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M. Antoniotti · SciRah

Researcher profile · Semantic Scholar

M. Antoniotti

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M. Antoniotti — researcher profile on SciRah

h-index: 24
Works: 143
Citations: 2,094

Most-cited papers

SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah M. Keating, D. Waltemath, Matthias König, Feng-Kai Zhang +137 more
2020Molecular Systems Biology269 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
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
A review of computational strategies for denoising and imputation of single-cell transcriptomic data.
Lucrezia Patruno, Davide Maspero, Francesco Craighero, Fabrizio Angaroni +2 more
2020Briefings in Bioinformatics60 citations
Semantic Scholar
A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development
G. de Matteis, A. Graudenzi, M. Antoniotti
2013Journal of Mathematical Biology56 citations
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
Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power
A. Graudenzi, Davide Maspero, M. D. Filippo, M. Gnugnoli +5 more
2018Journal of Biomedical Informatics33 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
Reverse engineering dynamic temporal models of biological processes and their relationships
Naren Ramakrishnan, Satish Tadepalli, L. Watson, R. Helm +2 more
2010Proceedings of the National Academy of Sciences of the United States of America30 citations Open access
Semantic Scholar
An Optimal Control Framework for the Automated Design of Personalized Cancer Treatments
Fabrizio Angaroni, A. Graudenzi, M. Rossignolo, Davide Maspero +4 more
2020Frontiers in Bioengineering and Biotechnology26 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
Chemotherapy after PD‐1 inhibitors in relapsed/refractory Hodgkin lymphoma: Outcomes and clonal evolution dynamics
E. Calabretta, A. Guidetti, F. Ricci, M. di Trani +14 more
2022British Journal of Haematology19 citations Open access
Semantic Scholar
CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks
Andrea Paroni, A. Graudenzi, G. Caravagna, Chiara Damiani +2 more
2015BMC Bioinformatics19 citations Open access
Semantic Scholar
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
2014PLoS ONE19 citations Open access
Semantic Scholar
An ontological modeling approach to cerebrovascular disease studies: The NEUROWEB case
G. Colombo, D. Merico, G. Boncoraglio, F. De Paoli +6 more
2010Journal of Biomedical Informatics19 citations Open access
Semantic Scholar
Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference
C. Cava, I. Zoppis, M. Gariboldi, I. Castiglioni +2 more
2014Journal of Clinical Bioinformatics18 citations Open access
Semantic Scholar
Different regulation of miR‐29a‐3p in glomeruli and tubules in an experimental model of angiotensin II‐dependent hypertension: potential role in renal fibrosis
G. Castoldi, C. D. di Gioia, F. Giollo, R. Carletti +5 more
2016Clinical and Experimental Pharmacology and Physiology17 citations
Semantic Scholar
Copy-Number Alterations for Tumor Progression Inference
C. Cava, I. Zoppis, M. Gariboldi, I. Castiglioni +2 more
2013Conference on Artificial Intelligence in Medicine in Europe17 citations
Semantic Scholar
Early tolerance and late persistence as alternative drug responses in cancer
Simona Punzi, D. Cittaro, Guido Gatti, Gemma Crupi +22 more
2025Nature Communications16 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
CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer
S. Rubinacci, A. Graudenzi, G. Caravagna, G. Mauri +3 more
2015Cancer Informatics16 citations Open access
Semantic Scholar
Unity is strength: Improving the detection of adversarial examples with ensemble approaches
Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani +2 more
2021Neurocomputing15 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
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
Longitudinal cancer evolution from single cells
Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani +4 more
2020bioRxiv13 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
Mutual Information Optimization for Mass Spectra Data Alignment
I. Zoppis, E. Gianazza, M. Borsani, C. Chinello +9 more
2012IEEE/ACM Transactions on Computational Biology & Bioinformatics11 citations
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
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing
Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, N. Calonaci +5 more
2023bioRxiv9 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
An application of kernel methods to gene cluster temporal meta-analysis
M. Antoniotti, Marco Carreras, Antonella Farinaccio, G. Mauri +2 more
2010Computers & Operations Research9 citations
Semantic Scholar
Scalable integration of multiomic single-cell data using generative adversarial networks
Valentina Giansanti, Francesca Giannese, O. Botrugno, Giorgia Gandolfi +4 more
2023bioRxiv8 citations Open access
Semantic Scholar
MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy
Chiara Damiani, Lorenzo Rovida, Davide Maspero, Irene Sala +6 more
2020Computational and Structural Biotechnology Journal8 citations Open access
Semantic Scholar
J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments
Fabrizio Angaroni, A. Guidi, Gianluca Ascolani, A. d'Onofrio +2 more
2022BMC Bioinformatics7 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
GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process
M. Antoniotti, Gary D Bader, G. Caravagna, Silvia Crippa +2 more
2013Bioinform.7 citations Open access
Semantic Scholar
Identification of Individualized Feature Combinations for Survival Prediction in Breast Cancer: A Comparison of Machine Learning Techniques
L. Vanneschi, Antonella Farinaccio, M. Giacobini, G. Mauri +2 more
2010Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics7 citations
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
Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays
G. Caravagna, A. d'Onofrio, M. Antoniotti, G. Mauri
2014Information and Computation6 citations Open access
Semantic Scholar
Effects of delayed immune-response in tumor immune-system interplay
G. Caravagna, A. Graudenzi, M. Antoniotti, G. Mauri +1 more
2012International Workshop on Hybrid Systems Biology6 citations Open access
Semantic Scholar
Investigating the Compositional Structure Of Deep Neural Networks
Francesco Craighero, Fabrizio Angaroni, A. Graudenzi, Fabio Stella +1 more
2020International Conference on Machine Learning, Optimization, and Data Science5 citations Open access
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
A multiscale model of intestinal crypts dynamics
A. Graudenzi, G. Caravagna, G. de Matteis, G. Mauri +1 more
20125 citations
Semantic Scholar
Analysis of Correlation Structures in Renal Cell Carcinoma Patient Data
I. Zoppis, M. Borsani, E. Gianazza, C. Chinello +7 more
2012Bioinformatics5 citations
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
A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development
G. de Matteis, A. Graudenzi, M. Antoniotti
2012Journal of Mathematical Biology4 citations
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
On the Use of Topological Features of Metabolic Networks for the Classification of Cancer Samples
Jeaneth Machicao, Francesco Craighero, Davide Maspero, Fabrizio Angaroni +4 more
2021Current Genomics3 citations Open access
Semantic Scholar

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