GRAUDENZI, ALEX
GRAUDENZI, ALEX
Istituto di Bioimmagini e Fisiologia Molecolare - IBFM
Chemotherapy after PD-1 inhibitors in relapsed/refractory Hodgkin lymphoma: Outcomes and clonal evolution dynamics
2022 Calabretta E.; Guidetti A.; Ricci F.; Di Trani M.; Monfrini C.; Magagnoli M.; Bramanti S.; Maspero D.; Morello L.; Merli M.; Di Rocco A.; Graudenzi A.; Derenzini E.; Antoniotti M.; Rossi D.; Corradini P.; Santoro A.; CarloStella C.
Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data
2022 Ramazzotti, D; Maspero, D; Angaroni, F; Spinelli, S; Antoniotti, M; Piazza, R; Graudenzi, A
J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments
2022 Angaroni F.; Guidi A.; Ascolani G.; d'Onofrio A.; Antoniotti M.; Graudenzi A.
LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data
2022 Ramazzotti D.; Angaroni F.; Maspero D.; Ascolani G.; Castiglioni I.; Piazza R.; Antoniotti M.; Graudenzi A.
Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution
2022 Ramazzotti, D; Angaroni, F; Maspero, D; Mauri, M; D'Aliberti, D; Fontana, D; Antoniotti, M; Elli, Em; Graudenzi, A; Piazza, R
PMCE: efficient inference of expressive models of cancer evolution with high prognostic power
2022 Angaroni, F; Chen, K; Damiani, C; Caravagna, G; Graudenzi, A; Ramazotti, D
SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples
2022 Mella L.; Lal A.; Angaroni F.;, Maspero D.; Piazza R.; Sidow A.; Antoniotti M.; Graudenzi A.; Ramazzotti D.
Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines
2022 Ramazzotti D.; Angaroni F.; Maspero D.; Ascolani G.; Castiglioni I.; Piazza R.; Antoniotti M.; Graudenzi A.
A review of computational strategies for denoising and imputation of single-cell transcriptomic data
2021 Patruno, L; Maspero, M; Craighero, F; Angaroni, F; Antoniotti, M; Graudenzi, A
Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems
2021 Patruno, L; Craighero, F; Maspero, D; Graudenzi, A; Damiani, C
On the Use of Topological Features of Metabolic Networks for the Classification of Cancer Samples
2021 Machicao J.; Craighero F.; Maspero D.; Angaroni F.; Damiani C.; Graudenzi A.; Antoniotti M.; Bruno O.M.
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
2021 Ramazzotti, D; Angaroni, F; Maspero, D; Gambacortipasserini, C; Antoniotti, M; Graudenzi, A; Piazza, R
VirMutSig: Discovery and assignment of viral mutational signatures from sequencing data
2021 Maspero, D; Angaroni, F; Porro, D; Piazza, R; Graudenzi, A; Ramazzotti, D
An Optimal Control Framework for the Automated Design of Personalized Cancer Treatments
2020 Angaroni F.; Graudenzi A.; Rossignolo M.; Maspero D.; Calarco T.; Piazza R.; Montangero S.; Antoniotti M.
FBCA, A multiscale modeling framework combining cellular automata and flux balance analysis
2020 Graudenzi, A; Maspero, D; Damiani, C
MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy
2020 Damiani, C; Rovida, L; Maspero, D; Sala, I; Rosato, L; Di Filippo, M; Pescini, D; Graudenzi, A; Antoniotti, M; Mauri, G
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data
2019 Daniele Ramazzotti ; Alex Graudenzi ; Luca De Sano ; Marco Antoniotti ;Giulio Caravagna
Pathway-based classification of breast cancer subtypes
2017 Graudenzi, Alex; Cava, Claudia; Bertoli, Gloria; Fromm, Bastian; Flatmark, Kjersti; Mauri, Giancarlo; Castiglioni, Isabella
SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data
2017 Cava, Claudia; Colaprico, Antonio; Bertoli, Gloria; Graudenzi, Alex; C Silva, Tiago; Olsen, Catharina; Noushmehr, Houtan; Bontempi, Gianluca; Mauri, Giancarlo; Castiglioni, Isabella
Algorithmic methods to infer the evolutionary trajectories in cancer progression
2016 Caravagna, Giulio; Graudenzi, Alex; Ramazzotti, Daniele; Sanzpamplona, Rebeca; De Sano, Luca; Mauri, Giancarlo; Moreno, Victor; Antoniotti, Marco; Mishra, Bud
| Titolo | Data di pubblicazione | Autore(i) | File |
|---|---|---|---|
