Doctorate School in Integrated Genomics Research

Informations projet

INTEGRATE

N° de convention de subvention: 945385

DOI

10.3030/945385

Projet clôturé

Date de signature de la CE 10 Avril 2020

Date de début 1 Septembre 2020

Date de fin 31 Août 2026

Financé au titre de

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Coût total

€ 4 339 200,00

Contribution de l’UE

€ 2 169 600,00

Coordonné par

UNIVERSITY OF GALWAY
Ireland

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Documents, reports (2)

Link to Euraxess website for the first call for proposals

Project Officer informed on publishing each call for proposals, by sending the link to the Euraxess website and a screen shot of the related call announcement.

Link to Euraxess website for the second call for proposals

Project Officer informed on publishing each call for proposals by sending the link to the Euraxess website and a screen shot of the related call announcement

Publications

Peer reviewed articles (35)

Small Extracellular Vesicles Secreted by Cisplatin-Resistant Neuroblastoma Cells Increase Lactate Secretion and Alter Metabolic Pathways in Primary Human Umbilical Vein Endothelial Cells (HUVECs)

Auteurs: Thomas Frawley, Lin Ma, Muhammad Zainul Arifin, Dan Wu, Alysia Scott, Brenton Cavanagh, Donal F. O’Shea, Vadim Zhernovkov, Mi Liu, Marco P. Monopoli, Olga Piskareva
Publié dans: Journal of Personalized Medicine, Numéro 15, 2025, Page(s) 584, ISSN 2075-4426
Éditeur: MDPI AG
DOI: 10.3390/jpm15120584

Multiomic Sequencing Reveals Distinctive Gene Expression and Epigenetic Alterations Associated With Primary Sclerosing Cholangitis Development in Treatment-Naïve Pediatric Ulcerative Colitis

Auteurs: Alejandra Rodriguez-Sosa, Ololade Lawal, Ciaran McDonnell, Luke Grant, John O’Brien, Muhammad Ali, Ian Stephens, Grainne Kirwan, Flavia Genua, Alexander Kel, Anna Dominik, Roisin Stack, Gregory Yochum, Michael McDermot, Glen Doherty, Seamus Hussey, Sudipto Das
Publié dans: Gastro Hep Advances, 2025, ISSN 2772-5723
Éditeur: Elsevier Inc.
DOI: 10.1016/j.gastha.2024.11.002

Identification of unique rectal cancer-specific subtypes

Auteurs: Batuhan Kisakol, Anna Matveeva, Manuela Salvucci, Alexander Kel, Elizabeth McDonough, Fiona Ginty, Daniel B. Longley, Jochen H. M. Prehn
Publié dans: British Journal of Cancer, Numéro 130, 2024, Page(s) 1809-1818, ISSN 0007-0920
Éditeur: Nature Publishing Group
DOI: 10.1038/s41416-024-02656-0

Comprehensive Analysis of Seasonal and Geographical Variation in UVB Radiation Relevant for Vitamin D Production in Europe

Auteurs: Tarinee Khanna, Rasha Shraim, Masa Zarkovic, Michiel van Weele, Jos van Geffen, and Lina Zgaga
Publié dans: Nutrients, Numéro Vol. 14, No. 23, 2022, Page(s) 5189, ISSN 2072-6643
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14235189

Ancient genomes reveal demographic trajectories during the Classic Maya period

Auteurs: Madeleine Murray, Seiichi Nakamura, Melvin Fuentes, Rolando Canizales, Omar Talavera, Salvador Varela, Zoila Madrid, Carlos Carbajal, Masahiro Ogawa, Minoru Yoneda, Lara M. Cassidy, Takashi Gakuhari, Shigeki Nakagome
Publié dans: Current Biology, Numéro 35, 2025, Page(s) 2709-2719.e5, ISSN 0960-9822
Éditeur: Cell Press
DOI: 10.1016/j.cub.2025.05.002

Spatial transcriptomic analysis reveals local effects of intratumoral fusobacterial infection on DNA damage and immune signaling in rectal cancer

