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

Informazioni relative al progetto

MicroC

ID dell’accordo di sovvenzione: 772970

DOI

10.3030/772970

Progetto chiuso

Data della firma CE 7 Marzo 2018

Data di avvio 1 Giugno 2018

Data di completamento 30 Novembre 2024

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 996 325,00

Contributo UE

€ 1 996 325,00

Coordinato da

UNIVERSITA COMMERCIALE LUIGI BOCCONI
Italy

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (25)

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

Autori: 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
Pubblicato in: Cell Genomics, Numero 5, 2025, Pagina/e 100764, ISSN 2666-979X
Editore: Cell
DOI: 10.1016/j.xgen.2025.100764

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

Autori: Evangelos Chatzaroulas, Vytenis Sliogeris, Pedro Victori, Francesca M. Buffa, Sotiris Moschoyiannis, Roman Bauer
Pubblicato in: Symmetry, Numero 14, 2025, Pagina/e 1009, ISSN 2073-8994
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/sym14051009

A role for SETD2 loss in tumorigenesis through DNA methylation dysregulation

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

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

Autori: May Ke, Badran Elshenawy, Helen Sheldon, Anjali Arora, Francesca M Buffa
Pubblicato in: BioEssays, Numero 44, 2023, ISSN 0265-9247
Editore: 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

Autori: 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
Pubblicato in: British Journal of Cancer, Numero 122, 2024, Pagina/e 258-265, ISSN 0007-0920
Editore: Nature Publishing Group
DOI: 10.1038/s41416-019-0665-5

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

Autori: Andrea Tangherloni, Simone G. Riva, Brynelle Myers, Francesca M. Buffa, Paolo Cazzaniga
Pubblicato in: Journal of Biomedical Informatics, Numero 147, 2024, Pagina/e 104510, ISSN 1532-0464
Editore: 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

Autori: 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
Pubblicato in: The Prostate, Numero 84, 2024, Pagina/e 977-990, ISSN 0270-4137
Editore: John Wiley & Sons Inc.
DOI: 10.1002/pros.24715

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

Autori: 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,
Pubblicato in: Cell Metabolism, Numero 28, 2024, Pagina/e 679-688.e4, ISSN 1550-4131
Editore: Cell Press
DOI: 10.1016/j.cmet.2018.08.021

Robustness and reproducibility for AI learning in biomedical sciences: RENOIR

Autori: Alessandro Barberis, Hugo J. W. L. Aerts, Francesca M. Buffa
Pubblicato in: Scientific Reports, Numero 14, 2024, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-024-51381-4

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

Autori: Charalampos P. Triantafyllidis, Alessandro Barberis, Fiona Hartley, Ana Miar Cuervo, Enio Gjerga, Philip Charlton, Linda van Bijsterveldt, Julio Saez Rodriguez, Francesca M. Buffa
Pubblicato in: iScience, Numero 26, 2025, Pagina/e 108291, ISSN 2589-0042
Editore: Cell Press
DOI: 10.1016/j.isci.2023.108291

The many faces of mathematical modelling in oncology

Autori: Pedro Victori, Francesca M Buffa
Pubblicato in: The British Journal of Radiology, Numero 92, 2024, ISSN 0007-1285
Editore: British Institute of Radiology
DOI: 10.1259/bjr.20180856

Guidelines for using sigQC for systematic evaluation of gene signatures

Autori: Andrew Dhawan, Alessandro Barberis, Wei-Chen Cheng, Enric Domingo, Catharine West, Tim Maughan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
Pubblicato in: Nature Protocols, Numero 14/5, 2019, Pagina/e 1377-1400, ISSN 1754-2189
Editore: Nature Publishing Group
DOI: 10.1038/s41596-019-0136-8

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

Autori: Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa
Pubblicato in: GigaScience, Numero 8/3, 2019, ISSN 2047-217X
Editore: Oxford University Press
DOI: 10.1093/gigascience/giz010

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

Autori: Andrew Dhawan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
Pubblicato in: Nature Communications, Numero 9/1, 2018, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-018-07657-1

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

Autori: 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
Pubblicato in: Cell Death & Differentiation, Numero 29, 2022, Pagina/e 1955-1969, ISSN 1350-9047
Editore: Nature Publishing Group
DOI: 10.1038/s41418-022-00983-4

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

Autori: 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
Pubblicato in: Cancer Research Communications, Numero 4, 2024, Pagina/e 1765-1776, ISSN 2767-9764
Editore: 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

Autori: 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
Pubblicato in: eBioMedicine, Numero 106, 2024, Pagina/e 105228, ISSN 2352-3964
Editore: Elsevier BV
DOI: 10.1016/j.ebiom.2024.105228

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

Autori: 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
Pubblicato in: Scientific Reports, Numero 14, 2024, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-024-54291-7

Obesity: a perfect storm for carcinogenesis

Autori: Benjamin H. L. Harris, Valentine M. Macaulay, David A. Harris, Paul Klenerman, Fredrik Karpe, Simon R. Lord, Adrian L. Harris, Francesca M. Buffa
Pubblicato in: Cancer and Metastasis Reviews, Numero 41, 2022, Pagina/e 491-515, ISSN 0167-7659
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10555-022-10046-2

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

Autori: 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
Pubblicato in: PLOS Computational Biology, Numero 20, 2024, Pagina/e e1011944, ISSN 1553-7358
Editore: PLOS
DOI: 10.1371/journal.pcbi.1011944

Replication catastrophe induced by cyclic hypoxia leads to increased APOBEC3B activity

Autori: Samuel B Bader, Tiffany S Ma, Charlotte J Simpson, Jiachen Liang, Sakura Eri B Maezono, Monica M Olcina, Francesca M Buffa, Ester M Hammond
Pubblicato in: Nucleic Acids Research, Numero 49, 2021, Pagina/e 7492-7506, ISSN 0305-1048
Editore: 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

Autori: 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
Pubblicato in: The EMBO Journal, Numero 38, 2023, ISSN 0261-4189
Editore: Nature Publishing Group
DOI: 10.15252/embj.2018101443

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

Autori: 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
Pubblicato in: Science Advances, Numero 10, 2024, ISSN 2375-2548
Editore: 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

Autori: 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
Pubblicato in: Journal of Extracellular Biology, Numero 1, 2023, ISSN 2768-2811
Editore: Wiley
DOI: 10.1002/jex2.52

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

Autori: 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
Pubblicato in: Journal of Medical Genetics, 2020, Pagina/e jmedgenet-2019-106799, ISSN 0022-2593
Editore: British Medical Association
DOI: 10.1136/jmedgenet-2019-106799

Book chapters (1)

Machine Learning Using Gene-Sets to Infer miRNA Function

Autori: Andrew Dhawan, Francesca M. Buffa
Pubblicato in: Advances in Experimental Medicine and Biology, Systems Biology of MicroRNAs in Cancer, 2022, Pagina/e 229-240
Editore: Springer International Publishing
DOI: 10.1007/978-3-031-08356-3_8