publications | Salvatore Milite

2024

Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc

Alice Antonello, Riccardo Bergamin, Nicola Calonaci, and 8 more authors

Genome Biology, 2024

@article{antonello2024computational,
  title = {Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc},
  author = {Antonello, Alice and Bergamin, Riccardo and Calonaci, Nicola and Househam, Jacob and Milite, Salvatore and Williams, Marc J and Anselmi, Fabio and d’Onofrio, Alberto and Sundaram, Vasavi and Sosinsky, Alona and others},
  journal = {Genome Biology},
  volume = {25},
  number = {1},
  pages = {1--40},
  year = {2024},
  publisher = {Springer},
}

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

Salvatore Milite, Giulio Caravagna, and Andrea Sottoriva

bioRxiv, 2024

Bib

@article{milite2024deep,
  title = {Deep Archetypal Analysis for interpretable multi-omic data integration based on biological principles},
  author = {Milite, Salvatore and Caravagna, Giulio and Sottoriva, Andrea},
  journal = {bioRxiv},
  pages = {2024--04},
  year = {2024},
  publisher = {Cold Spring Harbor Laboratory},
}

Clinical application of tumour-in-normal contamination assessment from whole genome sequencing

Jonathan Mitchell, Salvatore Milite, Jack Bartram, and 8 more authors

Nature Communications, 2024

Bib

@article{mitchell2024clinical,
  title = {Clinical application of tumour-in-normal contamination assessment from whole genome sequencing},
  author = {Mitchell, Jonathan and Milite, Salvatore and Bartram, Jack and Walker, Susan and Volkova, Nadezda and Yavorska, Olena and Zarowiecki, Magdalena and Chalker, Jane and Thomas, Rebecca and Vago, Luca and others},
  journal = {Nature Communications},
  volume = {15},
  number = {1},
  pages = {323},
  year = {2024},
  publisher = {Nature Publishing Group UK London},
}

2023

Blood

Time of Origin and Environmental Drivers of Leukemia Immune Escape after Transplantation

Cristina Toffalori, Riccardo Bergamin, Alice Antonello, and 8 more authors

Blood, 2023

Bib

@article{toffalori2023time,
  title = {Time of Origin and Environmental Drivers of Leukemia Immune Escape after Transplantation},
  author = {Toffalori, Cristina and Bergamin, Riccardo and Antonello, Alice and Tortorelli, Anna Francesca and Orofino, Giorgio and Cristante, Matteo and Della Volpe, Lucrezia and Milite, Salvatore and Calonaci, Nicola and Gandolfi, Giorgia and others},
  journal = {Blood},
  volume = {142},
  pages = {362},
  year = {2023},
  publisher = {Elsevier},
}

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

Idris Kouadri Boudjelthia, Salvatore Milite, Nour El Kazwini, and 5 more authors

bioRxiv, 2023

Bib

@article{kouadri2023neurovelo,
  title = {NeuroVelo: interpretable learning of cellular dynamics from single-cell transcriptomic data},
  author = {Kouadri Boudjelthia, Idris and Milite, Salvatore and El Kazwini, Nour and Fernandez-Mateos, Javier and Valeri, Nicola and Huang, Yuanhua and Sottoriva, Andrea and Sanguinetti, Guido},
  journal = {bioRxiv},
  pages = {2023--11},
  year = {2023},
  publisher = {Cold Spring Harbor Laboratory},
}

PLOS Comp. Bio.

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing

Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, and 6 more authors

PLOS Computational Biology, 2023

Bib

@article{patruno2023bayesian,
  title = {A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing},
  author = {Patruno, Lucrezia and Milite, Salvatore and Bergamin, Riccardo and Calonaci, Nicola and D’Onofrio, Alberto and Anselmi, Fabio and Antoniotti, Marco and Graudenzi, Alex and Caravagna, Giulio},
  journal = {PLOS Computational Biology},
  volume = {19},
  number = {11},
  pages = {e1011557},
  year = {2023},
  publisher = {Public Library of Science San Francisco, CA USA},
}

Nature Genetics

Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors

Luis Zapata, Giulio Caravagna, Marc J Williams, and 8 more authors

Nature Genetics, 2023

Bib

@article{zapata2023immune,
  title = {Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors},
  author = {Zapata, Luis and Caravagna, Giulio and Williams, Marc J and Lakatos, Eszter and AbdulJabbar, Khalid and Werner, Benjamin and Chowell, Diego and James, Chela and Gourmet, Lucie and Milite, Salvatore and others},
  journal = {Nature Genetics},
  volume = {55},
  number = {3},
  pages = {451--460},
  year = {2023},
  publisher = {Nature Publishing Group US New York},
}

Annals of Onc.

