Giulio Caravagna

Scopus Author ID ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 32

Top Venues

Nature genetics

Nature communications

Genome biology

Nature

Università degli Studi di Trieste

Universita degli Studi di Pisa (MSC)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Università degli Studi di Trieste Jun 01 2020

Italy

Tenure-track researcher :: Mathematics and Geosciences

Institute of Cancer Research - May 31 2020

United Kingdom

Postdoctoral Researcher :: Molecular Pathology

University of Edinburgh

United Kingdom

Research Associate :: School of Informatics

Universita degli Studi di Milano-Bicocca

Italy

Postdoctoral research fellow :: Computer Science

Universita degli Studi di Milano-Bicocca

Italy

Postdoctoral research fellow :: Computer Science

Universita degli Studi di Milano-Bicocca

Italy

Postdoctoral research fellow :: Computer Science

Consiglio Nazionale delle Ricerche

Italy

Postdoctoral research fellow

Education History

Universita degli Studi di Pisa

Italy

MSC :: Computer Science

Universita degli Studi di Pisa

Italy

BSC :: Computer Science

Publications

Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J Williams, Fabio Anselmi, Alberto d'Onofrio, Vasavi Sundaram, Alona Sosinsky, William C H Cross, Giulio Caravagna
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome biology 25 (1) (2024)
Hamzeh Kayhanian, William Cross, Suzanne E M van der Horst, Panagiotis Barmpoutis, Eszter Lakatos, Giulio Caravagna, Luis Zapata, Arne Van Hoeck, Sjors Middelkamp, Kevin Litchfield, Christopher Steele, William Waddingham, Dominic Patel, Salvatore Milite, Chen Jin, Ann-Marie C Baker, Daniel C Alexander, Khurum Khan, Daniel Hochhauser, Marco Novelli, Benjamin Werner, Ruben van Boxtel, Joris H Hageman, Julian R Buissant des Amorie, Josep Linares, Marjolijn J L Ligtenberg, Iris D Nagtegaal, Miangela M Laclé, Leon M G Moons, Lodewijk A A Brosens, Nischalan Pillay, Andrea Sottoriva, Trevor A Graham, Manuel Rodriguez, Kai-Keen Shiu, Hugo J G Snippert, Marnix Jansen
Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer. Nature genetics 56 (7) (2024)
Jonathan Mitchell, Salvatore Milite, Jack Bartram, Susan Walker, Nadezda Volkova, Olena Yavorska, Magdalena Zarowiecki, Jane Chalker, Rebecca Thomas, Luca Vago, Alona Sosinsky, Giulio Caravagna
Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nature communications 15 (1) (2024)
Stefano Scalera, Biagio Ricciuti, Daniele Marinelli, Marco Mazzotta, Laura Cipriani, Giulia Bon, Giulia Schiavoni, Irene Terrenato, Alessandro Di Federico, Joao M Victor Alessi, Maurizio Fanciulli, Ludovica Ciuffreda, Francesca De Nicola, Frauke Goeman, Giulio Caravagna, Daniele Santini, Ruggero De Maria, Federico Cappuzzo, Gennaro Ciliberto, Mariam Jamal-Hanjani, Mark M Awad, Nicholas McGranahan, Marcello Maugeri-Saccà
Transcriptional phenocopies of deleterious KEAP1 mutations correlate with survival outcomes in lung cancer treated with immunotherapy. Clinical cancer research : an official journal of the American Association for Cancer Research (2024)
Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J Williams, Fabio Anselmi, Alberto d'Onofrio, Vasavi Sundaram, Alona Sosinsky, William C H Cross, Giulio Caravagna
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome biology 25 (1) (2024)
Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J Williams, Fabio Anselmi, Alberto d'Onofrio, Vasavi Sundaram, Alona Sosinsky, William C H Cross, Giulio Caravagna
