Pre-prints

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.

dN/dS dynamics quantify tumour immunogenicity and predict response to immunotherapy
Zapata L, Caravagna G, Williams MJ, Lakatos E, Abduljabbar K, Werner B, Graham TA*, Sottoriva A*. 
​Biorxiv, 2020, 10.1101/2020.07.21.21.50.38.

Publications

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.
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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.

Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios
Williams MJ*, Zapata L, Werner B, Barnes CP, Sottoriva A*, Graham TA*.
​eLife, 2020, 9e48714.
​
Measuring single cell divisions in human cancers from multi-region sequencing data
Werner B*, Case J, Williams MJ, Chkhaidze K, Temko D, Fernandez-Mateos J, Cresswell GD, Nichol D, Cross W, Spiteri I, Huang W, Tomlinson IPM, Barnes CP, Graham TA*, Sottoriva A*. 
Nature Communications, 2020, 11(1):1035.

Prediction of benefit from checkpoint inhibitors in mismatch repair deficient metastatic colorectal cancer: role of tumor infiltrating lymphocytes
Loupakis F, Depretis I, Biason I, Intini R, Prete AA, Leone F, Lombardi P, Filippi R, Spallanzani A, Cascinu S, Reggiani Bonetti L, Maddalena G, Valeri N, Sottoriva A, Zapata L, Salmaso R, Munari G, Rugge M, Dei Tos AP, Golovato J, Sanborn JZ, Nguyen A, Schirripa M, Zagonel V, Lonardi S, Fassan M. 
The Oncologist, 2020, 25:1-7.​

EGFR amplification and outcome in a randomised phase III trial of chemotherapy alone or chemotherapy plus panitumumab for advanced gastro-oesophageal cancers
Smyth EC, Vlachogiannis G, Hedayat S, Harbery A, Hulkki-Wilson S, Salati M, Kouvelakis K, Fernandez-Mateos J, Cresswell GA, Fontana E, Seidlitz T, Peckitt C, Hahne JC, Lampis A, Begum R, Watkins D, Rao S, Starling N, Waddel T, Okines A, Crosby T, Mansoor W, Wadsley J, Middleton G, Fassan M, Wotherspoon A, Braconi C, Chau I, Vivanco I, Sottoriva A, Stange DE, Cunningham D, Valeri N.
Gut, 2020, 322658.​

Colorectal cancer residual disease at maximal response to EGFR blockade displays a druggable Paneth cell-like phenotype
Lupo B, Sassi F, Pinnelli M, Galimi F, Zanella ER, Vurchio V, Migliardi G, Gagliardi PA, Puliafito A, Manganaro D, Luraghi P, Kragh M, Pedersen MW, Horak ID, Boccaccio C, Medico E, Primo L, Nichol D, Spiteri I, Heide T, Vatsiou A, Graham TA, Elez E, Argiles G, Nuciforo P, Sottoriva A, Dienstmann R, Pasini D, Grassi E, Isella C, Bertotti A, Trusolino L. 
Science Translational Medicine, 2020, 12:eaax8313.​

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.

Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer
Nawaz S, Trahearn NA, Heidl A, Banerjee S, Maley CC, Sottoriva A, Yuan Y. 
EBioMedicine, 2019, doi.org/10.1016/j.ebiom.2019.10.001.

Measuring clonal evolution in cancer with genomics
Williams MJ, Sottoriva A*, Graham TA*. 
Annual Review of Genomics and Human Genetics, 2019, 20:309-329.

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.

The spatio-temporal evolution of lymph node spread in early breast cancer
Barry P*, Vatsiou A*, Spiteri I*, Nichol D, Cresswell GD, Acar A, Trahearn NA, Hrebien S, Garcia-Murillas I, Chkhaidze K, Ermini L, Huntingford IS, Cottom H, Zabaglio L, Koeble K, Khalique S, Rusby JE, Muscara F, Dowsett M, Maley CC, Natrajan R, Yuan Y, Schiavon G, Turner N, Sottoriva A. 
Clinical Cancer Research, 2018, doi:10.1158/1078-0432.CCR-17-3374.

The evolutionary landscape of colorectal carcinogenesis
Cross W, Kovac M, Mustonen V, Temko D, Davis H, Baker A, Biswas S, Arnold R, Chegwidden L, Gatenbee G, Anderson AR, Koelzer VH, Martinez P, Jiang X, Domingo E, Woodcock D, Feng Y, Kovacova M, Jansen M, Rodriguez-Justo M, Ashraf S, Guy R, Cunningham C, East JE, Wedge DC, Wang LM, Palles C, Heinimann K, Sottoriva A, Leedham SJ, Graham TA*, Tomlinson IPM*. 
Nature Ecology and Evolution, 2018, doi:10.1038/s41559-018-0642-z.

Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity
Heindl A, Khan AM, Rodrigues Nava D, Eason K, Sadanandam A, Orbegoso C, Punta M, Sottoriva A, Lise S, Banerjee S, Yuan Y. 
Nature Communications, 2018, 9, 3917.

Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rate
Werner B., Sottoriva A. 
PLoS Computational Biology, 2018, 16(4):e1006233.

Reply to 'Neutral tumor evolution?'
Heide T, Zapata L, Williams MJ, Werner B, Barnes CP, Graham TA*, Sottoriva A*.
Nature Genetics, 2018, 50:1633-1637.

Reply to 'Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution'
Werner B, Williams MJ, Barnes CP, Graham TA*, Sottoriva A*.
​Nature Genetics, 2018, 50:1624-1626.

Reply to 'Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data'
Williams MJ, Werner B, Heide T, Barnes CP, Graham TA*, Sottoriva A*.
Nature Genetics, 2018, 50:1628-1630

Reply: Is the evolution in tumors Darwinian or non-Darwinian?
Williams MJ, Werner B, Barnes CP, Graham TA*, Sottoriva A*. 
National Science Review, 2018, 5(1):17-19.

2017

Carbon dating cancer: defining the chronology of metastatic progression in colorectal cancer
Lote H, Spiteri I, Ermini L, Vatsiou A, Roy A, McDonald A, Maka N, Balsitis M, Bose N, Simbolo M, Mafficini A, Lampis A, Hahne JC, Trevisani F, Eltahir Z, Mentrasti G, Findlay C, Kalkman EAJ, Punta M, Werner B, Lise S, Aktipis A, Maley C, Greaves M, Braconi C, White J, Fassan M, Scarpa A, Sottoriva A*, Valeri N*. 
Annals of Oncology, 2017, 28(6):1243-1249.

Detecting truly clonal alterations from multi-region profiling of tumours
Werner B, Traulsen A, Sottoriva A*, Dingli D*. 
Scientific Reports, 2017, 7:44991.

Classifying the evolutionary and ecological features of neoplasms
Maley CC, Aktipis A, Graham TA, Sottoriva A, Boddy AM, Janiszewska M, Silva AS, Gerlinger M, Yuan Y, Pienta KJ, Anderson KS, Gatenby R, Swanton C, Posada D, Wu CI, Schiffman JD, Hwang ES, Polyak K, Anderson ARA, Brown JS, Greaves M, Shibata D. 
Nature Reviews Cancer, 2017, 17(10):605-619.

Between-region genetic diversity reflects the mode and tempo of tumor evolution
Sun R, Hu Z, Sottoriva A, Graham TA, Harpak A, Ma Z, Fischer JM, Shibata D, Curtis C. 
Nature Genetics, 2017, 49(7):1015-1024

Catch my drift? Making sense of genomic intra-tumour heterogeneity
Sottoriva A, Barnes CP, Graham TA. 
BBA - Reviews on Cancer, 2017, doi:10.1016/j.bbcan.2016.12.003.

Reply: Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures
Williams MJ, Werner B, Barnes CP, Graham TA*, Sottoriva A* 
Nature Genetics, 2017, 49:1289-1291.
​
2016

Measuring cancer evolution from the genome
Graham TA, Sottoriva A. 
Journal of Pathology, 2016, 241(2):183-191.

Identification of neutral tumor evolution across cancer types
Williams MJ, Werner B, Barnes CP, Graham TA*, Sottoriva A*. 
Nature Genetics, 2016, 48:238-244.

The cancer stem cell fraction in hierarchically organized tumors can be estimated using mathematical modeling and patient-specific treatment trajectories
Werner B, Scott JG, Sottoriva A, Anderson ARA, Traulsen A, Altrock PM. 
Cancer Research, 2016, 76(7):1705-1713.

Cancer Evolution and the limits of predictability in precision cancer medicine
Lipinski KA, Barber LJ, Davies MN, Ashenden M, Sottoriva A, Gerlinger M. 
Trends in Cancer, 2016, 2(1):49-63.

2015 and earlier (pre-ICR) selected publications

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.​

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone
Piccirillo SGM, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, Watts C. 
Cancer Research, 2015, 75(1): 1-9.

Defining stem cell dynamics in models of intestinal tumor initiation
Vermeulen L, Morrissey E, van der Heijden M, Nicholson AM, Sottoriva A, Buczacki S, Kemp R, Tavaré S, Winton DJ. 
Science, 2013, 342:995-998.

The shaping and functional consequence of the miRNA landscape in breast cancer
Dvinge H, Git A, Graf S, Salmon-Divon M, Curtis C, Sottoriva A, Zhao Y, Hirst M, Armisen J, Miska EA, Chin SF, Provenzano E, Turashvili G, Green A, Aparicio S, Caldas C. 
Nature, 2013, 497: 378-382.

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.