Agent-Based Modelling of Gene Networks to model clonal selection in the tumour microenvironment and predict therapeutic resistance

Informacje na temat projektu

MicroC

Identyfikator umowy o grant: 772970

DOI

10.3030/772970

Projekt został zamknięty

Data podpisania przez KE 7 Marca 2018

Data rozpoczęcia 1 Czerwca 2018

Data zakończenia 30 Listopada 2024

Finansowanie w ramach

• EXCELLENT SCIENCE - European Research Council (ERC)

Koszt całkowity

€ 1 996 325,00

Wkład UE

€ 1 996 325,00

Koordynowany przez

UNIVERSITA COMMERCIALE LUIGI BOCCONI
Italy

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Publikacje

Peer reviewed articles (25)

Defining hypoxia in cancer: A landmark evaluation of hypoxia gene expression signatures

Autorzy: Matteo Di Giovannantonio, Fiona Hartley, Badran Elshenawy, Alessandro Barberis, Dan Hudson, Hana S. Shafique, Vincent E.S. Allott, David A. Harris, Simon R. Lord, Syed Haider, Adrian L. Harris, Francesca M. Buffa, Benjamin H.L. Harris
Opublikowane w: Cell Genomics, Numer 5, 2025, Strona(/y) 100764, ISSN 2666-979X
Wydawca: Cell
DOI: 10.1016/j.xgen.2025.100764

A Structural Characterisation of the Mitogen-Activated Protein Kinase Network in Cancer

Autorzy: Evangelos Chatzaroulas, Vytenis Sliogeris, Pedro Victori, Francesca M. Buffa, Sotiris Moschoyiannis, Roman Bauer
Opublikowane w: Symmetry, Numer 14, 2025, Strona(/y) 1009, ISSN 2073-8994
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/sym14051009

A role for SETD2 loss in tumorigenesis through DNA methylation dysregulation

Autorzy: Hira Javaid, Alessandro Barberis, Olga Chervova, Isar Nassiri, Vitaly Voloshin, Yusuke Sato, Seishi Ogawa, Benjamin Fairfax, Francesca Buffa, Timothy C. Humphrey
Opublikowane w: BMC Cancer, Numer 23, 2024, ISSN 1471-2407
Wydawca: BioMed Central
DOI: 10.1186/s12885-023-11162-0

Single cell RNA‐sequencing: A powerful yet still challenging technology to study cellular heterogeneity

Autorzy: May Ke, Badran Elshenawy, Helen Sheldon, Anjali Arora, Francesca M Buffa
Opublikowane w: BioEssays, Numer 44, 2023, ISSN 0265-9247
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/bies.202200084

Transcriptomic analysis of human primary breast cancer identifies fatty acid oxidation as a target for metformin

Autorzy: Simon R. Lord, Jennifer M. Collins, Wei-Chen Cheng, Syed Haider, Simon Wigfield, Edoardo Gaude, Barbara A. Fielding, Katherine E. Pinnick, Ulrike Harjes, Ashvina Segaran, Pooja Jha, Gerald Hoefler, Michael N. Pollak, Alastair M. Thompson, Pankaj G. Roy, Ruth. English, Rosie F. Adams, Christian Frezza, Francesca M. Buffa, Fredrik Karpe, Adrian L. Harris
Opublikowane w: British Journal of Cancer, Numer 122, 2024, Strona(/y) 258-265, ISSN 0007-0920
Wydawca: Nature Publishing Group
DOI: 10.1038/s41416-019-0665-5

MAGNETO: Cell type marker panel generator from single-cell transcriptomic data

Autorzy: Andrea Tangherloni, Simone G. Riva, Brynelle Myers, Francesca M. Buffa, Paolo Cazzaniga
Opublikowane w: Journal of Biomedical Informatics, Numer 147, 2024, Strona(/y) 104510, ISSN 1532-0464
Wydawca: Academic Press
DOI: 10.1016/j.jbi.2023.104510

Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post‐radiotherapy, and those with de novo metastatic disease

Autorzy: Philip Vincent Charlton, Dawn O'Reilly, Yiannis Philippou, Srinivasa Rao Rao, Alastair David Gordon Lamb, Ian Geoffrey Mills, Geoff Stuart Higgins, Freddie Charles Hamdy, Clare Verrill, Francesca Meteora Buffa, Richard John Bryant
Opublikowane w: The Prostate, Numer 84, 2024, Strona(/y) 977-990, ISSN 0270-4137
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/pros.24715

Integrated Pharmacodynamic Analysis Identifies Two Metabolic Adaption Pathways to Metformin in Breast Cancer

