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Khabre desk
Recent reporting, analysis and explainers from the genomics desk.
health
A bioRxiv preprint describes CIDER, a whole-genome sequencing score based on reconstructed T-cell receptor sequences. In patient cohorts, higher scores were associated with better outcomes among people treated with immune checkpoint inhibitors.
science
A bioRxiv preprint describes Carbon-A, a 1.2-billion-parameter model for predicting protein-coding genes across eukaryotes. Its authors used the model to create a database covering 48,167 genome assemblies and report strong performance across 42 benchmarks.
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.
health
A Japanese medRxiv preprint reports clinically concordant genomic diagnoses in 10 of 108 sequenced patients who began dialysis by age 50, after clinically apparent polycystic kidney disease was excluded. Nine diagnoses had pathogenic or likely pathogenic genetic support.
science
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.
science
A bioRxiv preprint reports that wheat resistance to four soil-borne pathogens is shaped by many genetic factors, with some genomic regions shared across diseases. The authors say the patterns also depend on pathogen, environment and local genetic context.
science
A bioRxiv preprint maps nucleosome patterns across 410 tumours from 23 cancer types and reports that tissue-derived patterns could distinguish cancers using circulating cell-free DNA. The findings point to a possible source of information for non-invasive cancer detection, but the reported results are from research analyses rather than a demonstrated clinical test.
science
A bioRxiv preprint reports that correcting ambient RNA before detecting doublets can leave more doublet-containing droplets in single-cell RNA-sequencing data. The authors recommend detecting doublets first, except when using CellBender.
health
A bioRxiv preprint describes NeoOmni Atlas, a database built by reanalysing mass-spectrometry data from 26 cancer types. It catalogues HLA-presented peptides and computationally prioritises potential tumour-associated and tumour-specific targets.
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 describes DeepMM, a method that detects suspected misassembly junctions and splits contigs before microbial genomes are grouped into bins. In benchmark datasets, this reduced gene annotations that disagreed with sample-matched reference genomes.
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.
health
A bioRxiv preprint analysing 1,501 publicly available Enterobacterales genomes found 241 combinations of genes from five carbapenemase families. It also reports that cross-family combinations increased over time in the dataset.
health
A 12-patient preprint reports that duplex sequencing detected the aristolochic acid-associated SBS22a mutation signature in blood and urine from patients with signature-positive urothelial tumours. The findings are a proof of concept, not yet a validated population screening test.
science
A bioRxiv preprint reports that oversampling closely related prokaryotic strains makes genome collections less informative than their raw counts suggest. Applying the authors’ PhyloThin method to 402 species, the study estimates that the effective sample count is 41% below the actual count.
health
A bioRxiv preprint reports a ClinVar-derived AlphaGenome Variant Impact quantile cutoff of 0.9938 for prioritising single-nucleotide variants. Nearly half of the uncertain variants assessed exceeded that threshold, but the result is a prioritisation signal, not a clinical reclassification.
health
A bioRxiv preprint found that many capsule types in Pakistani carbapenem-resistant Klebsiella pneumoniae genomes have no phage described in the literature. It identifies the South Asian capsule type KL81 as a target for future phage-isolation work.
science
A genome-scale analysis combining bat DNA with fossil anatomy identifies Europe as the probable origin of bats, and therefore powered flight, in the late Palaeocene. The study also revises relationships among bat families and places laryngeal echolocation before the diversification of living bats.
