Chenxi Zhou

The paper presents nine T2T genomes of Lake Malawi cichlids, revealing a novel centromeric satellite structure with inverted elements and potential implications for speciation.

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

This study shows hybridisation enables Amazonian trees to rapidly evolve chemical defences against herbivores, driving diversification in response to shifting herbivore communities.

LRGE estimates genome size from long read overlaps, outperforming k-mer-based methods and being more efficient than assembly-based approaches.

The paper presents 40 new microsporidian genomes, revealing evidence of sexual reproduction and autopolyploidy, with tetraploid genomes organized into diploid compartments.

Oatk combines a sparse syncmer assembler, profile HMM gene databases and graph path search to assemble plastomes and mitogenomes from HiFi reads for 195 plant species.

This paper introduces a pangenome-guided sequence assembly framework that reduces contigs in complex regions using graph traversal optimisation, with potential for quantum computing implementation.

Hi-reComb estimates recombination maps from bulk gamete Hi-C data, showing accurate results in fish sperm and enabling structural variant analysis.

The paper analyzes 1,375 Malawi cichlid genomes to show that sex-linked chromosomal inversions drive adaptive speciation through introgression and selection on neuro-sensory, physiological, and reproductive genes.

This paper introduces FS-PLS, a feature selection method that generates minimal disease signatures from omics data without requiring library size normalization, achieving smaller and comparable performance to existing methods.

FastGA aligns genomes significantly faster than existing methods while maintaining sensitivity and efficiently storing alignments.

The paper uses long-read sperm sequencing to analyze non-crossover recombination events, finding variation in recombination rates and distinct mechanisms for non-crossover gene conversions.

YaHS, a C command-line Hi-C scaffolder, normalises inter-contig contacts by intra-contig medians, yielding more contiguous, accurate chromosome-scale scaffolds than SALSA2 and pin_hic.

The paper identifies reduced host transcriptomic signatures for tuberculosis using microarray data and validates them with digital PCR, showing high accuracy in distinguishing TB from other conditions and latent TB.

This paper develops a method to assemble whole-chromosome pseudomolecules for polyploid plant genomes using genotyping-by-sequencing and reference genome data, showing improved accuracy over existing tools.

This paper develops a targeted long-read sequencing method for high-throughput tandem repeat genotyping, achieving high accuracy and scalability.

The paper uses BioNano and nanopore data to analyze human chromosome ends, revealing heritable extensions and sequence duplications across primate lineages.

CapSim simulates targeted sequencing dynamics to evaluate probe design efficiency and sequencing pipeline performance.