Doctorate School in Integrated Genomics Research

Información del proyecto

INTEGRATE

Identificador del acuerdo de subvención: 945385

DOI

10.3030/945385

Proyecto cerrado

Fecha de la firma de la CE 10 Abril 2020

Fecha de inicio 1 Septiembre 2020

Fecha de finalización 31 Agosto 2026

Financiado con arreglo a

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Coste total

€ 4 339 200,00

Aportación de la UE

€ 2 169 600,00

Coordinado por

UNIVERSITY OF GALWAY
Ireland

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

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

Publicaciones

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)

Autores: 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
Publicado en: Journal of Personalized Medicine, Edición 15, 2025, Página(s) 584, ISSN 2075-4426
Editor: 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

Autores: 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
Publicado en: Gastro Hep Advances, 2025, ISSN 2772-5723
Editor: Elsevier Inc.
DOI: 10.1016/j.gastha.2024.11.002

Identification of unique rectal cancer-specific subtypes

Autores: Batuhan Kisakol, Anna Matveeva, Manuela Salvucci, Alexander Kel, Elizabeth McDonough, Fiona Ginty, Daniel B. Longley, Jochen H. M. Prehn
Publicado en: British Journal of Cancer, Edición 130, 2024, Página(s) 1809-1818, ISSN 0007-0920
Editor: 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

Autores: Tarinee Khanna, Rasha Shraim, Masa Zarkovic, Michiel van Weele, Jos van Geffen, and Lina Zgaga
Publicado en: Nutrients, Edición Vol. 14, No. 23, 2022, Página(s) 5189, ISSN 2072-6643
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14235189

Ancient genomes reveal demographic trajectories during the Classic Maya period

Autores: 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
Publicado en: Current Biology, Edición 35, 2025, Página(s) 2709-2719.e5, ISSN 0960-9822
Editor: 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

Autores: 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
Publicado en: Gut Microbes, Edición 16, 2024, ISSN 1949-0984
Editor: 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

Autores: 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
Publicado en: Journal of Molecular Medicine, Edición 101, 2023, Página(s) 829-841, ISSN 0946-2716
Editor: 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

Autores: Sodiq A. Hameed, Walter Kolch, Donal J. Brennan, Vadim Zhernovkov
Publicado en: Scientific Reports, Edición 15, 2025, Página(s) 14484, ISSN 2045-2322
Editor: 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

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

Overview of Molecular Diagnostics in Irish Clinical Oncology

Autores: Tyler Medina, Seán O. Hynes, Maeve Lowery, Patrick Gillespie, Walter Kolch, Cathal Seoighe
Publicado en: HRB Open Research, Edición 7, 2025, Página(s) 16, ISSN 2515-4826
Editor: 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

Autores: Yezhao Zhong, Cathal Seoighe, Haixuan Yang
Publicado en: Bioinformatics Advances, Edición 4, 2024, Página(s) vbae009, ISSN 2635-0041
Editor: 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

Autores: 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
Publicado en: BMJ Oncology, Edición 3, 2024, Página(s) e000362, ISSN 2752-7948
Editor: 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

Autores: Rasha Shraim, Margaret M. Brennan, Jos van Geffen, Lina Zgaga
Publicado en: The Journal of Steroid Biochemistry and Molecular Biology, 2025, ISSN 1879-1220
Editor: 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

Autores: Cosmin Tudose, Jonathan Bond, Colm J Ryan
Publicado en: NAR Cancer, Edición 5, 2023, ISSN 2632-8674
Editor: Oxford University Press (OUP)
DOI: 10.1093/narcan/zcad056

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

Autores: Barry Maguire, Batuhan Kisakol, Jochen H.M. Prehn, John P. Burke
Publicado en: Clinical Colorectal Cancer, Edición 24, 2026, Página(s) 129-134.e7, ISSN 1533-0028
Editor: 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

Autores: 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
Publicado en: Diseases of the Colon &amp; Rectum, Edición 66, 2025, Página(s) 914-922, ISSN 0012-3706
Editor: Springer Verlag
DOI: 10.1097/dcr.0000000000002624

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

Autores: Sarah Ennis, Alessandra Conforte, Eimear O’Reilly, Javid Sabour Takanlu, Tatiana Cichocka, Sukhraj Pal Dhami, Pamela Nicholson, Philippe Krebs, Pilib Ó Broin, Eva Szegezdi
Publicado en: iScience, Edición 26, 2026, Página(s) 106943, ISSN 2589-0042
Editor: Elsevier BV
DOI: 10.1016/j.isci.2023.106943

Targeting synthetic lethal paralogs in cancer

Autores: Colm J. Ryan, Ishan Mehta, Narod Kebabci, David J. Adams
Publicado en: Trends in Cancer, Edición 9, 2023, Página(s) 397-409, ISSN 2405-8033
Editor: Elsevier Inc.
DOI: 10.1016/j.trecan.2023.02.002

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

Autores: Sarah Ennis, Pilib Ó Broin, Eva Szegezdi
Publicado en: Bioinformatics Advances, Edición 3, 2023, Página(s) vbad130, ISSN 2635-0041
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 16, 2025, Página(s) 10774, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-025-65820-x

