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Daniele Ramazzotti · SciRah

Researcher profile · Semantic Scholar

Daniele Ramazzotti

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Daniele Ramazzotti — researcher profile on SciRah

h-index: 21
Works: 79
Citations: 2,260

Most-cited papers

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning
Bo Wang, Junjie Zhu, E. Pierson, Daniele Ramazzotti +1 more
2016Nature Methods658 citations Open access
Semantic Scholar
Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival
Daniele Ramazzotti, Avantika Lal, Bo Wang, S. Batzoglou +1 more
2018Nature Communications173 citations Open access
Semantic Scholar
Detecting repeated cancer evolution in human tumours from multi-region sequencing data
G. Caravagna, Ylenia Giarratano, Daniele Ramazzotti, I. Tomlinson +3 more
2018Nature Methods153 citations Open access
Semantic Scholar
The co-evolution of the genome and epigenome in colorectal cancer
Timon Heide, J. Househam, George D. Cresswell, I. Spiteri +27 more
2021bioRxiv111 citations Open access
Semantic Scholar
Algorithmic methods to infer the evolutionary trajectories in cancer progression
G. Caravagna, A. Graudenzi, Daniele Ramazzotti, R. Sanz-Pamplona +5 more
2015Proceedings of the National Academy of Sciences of the United States of America89 citations Open access
Semantic Scholar
CAPRI: Efficient Inference of Cancer Progression Models from Cross-sectional Data
Daniele Ramazzotti, G. Caravagna, L. O. Olde Loohuis, A. Graudenzi +4 more
2014bioRxiv85 citations Open access
Semantic Scholar
Exposing the probabilistic causal structure of discrimination
F. Bonchi, S. Hajian, B. Mishra, Daniele Ramazzotti
2015International Journal of Data Science and Analysis81 citations Open access
Semantic Scholar
Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity
A. Graudenzi, Davide Maspero, Fabrizio Angaroni, R. Piazza +1 more
2020bioRxiv79 citations Open access
Semantic Scholar
Contribution of pks+ E. coli mutations to colorectal carcinogenesis
Bing-Jie Chen, Daniele Ramazzotti, Timon Heide, Inma Spiteri +5 more
2023Nature Communications68 citations Open access
Semantic Scholar
Inferring Tree Causal Models of Cancer Progression with Probability Raising
L. O. Olde Loohuis, G. Caravagna, A. Graudenzi, Daniele Ramazzotti +3 more
2013bioRxiv64 citations Open access
Semantic Scholar
SIMLR: a tool for large-scale single-cell analysis by multi-kernel learning
Bo Wang, Daniele Ramazzotti, Luca De Sano, Junjie Zhu +2 more
2017bioRxiv50 citations Open access
Semantic Scholar
Learning the Structure of Bayesian Networks: A Quantitative Assessment of the Effect of Different Algorithmic Schemes
S. Beretta, M. Castelli, Ivo Gonçalves, R. Henriques +1 more
2017Complex47 citations Open access
Semantic Scholar
De novo mutational signature discovery in tumor genomes using SparseSignatures
Avantika Lal, Keli Liu, R. Tibshirani, A. Sidow +1 more
2018bioRxiv45 citations Open access
Semantic Scholar
TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data
Luca De Sano, G. Caravagna, Daniele Ramazzotti, A. Graudenzi +3 more
2015bioRxiv40 citations Open access
Semantic Scholar
Improved Survival of Cancer Patients Admitted to the Intensive Care Unit between 2002 and 2011 at a U.S. Teaching Hospital
C. M. Sauer, Jing-Hui Dong, L. Celi, Daniele Ramazzotti
2018Cancer research and treatment : official journal of Korean Cancer Association39 citations Open access
Semantic Scholar
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, C. Gambacorti-Passerini +3 more
2020bioRxiv31 citations Open access
Semantic Scholar
Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations
Avantika Lal, Daniele Ramazzotti, Z. Weng, Keli Liu +2 more
2018BMC Medical Genomics30 citations Open access
Semantic Scholar
Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer
J. Fernández-Mateos, George D. Cresswell, Nick Trahearn, K. Webb +23 more
2024Nature Cancer25 citations Open access
Semantic Scholar
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data
Daniele Ramazzotti, A. Graudenzi, Luca De Sano, M. Antoniotti +1 more
2017BMC Bioinformatics25 citations Open access
Semantic Scholar
LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data
Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani +4 more
2021Journal of Computer Science23 citations Open access
Semantic Scholar
Machine learning can accurately predict pre-admission baseline hemoglobin and creatinine in intensive care patients
Antonin Dauvin, C. Donado, Patrik Bachtiger, Ke-Chun Huang +5 more
2019npj Digital Medicine23 citations Open access
Semantic Scholar
Integrated Genomic, Functional, and Prognostic Characterization of Atypical Chronic Myeloid Leukemia
D. Fontana, Daniele Ramazzotti, A. Aroldi, S. Redaelli +26 more
2020HemaSphere21 citations Open access
Semantic Scholar
Effects of blocking CD24 and CD47 ‘don't eat me’ signals in combination with rituximab in mantle‐cell lymphoma and chronic lymphocytic leukaemia
A. Aroldi, Mario Mauri, Daniele Ramazzotti, M. Villa +12 more
2023Journal of Cellular and Molecular Medicine18 citations Open access
Semantic Scholar
Efficient Simulation of Financial Stress Testing Scenarios with Suppes-Bayes Causal Networks
Ge-Lin Gao, B. Mishra, Daniele Ramazzotti
