Publications

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PRE-PRINTS

Deep Archetypal Analysis for interpretable multi-omic data integration based on biological principles

Salvatore Milite, Giulio Caravagna, Andrea. Biorxiv, 2024, 04.05/2024.04.05.588238.

Epigenome and early selection determine the tumour-immune evolutionary trajectory of colorectal cancer

Eszter Lakatos, et al. Biorxiv, 2024, 02.12/2024.02.12.579956v1.

Epigenetic heritability of cell plasticity drives cancer drug resistance through one-to-many genotype to phenotype mapping

Oliveira E*, Milite S*, Fernandez-Mateos J*, Vlachogiannis G, Chen B, Yata E, Cresswell GD, James C, Patruno L, Ascolani G, Acar A, Heide T, Spiteri I, Graudenzi A, Caravagna G, Graham TA, Magnani L, Valeri N*, Sottoriva A*. Biorxiv, 2023, 10.1101/2023.11.15.567140.

NeuroVelo: interpretable learning of cellular dynamics from single-cell transcriptomic data

Kouadri Boudjelthia I, Milite S, El Kazwini N, Mateos-Fernandez J, Valeri N, Huang Y, Sottoriva A, Sanguinetti G. Biorxiv, 2023, 10.1101/2023.11.17.567500.

Stabilising selection causes grossly altered but stable karyotypes in metastatic colorectal cancer

Cross W, et al. Biorxiv, 2020, 10.1101/2020.03.26.007138.

SELECTED PUBLICATIONS

computational pathology applied to clinical colorectal cancer cohorts identifies immune and endothelial cell spatial patterns predictive of outcome

Trahearn N, et al. The Journal of Pathlogy, 265(2) 198–210 (2025).

stratified medicine paediatrics: cell free dna and serial tumour sequencing identifies subtype specific cancer evolution and epigenetic states

George SL, Lynn C, Stankunaite R, et al. Cancer Discovery, OF1–OF16 (2024). https://doi.org/10.1158/2159-8290.CD-24-0916.

The genomic landscape of 2,023 colorectal cancers

Cornish AJ, et al. Nature 633, 127–136 (2024).

Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer

Fernandez-Mateos J, Cresswell GD, Trahearn, N et al. Nature Cancer 5 , 1334–1351 (2024).

Contribution of pks+ E.coli mutations to colorectal carcinogenesis

Chen B*, Ramazzotti D, Heide T, Spiteri I, Fernandez-Mateos J, James C, Magnani L, Graham TA*, Sottoriva A*. Nature Communications, 2023, 14:7827.

Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors

Zapata L*, Caravagna G, Williams MJ, Lakatos E, Abduljabbar K, Werner B, Chowell D, James C, Gourmet L, Milite S, Acar A, Riaz N, Chan TA, Graham TA*, Sottoriva A*. Nature Genetics, 2023, 55:451-460.

The co-evolution of the genome and epigenome in colorectal cancer

Heide T*, Househam J*, Cresswell GD, Spiteri I, Lynn C, Mossner M, Kimberley C, Fernandez-Mateos J, Chen B, Zapata L, James C, Barozzi I, Chkhaidze K, Nichol D, Gunasri V, Berner A, Schmidt M, Lakatos E, Baker AM, Costa H, Mitchinson M, Piazza R, Jansen M, Caravagna G, Ramazzotti D, Shibata D, Bridgewater J, Rodrigues-Justo M, Magnani L, Graham TA*, Sottoriva A*. Nature, 2022, 611:733-743.

Phenotypic plasticity and genetic control in colorectal cancer evolution

Househam J*, Heide T*, Cresswell GD, Spiteri I, Kimberley C, Zapata L, Lynn C, James C, Mossner M, Fernandez-Mateos J, Vinceti A, Baker AM, Gabbutt C, Berner A, Schmidt M, Chen B, Lakatos E, Gunasri V, Nichol D, Costa H, Mitchinson M, Ramazzotti D, Werner B, Iorio F, Jansen M, Caravagna G, Barnes C, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Sottoriva A*, Graham TA*. Nature, 2022, 611:744-753.

Quantification of spatial subclonal interactions enhancing the invasive phenotype of paediatric glioma

Tari H, Kessler K, Trahearn N, Werner B, Vinci M, Jones C*, Sottoriva A*. Cell Reports, 2022, 40(9):111283.

Subclonal reconstruction of tumors by using machine learning and population genetics

Caravagna G, Heide T, Williams MJ, Zapata L, Nichol D, Chkhaidze K, Cross WH, Cresswell GD, Werner B, Acar A, Chesler L, Barnes CP, Sanguinetti G, Graham TA*, Sottoriva A*. Nature Genetics, 2020, 52:898-907.

Evolutionary dynamics of neoantigens in growing tumours

Lakatos E, Williams MJ, Schenck RO, Cross WCH, Househam J, Zapata L, Werner B, Gatenbee C, Robertson-Tessi M, Barnes CP, Anderson ARA, Sottoriva A*, Graham TA*. Nature Genetics, 2020, 52:1057-1066.

Exploiting evolutionary steering to induce collateral drug sensitivity in cancer

Acar A*, Nichol D*, Fernandez-Mateos J, Cresswell GD, Barozzi I, Hong SP, Trahearn N, Spiteri I, Stubbs M, Burke R, Stewart A, Caravagna G, Werner B, Vlachogiannis G, Maley CC, Magnani L, Valeri L, Banerji U*, Sottoriva A*. Nature Communications, 2020, 11(1):1923.

Detecting repeated cancer evolution from multi-region tumor sequencing data

Caravagna G, Giarratano Y, Ramazzotti D, Tomlinson I, Graham TA, Sanguinetti G*, Sottoriva A*. Nature Methods, 2018, 15:707-714.

Longitudinal liquid biopsy and mathematical modelling of clonal evolution forecast waiting time to treatment failure in a phase II colorectal cancer clinical trial

Khan K, Cunningham D, Werner B, Vlachogiannis G, Spiteri I, Heide T, Fernandez-Mateos J, Vatsiou A, Lampis A, Damavandi MD, Lote H, Huntingford IS, Hedayat S, Chau I, Tunariu N, Mentrasti G, Trevisani F, Rao S, Anandappa G, Watkins D, Starling N, Thomas J, Peckitt C, Khan N, Rugge M, Begum R, Hezelova B, Bryant A, Jones T, Proszek P, Fassan M, Hahne JC, Hubank M, Braconi C, Sottoriva A*, Valeri N*. Cancer Discovery, 2018, 8(10):1-16.

Quantification of subclonal selection in cancer from bulk sequencing data

Williams MJ, Werner B, Heide T, Curtis C, Barnes CP*, Sottoriva A*, Graham TA*. Nature Genetics, 2018, 50(6):895-903.

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

Vlachogiannis G, Hedayat S, Vatsiou A, Jamin Y, Fernandez-Mateos J, Khan K, Lampis A, Eason K, Huntingford I, Burke R, Rata M, Koh D, Tunariu N, Collins D, Hulkki-Wilson S, Regulan C, Spiteri I, Moorcraft SY, Chau I, Rao S, Watkins D, Fotiadis N, Bali M, Darvish-Damavandi M, Lote H, Eltahir Z, Smyth EC, Begum R, Clarke PA, Hahne JC, Dowsett M, de Bono J, Workman P, Sadanandam A, Fassan M, Sansom OJ, Eccles S, Starling N, Braconi C, Sottoriva A, Robinson SP, Cunningham D, Valeri N. Science, 2018, 359(6378):920-926.

SELECTED PUBLICATIONS and pre-prints