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

Autores: 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
Publicado en: International Journal of Molecular Sciences, Edición 25, 2025, Página(s) 5239, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms25105239

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

Autores: 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
Publicado en: Genome Biology, Edición 26, 2025, Página(s) 284, ISSN 1474-760X
Editor: 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

Autores: Tyler D Medina, Declan Bennett, Cathal Seoighe
Publicado en: NAR Genomics and Bioinformatics, Edición 7, 2025, ISSN 2631-9268
Editor: Oxford University Press (OUP)
DOI: 10.1093/nargab/lqaf120

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

Autores: Anna Großbach, Matthew J. Suderman, Anke Hüls, Alexandre A. Lussier, Andrew D.A.C. Smith, Esther Walton, Erin C. Dunn, Andrew J. Simpkin
Publicado en: Clinical Epigenetics, Edición 16, 2024, ISSN 1868-7083
Editor: 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

Autores: Rasha Shraim, Conor MacDonnchadha, Lauren Vrbanic, Ross McManus, Lina Zgaga
Publicado en: Nutrients, Edición 14, 2022, Página(s) 2735, ISSN 2072-6643
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14132735

Systematic review on gene–sun exposure interactions in skin cancer

Autores: Rasha Shraim, Mohamed Ziad Farran, George He, Jelena Marunica Karsaj, Lina Zgaga, Ross McManus
Publicado en: Molecular Genetics &amp; Genomic Medicine, Edición 11, 2023, ISSN 2324-9269
Editor: Wiley Periodicals LLC
DOI: 10.1002/mgg3.2259

Tumour mutations in long noncoding RNAs enhance cell fitness

Autores: 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
Publicado en: Nature Communications, Edición 14, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-39160-7

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

Autores: Lina Zgaga, Rasha Shraim, Elizabeth Bolger, Jason Wyse
Publicado en: The Journal of Steroid Biochemistry and Molecular Biology, Edición 09600760, 2022, ISSN 0960-0760
Editor: 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

Autores: 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
Publicado en: Nucleic Acids Research, Edición 52, 2024, Página(s) 2821-2835, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkae075

Systematic prioritisation of context-specific paralog pair vulnerabilities in cancer

Autores: Narod Daldal, Hamda B. Ajmal, David J. Adams, Colm J. Ryan
Publicado en: Genome Medicine, Edición Published 12 September 2026, 2026, Página(s) N/A, ISSN 1756-994X
Editor: 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

Autores: Zoe Hart, Anna Großbach, Andrew J Simpkin, Esther Walton
Publicado en: Psychological Medicine, Edición 55, 2026, Página(s) Article e182, pp. 1–9, ISSN 0033-2917
Editor: 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

Autores: 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
Publicado en: Clinical Epigenetics, Edición 16, 2024, Página(s) 166, ISSN 1868-7083
Editor: 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

Autores: Margaret M. Brennan, Jos van Geffen, Michiel van Weele, Lina Zgaga, Rasha Shraim
Publicado en: Clinical Nutrition, Edición 43, 2024, Página(s) 1308-1317, ISSN 0261-5614
Editor: Churchill Livingstone
DOI: 10.1016/j.clnu.2024.04.006

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

Autores: Muhammad Zainul Arifin, Judith Leitner, Donagh Egan, Petra Waidhofer-Söllner, Walter Kolch, Vadim Zhernovkov, Peter Steinberger
Publicado en: iScience, Edición 27, 2025, Página(s) 110253, ISSN 2589-0042
Editor: 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

Autores: Emma Grady, Sharmila Biswas, Tânia Dias, Peter McCarthy, Cosmin Tudose, David Betts, Andrea Malone, Jonathan Bond
Publicado en: British Journal of Haematology, Edición 205, 2024, ISSN 1365-2141
Editor: John Wiley & Sons Ltd.
DOI: 10.1111/bjh.19587

Non-peer reviewed articles (4)

A predicted cancer dependency map for paralog pairs

Autores: Narod Kebabci, Hamda Ajmal, David J. Adams, Colm J. Ryan
Publicado en: BioRxiv, Edición Posted 19 January 2026; Version 1, 2026, Página(s) N/A, ISSN 0000-0000
Editor: 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

Autores: 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
Publicado en: BioRxiv, Edición Posted 12 June 2026, 2026, Página(s) N/A, ISSN 0000-0000
Editor: openRxiv
DOI: 10.64898/2026.06.10.730876

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

Autores: Bhavya Dhaka, Jiahao Gao, Trey Ideker
Publicado en: BioRxiv, Edición Posted 27 April 2026; Version 1, 2026, Página(s) N/A, ISSN 0000-0000
Editor: openRxiv, Cold Spring Harbor Laboratories
DOI: 10.64898/2026.04.23.720505

How philosophy is making me a better scientist

Autores: Rasha Shraim
Publicado en: Nature, Edición 23 April 2021, 2023, Página(s) N/A, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/d41586-021-01103-x