Autorzy: Simon R. Lord, Wei-Chen Cheng, Dan Liu, Edoardo Gaude, Syed Haider, Tom Metcalf, Neel Patel, Eugene J. Teoh, Fergus Gleeson, Kevin Bradley, Simon Wigfield, Christos Zois, Daniel R. McGowan, Mei-Lin Ah-See, Alastair M. Thompson, Anand Sharma, Luc Bidaut, Michael Pollak, Pankaj G. Roy, Fredrik Karpe, Tim James, Ruth English, Rosie F. Adams, Leticia Campo, Lisa Ayers, Cameron Snell, Ioannis Roxanis,
Opublikowane w: Cell Metabolism, Numer 28, 2024, Strona(/y) 679-688.e4, ISSN 1550-4131
Wydawca: Cell Press
DOI: 10.1016/j.cmet.2018.08.021

Robustness and reproducibility for AI learning in biomedical sciences: RENOIR

Autorzy: Alessandro Barberis, Hugo J. W. L. Aerts, Francesca M. Buffa
Opublikowane w: Scientific Reports, Numer 14, 2024, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-024-51381-4

A machine learning and directed network optimization approach to uncover TP53 regulatory patterns

Autorzy: Charalampos P. Triantafyllidis, Alessandro Barberis, Fiona Hartley, Ana Miar Cuervo, Enio Gjerga, Philip Charlton, Linda van Bijsterveldt, Julio Saez Rodriguez, Francesca M. Buffa
Opublikowane w: iScience, Numer 26, 2025, Strona(/y) 108291, ISSN 2589-0042
Wydawca: Cell Press
DOI: 10.1016/j.isci.2023.108291

The many faces of mathematical modelling in oncology

Autorzy: Pedro Victori, Francesca M Buffa
Opublikowane w: The British Journal of Radiology, Numer 92, 2024, ISSN 0007-1285
Wydawca: British Institute of Radiology
DOI: 10.1259/bjr.20180856

Guidelines for using sigQC for systematic evaluation of gene signatures

Autorzy: Andrew Dhawan, Alessandro Barberis, Wei-Chen Cheng, Enric Domingo, Catharine West, Tim Maughan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
Opublikowane w: Nature Protocols, Numer 14/5, 2019, Strona(/y) 1377-1400, ISSN 1754-2189
Wydawca: Nature Publishing Group
DOI: 10.1038/s41596-019-0136-8

Modeling genotypes in their microenvironment to predict single- and multi-cellular behavior

Autorzy: Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa
Opublikowane w: GigaScience, Numer 8/3, 2019, ISSN 2047-217X
Wydawca: Oxford University Press
DOI: 10.1093/gigascience/giz010

Pan-cancer characterisation of microRNA across cancer hallmarks reveals microRNA-mediated downregulation of tumour suppressors

Autorzy: Andrew Dhawan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
Opublikowane w: Nature Communications, Numer 9/1, 2018, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-018-07657-1

Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST degradation

Autorzy: Zhuoyao Chen, Rafael M. Ioris, Stacey Richardson, Ava N. Van Ess, Iolanda Vendrell, Benedikt M. Kessler, Francesca M. Buffa, Luca Busino, Steven C. Clifford, Alex N. Bullock, Vincenzo D’Angiolella
Opublikowane w: Cell Death & Differentiation, Numer 29, 2022, Strona(/y) 1955-1969, ISSN 1350-9047
Wydawca: Nature Publishing Group
DOI: 10.1038/s41418-022-00983-4

Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures

Autorzy: Umair Mahmood, Andrew Blake, Sanjay Rathee, Leslie Samuel, Graeme Murray, David Sebag-Montefiore, Simon Gollins, Nicholas P. West, Rubina Begum, Simon P. Bach, Susan D. Richman, Phil Quirke, Keara L. Redmond, Manuel Salto-Tellez, Viktor H. Koelzer, Simon J. Leedham, Ian Tomlinson, Philip D. Dunne, Francesca M. Buffa, null null, Tim S. Maughan, Enric Domingo
Opublikowane w: Cancer Research Communications, Numer 4, 2024, Strona(/y) 1765-1776, ISSN 2767-9764
Wydawca: AACR journals
DOI: 10.1158/2767-9764.crc-23-0502

Identification and validation of a machine learning model of complete response to radiation in rectal cancer reveals immune infiltrate and TGFβ as key predictors

Autorzy: Enric Domingo, Sanjay Rathee, Andrew Blake, Leslie Samuel, Graeme Murray, David Sebag-Montefiore, Simon Gollins, Nicholas West, Rubina Begum, Susan Richman, Phil Quirke, Keara Redmond, Aikaterini Chatzipli, Alessandro Barberis, Sylvana Hassanieh, Umair Mahmood, Michael Youdell, Ultan McDermott, Viktor Koelzer, Simon Leedham, Ian Tomlinson, Philip Dunne, Andrew Blake, Francesca Buffa, Enric Domingo
Opublikowane w: eBioMedicine, Numer 106, 2024, Strona(/y) 105228, ISSN 2352-3964
Wydawca: Elsevier BV
DOI: 10.1016/j.ebiom.2024.105228

