Luke J. Tallon

Haplotype-phased, chromosome-level, annotated genome assembly of the soybean rust pathogen Phakopsora pachyrhizi

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

A chromosome-level genome assembly of Thecaphora frezzii, cause of peanut smut, reveals the largest genome among the true smut fungi

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.

Rapid reduction in global chromatin loop size after acute STAG2 reconstitution in human cancer cells

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.

GSTT1 mediates stemness and FGFR inhibitor sensitivity in pancreatic cancer through regulation of CD133 (PROM1)

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

High Coverage Highly Accurate Long-Read Sequencing of a Mouse Neuronal Cell Line Using the PacBio Revio Sequencer

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.

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

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

Comparison of long read sequencing technologies in resolving bacteria and fly genomes

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.

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

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

Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo- derived strain and reveals exceptional intra-specific genetic diversity

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.

No evidence for intermolecular recombination in human fibroblast and blood mtDNA from individuals with biparental mtDNA transmission

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

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

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

Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses

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

FADU: A Feature Counting Tool for Prokaryotic RNA-Seq Analysis

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.