麻豆传媒AV

We develop and maintain several software tools and data analysis solutions for plant science, infectious disease, food and plant science, as well as biomedical research, especially when genomic and genetic data is involved.

Learn more about our software and tools below.

• : a standalone software for visualising and interacting with optical mapping data and can be used for in-depth exploration of hybrid scaffolding alignments.

Above: Figure 1 - for visualising and processing optical mapping and sequencing data.

• : a command-line tool for super-fast querying of a large number of variant calling files.
• : an R package for disease-associated variant discovery and annotation.
• : a highly customizable genome browser supporting multiple visualization instances.

Above: Figure 2 -

Together with our colleagues in the Environment and Agrifood Theme, we are applying our expertise in bioinformatics to help solve a range of biological challenges funded by UKRI, EU and through direct industry funding. The group is leading all sequencing informatics at 麻豆传媒AV and has been involved in a number of Research Council and commercially-funded projects in this research area.

Learn more about our recent work below.

Chilbix

As part of this BBSRC-funded project, we developed a high-quality reference genome for two highly heterozygous, drought and salinity tolerant tomato species, Solanum chilense and Solanum sitiens.

Research team:
Andrew Thompson
Fady Mohareb
Tomasz Kurowski
Corentin Molitor

Adroots

We aim to understand the genetic control of adventitious rooting (AR) and to identify molecular markers and beneficial alleles that will allow AR to be controlled to the benefit of breeding in horticultural crops. AR formation from the hypocotyl is important for rootstock vigour in grafted annual crops like tomato, and AR formation is essential for propagation in all perennial crops.

Research team:
Andrew Thompson
Fady Mohareb
Zoltan Kevei
Tomasz Kurowski

Controlling dormancy and sprouting in potato and onion

We aim to provide a molecular understanding for the process of dormancy break in potato, through the identification of key genes and transcription factors responsible for the process of dormancy break. As part of this project, we developed a high-quality transcriptome assembly for onion and potato tubers during the process of dormancy break and early sprouting.

Read more about our potato transcriptome

Tea transcriptome - industrial partner: Unilever (Colworth)

Tea is one of the most popular beverages in the world. Together with Unilever and the Postharvest Group at Cranfield, we developed the most comprehensive tea transcriptome assembly using a commercial tea variety, as well as performing a global transcriptome profiling on plants treated under different withering processes to provide a differentially expressed gene analysis about the compounds related to tea flavour and aroma, such as flavonoids and caffeine.

Research team:
Professor Leon Terry
Dr Fady Mohareb
Dr M. Carmen Alamar
Dr Emma Collings

Minimally invasive biomarkers for a personalised treatment of neonatal hypoxic-ischemic encephalopathy (in collaboration with La Fe Hospital, Valencia, Spain)

The main objective of this work is to establish whether there is a correlation between metabolic biomarkers of neuronal damage and microRNAs (miRNAs), and the neurodevelopmental outcome of newborns with hypoxic-ischemic encephalopathy (HIE) at 24 months of age, determined by means of standardised scales. This is a clinical, observational study involving samples collected and stored at the Neonatal Research Unit (Health Research Institute, La Fe) in the frame of a multicentric, randomised, blinded placebo-control clinical trial with competitive funding (HYPOTOP study). This study proposes the dynamic monitoring of the effect moderate, whole body hypothermia treatment and the administration of topiramate versus placebo in newborns with HIE.

Research team:
Corentin Molitor
Fady Mohareb