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome biology 25 (1) (2024)
Alex J Cornish, Andreas J Gruber, Ben Kinnersley, Daniel Chubb, Anna Frangou, Giulio Caravagna, Boris Noyvert, Eszter Lakatos, Henry M Wood, Steve Thorn, Richard Culliford, Claudia Arnedo-Pac, Jacob Househam, William Cross, Amit Sud, Philip J Law, Maire Ni Leathlobhair, Aliah Hawari, Connor Woolley, Kitty Sherwood, Nathalie Feeley, Güler Gül, Juan Fernandez-Tajes, Luis Zapata, Ludmil B Alexandrov, Nirupa Murugaesu, Alona Sosinsky, Jonathan Mitchell, Núria López-Bigas, Philip Quirke, David N Church, Ian P M Tomlinson, Andrea Sottoriva, Trevor A Graham, David C Wedge, Richard S Houlston
The genomic landscape of 2,023 colorectal cancers. Nature (2024)
Jonathan Mitchell, Salvatore Milite, Jack Bartram, Susan Walker, Nadezda Volkova, Olena Yavorska, Magdalena Zarowiecki, Jane Chalker, Rebecca Thomas, Luca Vago, Alona Sosinsky, Giulio Caravagna
Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nature communications 15 (1) (2024)
Alex J Cornish, Andreas J Gruber, Ben Kinnersley, Daniel Chubb, Anna Frangou, Giulio Caravagna, Boris Noyvert, Eszter Lakatos, Henry M Wood, Steve Thorn, Richard Culliford, Claudia Arnedo-Pac, Jacob Househam, William Cross, Amit Sud, Philip J Law, Maire Ni Leathlobhair, Aliah Hawari, Connor Woolley, Kitty Sherwood, Nathalie Feeley, Güler Gül, Juan Fernandez-Tajes, Luis Zapata, Ludmil B Alexandrov, Nirupa Murugaesu, Alona Sosinsky, Jonathan Mitchell, Núria López-Bigas, Philip Quirke, David N Church, Ian P M Tomlinson, Andrea Sottoriva, Trevor A Graham, David C Wedge, Richard S Houlston
The genomic landscape of 2,023 colorectal cancers. Nature (2024)
Jonathan Mitchell, Salvatore Milite, Jack Bartram, Susan Walker, Nadezda Volkova, Olena Yavorska, Magdalena Zarowiecki, Jane Chalker, Rebecca Thomas, Luca Vago, Alona Sosinsky, Giulio Caravagna
Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nature communications 15 (1) (2024)
Hamzeh Kayhanian, William Cross, Suzanne E M van der Horst, Panagiotis Barmpoutis, Eszter Lakatos, Giulio Caravagna, Luis Zapata, Arne Van Hoeck, Sjors Middelkamp, Kevin Litchfield, Christopher Steele, William Waddingham, Dominic Patel, Salvatore Milite, Chen Jin, Ann-Marie C Baker, Daniel C Alexander, Khurum Khan, Daniel Hochhauser, Marco Novelli, Benjamin Werner, Ruben van Boxtel, Joris H Hageman, Julian R Buissant des Amorie, Josep Linares, Marjolijn J L Ligtenberg, Iris D Nagtegaal, Miangela M Laclé, Leon M G Moons, Lodewijk A A Brosens, Nischalan Pillay, Andrea Sottoriva, Trevor A Graham, Manuel Rodriguez, Kai-Keen Shiu, Hugo J G Snippert, Marnix Jansen
Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer. Nature genetics (2024)
Jonathan Mitchell, Salvatore Milite, Jack Bartram, Susan Walker, Nadezda Volkova, Olena Yavorska, Magdalena Zarowiecki, Jane Chalker, Rebecca Thomas, Luca Vago, Alona Sosinsky, Giulio Caravagna
Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nature communications 15 (1) (2024)
Jonathan Mitchell, Salvatore Milite, Jack Bartram, Susan Walker, Nadezda Volkova, Olena Yavorska, Magdalena Zarowiecki, Jane Chalker, Rebecca Thomas, Luca Vago, Alona Sosinsky, Giulio Caravagna
Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nature communications 15 (1) (2024)