Auteurs: William P. Duggan, Batuhan Kisakol, Ina Woods, Mohammedreza Azimi, Heiko Dussmann, Joanna Fay, Tony O’Grady, Barry Maguire, Ian S. Reynolds, Manuela Salvucci, Daniel J. Slade, Deborah A. McNamara, John P. Burke, Jochen H.M. Prehn
Publié dans: Gut Microbes, Numéro 16, 2024, ISSN 1949-0984
Éditeur: Taylor & Francis
DOI: 10.1080/19490976.2024.2350149

Increased Fusobacterium tumoural abundance affects immunogenicity in mucinous colorectal cancer and may be associated with improved clinical outcome

Auteurs: William P. Duggan, Manuela Salvucci, Batuhan Kisakol, Andreas U. Lindner, Ian S. Reynolds, Heiko Dussmann, Joanna Fay, Tony O’Grady, Daniel B. Longley, Fiona Ginty, Elizabeth Mc Donough, Daniel J. Slade, John P. Burke, Jochen H. M. Prehn
Publié dans: Journal of Molecular Medicine, Numéro 101, 2023, Page(s) 829-841, ISSN 0946-2716
Éditeur: Springer Verlag
DOI: 10.1007/s00109-023-02324-5

Direct cell interactions potentially regulate transcriptional programmes that control the responses of high grade serous ovarian cancer patients to therapy

Auteurs: Sodiq A. Hameed, Walter Kolch, Donal J. Brennan, Vadim Zhernovkov
Publié dans: Scientific Reports, Numéro 15, 2025, Page(s) 14484, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-025-98463-5

Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics

Auteurs: Sai Ravi Chandra Nori, Calum J. Walsh, Fionnuala M. McAuliffe, Rebecca L. Moore, Douwe Van Sinderen, Conor Feehily, Paul D. Cotter
Publié dans: npj Biofilms and Microbiomes, Numéro 11, 2025, ISSN 2055-5008
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/s41522-025-00682-1

Overview of Molecular Diagnostics in Irish Clinical Oncology

Auteurs: Tyler Medina, Seán O. Hynes, Maeve Lowery, Patrick Gillespie, Walter Kolch, Cathal Seoighe
Publié dans: HRB Open Research, Numéro 7, 2025, Page(s) 16, ISSN 2515-4826
Éditeur: F1000 Research Ltd
DOI: 10.12688/hrbopenres.13822.1

Non-Negative matrix factorization combined with kernel regression for the prediction of adverse drug reaction profiles

Auteurs: Yezhao Zhong, Cathal Seoighe, Haixuan Yang
Publié dans: Bioinformatics Advances, Numéro 4, 2024, Page(s) vbae009, ISSN 2635-0041
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbae009

Integrated multiplex analysis of cell death regulators in stage II colorectal cancer suggests patients with ‘persister’ cell profiles fail to benefit from adjuvant chemotherapy

Auteurs: Sanghee Cho, Elizabeth McDonough, John Graf, Jinru Shia, Canan Firat, Nil Urganci, Christine Surrette, Andreas Lindner, Manuela Salvucci, Anna Matveeva, Batuhan Kisakol, Anthony O’Grady, Mohammadreza Azimi, John P Burke, Deborah A McNamara, Simon McDade, Daniel B Longley, Jochen HM Prehn, Fiona Ginty
Publié dans: BMJ Oncology, Numéro 3, 2024, Page(s) e000362, ISSN 2752-7948
Éditeur: BMJ
DOI: 10.1136/bmjonc-2024-000362

Prevalence and determinants of profound vitamin D deficiency (25-hydroxyvitamin D <10 nmol/L) in the UK Biobank and potential implications for disease association studies

Auteurs: Rasha Shraim, Margaret M. Brennan, Jos van Geffen, Lina Zgaga
Publié dans: The Journal of Steroid Biochemistry and Molecular Biology, 2025, ISSN 1879-1220
Éditeur: Elsevier Ltd.
DOI: 10.1016/j.jsbmb.2025.106737

Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity

Auteurs: Cosmin Tudose, Jonathan Bond, Colm J Ryan
Publié dans: NAR Cancer, Numéro 5, 2023, ISSN 2632-8674
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/narcan/zcad056

SATB2 Expression Affects Chemotherapy Metabolism and Immune Checkpoint Gene Expression in Colorectal Cancer