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.
health
A medRxiv preprint introduces GenSep, a framework that estimates how distinct disease subtypes could be using genetic information and compares that benchmark with polygenic risk scores. Across 18 subtype pairs, the authors report that current scores captured a small share of the estimated genetic separation.
science
A bioRxiv preprint describes BEACON, a method that learns background count patterns to assign single cells to their samples in multiplexed sequencing. The authors report improved classification across human datasets and applications in cancer-cell experiments and protein–transcriptome profiling.
science
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.
science
Researchers report a single-nucleus atlas spanning 21 adult human tissues and four donors, combining gene-expression and chromatin-accessibility data. It maps candidate regulatory elements and gene links, and uses sequence-to-function models to predict effects of fine-mapped variants.
science
Anthropic says Claude agents identified a previously uncharacterised system in bacteriophages, built around a reverse transcriptase and an array of DNA repeats. Early lab experiments found that the array is expressed as distinct short RNAs; the system’s function is still under investigation.
health
A Nature Medicine correspondence argues that debate over polygenic scores in England’s NHS depends partly on what prevention is meant to achieve. The authors say risk thresholds, outcome measures and comparators shape how the evidence is judged.
health
A medRxiv preprint reports different somatic mutation patterns in blood and arterial samples from patients undergoing coronary bypass surgery. Only four identical variants were found in both tissues among 221 matched pairs.
science
Anthropic says Claude agents identified a previously uncharacterized enzyme system in bacteriophages, built around a known reverse transcriptase and an array of DNA repeats. Early laboratory experiments found that the array is expressed as distinct short RNAs, but the system’s function is still being investigated.
science
A bioRxiv preprint reports genome-pattern evidence for an ancient whole-genome duplication shared by bryozoans. Few duplicate genes remain, but retained copies are enriched for cilia-related genes.
health
Researchers from the UK Health Security Agency and the University of Oxford say genetic material acquired from other bacteria may have made the strain behind a deadly Kent MenB outbreak unusually effective at causing severe disease. The same changes may also help explain why the strain has not continued to spread widely.
health
A six-month pilot in 138 cognitively normal adults used family history, genetics and plasma pTau217 to identify people at higher Alzheimer’s risk. Participants who received personalised lifestyle coaching reported less worry, while cognitive scores and lifestyle-risk measures remained unchanged and pTau217 showed only a slower rise.
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.
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A bioRxiv preprint reports that DNA recovered from museum hair samples attributed to Thomas Jefferson supports his direct paternity of children descended from Sally Hemings. The study compares inherited DNA shared with known and putative descendants and remains a preprint.
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A bioRxiv preprint links a focal 2026 meningococcal outbreak in Kent, UK, to genetic changes that may have been acquired from carriage-associated Neisseria. The researchers propose that such highly invasive variants can emerge briefly and then disappear because they are poorly suited to sustained transmission.
science
A bioRxiv preprint reports a previously uncharacterised porcine adenovirus in a New Zealand high-health pig herd affected by neonatal deaths and reproductive problems. Genome sequencing placed the virus in the Mastadenovirus genus but on a distinct lineage from characterised porcine adenoviruses.
science
A bioRxiv preprint presents GAVURD, a trio whole-genome analysis system for finding potentially pathogenic variants outside protein-coding regions. In a proof-of-concept involving 10 unresolved rare-disease cases, it prioritised six potentially causal variants for further study.
science
A bioRxiv preprint reports that synthetic, taxonomically complex bacterial communities rapidly evolved after adapting to novel plant hosts. The changes improved colonisation fitness while preserving the stability of the root microbiota.
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A bioRxiv preprint presents Sma3s v3, a scalable workflow for assigning functions to proteins in proteomes, pangenomes and metagenomes. In tests on a Vibrio cholerae pangenome and a metagenomic catalogue, it reported higher annotation coverage than the cited comparator tools.
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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 bioRxiv preprint presents Rsearch, an R package that integrates VSEARCH with visualisation, parameter optimisation and conversion tools for metabarcoding analysis. In a mock-community comparison with DADA2, the two pipelines produced abundance profiles that closely matched the expected composition, with differences in OTU counts and computational performance.
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A bioRxiv preprint reports that incomplete reference profiles can leave bulk RNA deconvolution targets non-identifiable even when an algorithm returns precise estimates. The authors propose measuring coverage and false-certification risk, and estimate the measurement precision needed for a decisive result in peripheral blood mononuclear cells.