Hamzeh Kayhanian, William Cross, Suzanne E M van der Horst, Panagiotis Barmpoutis, Eszter Lakatos, Giulio Caravagna, Luis Zapata, Arne Van Hoeck, Sjors Middelkamp, Kevin Litchfield, Christopher Steele, William Waddingham, Dominic Patel, Salvatore Milite, Chen Jin, Ann-Marie C Baker, Daniel C Alexander, Khurum Khan, Daniel Hochhauser, Marco Novelli, Benjamin Werner, Ruben van Boxtel, Joris H Hageman, Julian R Buissant des Amorie, Josep Linares, Marjolijn J L Ligtenberg, Iris D Nagtegaal, Miangela M Laclé, Leon M G Moons, Lodewijk A A Brosens, Nischalan Pillay, Andrea Sottoriva, Trevor A Graham, Manuel Rodriguez, Kai-Keen Shiu, Hugo J G Snippert, Marnix Jansen
Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer. Nature genetics 56 (7) (2024)
Hamzeh Kayhanian, William Cross, Suzanne E M van der Horst, Panagiotis Barmpoutis, Eszter Lakatos, Giulio Caravagna, Luis Zapata, Arne Van Hoeck, Sjors Middelkamp, Kevin Litchfield, Christopher Steele, William Waddingham, Dominic Patel, Salvatore Milite, Chen Jin, Ann-Marie C Baker, Daniel C Alexander, Khurum Khan, Daniel Hochhauser, Marco Novelli, Benjamin Werner, Ruben van Boxtel, Joris H Hageman, Julian R Buissant des Amorie, Josep Linares, Marjolijn J L Ligtenberg, Iris D Nagtegaal, Miangela M Laclé, Leon M G Moons, Lodewijk A A Brosens, Nischalan Pillay, Andrea Sottoriva, Trevor A Graham, Manuel Rodriguez, Kai-Keen Shiu, Hugo J G Snippert, Marnix Jansen
Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer. Nature genetics 56 (7) (2024)
Jonathan Mitchell, Salvatore Milite, Jack Bartram, Susan Walker, Nadezda Volkova, Olena Yavorska, Magdalena Zarowiecki, Jane Chalker, Rebecca Thomas, Luca Vago, Alona Sosinsky, Giulio Caravagna
Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nature communications 15 (1) (2024)
Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J Williams, Fabio Anselmi, Alberto d'Onofrio, Vasavi Sundaram, Alona Sosinsky, William C H Cross, Giulio Caravagna
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome biology 25 (1) (2024)
Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J Williams, Fabio Anselmi, Alberto d'Onofrio, Vasavi Sundaram, Alona Sosinsky, William C H Cross, Giulio Caravagna
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome biology 25 (1) (2024)
Hamzeh Kayhanian, William Cross, Suzanne E M van der Horst, Panagiotis Barmpoutis, Eszter Lakatos, Giulio Caravagna, Luis Zapata, Arne Van Hoeck, Sjors Middelkamp, Kevin Litchfield, Christopher Steele, William Waddingham, Dominic Patel, Salvatore Milite, Chen Jin, Ann-Marie C Baker, Daniel C Alexander, Khurum Khan, Daniel Hochhauser, Marco Novelli, Benjamin Werner, Ruben van Boxtel, Joris H Hageman, Julian R Buissant des Amorie, Josep Linares, Marjolijn J L Ligtenberg, Iris D Nagtegaal, Miangela M Laclé, Leon M G Moons, Lodewijk A A Brosens, Nischalan Pillay, Andrea Sottoriva, Trevor A Graham, Manuel Rodriguez, Kai-Keen Shiu, Hugo J G Snippert, Marnix Jansen
Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer. Nature genetics 56 (7) (2024)
Luis Zapata, Giulio Caravagna, Marc J Williams, Eszter Lakatos, Khalid AbdulJabbar, Benjamin Werner, Diego Chowell, Chela James, Lucie Gourmet, Salvatore Milite, Ahmet Acar, Nadeem Riaz, Timothy A Chan, Trevor A Graham, Andrea Sottoriva
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. Nature genetics (2023)