Auteurs: Barry Maguire, Batuhan Kisakol, Jochen H.M. Prehn, John P. Burke
Publié dans: Clinical Colorectal Cancer, Numéro 24, 2026, Page(s) 129-134.e7, ISSN 1533-0028
Éditeur: Cancer Information Group
DOI: 10.1016/j.clcc.2024.12.004

Multiplexed Immunofluorescence Imaging Reveals an Immune-Rich Tumor Microenvironment in Mucinous Rectal Cancer Characterized by Increased Lymphocyte Infiltration and Enhanced Programmed Cell Death Protein 1 Expression

Auteurs: William P. Duggan, Batuhan Kisakol, Emer O’Connell, Anna Matveeva, Tony O’Grady, Elizabeth McDonough, Andreas U. Lindner, Deborah McNamara, Daniel Longley, Fiona Ginty, John P. Burke, Jochen H.M. Prehn
Publié dans: Diseases of the Colon &amp; Rectum, Numéro 66, 2025, Page(s) 914-922, ISSN 0012-3706
Éditeur: Springer Verlag
DOI: 10.1097/dcr.0000000000002624

Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia

Auteurs: Sarah Ennis, Alessandra Conforte, Eimear O’Reilly, Javid Sabour Takanlu, Tatiana Cichocka, Sukhraj Pal Dhami, Pamela Nicholson, Philippe Krebs, Pilib Ó Broin, Eva Szegezdi
Publié dans: iScience, Numéro 26, 2026, Page(s) 106943, ISSN 2589-0042
Éditeur: Elsevier BV
DOI: 10.1016/j.isci.2023.106943

Targeting synthetic lethal paralogs in cancer

Auteurs: Colm J. Ryan, Ishan Mehta, Narod Kebabci, David J. Adams
Publié dans: Trends in Cancer, Numéro 9, 2023, Page(s) 397-409, ISSN 2405-8033
Éditeur: Elsevier Inc.
DOI: 10.1016/j.trecan.2023.02.002

CCPlotR: an R package for the visualization of cell–cell interactions

Auteurs: Sarah Ennis, Pilib Ó Broin, Eva Szegezdi
Publié dans: Bioinformatics Advances, Numéro 3, 2023, Page(s) vbad130, ISSN 2635-0041
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbad130

Genome-wide gene-environment interaction study uncovers 162 vitamin D status variants using a precise ambient UVB measure

Auteurs: Rasha Shraim, Maria Timofeeva, Cathy Wyse, Jos van Geffen, Michiel van Weele, Roman Romero-Ortuno, Lorna M. Lopez, Marcus E. Kleber, Stefan Pilz, Winfried März, Benjamin S. Fletcher, James F. Wilson, Evropi Theodoratou, Malcolm G. Dunlop, Ross McManus, Lina Zgaga
Publié dans: Nature Communications, Numéro 16, 2025, Page(s) 10774, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-025-65820-x

Effect of Immunosuppression on the Immune Response to SARS-CoV-2 Infection and Vaccination

Auteurs: Emma J. Leacy, Jia Wei Teh, Aoife M. O’Rourke, Gareth Brady, Siobhan Gargan, Niall Conlon, Jennifer Scott, Jean Dunne, Thomas Phelan, Matthew D. Griffin, Julie Power, Aoife Mooney, Aifric Naughton, Rachel Kiersey, Mary Gardiner, Caroline O’Brien, Ronan Mullan, Rachael Flood, Michael Clarkson, Liam Townsend, Michelle O’Shaughnessy, Adam H. Dyer, Barry Moran, Jean M. Fletcher, Lina Zgaga, Mark
Publié dans: International Journal of Molecular Sciences, Numéro 25, 2025, Page(s) 5239, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms25105239

A compendium of synthetic lethal gene pairs defined by extensive combinatorial pan-cancer CRISPR screening

Auteurs: Victoria Harle, Victoria Offord, Birkan Gökbağ, Lazaros Fotopoulos, Thomas Williams, Diana Alexander, Ishan Mehta, Nicola A. Thompson, Rebeca Olvera-León, Stefan Peidli, Vivek Iyer, Emanuel Gonçalves, Narod Kebabci, Barbara De Kegel, Joris van de Haar, Lang Li, Colm J. Ryan, David J. Adams
Publié dans: Genome Biology, Numéro 26, 2025, Page(s) 284, ISSN 1474-760X
Éditeur: Springer Science and Business Media LLC
DOI: 10.1186/s13059-025-03737-w