| Chemotherapy after PD-1 inhibitors in relapsed/refractory Hodgkin lymphoma: Outcomes and clonal evolution dynamics | 1-gen-2022 | Calabretta E.; Guidetti A.; Ricci F.; Di Trani M.; Monfrini C.; Magagnoli M.; Bramanti S.; Maspero D.; Morello L.; Merli M.; Di Rocco A.; Graudenzi A.; Derenzini E.; Antoniotti M.; Rossi D.; Corradini P.; Santoro A.; CarloStella C. | |
| Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data | 1-gen-2022 | Ramazzotti, D; Maspero, D; Angaroni, F; Spinelli, S; Antoniotti, M; Piazza, R; Graudenzi, A | |
| J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments | 1-gen-2022 | Angaroni F.; Guidi A.; Ascolani G.; d'Onofrio A.; Antoniotti M.; Graudenzi A. | |
| LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data | 1-gen-2022 | Ramazzotti D.; Angaroni F.; Maspero D.; Ascolani G.; Castiglioni I.; Piazza R.; Antoniotti M.; Graudenzi A. | |
| Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution | 1-gen-2022 | Ramazzotti, D; Angaroni, F; Maspero, D; Mauri, M; D'Aliberti, D; Fontana, D; Antoniotti, M; Elli, Em; Graudenzi, A; Piazza, R | |
| PMCE: efficient inference of expressive models of cancer evolution with high prognostic power | 1-gen-2022 | Angaroni, F; Chen, K; Damiani, C; Caravagna, G; Graudenzi, A; Ramazotti, D | |
| SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples | 1-gen-2022 | Mella L.; Lal A.; Angaroni F.;, Maspero D.; Piazza R.; Sidow A.; Antoniotti M.; Graudenzi A.; Ramazzotti D. | |
| Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines | 1-gen-2022 | Ramazzotti D.; Angaroni F.; Maspero D.; Ascolani G.; Castiglioni I.; Piazza R.; Antoniotti M.; Graudenzi A. | |
| A review of computational strategies for denoising and imputation of single-cell transcriptomic data | 1-gen-2021 | Patruno, L; Maspero, M; Craighero, F; Angaroni, F; Antoniotti, M; Graudenzi, A | |
| Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems | 1-gen-2021 | Patruno, L; Craighero, F; Maspero, D; Graudenzi, A; Damiani, C | |
| On the Use of Topological Features of Metabolic Networks for the Classification of Cancer Samples | 1-gen-2021 | Machicao J.; Craighero F.; Maspero D.; Angaroni F.; Damiani C.; Graudenzi A.; Antoniotti M.; Bruno O.M. | |
| VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples | 1-gen-2021 | Ramazzotti, D; Angaroni, F; Maspero, D; Gambacortipasserini, C; Antoniotti, M; Graudenzi, A; Piazza, R | |
| VirMutSig: Discovery and assignment of viral mutational signatures from sequencing data | 1-gen-2021 | Maspero, D; Angaroni, F; Porro, D; Piazza, R; Graudenzi, A; Ramazzotti, D | |
| An Optimal Control Framework for the Automated Design of Personalized Cancer Treatments | 1-gen-2020 | Angaroni F.; Graudenzi A.; Rossignolo M.; Maspero D.; Calarco T.; Piazza R.; Montangero S.; Antoniotti M. | |
| FBCA, A multiscale modeling framework combining cellular automata and flux balance analysis | 1-gen-2020 | Graudenzi, A; Maspero, D; Damiani, C | |
| MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy | 1-gen-2020 | Damiani, C; Rovida, L; Maspero, D; Sala, I; Rosato, L; Di Filippo, M; Pescini, D; Graudenzi, A; Antoniotti, M; Mauri, G | |
| Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data | 1-gen-2019 | Daniele Ramazzotti ; Alex Graudenzi ; Luca De Sano ; Marco Antoniotti ;Giulio Caravagna | |
| Pathway-based classification of breast cancer subtypes | 1-gen-2017 | Graudenzi, Alex; Cava, Claudia; Bertoli, Gloria; Fromm, Bastian; Flatmark, Kjersti; Mauri, Giancarlo; Castiglioni, Isabella | |
| SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data | 1-gen-2017 | Cava, Claudia; Colaprico, Antonio; Bertoli, Gloria; Graudenzi, Alex; C Silva, Tiago; Olsen, Catharina; Noushmehr, Houtan; Bontempi, Gianluca; Mauri, Giancarlo; Castiglioni, Isabella | |
| Algorithmic methods to infer the evolutionary trajectories in cancer progression | 1-gen-2016 | Caravagna, Giulio; Graudenzi, Alex; Ramazzotti, Daniele; Sanzpamplona, Rebeca; De Sano, Luca; Mauri, Giancarlo; Moreno, Victor; Antoniotti, Marco; Mishra, Bud |