Targetid

20/05/2024

Our video on the EU funded project TargetMI which continues to add more valuable data to the work we set up in TargetID.

https://www.youtube.com/watch?v=sylkIynnv7M

See also our website:
https://www.um.edu.mt/projects/targetmi/

TargetMI is an EIC Pathfinder project at the forefront of research on Cardio genomics. In this project a high throughput multi-omic approach for the rapid di...

02/01/2023

The latest feature on TargetID in The Sunday Times of Malta

The extensive data obtained will be useful beyond the end of this project

23/12/2022

TargetID: Novel Drug Targets for Infectious Diseases is a University of Malta project funded through the COVID-19 R&D Fund 2020 jointly administered by the Malta Council for Science & Technology and Malta Enterprise.

TargetID: Novel Drug Targets for Infectious Diseases huwa proġett li qed isir minn l-Università ta’ Malta b’fondi nazzjonali mill-COVID-19 R&D Fund 2020 amministrati mill-Kunsill Malti għax-Xjenza u t-Teknoloġija u Malta Enterprise.

22/12/2022

Hemm hi!

Wara sentejn xogħol it-tim tal-proġett TargetID laħaq l-għan tiegħu. Żviluppajna strateġija bbażata fuq analisi tal-ġenom u l-prodott tiegħu, t-transcriptome, biex nagħrfu molekoli li għandhom il-potenzjal biex jiġu żvilluppati għal mediċini ġodda kontra l-Covid19. Issa ngħaddu l-bastun lil proġett ġdid BioGeMT: Bioinformatics for Genomics in Malta, b’fondi Ewropej mill-programm Horizon Europe fejn id-data, l-programmi u l-istrateġija ġdida li żviluppajna fil-proġett TargetID jistgħu jigu applikati biex ntejbu d-djanjosi u biex insibu mediċini ġodda għal ħafna aktar mard.

TargetID: Novel Drug Targets for Infectious Diseases huwa proġett li qed isir minn l-Università ta’ Malta b’fondi nazzjonali mill-COVID-19 R&D Fund 2020 amministrati mill-Kunsill Malti għax-Xjenza u t-Teknoloġija u Malta Enterprise.

And there it is!

Two years of work and the team has completed the project TargetID. We have developed a strategy that uses genomic and transcriptomic data to identify novel drug targets. The baton passes to our new project BioGeMT: Bioinformatics for Genomics in Malta funded through Horizon Europe where the data, the bioinformatic tools and the strategy we have developed in TargetID will be used to help improve diagnostics and find drug targets for many other diseases.

TargetID: Novel Drug Targets for Infectious Diseases is a University of Malta project funded through the COVID-19 R&D Fund 2020 jointly administered by the Malta Council for Science & Technology and Malta Enterprise.

17/12/2022

Ultimately we still rely heavily on thought processes to analyse genomic and transcriptomic data - not just for the development of a strategy and the bioinformatic pipelines but also to interpret the results. The bioinformatic pipelines we developed are giving us promising outputs - shortlists of genes from 86 families that we have analysed amongst which are some that could be involved in severe Covid19. We are currently reanalysing those lists, seeing what biological pathways the highlighted genes fit into, getting hints from literature to select those that are most promising as drug targets and drawing our final conclusions as the TargetID project draws to a close.

TargetID: Novel Drug Targets for Infectious Diseases is a University of Malta project funded through the COVID-19 R&D Fund 2020 jointly administered by the Malta Council for Science & Technology and Malta Enterprise.

14/12/2022

The successes of a team depend on many people who are not visible on the field. This is especially so for the project TargetID. We would like to thank all the people and University of Malta offices that have supported us throughout this project.

Project Support Office
Research Support Services Directorate
Legal Office
Knowledge Transfer Office
Office for Human Resources, Management and Development
Procurement Office
Finance Office
Marketing, Communications and Alumni Office
IT Services
Laboratory support staff at the Department of Applied Biomedical Science, the Faculty of Health Sciences and at the Centre for Molecular Medicine and Biobanking
the Faculty of Health Sciences Research Ethics Committee and the University Research Ethics Committee
the Director for the Centre for Molecular Medicine and Biobanking
the past and present Dean of the Faculty for Health Sciences
past and present Prorector for Research
the rectorate and Rector Prof Alfred Vella
and of course the funding agencies Malta Council for Science and Technology and Malta Enterprise

A huge thank you to you all!

