Luke J. Tallon

The paper presents a haplotype-phased, chromosome-level genome assembly of the soybean rust pathogen Phakopsora pachyrhizi, improving upon previous fragmented assemblies.

The paper presents a chromosome-level genome assembly of Thecaphora frezzii, the largest genome among true smut fungi, and compares it with 49 other smut fungi genomes to explore genomic traits and evolutionary adaptations.

This study shows that restoring STAG2 in STAG2-mutant cancer cells rapidly reduces global chromatin loop size, with limited transcriptional changes, including induction of EFEMP1.

This study identifies GSTT1HighCD133High cells as a stem-like subpopulation in pancreatic cancer that is sensitive to FGFR inhibitors, highlighting a therapeutic target.

The paper tests the PacBio Revio sequencer by generating high-coverage long-read sequencing data for a mouse neuronal cell line and evaluates its performance in variant detection and genome assembly.

The paper develops a repeat-pangenome graph to analyze VNTR variation across populations and identifies population-specific VNTRs and expression quantitative trait loci.

This study compares PacBio and Oxford Nanopore long-read sequencing technologies for bacterial and fly genome assembly and methylation detection, finding no single technology outperforms others across all metrics.

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

The paper develops a capture-based DNA enrichment method to assemble the first buffalo-derived T. parva genome, revealing high genetic diversity between cattle- and buffalo-associated strains.

The paper analyzes mtDNA from individuals with biparental transmission and finds no evidence of intermolecular recombination, supporting strict maternal inheritance.

The paper compares genome structure, sequence, and immunogenic potential of Plasmodium falciparum strains used in vaccine trials and finds significant differences affecting vaccine efficacy.

This study compares enrichment techniques for multi-species RNA-Seq, finding that targeted enrichment with Agilent SureSelect improves read mapping to target organisms.

FADU improves RNA-Seq quantification for prokaryotes by better detecting genes missed by HTSeq and featurecounts, especially in organisms with overlapping transcriptional units and polycistronic transcripts.