2017International Conference on Conceptual Structures17 citations Open access
Semantic Scholar
PMCE: efficient inference of expressive models of cancer evolution with high prognostic power
Fabrizio Angaroni, Kevin G Chen, Chiara Damiani, G. Caravagna +2 more
2014bioRxiv17 citations Open access
Semantic Scholar
Modeling Cumulative Biological Phenomena with Suppes-Bayes Causal Networks
Daniele Ramazzotti, A. Graudenzi, G. Caravagna, M. Antoniotti
2016bioRxiv16 citations Open access
Semantic Scholar
Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena
Daniele Ramazzotti, Marco S. Nobile, M. Antoniotti, A. Graudenzi
2017Journal of Computer Science15 citations Open access
Semantic Scholar
Targeting the immune microenvironment in Waldenström Macroglobulinemia via halting the CD40/CD40-ligand axis.
A. Sacco, V. Desantis, J. Celay, V. Giustini +20 more
2023Blood14 citations
Semantic Scholar
Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution
Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Mario Mauri +6 more
2022bioRxiv13 citations Open access
Semantic Scholar
Learning the structure of Bayesian Networks via the bootstrap
G. Caravagna, Daniele Ramazzotti
2021Neurocomputing13 citations Open access
Semantic Scholar
Longitudinal cancer evolution from single cells
Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani +4 more
2020bioRxiv13 citations Open access
Semantic Scholar
Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer
Ryan N. Serio, Armin Scheben, Billy Lu, Domenic V Gargiulo +12 more
2024Cancer Discovery12 citations Open access
Semantic Scholar
Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients
D. Fontana, I. Crespiatico, Valentina Crippa, F. Malighetti +10 more
2023bioRxiv12 citations Open access
Semantic Scholar
Erratum: OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes
R. Piazza, Daniele Ramazzotti, R. Spinelli, A. Pirola +6 more
2017Scientific Reports11 citations Open access
Semantic Scholar
Characterization of cancer subtypes associated with clinical outcomes by multi-omics integrative clustering
Valentina Crippa, F. Malighetti, M. Villa, A. Graudenzi +3 more
2023Comput. Biol. Medicine10 citations Open access
Semantic Scholar
Learning mutational graphs of individual tumor evolution from multi-sample sequencing data
Daniele Ramazzotti, A. Graudenzi, Luca De Sano, M. Antoniotti +1 more
2017bioRxiv10 citations Open access
Semantic Scholar
Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines
Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani +4 more
2021Nature Communications9 citations Open access
Semantic Scholar
Data Pre-processing
B. Malley, Daniele Ramazzotti, Joy Y Wu
20169 citations Open access
Semantic Scholar
Oncoscore, a Novel, Internet-Based Tool to Assess the Oncogenic Potential of Genes Can Differentiate Between CP-CML and BC-CML Associated Genes, and Between CP-CML Patients with Good and Bad Prognosis
R. Piazza, L. Mologni, Daniele Ramazzotti, R. Spinelli +7 more
20169 citations
Semantic Scholar
Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response
I. Hernández-Verdin, K. Akdemir, Daniele Ramazzotti, G. Caravagna +10 more
2022npj Precision Oncology8 citations Open access
Semantic Scholar
Withholding or withdrawing invasive interventions may not accelerate time to death among dying ICU patients
Daniele Ramazzotti, P. Clardy, L. Celi, David J. Stone +1 more
2018PLoS ONE7 citations Open access
Semantic Scholar
Parallel implementation of efficient search schemes for the inference of cancer progression models
Daniele Ramazzotti, Marco S. Nobile, P. Cazzaniga, G. Mauri +1 more
2016IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology7 citations Open access
Semantic Scholar
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution
Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero +6 more
2023BMC Bioinformatics6 citations Open access
Semantic Scholar
Probabilistic Causal Analysis of Social Influence
F. Bonchi, Francesco Gullo, B. Mishra, Daniele Ramazzotti
2018International Conference on Information and Knowledge Management6 citations
Semantic Scholar
A quantitative assessment of the effect of different algorithmic schemes to the task of learning the structure of Bayesian Networks
S. Beretta, M. Castelli, Ivo Gonçalves, Daniele Ramazzotti
2017arXiv.org5 citations
Semantic Scholar
A Model of Selective Advantage for the Efficient Inference of Cancer Clonal Evolution
Daniele Ramazzotti
2016arXiv.org5 citations
Semantic Scholar
Design of the TRONCO BioConductor Package for TRanslational ONCOlogy
M. Antoniotti, G. Caravagna, Luca De Sano, A. Graudenzi +3 more
2015bioRxiv5 citations Open access
Semantic Scholar
Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks
Daniele Ramazzotti, Marco S. Nobile, M. Antoniotti, A. Graudenzi
2017International Conference on Conceptual Structures4 citations
Semantic Scholar
BASCULE: bayesian inference and clustering of mutational signatures leveraging biological priors
Elena Buscaroli, Azad Sadr, Riccardo Bergamin, S. Milite +6 more
2025bioRxiv3 citations Open access
Semantic Scholar
SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples
L. Mella, Avantika Lal, Fabrizio Angaroni, Davide Maspero +5 more
2022STAR Protocols3 citations Open access
Semantic Scholar

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