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

Información del proyecto

MicroC

Identificador del acuerdo de subvención: 772970

DOI

10.3030/772970

Proyecto cerrado

Fecha de la firma de la CE 7 Marzo 2018

Fecha de inicio 1 Junio 2018

Fecha de finalización 30 Noviembre 2024

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 1 996 325,00

Aportación de la UE

€ 1 996 325,00

Coordinado por

UNIVERSITA COMMERCIALE LUIGI BOCCONI
Italy

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 .

Publicaciones

Peer reviewed articles (25)

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

Autores: 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
Publicado en: Cell Genomics, Edición 5, 2025, Página(s) 100764, ISSN 2666-979X
Editor: Cell
DOI: 10.1016/j.xgen.2025.100764

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

Autores: Evangelos Chatzaroulas, Vytenis Sliogeris, Pedro Victori, Francesca M. Buffa, Sotiris Moschoyiannis, Roman Bauer
Publicado en: Symmetry, Edición 14, 2025, Página(s) 1009, ISSN 2073-8994
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/sym14051009

A role for SETD2 loss in tumorigenesis through DNA methylation dysregulation

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

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

Autores: May Ke, Badran Elshenawy, Helen Sheldon, Anjali Arora, Francesca M Buffa
Publicado en: BioEssays, Edición 44, 2023, ISSN 0265-9247
Editor: 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

Autores: 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
Publicado en: British Journal of Cancer, Edición 122, 2024, Página(s) 258-265, ISSN 0007-0920
Editor: Nature Publishing Group
DOI: 10.1038/s41416-019-0665-5

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

Autores: Andrea Tangherloni, Simone G. Riva, Brynelle Myers, Francesca M. Buffa, Paolo Cazzaniga
Publicado en: Journal of Biomedical Informatics, Edición 147, 2024, Página(s) 104510, ISSN 1532-0464
Editor: 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

Autores: 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
Publicado en: The Prostate, Edición 84, 2024, Página(s) 977-990, ISSN 0270-4137
Editor: John Wiley & Sons Inc.
DOI: 10.1002/pros.24715

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

Autores: 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,
Publicado en: Cell Metabolism, Edición 28, 2024, Página(s) 679-688.e4, ISSN 1550-4131
Editor: Cell Press
DOI: 10.1016/j.cmet.2018.08.021

Robustness and reproducibility for AI learning in biomedical sciences: RENOIR

Autores: Alessandro Barberis, Hugo J. W. L. Aerts, Francesca M. Buffa
Publicado en: Scientific Reports, Edición 14, 2024, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-024-51381-4

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

Autores: Charalampos P. Triantafyllidis, Alessandro Barberis, Fiona Hartley, Ana Miar Cuervo, Enio Gjerga, Philip Charlton, Linda van Bijsterveldt, Julio Saez Rodriguez, Francesca M. Buffa
Publicado en: iScience, Edición 26, 2025, Página(s) 108291, ISSN 2589-0042
Editor: Cell Press
DOI: 10.1016/j.isci.2023.108291

The many faces of mathematical modelling in oncology

Autores: Pedro Victori, Francesca M Buffa
Publicado en: The British Journal of Radiology, Edición 92, 2024, ISSN 0007-1285
Editor: British Institute of Radiology
DOI: 10.1259/bjr.20180856

Guidelines for using sigQC for systematic evaluation of gene signatures

Autores: Andrew Dhawan, Alessandro Barberis, Wei-Chen Cheng, Enric Domingo, Catharine West, Tim Maughan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
Publicado en: Nature Protocols, Edición 14/5, 2019, Página(s) 1377-1400, ISSN 1754-2189
Editor: Nature Publishing Group
DOI: 10.1038/s41596-019-0136-8

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

Autores: Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa
Publicado en: GigaScience, Edición 8/3, 2019, ISSN 2047-217X
Editor: Oxford University Press
DOI: 10.1093/gigascience/giz010

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

Autores: Andrew Dhawan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
Publicado en: Nature Communications, Edición 9/1, 2018, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-018-07657-1

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

Autores: 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
Publicado en: Cell Death & Differentiation, Edición 29, 2022, Página(s) 1955-1969, ISSN 1350-9047
Editor: Nature Publishing Group
DOI: 10.1038/s41418-022-00983-4

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

Autores: 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
Publicado en: Cancer Research Communications, Edición 4, 2024, Página(s) 1765-1776, ISSN 2767-9764
Editor: 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

Autores: 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
Publicado en: eBioMedicine, Edición 106, 2024, Página(s) 105228, ISSN 2352-3964
Editor: Elsevier BV
DOI: 10.1016/j.ebiom.2024.105228

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

Autores: 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
Publicado en: Scientific Reports, Edición 14, 2024, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-024-54291-7

Obesity: a perfect storm for carcinogenesis

Autores: Benjamin H. L. Harris, Valentine M. Macaulay, David A. Harris, Paul Klenerman, Fredrik Karpe, Simon R. Lord, Adrian L. Harris, Francesca M. Buffa
Publicado en: Cancer and Metastasis Reviews, Edición 41, 2022, Página(s) 491-515, ISSN 0167-7659
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10555-022-10046-2

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

Autores: 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
Publicado en: PLOS Computational Biology, Edición 20, 2024, Página(s) e1011944, ISSN 1553-7358
Editor: PLOS
DOI: 10.1371/journal.pcbi.1011944

Replication catastrophe induced by cyclic hypoxia leads to increased APOBEC3B activity

Autores: Samuel B Bader, Tiffany S Ma, Charlotte J Simpson, Jiachen Liang, Sakura Eri B Maezono, Monica M Olcina, Francesca M Buffa, Ester M Hammond
Publicado en: Nucleic Acids Research, Edición 49, 2021, Página(s) 7492-7506, ISSN 0305-1048
Editor: 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

Autores: 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
Publicado en: The EMBO Journal, Edición 38, 2023, ISSN 0261-4189
Editor: Nature Publishing Group
DOI: 10.15252/embj.2018101443

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

Autores: 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
Publicado en: Science Advances, Edición 10, 2024, ISSN 2375-2548
Editor: 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

Autores: 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
Publicado en: Journal of Extracellular Biology, Edición 1, 2023, ISSN 2768-2811
Editor: Wiley
DOI: 10.1002/jex2.52

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

Autores: 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
Publicado en: Journal of Medical Genetics, 2020, Página(s) jmedgenet-2019-106799, ISSN 0022-2593
Editor: British Medical Association
DOI: 10.1136/jmedgenet-2019-106799

Book chapters (1)

Machine Learning Using Gene-Sets to Infer miRNA Function

Autores: Andrew Dhawan, Francesca M. Buffa
Publicado en: Advances in Experimental Medicine and Biology, Systems Biology of MicroRNAs in Cancer, 2022, Página(s) 229-240
Editor: Springer International Publishing
DOI: 10.1007/978-3-031-08356-3_8