell CRISPRi benchmark.
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A bioRxiv preprint describes a graph neural network that incorporates viral evolutionary relationships when predicting the host associated with a paramyxovirus sequence. The authors report advantages over unstructured neural networks when training data are sparse, while finding that phylogeny alone explains much of the predictive performance.
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A bioRxiv preprint introduces ARCHER-LD, a multi-GPU tool for calculating linkage disequilibrium across very large sequencing datasets. The authors report speedups of about eightfold to 28-fold over PLINK in benchmark tests and complete a 10-quadrillion-element LD matrix in under six hours on 512 GPUs.
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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.
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A bioRxiv preprint describes miRstring, a biogenesis-aware RNA language model trained on 77,708 miRNA precursors from 414 species. The authors report cross-species mature-miRNA boundary decoding and artificial miRNA scaffold designs that repressed target mRNAs in validation experiments.
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A bioRxiv preprint reports that neonatal AAV-SIL1 gene therapy prevented neurological and muscle disease in a mouse model of Marinesco-Sjögren syndrome. The treatment preserved cerebellar Purkinje cells and maintained its effects through 26 weeks.
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A bioRxiv preprint reports severe growth depression in Chinese bahaba after two generations of closed captive breeding from 18 wild founders. Whole-genome analysis linked the decline to increased genomic inbreeding and identified candidate pathways relevant to conservation breeding.
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A UCSF-led bioRxiv preprint introduces CELL-FM, a bidirectional generative model that connects protein sequences and cellular context with fluorescence microscopy images. The authors use it for virtual localization, motif analysis and mutagenesis of intrinsically disordered peptides.
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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.
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A bioRxiv preprint integrates genome-wide maps of DNA breaks, replication and transcription in U2-OS and HeLa cancer cell lines. It reports that prolonged low-dose DNA polymerase inhibition redirects breaks toward late-replicating regions and identifies MUS81 as a regulator of recurrent break clusters.
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A bioRxiv preprint functionally profiled 80 human PRDM9 alleles and found that most produce similar genome-wide DNA-binding patterns despite extensive sequence diversity. Rare and infertility-associated variants showed unusually broad or minimal DNA binding, pointing to a possible role in disrupted meiotic recombination.
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A bioRxiv preprint describes RNA-fragment end joining (REJ), a modular system that joins separate RNA units into functional coding mRNAs. The reported platform supports gene complementation, intersectional cell labeling and expression of large proteins.
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A bioRxiv preprint introduces LucaCell, a foundation model that represents genes through mRNA sequence embeddings instead of fixed gene identifiers. The authors report applications spanning cross-species cell annotation, microbial analysis, chromatin accessibility and influenza infection states.
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A bioRxiv preprint comparing matched full-UDG and non-UDG libraries from two medieval Mongolian individuals found trade-offs between site retention, residual disagreement and kinship inference. Corrected mixed-library data supported a first-degree, likely mother–son relationship, while uncorrected data shifted one estimate towards second degree.
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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.
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A bioRxiv preprint describes Isocall, a deterministic method for jointly identifying known and novel transcripts across large PacBio long-read RNA-sequencing datasets. The authors report a joint call across 206 samples in 25 minutes after alignment and profiling.
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A bioRxiv preprint introduces RADIS, a chemical-probing strategy that maps RNA secondary structure across long, intron-rich genomic loci. The study applies it to splice sites, branchpoints and Alu elements, including deep intronic regions that are difficult to analyse experimentally.