Consistent asymmetry in DNA damage artefacts across target regions in exome sequencing data

Auteurs: Tyler D Medina, Declan Bennett, Cathal Seoighe
Publié dans: NAR Genomics and Bioinformatics, Numéro 7, 2025, ISSN 2631-9268
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/nargab/lqaf120

Maximizing Insights from Longitudinal Epigenetic Age Data: Simulations, Applications, and Practical Guidance

Auteurs: Anna Großbach, Matthew J. Suderman, Anke Hüls, Alexandre A. Lussier, Andrew D.A.C. Smith, Esther Walton, Erin C. Dunn, Andrew J. Simpkin
Publié dans: Clinical Epigenetics, Numéro 16, 2024, ISSN 1868-7083
Éditeur: BioMed Central Ltd
DOI: 10.21203/rs.3.rs-4482915/v1

Gene-Environment Interactions in Vitamin D Status and Sun Exposure: A Systematic Review with Recommendations for Future Research

Auteurs: Rasha Shraim, Conor MacDonnchadha, Lauren Vrbanic, Ross McManus, Lina Zgaga
Publié dans: Nutrients, Numéro 14, 2022, Page(s) 2735, ISSN 2072-6643
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14132735

Systematic review on gene–sun exposure interactions in skin cancer

Auteurs: Rasha Shraim, Mohamed Ziad Farran, George He, Jelena Marunica Karsaj, Lina Zgaga, Ross McManus
Publié dans: Molecular Genetics &amp; Genomic Medicine, Numéro 11, 2023, ISSN 2324-9269
Éditeur: Wiley Periodicals LLC
DOI: 10.1002/mgg3.2259

Tumour mutations in long noncoding RNAs enhance cell fitness

Auteurs: Roberta Esposito, Andrés Lanzós, Tina Uroda, Sunandini Ramnarayanan, Isabel Büchi, Taisia Polidori, Hugo Guillen-Ramirez, Ante Mihaljevic, Bernard Mefi Merlin, Lia Mela, Eugenio Zoni, Lusine Hovhannisyan, Finn McCluggage, Matúš Medo, Giulia Basile, Dominik F. Meise, Sandra Zwyssig, Corina Wenger, Kyriakos Schwarz, Adrienne Vancura, Núria Bosch-Guiteras, Álvaro Andrades, Ai Ming Tham, Michae
Publié dans: Nature Communications, Numéro 14, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-39160-7

Statistical power in vitamin D randomized control trials investigating biomarkers as continuous outcomes

Auteurs: Lina Zgaga, Rasha Shraim, Elizabeth Bolger, Jason Wyse
Publié dans: The Journal of Steroid Biochemistry and Molecular Biology, Numéro 09600760, 2022, ISSN 0960-0760
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.jsbmb.2022.106148

Functional identification of <i>cis</i> -regulatory long noncoding RNAs at controlled false discovery rates

Auteurs: Bhavya Dhaka, Marc Zimmerli, Daniel Hanhart, Mario B Moser, Hugo Guillen-Ramirez, Sanat Mishra, Roberta Esposito, Taisia Polidori, Maro Widmer, Raquel García-Pérez, Marianna Kruithof-de Julio, Dmitri Pervouchine, Marta Melé, Panagiotis Chouvardas, Rory Johnson
Publié dans: Nucleic Acids Research, Numéro 52, 2024, Page(s) 2821-2835, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkae075

Systematic prioritisation of context-specific paralog pair vulnerabilities in cancer

Auteurs: Narod Daldal, Hamda B. Ajmal, David J. Adams, Colm J. Ryan
Publié dans: Genome Medicine, Numéro Published 12 September 2026, 2026, Page(s) N/A, ISSN 1756-994X
Éditeur: BioMed Central
DOI: 10.1186/s13073-026-01759-y

The association between epigenetic ageing from childhood to early adulthood and psychotic-like experiences in early adulthood

