About
I am a PhD student in Systems Biology Ireland as part of the Centre for Research Training (CRT) Genomics Data Science programme, co-funded by the European Commission’s Marie Sklodowska Curie Actions (MSCA) COFUND programme. My work involves finding molecular vulnerabilities in high-risk pediatric leukemia through biological network analysis. I am interested in exploiting omics data to better understand childhood leukemia to aid in the development of better treatments. I am currently part of the Bond and Ryan groups in SBI, UCD.
Interests
Cancer biology | Childhood leukaemia | Epigenomics | Data viz | NGS |
Data science | Bioinformatics | Chromatin architecture |
Background
PhD student, Systems Biology Ireland, UCD 2020 - present Identifying molecular vulenarabilities in childhood leukaemia through biological network analysis. | |
MSci Hons Genetics 2016 - 2020 Awarded a first class MSci Hons degree in Genetics. |
Projects
PhD 2020 - present Supervisors: Prof Jonathan Bond and Dr Colm Ryan Currently working on using biological networks to uncover vulnerabilities in childhood leukaemia. I am using large datasets from patients and cell-line models such as WGS, RNA-Seq, proteomics, CRISPR screens to compare leukaemia subtypes. | |
Masters project Sep 2019 - May 2020 Supervisor: Prof John Armour Studied copy-number variations in the human genome using Nanopore reads. Developed a pipeline that can identify copy-number variants and separate the two haplotypes based on read depth and read length. | |
Summer internship Jun 2019 - Aug 2019 Supervisor: Dr Martin Gering Worked on zebrafish mutant embryos to investigate how the expression of macrophage marker genes changes over different time-points post fertilisation. Learnt about developmental biology and gene regulation. Methods used: embryo handling, RNA in-situ hybridization, PCR and light microscopy. |
Publications
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Cosmin Tudose, Jonathan Bond, Colm J Ryan - Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity. NAR Cancer, Volume 5, Issue 4, December 2023
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Thomas Lefeivre, Cosmin Tudose, Theodora-Ioana Grosu, Luke Jones, Theresa E. León, Kieran Wynne, Giorgio Oliviero, Owen P. Smith, Amélie Trinquand, Marc R. Mansour, Colm J. Ryan, Jonathan Bond - Loss of Polycomb Repressive Complex 2 function causes asparaginase resistance in T-acute lymphoblastic leukemia through decreased WNT pathway activity - bioRxiv
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Emma Grady, Sharmila Biswas, Tânia Dias, Peter McCarthy, Cosmin Tudose, David Betts, Andrea Malone, Jonathan Bond - A novel TCF3::PIK3R1 fusion linked to decreased PI3K‐AKT signalling activity in paediatric B‐acute lymphoblastic leukaemia. British Journal of Haematology, June 2024
Presentations
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June 2024 - European Hematology Association Congress - Madrid, Spain
Poster: The role of PRC2 in gene regulation and 3D chromatin architecture in acute myeloid leukaemia -
May 2024 - EMBO Intercepting Childhood Blood Cancer: From Single Cells To Malignant Clones - Düsseldorf, Germany
Flash Talk: The role of PRC2 in gene regulation and 3D chromatin architecture in acute myeloid leukaemia -
April 2024 - EACR Cancer Genomics, Multiomics and Computational Biology - Bergamo, Italy
Poster: The role of PRC2 in gene regulation and 3D chromatin architecture in acute myeloid leukaemia -
February 2024 - EACR-AACR-IACR 2024 - Dublin, Ireland
Poster: The role of PRC2 in gene regulation and 3D chromatin architecture in acute myeloid leukaemia -
December 2023 - Irish Computational Biology and Genomics Symposium - University of Galway, Ireland
Poster: The role of PRC2 in gene regulation and 3D chromatin architecture in acute myeloid leukaemia -
October 2023 - IUBMB Focused Meeting on Integrative Omics of Nuclear Functions - Avra Imperial Hotel, Kolymvari, Greece
Talk: The role of PRC2 in gene regulation and 3D chromatin architecture in acute myeloid leukaemia -
September 2023 - 20th Anniversary of Childhood Leukaemia Research UK - University of Strathclyde, Glasgow, UK
Talk: The role of PRC2 in gene regulation and 3D chromatin architecture in acute myeloid leukaemia -
September 2023 - BCNI Blood Cancer Symposium - Hilton Kilmainham, Dublin, Ireland
Poster: The role of PRC2 in gene regulation in acute myeloid leukaemia -
July 2023 - All-Ireland Haematology Forum - Queen’s University Belfast, UK
Poster: The role of PRC2 in gene regulation in acute myeloid leukaemia -
May 2023 - All-Ireland Chromatin Consortium - University College Dublin, Ireland
Poster: The role of PRC2 in gene regulation in acute myeloid leukaemia -
May 2023 - VIBE Conference - Queen’s University Belfast, UK
Poster: The role of PRC2 in gene regulation in acute myeloid leukaemia -
December 2022 - Irish Computational Biology and Genomics Symposium - University of Galway, Ireland
Talk: The dual role of PRC2 in gene regulation in acute myeloid leukaemia -
September 2022 - CRISPR and Beyond: Perturbations at Scale to Understand Genomes - Wellcome Genome Campus, UK
Talk: Sensitivity to gene inhibition in cancer cells is better predicted by mRNA abundance than by gene regulatory network-inferred activity -
June 2022 - VIBE Conference - Limerick, Ireland
Talk: Sensitivity to gene inhibition in cancer cells is better predicted by mRNA abundance than by gene regulatory network-inferred activity -
February 2022 - Systems Genomics Summit - Virtual
Poster: Gene regulatory network-inferred driver activity as a predictor of cancer cells sensitivity to gene inhibition -
October 2021 - Conway Festival - Virtual
Poster: Gene regulatory network-inferred driver activity as a predictor of cancer cells sensitivity to gene inhibition