Luis Zapata, Giulio Caravagna, Marc J Williams, Eszter Lakatos, Khalid AbdulJabbar, Benjamin Werner, Diego Chowell, Chela James, Lucie Gourmet, Salvatore Milite, Ahmet Acar, Nadeem Riaz, Timothy A Chan, Trevor A Graham, Andrea Sottoriva
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. Nature genetics 55 (3) (2023)
Luis Zapata, Giulio Caravagna, Marc J Williams, Eszter Lakatos, Khalid AbdulJabbar, Benjamin Werner, Diego Chowell, Chela James, Lucie Gourmet, Salvatore Milite, Ahmet Acar, Nadeem Riaz, Timothy A Chan, Trevor A Graham, Andrea Sottoriva
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. Nature genetics 55 (3) (2023)
Giulio Caravagna
Mathematical modeling of neuroblastoma associates evolutionary patterns with outcomes. Nature genetics (2023)
Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto d'Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. PLoS computational biology 19 (11) (2023)
Luis Zapata, Giulio Caravagna, Marc J Williams, Eszter Lakatos, Khalid AbdulJabbar, Benjamin Werner, Diego Chowell, Chela James, Lucie Gourmet, Salvatore Milite, Ahmet Acar, Nadeem Riaz, Timothy A Chan, Trevor A Graham, Andrea Sottoriva
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. Nature genetics 55 (3) (2023)
Luis Zapata, Giulio Caravagna, Marc J Williams, Eszter Lakatos, Khalid AbdulJabbar, Benjamin Werner, Diego Chowell, Chela James, Lucie Gourmet, Salvatore Milite, Ahmet Acar, Nadeem Riaz, Timothy A Chan, Trevor A Graham, Andrea Sottoriva
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. Nature genetics 55 (3) (2023)
Jacob Househam, Timon Heide, George D Cresswell, Inmaculada Spiteri, Chris Kimberley, Luis Zapata, Claire Lynn, Chela James, Maximilian Mossner, Javier Fernandez-Mateos, Alessandro Vinceti, Ann-Marie C Baker, Calum Gabbutt, Alison Berner, Melissa Schmidt, Bingjie Chen, Eszter Lakatos, Vinaya Gunasri, Daniel Nichol, Helena Costa, Miriam Mitchinson, Daniele Ramazzotti, Benjamin Werner, Francesco Iorio, Marnix Jansen, Giulio Caravagna, Christopher P Barnes, Darryl Shibata, John A Bridgewater, Manuel Rodriguez, Luca Magnani, Andrea Sottoriva, Trevor A Graham
Phenotypic plasticity and genetic control in colorectal cancer evolution. Nature 611 (7937) (2022)
Salvatore Milite, Riccardo Bergamin, Lucrezia Patruno, Nicola Calonaci, Giulio Caravagna
A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations. Bioinformatics (Oxford, England) 38 (9) (2022)
Giulio Caravagna, Guido Sanguinetti, Trevor A Graham, Andrea Sottoriva
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. BMC bioinformatics 21 (1) (2020)
Ketevan Chkhaidze, Timon Heide, Benjamin Werner, Marc J Williams, Weini Huang, Giulio Caravagna, Trevor A Graham, Andrea Sottoriva
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. PLoS computational biology 15 (7) (2019)
Giulio Caravagna, Ylenia Giarratano, Daniele Ramazzotti, Ian P M Tomlinson, Trevor A Graham, Guido Sanguinetti, Andrea Sottoriva
Detecting repeated cancer evolution from multi-region tumor sequencing data. Nature methods 15 (9) (2018)
Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti, Rebeca Sanz-Pamplona, Luca De Sano, Giancarlo Mauri, Victor Moreno, Marco Antoniotti, Bud Mishra
Algorithmic methods to infer the evolutionary trajectories in cancer progression. Proceedings of the National Academy of Sciences of the United States of America 113 (28) (2016)

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Publication Activity (10 Years)

Top Topics

Top Venues

Giulio Caravagna