TargetID: Novel Drug Targets for Infectious Diseases is a University of Malta project funded through the COVID-19 R&D Fund 2020 jointly administered by the Malta Council for Science & Technology and Malta Enterprise.

10/12/2022

The analysis of millions of genetic variants in over 1000 individuals from a Mediterranean population is revealing known pathogenic genetic variants which will facilitate genetic diagnostics in the region. Whereas previously we had to test every candidate genetic variant in a few hundred samples we can now rapidly determine the frequency of any variant in the Maltese using the TargetID genomic data. Together with the medical and family history, and extensive laboratory and physical measurements, as well as ten-year follow up data on all the participants from the Maltese Acute Myocardial Infarction (MAMI) Study makes it simpler and faster to determine if a gene is disease-causing. This helps us reach our overall goal to give tools to clinicians and researchers to improve healthcare.

TargetID: Novel Drug Targets for Infectious Diseases is a University of Malta project funded through the COVID-19 R&D Fund 2020 jointly administered by the Malta Council for Science & Technology and Malta Enterprise.

The MAMI Study was conducted as a collaboration between the University of Malta and the Malta Department of Health. The sample and data collection was funded through the MCST R&I 2008 programme and a number of Malta Government Scholarship Scheme (MGSS) grants.

08/12/2022

Measure a hundred times and cut once

A Maltese proverb teaches us to plan well and consider all aspects before starting a project. The most crucial step in planning a multi-omic study is deciding how to collect and process the biological samples. TargetID uses samples from the Maltese Acute Myocardial Infarction Study funded through the MCST R&I 2008 Programme. These samples were collected with meticulous attention to details. Participants were fasted and asked not to smoke for a number of hours before blood sampling, postponing collection if they had recent infection, vaccination or surgery, collecting samples within a specified timeframe at the same time of day, collecting blood with the participant in the same position, rapid processing of sample. These are just some of the precautions taken to have data that is comparable between one sample and another. This is particularly important for transcriptomic, metabolomic and proteomic work. The plan for the ethics framework of a project is also crucial. Once taken, these decisions determine the suitability of a sample collection for specific applications. It pays to plan well!

07/12/2022

Bioinformatics helps us put the pieces of the puzzle together. There are around 4-5 million variants in one single genome but only a few cause serious effects resulting in disease. Identifying and recognising which are truly disease-causing is a difficult task. Luckily we have more tools available to analyse the increasing volumes of genetic data including combining information from the genome to other layers of data - such as the transcriptome, metabolome and proteome. In TargetID we are analysing the genome of 1000 individuals together with the gene expression (or productivity) from the transcriptome.

TargetID: Novel Drug Targets for Infectious Diseases is a University of Malta project funded through the COVID-19 R&D Fund 2020 jointly administered by the Malta Council for Science & Technology and Malta Enterprise.

06/12/2022

TargetID may be a springboard, but it also builds on the successes of several past University of Malta projects including:

- European Regional Development Funds (ERDF) 081: Enhancing Health Biotechnology Facilities at the University (https://investinginyourfuture.gov.mt/project/research-science-and-technology/enhancing-health-biotechnology-facilities-at-the-university-33947675) which involved multiple departments at the University fo Malta (UM) and helped equip our labs;

- the Maltese Acute Myocardial Infarction (MAMI) Study in which we collected data and samples from around 1000 research subjects (National R&I Programme 2008 organised by the Malta Council for Science and Technology ),

- The Malta Next Generation Sequencing (NGS) Project where we started work on high throughput sequencing ( National R&I Programme 2012),

- the EU Twinning project TrainMALTA led by Dr Rosienne Farrugia where students and staff at the University of Malta received training in Bioinformatics and functional work from researchers at the University of Cambridge (UCAM) and the Katholieke Universiteit Leuven (KU Leuven) (https://www.um.edu.mt/r/projects/trainmalta).

Like a stepping stone each of these helped us move forward. It is amazing to see the years of work and preparation by so many people that leads us to today where we are developing and using bioinformatic tools to analyse 1000 whole genomes and transcriptomes to understand diseases better and find new drugs to treat them.