Clonal KEAP1 mutations with loss of heterozygosity share reduced immunotherapy efficacy and low immune cell infiltration in lung adenocarcinoma

S Scalera, B Ricciuti, M Mazzotta, and 8 more authors

Annals of Oncology, 2023

Bib

@article{scalera2023clonal,
  title = {Clonal KEAP1 mutations with loss of heterozygosity share reduced immunotherapy efficacy and low immune cell infiltration in lung adenocarcinoma},
  author = {Scalera, S and Ricciuti, B and Mazzotta, M and Calonaci, N and Alessi, Joao V and Cipriani, L and Bon, G and Messina, B and Lamberti, G and Di Federico, A and others},
  journal = {Annals of Oncology},
  volume = {34},
  number = {3},
  pages = {275--288},
  year = {2023},
  publisher = {Elsevier},
}

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

Javier Fernandez-Mateos, Salvatore Milite, Erica Oliveira, and 8 more authors

bioRxiv, 2023

Bib

@article{fernandez2023epigenetic,
  title = {Epigenetic heritability of cell plasticity drives cancer drug resistance through one-to-many genotype to phenotype mapping},
  author = {Fernandez-Mateos, Javier and Milite, Salvatore and Oliveira, Erica and Vlachogiannis, Georgios and Chen, Bingjie and Yara, Erika and Cresswell, George D and James, Chela and Patruno, Lucrezia and Ascolani, Gianluca and others},
  journal = {bioRxiv},
  pages = {2023--11},
  year = {2023},
  publisher = {Cold Spring Harbor Laboratory},
}

2022

Blood

Clonal Evolution of Chronic Lymphocytic Leukemia with Bimodal CD49d Expression Reveals CD49d Plasticity

Erika Tissino, Nicola Calonaci, Federico Pozzo, and 8 more authors

Blood, 2022

Bib

@article{tissino2022clonal,
  title = {Clonal Evolution of Chronic Lymphocytic Leukemia with Bimodal CD49d Expression Reveals CD49d Plasticity},
  author = {Tissino, Erika and Calonaci, Nicola and Pozzo, Federico and Forestieri, Gabriela and Terzi Di Bergamo, Lodovico and Vit, Filippo and Gaglio, Annalisa and Bergamin, Riccardo and Milite, Salvatore and Cozzini, Stefano and others},
  journal = {Blood},
  volume = {140},
  number = {Supplement 1},
  pages = {9844--9846},
  year = {2022},
  publisher = {American Society of Hematology},
}

Cancer Research

A study of evolutionary dynamics induced by carboplatin, olaparib and paclitaxel in high-grade serous ovarian cancer cell line models

Alvaro H Ingles Russo Garces, Salvatore Milite, Javier Fernandez-Mateos, and 8 more authors

Cancer Research, 2022

Bib

@article{garces2022study,
  title = {A study of evolutionary dynamics induced by carboplatin, olaparib and paclitaxel in high-grade serous ovarian cancer cell line models},
  author = {Garces, Alvaro H Ingles Russo and Milite, Salvatore and Fernandez-Mateos, Javier and Chen, Bingjie and Pickard, Lisa and Stewart, Adam and Sanchez, Sara Diaz and Lau, Rachel and Oliveira, Erica and Banerjee, Susana and others},
  journal = {Cancer Research},
  volume = {82},
  number = {12\_Supplement},
  pages = {3790--3790},
  year = {2022},
  publisher = {AACR},
}

A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations

Salvatore Milite, Riccardo Bergamin, Lucrezia Patruno, and 2 more authors

Bioinformatics, 2022

Bib

@article{milite2022bayesian,
  title = {A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations},
  author = {Milite, Salvatore and Bergamin, Riccardo and Patruno, Lucrezia and Calonaci, Nicola and Caravagna, Giulio},
  journal = {Bioinformatics},
  volume = {38},
  number = {9},
  pages = {2512--2518},
  year = {2022},
  publisher = {Oxford University Press},
}

bioRxiv

Mutation Rate Evolution Drives Immune Escape in Mismatch Repair-Deficient Cancer

Hamzeh Kayhanian, Panagiotis Barmpoutis, Eszter Lakatos, and 8 more authors

bioRxiv, 2022

Bib

@article{kayhanian2022mutation,
  title = {Mutation Rate Evolution Drives Immune Escape in Mismatch Repair-Deficient Cancer},
  author = {Kayhanian, Hamzeh and Barmpoutis, Panagiotis and Lakatos, Eszter and Cross, William and Caravagna, Giulio and Zapata, Luis and Litchfield, Kevin and Steele, Christopher and Waddingham, William and Patel, Dominic and others},
  journal = {bioRxiv},
  pages = {2022--03},
  year = {2022},
  publisher = {Cold Spring Harbor Laboratory},
}

2019

Cells

Transcriptional characterization of stage I epithelial ovarian cancer: a multicentric study

Enrica Calura, Matteo Ciciani, Andrea Sambugaro, and 8 more authors

Cells, 2019

Bib

@article{calura2019transcriptional,
  title = {Transcriptional characterization of stage I epithelial ovarian cancer: a multicentric study},
  author = {Calura, Enrica and Ciciani, Matteo and Sambugaro, Andrea and Paracchini, Lara and Benvenuto, Giuseppe and Milite, Salvatore and Martini, Paolo and Beltrame, Luca and Zane, Flaminia and Fruscio, Robert and others},
  journal = {Cells},
  volume = {8},
  number = {12},
  pages = {1554},
  year = {2019},
  publisher = {MDPI},
}