Search articles by title, topic or section.
Khabre desk
Recent reporting, analysis and explainers from the Genetics desk.
science
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.
science
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.
science
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.
science
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.
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 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.
science
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.
science
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.
science
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.
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 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.
science
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.
science
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.
science
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.
science
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.
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.
science
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.
science
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.