Publications | Matthew A. Clarke

Tumor digital twins uncover therapeutic strategies in triple-negative breast cancer

Pedro Victori, Kui Hua, Alecia-Jane Twigger, Akanksha Anand, Zera M. Bose, Matthew A. Clarke, Steven Bell, Katrina J.Q. Xian, Lama Zakarneh, Karen Pinilla, Colin Y.C. Lee, Menna R. Clatworthy, Walid T. Khaled, Jean E. Abraham, PARTNER Trial Group, Personalised Breast Cancer Program Group, Gregory J. Hannon and Jasmin Fisher

The Effectiveness and Durability of Pretraining Data Filtering in Protein Language Models

Aaron Maiwald, Roderick McNeill, Jaeyoung Lee, Matthew A. Clarke, Lennart Justen, Alejandro Acelas, Ivo Andrews, Giles Harper-Donnelly, Adam Moore, Sophie Rose, Oliver M. Crook, Felix Jackson

NANSEN: Network Analysis and Screening

Matthew A. Clarke, Pedro Victori, Jasmin Fisher

Selective Generalization: Improving Capabilities While Maintaining Alignment

Ariana Azarbal, Matthew A. Clarke, Jorio Cocolla, Cailley Factor, Alex Cloud

MAGELLAN: Automated Generation of Interpretable Computational Models for Biological Reasoning

Matthew A. Clarke, Charlie George Barker, Yuxin Sun, Theodoros I. Roumeliotis, Jyoti S. Choudhary, Jasmin Fisher

Virtual Tumors Enable Prediction of Personalized Therapeutic Combinations for Non-Small Cell Lung Cancer

Matthew A. Clarke, Charlie George Barker, Ashley Nicholls, Matt P. Handler, Lisa Pickard, Amna Shah, David Walter, Etienne De Braekeleer, Udai Banerji, Jyoti Choudhary, Saif Ahmed, Ultan McDermott, Gregory J. Hannon, Jasmin Fisher

Compositionality and Ambiguity: Latent Co-occurrence and Interpretable Subspaces

Matthew A. Clarke, Hardik Bhatnagar, Joseph Bloom

Localized immune surveillance of primary melanoma in the skin deciphered through executable modeling

Rowan Howell, James Davies, Matthew A. Clarke, Anna Appios, Inês Mesquita, Yashoda Jayal, Ben Ringham-Terry, Isabel Boned Del Rio, Jasmin Fisher, Clare L. Bennett

HOXA9 has the hallmarks of a biological switch with implications in blood cancers

Laure Talarmain, Matthew A. Clarke, David Shorthouse, Lilia Cabrera-Cosme, David G. Kent, Jasmin Fisher, Benjamin A. Hall

Executable Network of SARS-CoV-2-Host Interaction Predicts Drug Combination Treatments

Rowan Howell, Matthew A. Clarke, Ann-Kathrin Reuschl, Tianyi Chen, Sean Abbott-Imboden, Mervyn Singer, David M. Lowe, Clare L. Bennett, Benjamin Chain, Clare Jolly, Jasmin Fisher

Executable cancer models: successes and challenges

Matthew A. Clarke, Jasmin Fisher

Prognostic hallmarks in AML

Matthew A. Clarke, Jasmin Fisher

Heterogeneity of Myc expression in breast cancer exposes pharmacological vulnerabilities revealed through executable mechanistic modeling

Peter Kreuzaler, Matthew A. Clarke, Elizabeth J. Brown, Catherine H. Wilson, Roderik M. Kortlever, Nir Piterman, Trevor Littlewood, Gerard I. Evan, Jasmin Fisher

Using State Space Exploration to Determine How Gene Regulatory Networks Constrain Mutation Order in Cancer Evolution

Matthew A. Clarke, Steven Woodhouse, Nir Piterman, Benjamin A. Hall, Jasmin Fisher

Predictive Computational Modelling of the c-myc Gene Regulatory Network for Combinatorial Treatments of Breast Cancer

Matthew A. Clarke