04/12/2022

TargetID has been an important springboard towards obtaining 2.5 million Euros in EU funds through Horizon Europe. The data, tools and skills acquired through this project have helped us secure an ERA Chair grant, BioGeMT: Bioinformatics for Genomics in Malta, which will allow UM to have an expert and team in bioinformatics for 5 years. This in turn guarantees that the whole genome sequencing and transcriptomic data on 1000 samples acquired through TargetID will continue to deliver results that will be useful to science and society.

TargetID: Novel Drug Targets for Infectious Diseases is a University of Malta project funded through the COVID-19 R&D Fund 2020 jointly administered by the Malta Council for Science & Technology and Malta Enterprise.

02/12/2022

The cogwheels are coming together and the engine has been set in motion.

Millions of variants from one thousand whole genomes are being analysed together with RNA expression levels from transcriptomes in innovative ways on our processing server to give us lists of candidate drug targets that may serve to eventually prevent severe COVID19. We have analysed 86 families over a weekend using our variant prioritisation tool. The output of that has fed into another tool last Monday, and that output is feeding into yet another tool, which feeds into another one....... all of them designed specifically by our multidisciplinary team at for the project TargetID. It's all coming together and the engine has been set in motion! A very exciting time as we start to see the final outputs of all this hard work!

TargetID: Novel Drug Targets for Infectious Diseases is funded through the COVID-19 R&D Fund 2020 jointly administered by the Malta Council for Science & Technology and Malta Enterprise.

01/12/2022

Looking for a needle in a haystack!

It takes on a new meaning as we sift through millions of genetic variants in the 1000 whole genome sequences looking for those that alter genes that go out of control during COVID19 resulting in severe COVID19.

We have developed a novel strategy and various bioinformatics tools to search for and hone in on these genetic variants using a combination of approaches. We then gather more evidence from our MAMI Study and COVID19 data.

This is an important step towards finding new drug targets - identifying genes that regulate the factors that go wrong in severe COVID19.

Fingers crossed!

25/11/2022

Bioinformatics Job Opportunities at the University of Malta:

Applications are now open for the posts of Research Support Officers (RSO) I (Graduate level), II (Masters level/PhD students), III (With PhD) and IV (with PhD and postdoc experience) to join the BioGeMT Horizon Europe ERA Chair team.

The overall objective of BioGeMT:Bioinformatics for Genomics in Malta is to merge the strengths of the University of Malta in Information and Communications Technology, Statistics, and Molecular Genetics and Genomics by setting up a bioinformatics team which will focus primarily on the development and application of methods (including machine learning) for interpreting combined genomic, transcriptomic, metabolomic and phenotypic data.

For complete details on the positions and how to apply please see:

https://www.um.edu.mt/hrmd/recruitment/projects

Further information may be obtained by contacting Dr Jean Paul Ebejer at jean.p.ebejer@um.edu.mt .

Please note that there are different deadlines for the calls. The deadline for the RSOI, RSOII and RSOIII positions are 4th December 2022, for the RSOIV the deadline is 31st January 2023.

18/10/2022

TargetID: Novel Drug Targets for Infectious Diseases Covid-19 R&D Fund 2000

The interesting work starts now! Using bioinformatic tools we have developed, we can now rapidly assess the effects of millions of genetic variants on the entire transcriptome, on levels of over 130 haematological, coagulation, biochemical and other variables we have measured, and on disease, using all the clinical data and 10 year follow up study data we have on the 1000 individuals from the Maltese Acute Myocardial Infarction (MAMI) Study, a collaboration between the University of Malta and the Malta Department of Health, funded through Maltese national research funds (MCST R&I 2008). What used to take us years and decades to assess now takes us minutes. The insight one gets through harnessing all this data together is amazing.

18/10/2022

We have successfully completed all the initial processing and quality control of the 1000 whole genome sequences and transcriptomes we obtained through the MCST COVID-19 R&D Fund 2020 TargetID. We have developed a number of tools to help us analyse this wealth of data and we are now acquiring new knowledge that will be relevant to COVID19 and to other diseases. Exciting times!

19/10/2021