Recent Publications

Simulations reveal that different responses to cell crowding determine the expansion of p53 and Notch mutant clones in squamous epithelia.

Vasiliki Kostiou, Michael W. J. Hall, Philip H. Jones, Benjamin A Hall. Journal of the Royal Society: Interface (2021)

SARS-CoV-2 Variants are Selecting for Spike Protein Mutations that Increase Protein Stability

David Shorthouse & Benjamin A Hall. JCIM (2021)

Mutant clones in normal epithelium outcompete and eliminate emerging tumours

Bartomeu Colom , Albert Herms , Michael Hall , Stefan Dentro , Charlotte King , Roshan Sood , Maria Alcolea , Gabriel Piedrafita , David Fernandez-Antoran , Swee Hoe Ong , Joanna Fowler , Krishnaa Mahbubani , Kourosh Saeb-Parsy , Moritz Gerstung , Benjamin A Hall, Philip H. Jones. Nature (2021)

Cancer-causing BRCA2 missense mutations disrupt an intracellular protein assembly mechanism to disable genome maintenance

Miyoung Lee,  David Shorthouse,  Robert Mahen,  Benjamin A Hall, Ashok R Venkitaraman. Nucleic Acids Research, Volume 49, Issue 10, 4 June 2021, Pages 5588–5604

Computational Saturation Screen Reveals the Landscape of Mutations in Human Fumarate Hydratase

David Shorthouse, Michael WJ Hall & Benjamin A Hall. Journal of Chemical Information and Modelling, Issue 61(4) pages 1970-1980 (2021)

Methods for analysing lineage tracing datasets

Vasiliki Kostiou, Huairen Zhang, Michael W J Hall, Philip H Jones, Benjamin A Hall. Royal Society Open Science 8(5), article 202231 (2021)

Selection of oncogenic mutant clones in normal human skin varies with body site

Joanna C Fowler, Charlotte King, Christopher Bryant, Michael Hall, Roshan Sood, Swee Hoe Ong, Eleanor Earp, David Fernandez-Antoran, Jonas Koeppel, Stefan C Dentro, David Shorthouse, Amer Durrani, Kate Fife, Edward Rytina, Doreen Milne, Amit Roshan, Krishnaa Mahububani, Kourosh Saeb-Parsy, Benjamin A Hall, Moritz Gerstung & Philip H Jones.  Cancer Discovery (2020)

Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium

Bartomeu Colom, Maria P. Alcolea, Gabriel Piedrafita, Michael W. J. Hall, Agnieszka Wabik, Stefan C. Dentro, Joanna C. Fowler, Albert Herms, Charlotte King, Swee Hoe Ong, Roshan K. Sood, Moritz Gerstung, Inigo Martincorena, Benjamin A. Hall & Philip H. Jones.  Nature Genetics volume 52, pages 604–614 (2020)

The single-progenitor model as the unifying paradigm of squamous epithelial maintenance

Gabriel Piedrafita, Vasiliki Kostiou, Agnieszka Wabik, Bartomeu Colom, David Fernandez-Antoran, Albert Herms, Kasumi Murai, Benjamin A Hall, Philip H Jones. Nature Communications, 11, Article number: 1429 (2020)

Relating evolutionary selection and mutant clonal dynamics in normal epithelia

Michael Hall, Philip H Jones, Benjamin A Hall. Journal of the Royal Society: Interface, 16(156) 2019

Pre-cancer: how p53 mutant progenitors colonize normal epidermis

Kasumi Murai, Greta Skrupskelyte, Gabriel Piedrafita, Michael Hall, Vasiliki Kostiou, Swee Hoe Ong, Tibor Nagy, Alex Cagan, David Goulding, Allon M Klein, Benjamin A Hall, Philip H Jones. Cell Stem Cell 23(5)/2018

Exploring the role of stromal osmoregulation in cancer and disease using executable modelling

David Shorthouse, Angela Riedel, Emma Kerr, Luisa Pedro, Dóra Bihary, Shamith Samarajiwa, Carla P. Martins, Jacqueline Shields, Benjamin A. Hall.  Nature Communications volume 9, Article number: 3011 (2018)

 

Preprints

p53 mutation in normal esophagus promotes multiple stages of carcinogenesis but is constrained by clonal competition

Kasumi Murai, Stefan Dentro, Swee Hoe Ong, Roshan Sood, David Fernandez-Antoran, Albert Herms, Vasiliki Kostiou,  Benjamin A Hall,  Moritz Gerstung,  Philip H Jones, bioRxiv

Heterogeneity of the Cancer Cell Line Metabolic Landscape

David Shorthouse, Jenna Bradley, Susan E. Critchlow, Claus Bendtsen, Benjamin A Hall, bioRxiv

Notch1 mutation drives clonal expansion in normal esophageal epithelium but impairs tumor growth

Emilie Abby, Stefan C Dentro, Michael W J Hall, Joanna C Fowler, Swee Hoe Ong, Roshan Sood, Christian W Siebel,  Moritz Gerstung,  Benjamin A Hall,  Philip H Jones, bioRxiv

HOXA9 acts as a regulatory switch in acute myeloid leukaemia and myeloproliferative neoplasms

Laure Talarmain, Matthew A. Clarke, David Shorthouse, Jasmin Fisher, Benjamin A Hall, bioRxiv

KCNQ gene family members act as both tumor suppressors and oncogenes in gastrointestinal cancers

David Shorthouse, Cassandra Kosmidou, Eric Rahrmann, Benedict Greenwood, Michael W. J. Hall, Richard J. Gilbertson, Rebecca C. Fitzgerald, Benjamin A Hall , bioRxiv

Missense mutations of NOTCH1 reveal underlying mechanisms

Michael W. J. Hall., David Shorthouse, Philip H. Jones, Benjamin A Hall, bioRxiv

Tumor pre-conditioning of draining lymph node stroma by lactic acid

Angela Riedel, Jonathan Swietlik, David Shorthouse, Lisa Haas, Tim Young, Ana S H Costa, Sarah Davidson, Luisa Pedro, Thordur Oskarsson, Benjamin A Hall, Christian Frezza, Jacqueline Shields, BioRxiv

In vivo cross-linking and transmembrane helix dynamics support a non-piston model of signaling within E. coli EnvZ

Rahmi Yusuf, Tuyet Linh Nguyen, Annika Heininger, Robert J. Lawrence, Benjamin A. Hall*,  Roger R. Draheim*, BioRxiv

 

Reviews and book chapters

Data integration in logic-based models of biological mechanisms.

Benjamin A Hall and Anna Niaraki. Current Opinion In Systems Biology (2021)

Cellular survival over genomic perfection.

S Nik-Zainal, Benjamin A Hall, Science (2019)

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 and Jasmin Fisher.
Automated Reasoning for Systems Biology and Medicine (2018)

Bacterial Chemotaxis

Kathryn A Scott, Elizabeth E Jefferys, Benjamin A Hall, Mark AJ Roberts, Judith P Armitage. Bacterial Regulatory Networks (2012)