Doctorate School in Integrated Genomics Research

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

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

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

Author(s): 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
Published in: Journal of Personalized Medicine, Issue 15, 2025, Page(s) 584, ISSN 2075-4426
Publisher: 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

Author(s): 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
Published in: Gastro Hep Advances, 2025, ISSN 2772-5723
Publisher: Elsevier Inc.
DOI: 10.1016/j.gastha.2024.11.002

Identification of unique rectal cancer-specific subtypes

Author(s): Batuhan Kisakol, Anna Matveeva, Manuela Salvucci, Alexander Kel, Elizabeth McDonough, Fiona Ginty, Daniel B. Longley, Jochen H. M. Prehn
Published in: British Journal of Cancer, Issue 130, 2024, Page(s) 1809-1818, ISSN 0007-0920
Publisher: 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

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

Ancient genomes reveal demographic trajectories during the Classic Maya period

Author(s): 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
Published in: Current Biology, Issue 35, 2025, Page(s) 2709-2719.e5, ISSN 0960-9822
Publisher: 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

Author(s): 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
Published in: Gut Microbes, Issue 16, 2024, ISSN 1949-0984
Publisher: 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

Author(s): 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
Published in: Journal of Molecular Medicine, Issue 101, 2023, Page(s) 829-841, ISSN 0946-2716
Publisher: 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

Author(s): Sodiq A. Hameed, Walter Kolch, Donal J. Brennan, Vadim Zhernovkov
Published in: Scientific Reports, Issue 15, 2025, Page(s) 14484, ISSN 2045-2322
Publisher: 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

Author(s): Sai Ravi Chandra Nori, Calum J. Walsh, Fionnuala M. McAuliffe, Rebecca L. Moore, Douwe Van Sinderen, Conor Feehily, Paul D. Cotter
Published in: npj Biofilms and Microbiomes, Issue 11, 2025, ISSN 2055-5008
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41522-025-00682-1

Overview of Molecular Diagnostics in Irish Clinical Oncology

Author(s): Tyler Medina, Seán O. Hynes, Maeve Lowery, Patrick Gillespie, Walter Kolch, Cathal Seoighe
Published in: HRB Open Research, Issue 7, 2025, Page(s) 16, ISSN 2515-4826
Publisher: 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

Author(s): Yezhao Zhong, Cathal Seoighe, Haixuan Yang
Published in: Bioinformatics Advances, Issue 4, 2024, Page(s) vbae009, ISSN 2635-0041
Publisher: 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

Author(s): 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
Published in: BMJ Oncology, Issue 3, 2024, Page(s) e000362, ISSN 2752-7948
Publisher: 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

Author(s): Rasha Shraim, Margaret M. Brennan, Jos van Geffen, Lina Zgaga
Published in: The Journal of Steroid Biochemistry and Molecular Biology, 2025, ISSN 1879-1220
Publisher: 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

Author(s): Cosmin Tudose, Jonathan Bond, Colm J Ryan
Published in: NAR Cancer, Issue 5, 2023, ISSN 2632-8674
Publisher: Oxford University Press (OUP)
DOI: 10.1093/narcan/zcad056

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

Author(s): Barry Maguire, Batuhan Kisakol, Jochen H.M. Prehn, John P. Burke
Published in: Clinical Colorectal Cancer, Issue 24, 2026, Page(s) 129-134.e7, ISSN 1533-0028
Publisher: 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

Author(s): 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
Published in: Diseases of the Colon & Rectum, Issue 66, 2025, Page(s) 914-922, ISSN 0012-3706
Publisher: Springer Verlag
DOI: 10.1097/dcr.0000000000002624

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

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

Targeting synthetic lethal paralogs in cancer

Author(s): Colm J. Ryan, Ishan Mehta, Narod Kebabci, David J. Adams
Published in: Trends in Cancer, Issue 9, 2023, Page(s) 397-409, ISSN 2405-8033
Publisher: Elsevier Inc.
DOI: 10.1016/j.trecan.2023.02.002

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

Author(s): Sarah Ennis, Pilib Ó Broin, Eva Szegezdi
Published in: Bioinformatics Advances, Issue 3, 2023, Page(s) vbad130, ISSN 2635-0041
Publisher: 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

Author(s): 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
Published in: Nature Communications, Issue 16, 2025, Page(s) 10774, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-025-65820-x

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

Author(s): 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
Published in: International Journal of Molecular Sciences, Issue 25, 2025, Page(s) 5239, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms25105239

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

Author(s): 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
Published in: Genome Biology, Issue 26, 2025, Page(s) 284, ISSN 1474-760X
Publisher: 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

