Giulio Caravagna

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Alex GraudenziDept. of Informatics, Systems and Communication, Univ. of Milan-BicoccaVerified email at unimib.it
Marco AntoniottiProfessor of Computer Science, Università degli Studi di Milano-BicoccaVerified email at unimib.it
Daniele RamazzottiDepartment of Medicine and Surgery, University of Milano-Bicocca, Milano, ItalyVerified email at unimib.it
Andrea SottorivaHuman TechnopoleVerified email at fht.org
Trevor A GrahamDirector, Centre for Evolution and Cancer, ICR, LondonVerified email at icr.ac.uk
Alberto d'OnofrioComputer Sciences for Complex Systems Lab, Università di TriesteVerified email at units.it
Bud MishraProfessor of Computer Science and MathematicsVerified email at nyu.edu
Benjamin WernerReader, Barts Cancer Institute, Queen Mary University LondonVerified email at qmul.ac.uk
Guido SanguinettiReader in Informatics, University of EdinburghVerified email at inf.ed.ac.uk
Dr George D CresswellSt. Anna Children's Cancer Research InstituteVerified email at ccri.at
Ahmet AcarMiddle East Technical UniversityVerified email at metu.edu.tr
Marc J WilliamsMemorial Sloan Kettering Cancer CenterVerified email at mskcc.org
William CrossPostdoctoral Research Fellow, University College LondonVerified email at ucl.ac.uk
Luis ZapataICR fellow, Center For Evolution And Cancer, ICRVerified email at icr.ac.uk
Salvatore MiliteHuman TechnopoleVerified email at fht.org
Chris P BarnesUniversity College LondonVerified email at ucl.ac.uk
Javier Fernández-MateosPDTF University of Oviedo, SpainVerified email at uniovi.es
Luca MagnaniBreast Epigenetic Plasticity and Evolution Lab, Institute of Cancer ResearchVerified email at icr.ac.uk
Nicola ValeriThe Institute of Cancer Research LondonVerified email at icr.ac.uk
Jacob HousehamGenomics and Evolutionary Dynamics Team, Centre for Evolution and Cancer, The Institute for CancerVerified email at icr.ac.uk

Giulio Caravagna

Cancer Data Science Laboratory, University of Trieste

Verified email at units.it - Homepage

Cancer Data Science Cancer Evolution Bioinformatics Computational Biology


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Detecting repeated cancer evolution from multi-region tumor sequencing data G Caravagna, Y Giarratano, D Ramazzotti, I Tomlinson, TA Graham, ... Nature methods 15 (9), 707-714, 2018	146	2018
CAPRI: efficient inference of cancer progression models from cross-sectional data D Ramazzotti, G Caravagna, L Olde Loohuis, A Graudenzi, I Korsunsky, ... Bioinformatics 31 (18), 3016-3026, 2015	93	2015
Algorithmic methods to infer the evolutionary trajectories in cancer progression G Caravagna, A Graudenzi, D Ramazzotti, R Sanz-Pamplona, L De Sano, ... PNAS 113 (28), E4025–E4034, 2016	89	2016
Subclonal reconstruction of tumors by using machine learning and population genetics G Caravagna, T Heide, MJ Williams, L Zapata, D Nichol, K Chkhaidze, ... Nature genetics 52 (9), 898-907, 2020	86	2020
Exploiting evolutionary steering to induce collateral drug sensitivity in cancer A Acar, D Nichol, J Fernandez-Mateos, GD Cresswell, I Barozzi, SP Hong, ... Nature communications 11 (1), 1923, 2020	80	2020
Tumour suppression by immune system through stochastic oscillations G Caravagna, A d’Onofrio, P Milazzo, R Barbuti Journal of theoretical biology 265 (3), 336-345, 2010	69*	2010
Inferring tree causal models of cancer progression with probability raising LO Loohuis, G Caravagna, A Graudenzi, D Ramazzotti, G Mauri, ... PloS one 9 (10), e108358, 2014	67	2014
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data K Chkhaidze, T Heide, B Werner, MJ Williams, W Huang, G Caravagna, ... PLoS computational biology 15 (7), e1007243, 2019	66	2019
Evolutionary dynamics of residual disease in human glioblastoma I Spiteri, G Caravagna, GD Cresswell, A Vatsiou, D Nichol, A Acar, ... Annals of Oncology 30 (3), 456-463, 2019	61	2019
Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin M Tedesco, F Giannese, D Lazarević, V Giansanti, D Rosano, S Monzani, ... Nature biotechnology 40 (2), 235-244, 2022	60	2022
Phenotypic plasticity and genetic control in colorectal cancer evolution J Househam, T Heide, GD Cresswell, I Spiteri, C Kimberley, L Zapata, ... Nature 611 (7937), 744-753, 2022	53	2022
The interplay of intrinsic and extrinsic bounded noises in biomolecular networks G Caravagna, G Mauri, A d'Onofrio PLoS one 8 (2), e51174, 2013	50	2013
The calculus of looping sequences R Barbuti, G Caravagna, A Maggiolo–Schettini, P Milazzo, G Pardini Formal Methods for Computational Systems Biology: 8th International School …, 2008	48	2008
TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data L De Sano, G Caravagna, D Ramazzotti, A Graudenzi, G Mauri, B Mishra, ... Bioinformatics 32 (12), 1911-1913, 2016	45	2016
The co-evolution of the genome and epigenome in colorectal cancer T Heide, J Househam, GD Cresswell, I Spiteri, C Lynn, M Mossner, ... Nature 611 (7937), 733-743, 2022	37	2022
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data D Ramazzotti, A Graudenzi, L De Sano, M Antoniotti, G Caravagna BMC bioinformatics 20 (1), 1-13, 2019	37	2019
Reply to ‘Neutral tumor evolution?’ T Heide, L Zapata, MJ Williams, B Werner, G Caravagna, CP Barnes, ... Nature genetics 50 (12), 1633-1637, 2018	31	2018
Investigating the relation between stochastic differentiation, homeostasis and clonal expansion in intestinal crypts via multiscale modeling A Graudenzi, G Caravagna, G De Matteis, M Antoniotti PLoS One 9 (5), e97272, 2014	30*	2014
Delay stochastic simulation of biological systems: a purely delayed approach R Barbuti, G Caravagna, A Maggiolo-Schettini, P Milazzo Transactions on Computational Systems Biology XIII, 61-84, 2011	28	2011
Signatures of TOP1 transcription-associated mutagenesis in cancer and germline MAM Reijns, DA Parry, TC Williams, F Nadeu, RL Hindshaw, ... Nature, 2022	26	2022

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