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A bioRxiv preprint using data from 1,494 donors finds that many single-cell gene-expression studies may lack sufficient statistical power to detect small effects. Cell counts, gene-expression levels and sequencing depth strongly influenced which findings were detected and reproduced.
health
A genome-wide association study involving more than one million people examined how genetic variation contributes to personality traits and may influence physical health, mental health and behaviour. The findings highlight genetic effects without separating them from the role of environment.
science
A bioRxiv preprint maps bacterial host factors involved in infection by single-stranded RNA and DNA bacteriophages. The study identifies conserved requirements for F-pilus-dependent infection and links an E. coli capsule architecture to selective phage access.
science
A bioRxiv preprint identifies the soil bacterium genus Trinickia as a candidate for supporting soybean drought resilience. Its abundance was strongly associated with greater root biomass during drought, while drought and rewetting produced different responses in the rhizosphere and bulk soil.
science
A University of Michigan team has introduced AmbientMapper, a computational method that estimates ambient chromatin contamination in combinatorial single-cell experiments. In a bioRxiv preprint, the authors report a 0.19% wrong-genome rate on a 26-genome reference panel and recovery of low-depth nuclei that standard pipelines discarded.
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A bioRxiv preprint identifies a previously undescribed association between the Saccharimonadia bacterium Candidatus Lutisaccharimonas and the phosphorus-accumulating Candidatus Phosphoribacter in wastewater treatment plants. The findings suggest that this microbial interaction could be relevant to biological phosphorus removal.
science
A chromosome-level reference genome and resequencing data from 80 Saimaa ringed seals show extremely limited Y-chromosomal diversity compared with other ringed seals. The bioRxiv preprint estimates that the population retains about 1% of the broader Y-chromosomal diversity and 5% of mitochondrial diversity.
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A bioRxiv preprint presents the first genome-wide maps of four major histone modifications in the reef-building coral Pocillopora damicornis. The maps associate distinct chromatin states with gene expression, receptor-related genes, developmental functions and transposable element-like regions.
science
Researchers mapped 4,321 microproteins in 608 post-mortem human brain samples, including dozens with altered expression in Alzheimer’s disease. The atlas expands the molecular inventory available for studying neurodegeneration, while the proteins’ biological roles still require experimental validation.
science
Researchers at Shandong University and BGI Research describe DiffGSP, a computational framework that models mRNA diffusion to reconstruct spatial gene-expression patterns. The work is a bioRxiv preprint evaluated across diverse spatial-transcriptomics datasets.
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A bioRxiv preprint finds that randomly dividing single-cell data can leak information between training and test sets when related cells share labels. The authors propose eakcheck, a tool that estimates this leakage before a predictive model is trained.
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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.
science
A bioRxiv preprint presents PHACTn, a training-free method that uses mammalian evolutionary history to infer how tolerable single-nucleotide variants may be across the human genome. The authors report strong performance on benchmark sets of non-coding variants using four interpretable parameters and no GPU.
health
A medRxiv preprint reports seven genomic risk loci associated with myalgic encephalomyelitis/chronic fatigue syndrome after analysis of UK Biobank and All of Us data. The findings provide leads for studying the condition’s biology, but the study is based on a preprint and no locus was significant across all three cohorts.
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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 reports using six-base sequencing to analyse DNA modifications in cell-free DNA released by neural cells into cerebrospinal fluid. The authors say the approach could support liquid-biopsy research into neurodegenerative disease.
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Google DeepMind says AlphaGenome Atlas pre-calculates predicted molecular effects for approximately 9 billion possible single-nucleotide changes, giving researchers a searchable tool for prioritising variants.
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Google DeepMind says AlphaGenome Atlas precomputes molecular-effect predictions for approximately 9 billion single-nucleotide variants and provides scores and interpretation tools for non-commercial academic research.