Author(s): Tyler D Medina, Declan Bennett, Cathal Seoighe
Published in: NAR Genomics and Bioinformatics, Issue 7, 2025, ISSN 2631-9268
Publisher: Oxford University Press (OUP)
DOI: 10.1093/nargab/lqaf120

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

Author(s): Anna Großbach, Matthew J. Suderman, Anke Hüls, Alexandre A. Lussier, Andrew D.A.C. Smith, Esther Walton, Erin C. Dunn, Andrew J. Simpkin
Published in: Clinical Epigenetics, Issue 16, 2024, ISSN 1868-7083
Publisher: 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

Author(s): Rasha Shraim, Conor MacDonnchadha, Lauren Vrbanic, Ross McManus, Lina Zgaga
Published in: Nutrients, Issue 14, 2022, Page(s) 2735, ISSN 2072-6643
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14132735

Systematic review on gene–sun exposure interactions in skin cancer

Author(s): Rasha Shraim, Mohamed Ziad Farran, George He, Jelena Marunica Karsaj, Lina Zgaga, Ross McManus
Published in: Molecular Genetics & Genomic Medicine, Issue 11, 2023, ISSN 2324-9269
Publisher: Wiley Periodicals LLC
DOI: 10.1002/mgg3.2259

Tumour mutations in long noncoding RNAs enhance cell fitness

Author(s): 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
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-39160-7

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

Author(s): Lina Zgaga, Rasha Shraim, Elizabeth Bolger, Jason Wyse
Published in: The Journal of Steroid Biochemistry and Molecular Biology, Issue 09600760, 2022, ISSN 0960-0760
Publisher: 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

Author(s): 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
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 2821-2835, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae075

Systematic prioritisation of context-specific paralog pair vulnerabilities in cancer

Author(s): Narod Daldal, Hamda B. Ajmal, David J. Adams, Colm J. Ryan
Published in: Genome Medicine, Issue Published 12 September 2026, 2026, Page(s) N/A, ISSN 1756-994X
Publisher: 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

Author(s): Zoe Hart, Anna Großbach, Andrew J Simpkin, Esther Walton
Published in: Psychological Medicine, Issue 55, 2026, Page(s) Article e182, pp. 1–9, ISSN 0033-2917
Publisher: 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

Author(s): 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
Published in: Clinical Epigenetics, Issue 16, 2024, Page(s) 166, ISSN 1868-7083
Publisher: 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

Author(s): Margaret M. Brennan, Jos van Geffen, Michiel van Weele, Lina Zgaga, Rasha Shraim
Published in: Clinical Nutrition, Issue 43, 2024, Page(s) 1308-1317, ISSN 0261-5614
Publisher: Churchill Livingstone
DOI: 10.1016/j.clnu.2024.04.006

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

Author(s): Muhammad Zainul Arifin, Judith Leitner, Donagh Egan, Petra Waidhofer-Söllner, Walter Kolch, Vadim Zhernovkov, Peter Steinberger
Published in: iScience, Issue 27, 2025, Page(s) 110253, ISSN 2589-0042
Publisher: 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

Author(s): Emma Grady, Sharmila Biswas, Tânia Dias, Peter McCarthy, Cosmin Tudose, David Betts, Andrea Malone, Jonathan Bond
Published in: British Journal of Haematology, Issue 205, 2024, ISSN 1365-2141
Publisher: John Wiley & Sons Ltd.
DOI: 10.1111/bjh.19587

A predicted cancer dependency map for paralog pairs

Author(s): Narod Kebabci, Hamda Ajmal, David J. Adams, Colm J. Ryan
Published in: BioRxiv, Issue Posted 19 January 2026; Version 1, 2026, Page(s) N/A, ISSN 0000-0000
Publisher: 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

Author(s): 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
Published in: BioRxiv, Issue Posted 12 June 2026, 2026, Page(s) N/A, ISSN 0000-0000
Publisher: openRxiv
DOI: 10.64898/2026.06.10.730876

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

Author(s): Bhavya Dhaka, Jiahao Gao, Trey Ideker
Published in: BioRxiv, Issue Posted 27 April 2026; Version 1, 2026, Page(s) N/A, ISSN 0000-0000
Publisher: openRxiv, Cold Spring Harbor Laboratories
DOI: 10.64898/2026.04.23.720505

How philosophy is making me a better scientist

Author(s): Rasha Shraim
Published in: Nature, Issue 23 April 2021, 2023, Page(s) N/A, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/d41586-021-01103-x

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