New role of fat-free mass in cancer risk linked with genetic predisposition

Autorzy: Benjamin H. L. Harris, Matteo Di Giovannantonio, Ping Zhang, David A. Harris, Simon R. Lord, Naomi E. Allen, Tim S. Maughan, Richard J. Bryant, Adrian L. Harris, Gareth L. Bond, Francesca M. Buffa
Opublikowane w: Scientific Reports, Numer 14, 2024, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-024-54291-7

Obesity: a perfect storm for carcinogenesis

Autorzy: Benjamin H. L. Harris, Valentine M. Macaulay, David A. Harris, Paul Klenerman, Fredrik Karpe, Simon R. Lord, Adrian L. Harris, Francesca M. Buffa
Opublikowane w: Cancer and Metastasis Reviews, Numer 41, 2022, Strona(/y) 491-515, ISSN 0167-7659
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10555-022-10046-2

Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study

Autorzy: Pahala Gedara Jayathilake, Pedro Victori, Clara E. Pavillet, Chang Heon Lee, Dimitrios Voukantsis, Ana Miar, Anjali Arora, Adrian L. Harris, Karl J. Morten, Francesca M. Buffa
Opublikowane w: PLOS Computational Biology, Numer 20, 2024, Strona(/y) e1011944, ISSN 1553-7358
Wydawca: PLOS
DOI: 10.1371/journal.pcbi.1011944

Replication catastrophe induced by cyclic hypoxia leads to increased APOBEC3B activity

Autorzy: Samuel B Bader, Tiffany S Ma, Charlotte J Simpson, Jiachen Liang, Sakura Eri B Maezono, Monica M Olcina, Francesca M Buffa, Ester M Hammond
Opublikowane w: Nucleic Acids Research, Numer 49, 2021, Strona(/y) 7492-7506, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkab551

E2F1 proteolysis via <scp>SCF</scp> ‐cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition

Autorzy: Kamila Burdova, Hongbin Yang, Roberta Faedda, Samuel Hume, Jagat Chauhan, Daniel Ebner, Benedikt M Kessler, Iolanda Vendrell, David H Drewry, Carrow I Wells, Stephanie B Hatch, Grigory L Dianov, Francesca M Buffa, Vincenzo D'Angiolella
Opublikowane w: The EMBO Journal, Numer 38, 2023, ISSN 0261-4189
Wydawca: Nature Publishing Group
DOI: 10.15252/embj.2018101443

Cyclin F–EXO1 axis controls cell cycle–dependent execution of double-strand break repair

Autorzy: Hongbin Yang, Shahd Fouad, Paul Smith, Eun Young Bae, Yu Ji, Xinhui Lan, Ava Van Ess, Francesca M. Buffa, Roman Fischer, Iolanda Vendrell, Benedikt M. Kessler, Vincenzo D’Angiolella
Opublikowane w: Science Advances, Numer 10, 2024, ISSN 2375-2548
Wydawca: Science
DOI: 10.1126/sciadv.ado0636

ELTD1 is present in extracellular vesicles derived from endothelial cells as a cleaved extracellular domain which induces in vivo angiogenesis

Autorzy: Helen Sheldon, Wei Zhang, Esther Bridges, Koon Hwee Ang, Salwa Lin, Massimo Masiero, Demin Li, Penny A. Handford, Pat Whiteman, Roman Fischer, Francesca Buffa, Manu Vatish, Alison H. Banham, Adrian L. Harris
Opublikowane w: Journal of Extracellular Biology, Numer 1, 2023, ISSN 2768-2811
Wydawca: Wiley
DOI: 10.1002/jex2.52

Heritable genetic variants in key cancer genes link cancer risk with anthropometric traits

Autorzy: Matteo Di Giovannantonio, Benjamin HL Harris, Ping Zhang, Isaac Kitchen-Smith, Lingyun Xiong, Natasha Sahgal, Giovanni Stracquadanio, Marsha Wallace, Sarah Blagden, Simon Lord, David Harris, Adrian H.L. Harris, Francesca M. Buffa, Gareth L. Bond
Opublikowane w: Journal of Medical Genetics, 2020, Strona(/y) jmedgenet-2019-106799, ISSN 0022-2593
Wydawca: British Medical Association
DOI: 10.1136/jmedgenet-2019-106799

Book chapters (1)

Machine Learning Using Gene-Sets to Infer miRNA Function

Autorzy: Andrew Dhawan, Francesca M. Buffa
Opublikowane w: Advances in Experimental Medicine and Biology, Systems Biology of MicroRNAs in Cancer, 2022, Strona(/y) 229-240
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-031-08356-3_8