Auteurs: Zoe Hart, Anna Großbach, Andrew J Simpkin, Esther Walton
Publié dans: Psychological Medicine, Numéro 55, 2026, Page(s) Article e182, pp. 1–9, ISSN 0033-2917
Éditeur: Cambridge University Press
DOI: 10.1017/s003329172510055x

Technical variability across the 450K, EPICv1, and EPICv2 DNA methylation arrays: lessons learned for clinical and longitudinal studies

Auteurs: Alexandre A. Lussier, Isabel K. Schuurmans, Anna Großbach, Julie Maclsaac, Kristy Dever, Nastassja Koen, Heather J. Zar, Dan J. Stein, Michael S. Kobor, Erin C. Dunn
Publié dans: Clinical Epigenetics, Numéro 16, 2024, Page(s) 166, ISSN 1868-7083
Éditeur: Springer Science and Business Media LLC
DOI: 10.1186/s13148-024-01761-4

Ambient ultraviolet-B radiation, supplements and other factors interact to impact vitamin D status differently depending on ethnicity: A cross-sectional study

Auteurs: Margaret M. Brennan, Jos van Geffen, Michiel van Weele, Lina Zgaga, Rasha Shraim
Publié dans: Clinical Nutrition, Numéro 43, 2024, Page(s) 1308-1317, ISSN 0261-5614
Éditeur: Churchill Livingstone
DOI: 10.1016/j.clnu.2024.04.006

BTLA and PD-1 signals attenuate TCR-mediated transcriptomic changes

Auteurs: Muhammad Zainul Arifin, Judith Leitner, Donagh Egan, Petra Waidhofer-Söllner, Walter Kolch, Vadim Zhernovkov, Peter Steinberger
Publié dans: iScience, Numéro 27, 2025, Page(s) 110253, ISSN 2589-0042
Éditeur: Elsevier Inc.
DOI: 10.1016/j.isci.2024.110253

A novel TCF3::PIK3R1 fusion linked to decreased PI3K-AKT signalling activity in paediatric B-acute lymphoblastic leukaemia

Auteurs: Emma Grady, Sharmila Biswas, Tânia Dias, Peter McCarthy, Cosmin Tudose, David Betts, Andrea Malone, Jonathan Bond
Publié dans: British Journal of Haematology, Numéro 205, 2024, ISSN 1365-2141
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1111/bjh.19587

Non-peer reviewed articles (4)

A predicted cancer dependency map for paralog pairs

Auteurs: Narod Kebabci, Hamda Ajmal, David J. Adams, Colm J. Ryan
Publié dans: BioRxiv, Numéro Posted 19 January 2026; Version 1, 2026, Page(s) N/A, ISSN 0000-0000
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.64898/2026.01.19.700065

Pan-cancer discovery of driver mutations in long noncoding RNAs reveals widespread functional rewiring of RNA regulatory elements

Auteurs: Sunandini Ramnarayanan, Roofiya Koya, Marta Soszynska-Jozwiak, Marta Szabat, Jack Roban, Sarang Bhutada, Bhavya Dhaka, Tilman Schaefer, Ai Ming Tham, Hugo A. Guillen Ramirez, Francesca Alessandroni, Michela Coan, Artem Baranovskii, Lambert Moyon, Annalisa Marsico, Colm Ryan, Richard S Houlston, Ryszard Kierzek, Elzbieta Kierzek, Rory Johnson
Publié dans: BioRxiv, Numéro Posted 12 June 2026, 2026, Page(s) N/A, ISSN 0000-0000
Éditeur: openRxiv
DOI: 10.64898/2026.06.10.730876

HyperMap: An Efficient Framework for Transferring Perturbation Responses Across Diverse Biological Contexts

Auteurs: Bhavya Dhaka, Jiahao Gao, Trey Ideker
Publié dans: BioRxiv, Numéro Posted 27 April 2026; Version 1, 2026, Page(s) N/A, ISSN 0000-0000
Éditeur: openRxiv, Cold Spring Harbor Laboratories
DOI: 10.64898/2026.04.23.720505

How philosophy is making me a better scientist

Auteurs: Rasha Shraim
Publié dans: Nature, Numéro 23 April 2021, 2023, Page(s) N/A, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/d41586-021-01103-x