Rayan Chikhi

This study identifies host factors and cellular contexts governing anellovirus persistence through genomic, transcriptomic, and functional analyses.

The paper introduces resources for large-scale metagenome comparison in the SRA, revealing trends in microbial discovery and improving assembly quality.

The paper identifies and characterizes defence hotspots in P2-like phages and P4-like satellites, revealing rapid modular evolution of antiviral systems through gene swapping and recombination.

The paper introduces kmcomp, a lossless compression method for k-mer matrices that enables fast random access, achieving significant storage savings with minimal query overhead.

The paper searches a petabase-scale dataset to discover new Papillomaviruses, identifying 383 novel types across 105 host species and highlighting biodiversity hotspots.

nanoMDBG improves metagenome assembly from ONT reads, producing more high-quality MAGs with less computational resources than existing assemblers.

The paper develops a taxonomy-free GWAS method using k-mers to analyze gut microbiome associations with host phenotypes, identifying significant links to seven traits in a cohort of healthy participants.

The paper introduces kloe, a compression method for k-mer multi-sets that enables targeted decompression of specific samples' k-mer content.

This study evaluates structural variant callers using long-read sequencing data, showing performance variation based on ground truth, reference genome, and genomic regions.

This paper introduces phylogenetic compression to efficiently search large microbial genome collections, achieving significant compression improvements and enabling fast BLAST-like searches on desktop computers.

This paper introduces an assembly-free method to augment pangenome graphs using long reads from new samples, without aligning to a reference or calling variants.

BFVD provides a large repository of predicted viral protein structures, enhancing annotation of bacteriophage proteins compared to sequence-based methods.

Assembling the Sequence Read Archive (27.3 million accessions) with over 100-fold compression enables minutes-scale k-mer search and mining of enzymes, plasmids, proteins and viral reactivation.

The paper introduces statistical methods to detect subtle behavioural changes in Drosophila larvae from large-scale behavioural assays.

This paper introduces rhea, a reference-free method for detecting structural variants in microbiomes using long-read coassembly graphs, showing improved performance over existing methods in simulated and real metagenomic data.

The paper introduces a k-mer-based method to quantify RNA sequences from large RNA-seq datasets, demonstrating its accuracy for variant RNA detection in cancer cell lines.

The paper introduces kmindex for fast indexing of complex genomic datasets and ORA for real-time querying of the Tara Oceans metagenomes.

decOM improves microbial source tracking in ancient oral metagenomes by using k-mer matrices, outperforming existing methods in accuracy.

The paper uses petabase-scale homology searches from SRA data to improve protein structure prediction accuracy using ColabFold, achieving better results than default methods.

The paper introduces a metagenomics assembler that improves efficiency and assembly quality for long reads, achieving faster performance and better recovery of MAGs and viral/plasmid sequences.

mapquik accelerates long-read mapping by using minimizer-space seeding and a pseudo-chaining algorithm, achieving high sensitivity and speed on human and maize genomes.

This work constructs the largest human pangenome graphs by integrating 52 haplotypes and two synthetic references, comparing five tools to evaluate their representation of genetic variation.

The paper develops ChoruMM, a multi-components mixed model for bacterial GWAS, showing that standard human genetics models are inadequate for highly structured bacterial genomes.

The paper presents a draft genome assembly of the lowland anoa and compares it to buffalo genomes, showing good completeness for downstream analyses.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

SVDSS improves structural variant discovery in hard-to-call regions using long-read sequencing by combining multiple methodologies, outperforming existing methods in repetitive genomic regions.

The paper develops a cloud computing infrastructure for petabase-scale sequence alignment, identifying over 105 novel RNA viruses and expanding known species by an order of magnitude.

kmtricks improves Bloom filter construction for large sequencing data by efficiently counting k-mers and preserving low-abundant ones, enhancing metagenomics analysis.

The paper studies the molecular evolution of a recently endogenized retrovirus in mule deer, showing increased diversity through horizontal acquisition and recombination.

Strainberry uses long-read data to separate microbial strains in low-complexity metagenomes, achieving high accuracy and additional genomic material in real datasets.