Pre-prints
Epigenetic heritability of cell plasticity drives cancer drug resistance through one-to-many genotype to phenotype mapping
Fernandez-Mateos J*, Milite S*, Oliveira E, 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, 20203, 10.1101/2023.11.15.567140.
NeuroVelo: interpretable learning of cellular dynamics from single-cell transcriptomic data
Kouadri Boudjelthia, 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*, Mossner M*, Nowinski S*, Cresswell GD*, Banerjee A*, Williams MJ*, Gay L*, Baker A*, Kimberley K, Davis H, Martinez P, Traki M, Walther V, Smith K, Caravagna G, Amarisgam S, Elia G, Berner A, Choi RC, Ramagiri P, Chauhan, Matthews N, Murphy J, Antoniu A, Clark S, Aleong JC, Domingo E, Spiteri I, McDonald SAC, Shibata D, Lacie MM, Want LM, Moorghen M, Tomlinson IPM, Novelli M, Jansen M, Watson A, Wright NA, Bridgewater J, Rodriguez-Justo M, Kocher H, Leedham SJ, Sottoriva A*, Graham TA*.
Biorxiv, 2020, 10.1101/2020.03.26.007138.
Key Publications (see Google Scholar for full list)
2023
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.
2022
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.
2020
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.
Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking
Cresswell GD*, Nichol D*, Spiteri I, Tari H, Zapata L, Heide T, Maley CC, Magnani L, Schiavon G, Ashworth A, Barry P*, Sottoriva A*.
Nature Communications, 2020, 11(1):1446.
2019
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data
Chkhaidze K, Heide T, Werner B, Williams MJ, Huang W, Caravagna G, Graham TA*, Sottoriva A*.
PLoS Computational Biology, 2019, 15(7) e1007243.
Resolving genetic heterogeneity in cancers
Turajlic S, Sottoriva A, Graham TA, Swanton C.
Nature Reviews Genetics, 2019, 20:404-416.
Evolutionary dynamics of residual disease in human glioblastoma
Spiteri I, Caravagna G, Cresswell GD, Vatsiou A, Nichol D, Acar A, Ermini L, Chkhaidze K, Werner B, Mair R, Brognaro E, Verhaak RGW, Sanguinetti G, Piccirillo SGM*, Watts C*, Sottoriva A*.
Annals of Oncology, 2019, 30(3):456-463.
2018
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.
2016
Identification of neutral tumor evolution across cancer types
Williams MJ, Werner B, Barnes CP, Graham TA*, Sottoriva A*.
Nature Genetics, 2016, 48:238-244.
2015 and earlier
A Big Bang model of human colorectal tumor growth
Sottoriva A, Kang H, Ma Z, Graham TA, Salomon M, Zhao J, Marjoram P, Siegmund K, Press MF, Shibata D, Curtis C.
Nature Genetics, 2015, 47 (3): 209-216.
Intra-tumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics
Sottoriva A, Spiteri I, Piccirillo SGM, Touloumis A, Collins PV, Marioni JC, Curtis C, Watts C, Tavaré S.
Proc Natl Acad Sci USA, 2013, 110(10):4009-4014.
Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization
Sottoriva A, Spiteri I, Shibata D, Curtis C, Tavaré S.
Cancer Research, 2013, 73(1):41-49.
Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors
Sottoriva A, Vermeulen L, Tavaré S.
PLoS Computational Biology, 2011, 7(5) doi: 10.1371/journal.pcbi.1001132.
Epigenetic heritability of cell plasticity drives cancer drug resistance through one-to-many genotype to phenotype mapping
Fernandez-Mateos J*, Milite S*, Oliveira E, 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, 20203, 10.1101/2023.11.15.567140.
NeuroVelo: interpretable learning of cellular dynamics from single-cell transcriptomic data
Kouadri Boudjelthia, 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*, Mossner M*, Nowinski S*, Cresswell GD*, Banerjee A*, Williams MJ*, Gay L*, Baker A*, Kimberley K, Davis H, Martinez P, Traki M, Walther V, Smith K, Caravagna G, Amarisgam S, Elia G, Berner A, Choi RC, Ramagiri P, Chauhan, Matthews N, Murphy J, Antoniu A, Clark S, Aleong JC, Domingo E, Spiteri I, McDonald SAC, Shibata D, Lacie MM, Want LM, Moorghen M, Tomlinson IPM, Novelli M, Jansen M, Watson A, Wright NA, Bridgewater J, Rodriguez-Justo M, Kocher H, Leedham SJ, Sottoriva A*, Graham TA*.
Biorxiv, 2020, 10.1101/2020.03.26.007138.
Key Publications (see Google Scholar for full list)
2023
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.
2022
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.
2020
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.
Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking
Cresswell GD*, Nichol D*, Spiteri I, Tari H, Zapata L, Heide T, Maley CC, Magnani L, Schiavon G, Ashworth A, Barry P*, Sottoriva A*.
Nature Communications, 2020, 11(1):1446.
2019
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data
Chkhaidze K, Heide T, Werner B, Williams MJ, Huang W, Caravagna G, Graham TA*, Sottoriva A*.
PLoS Computational Biology, 2019, 15(7) e1007243.
Resolving genetic heterogeneity in cancers
Turajlic S, Sottoriva A, Graham TA, Swanton C.
Nature Reviews Genetics, 2019, 20:404-416.
Evolutionary dynamics of residual disease in human glioblastoma
Spiteri I, Caravagna G, Cresswell GD, Vatsiou A, Nichol D, Acar A, Ermini L, Chkhaidze K, Werner B, Mair R, Brognaro E, Verhaak RGW, Sanguinetti G, Piccirillo SGM*, Watts C*, Sottoriva A*.
Annals of Oncology, 2019, 30(3):456-463.
2018
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.
2016
Identification of neutral tumor evolution across cancer types
Williams MJ, Werner B, Barnes CP, Graham TA*, Sottoriva A*.
Nature Genetics, 2016, 48:238-244.
2015 and earlier
A Big Bang model of human colorectal tumor growth
Sottoriva A, Kang H, Ma Z, Graham TA, Salomon M, Zhao J, Marjoram P, Siegmund K, Press MF, Shibata D, Curtis C.
Nature Genetics, 2015, 47 (3): 209-216.
Intra-tumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics
Sottoriva A, Spiteri I, Piccirillo SGM, Touloumis A, Collins PV, Marioni JC, Curtis C, Watts C, Tavaré S.
Proc Natl Acad Sci USA, 2013, 110(10):4009-4014.
Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization
Sottoriva A, Spiteri I, Shibata D, Curtis C, Tavaré S.
Cancer Research, 2013, 73(1):41-49.
Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors
Sottoriva A, Vermeulen L, Tavaré S.
PLoS Computational Biology, 2011, 7(5) doi: 10.1371/journal.pcbi.1001132.