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Author Details

Daniele Ramazzotti
University of Milano-Bicocca
2015
32
14
PMIDPaper TitleJournal TitlePublished Year
36735903Targeting the immune microenvironment in Waldenström macroglobulinemia via halting the CD40/CD40-ligand axis.Blood2023
37749078Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients.Nat Commun2023
37654003Effects of blocking CD24 and CD47 'don't eat me' signals in combination with rituximab in mantle-cell lymphoma and chronic lymphocytic leukaemia.J Cell Mol Med2023
38030613Contribution of pks<sup>+</sup> E. coli mutations to colorectal carcinogenesis.Nat Commun2023
37267828Characterization of cancer subtypes associated with clinical outcomes by multi-omics integrative clustering.Comput Biol Med2023
36860269DNA Damage Response (DDR) Is Associated With Treatment-free Remission in Chronic Myeloid Leukemia Patients.Hemasphere2023
36932333LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution.BMC Bioinformatics2023
34647978PMCE: efficient inference of expressive models of cancer evolution with high prognostic power.Bioinformatics2022
35551450Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines.Nat Commun2022
35371557Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution.Virus Evol2022
35779264SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples.STAR Protoc2022
36680048Characterization of SARS-CoV-2 Mutational Signatures from 1.5+ Million Raw Sequencing Samples.Viruses2022
36456685Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response.NPJ Precis Oncol2022
34181655De novo mutational signature discovery in tumor genomes using SparseSignatures.PLoS Comput Biol2021
33728416VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples.Patterns (N Y)2021
33532709Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity.iScience2021
33196013Integrated Genomic, Functional, and Prognostic Characterization of Atypical Chronic Myeloid Leukemia.Hemasphere2020
30309220Improved Survival of Cancer Patients Admitted to the Intensive Care Unit between 2002 and 2011 at a U.S. Teaching Hospital.Cancer Res Treat2019
31815192Machine learning can accurately predict pre-admission baseline hemoglobin and creatinine in intensive care patients.NPJ Digit Med2019
31182087Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations.BMC Med Genomics2019
30763372Withholding or withdrawing invasive interventions may not accelerate time to death among dying ICU patients.PLoS One2019
31023236Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data.BMC Bioinformatics2019
29265724SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning.Proteomics2018
30013303Modeling Cumulative Biological Phenomena with Suppes-Bayes Causal Networks.Evol Bioinform Online2018
30171232Detecting repeated cancer evolution from multi-region tumor sequencing data.Nat Methods2018
30367051Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival.Nat Commun2018
28530230Erratum: OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes.Sci Rep2017
28387367OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes.Sci Rep2017
28263960Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.Nat Methods2017
26861821TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data.Bioinformatics2016
27357673Algorithmic methods to infer the evolutionary trajectories in cancer progression.Proc Natl Acad Sci U S A2016
25971740CAPRI: efficient inference of cancer progression models from cross-sectional data.Bioinformatics2015
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Collaborators

Arend Sidow
Co-authored papers 4
Serafim Batzoglou
Co-authored papers 3
Leo Anthony Celi
Harvard T.H. Chan School of Public Health, MIT
Co-authored papers 3
Emma Pierson
Co-authored papers 2
Andrea Sottoriva
The Institute of Cancer Research, UK Computational Biology Research Centre
Co-authored papers 2
Christopher M Sauer
Amsterdam Institute for Infection and Immunity (AII), Vrije Universiteit
Co-authored papers 2
Marc Sanson
Co-authored papers 1
Ke-Chun Huang
1Massachusetts Institute of Technology
Co-authored papers 1
Molly Douglas
University of Arizona
Co-authored papers 1
Robert S Rudin
RAND Corporation
Co-authored papers 1
Matteo Bonvini
Carnegie Mellon University
Co-authored papers 1
Karima Mokhtari
Co-authored papers 1
Peter Clardy
Mount Auburn Hospital
Co-authored papers 1
Carolina Donado
Boston Children's Hospital (C.D., Harvard Medical School (C.D.
Co-authored papers 1
Mehdi Touat
Co-authored papers 1
Ahmed Idbaih
Co-authored papers 1
Patrik Bachtiger
4Harvard T.H. Chan School of Public Health
Co-authored papers 1
Khê Hoang-Xuan
Co-authored papers 1
Jinghui Dong
Institute for Clinical Research and Health Policy Studies, Tufts Medical Center
Co-authored papers 1
Antonin Dauvin
1Massachusetts Institute of Technology
Co-authored papers 1
James M Ford
Stanford University
Co-authored papers 1
David J Stone
University of Virginia School of Medicine, USA Center for Advanced Medical Analytics
Co-authored papers 1
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