Sequencing & genome assembly
Next-generation sequencing for whole genomes, including chromosome-level assemblies — as built for the model plant Nicotiana benthamiana alongside its transcriptome, epigenome, microRNA and transposable-element datasets.
Technology
We combine high-throughput sequencing, mass spectrometry and computational genomics to study how genomes are encoded, regulated and expressed — often in non-model species that lack ready-made reference resources.
Next-generation sequencing for whole genomes, including chromosome-level assemblies — as built for the model plant Nicotiana benthamiana alongside its transcriptome, epigenome, microRNA and transposable-element datasets.
Whole-genome bisulfite sequencing and targeted mass spectrometry to quantify cytosine methylation — including the non-CG methylation distinguishing pupa and adult in Helicoverpa armigera — plus ChIP-seq for genome-wide histone modifications in non-model species.
Reference-free transcriptome assembly where no genome exists — assembling more than 600 million RNA-seq reads into a 333,000-transcript reference for the Norway lobster Nephrops norvegicus, validated by RT-PCR.
MS/MS-based proteomics integrated with genome data, including VPBrowse — a genome-based browser of the Bos taurus proteome that makes reliable protein libraries available for veterinary and non-laboratory species.
Whole-genome sequencing and targeted amplification of difficult templates — from enzyme discovery in a Great Artesian Basin Bacillus velezensis to rolling-circle amplification of circular polyomavirus genomes from low-load clinical samples.
De novo assembly, genome annotation and multi-omics integration — joined to interactive databases and web tools that turn raw data into reference resources the wider community can use.
Genome, epigenome, transcriptome and proteome rarely tell the whole story alone. Our work integrates these layers to connect DNA sequence and its chemical modifications to the genes, transcripts and proteins they ultimately produce.