Stefano Beretta

Publication Activity (10 Years)

Years Active: 2011-2023
Publications (10 Years): 23

Top Topics

Bayesian Approaches

Machine Learning

Parallel Implementation

Data Integration

Top Venues

Publications

Ivan Merelli, Stefano Beretta, Daniela Cesana, Alessandro Gennari, Fabrizio Benedicenti, Giulio Spinozzi, Daniele Cesini, Eugenio Montini, Daniele D'Agostino, Andrea Calabria
clonal tracking toward clinical genomics data integration. Database J. Biol. Databases Curation 2023 (2023)
Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites. Bioinform. 36 (5) (2020)
Valentina Giansanti, Mauro Castelli, Stefano Beretta, Ivan Merelli
Comparing Deep and Machine Learning Approaches in Bioinformatics: A miRNA-Target Prediction Case Study. ICCS (3) (2019)
Valentina Giansanti, Stefano Beretta, Daniele Cesini, Daniele D'Agostino, Ivan Merelli
Parallel Computing in Deep Learning: Bioinformatics Case Studiesa. PDP (2019)
Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni
Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era. Quant. Biol. 7 (4) (2019)
Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. BMC Bioinform. 19 (1) (2018)
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Kel, Valentina Giansanti, Ivan Merelli
Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: A Logistic Model Tree Solution. J. Comput. Biol. 25 (10) (2018)
Valentina Giansanti, Daniele D'Agostino, Carlo Maj, Stefano Beretta, Ivan Merelli
Computing Empirical P-Values for Estimating Gene-Gene Interactions in Genome-Wide Association Studies: A Parallel Computing Approach. PDP (2018)
Stefano Beretta, Murray Patterson, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinform. 19 (1) (2018)
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Roberto Henriques, Daniele Ramazzotti
Learning the Structure of Bayesian Networks: A Quantitative Assessment of the Effect of Different Algorithmic Schemes. Complex. 2018 (2018)
Stefano Beretta, Mauro Castelli, Luis Muñoz, Leonardo Trujillo, Yuliana Martínez, Ales Popovic, Luciano Milanesi, Ivan Merelli
A Scalable Genetic Programming Approach to Integrate miRNA-Target Predictions: Comparing Different Parallel Implementations of M3GP. Complex. 2018 (2018)
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Merelli, Daniele Ramazzotti
Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks. CoRR (2017)
Stefano Beretta, Paola Bonizzoni, Luca Denti, Marco Previtali, Raffaella Rizzi
Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext. AlCoB (2017)
Stefano Beretta, Lucia Morganti, Elena Corni, Andrea Ferraro, Daniele Cesini, Daniele D'Agostino, Luciano Milanesi, Ivan Merelli
Low-Power Architectures for miRNA-Target Genome Wide Analysis. PDP (2017)
Stefano Beretta, Carlo Maj, Ivan Merelli
Rank miRNA: a web tool for identifying polymorphisms altering miRNA target sites. ICCS (2017)
Giulio Spinozzi, Andrea Calabria, Stefano Brasca, Stefano Beretta, Ivan Merelli, Luciano Milanesi, Eugenio Montini
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites. BMC Bioinform. 18 (1) (2017)
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Daniele Ramazzotti
A quantitative assessment of the effect of different algorithmic schemes to the task of learning the structure of Bayesian Networks. CoRR (2017)
Stefano Beretta, Mauro Castelli, Riccardo Dondi
Parameterized tractability of the maximum-duo preservation string mapping problem. Theor. Comput. Sci. 646 (2016)
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Merelli, Daniele Ramazzotti
Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks. IJCCI (ECTA) (2016)
Stefano Beretta, Riccardo Dondi
Correcting Gene Trees by Leaf Insertions: Complexity and Approximation. Electron. Notes Theor. Comput. Sci. 322 (2016)
Stefano Beretta, Mauro Castelli, Yuliana Martínez, Luis Muñoz, Sara Silva, Leonardo Trujillo, Luciano Milanesi, Ivan Merelli
A Machine Learning Approach for the Integration of miRNA-Target Predictions. PDP (2016)
Stefano Beretta, Mario Cannataro, Mauro Castelli
Workshop on Biomedical and Bioinformatics Challenges for Computer Science - BBC2016. ICCS (2016)
Stefano Beretta, Mauro Castelli, Riccardo Dondi
Corrigendum to "Parameterized tractability of the maximum-duo preservation string mapping problem" [Theoret. Comput. Sci. 646(2016) 16-25]. Theor. Comput. Sci. 653 (2016)
Stefano Beretta, Mauro Castelli, Riccardo Dondi
Parameterized Tractability of the Maximum-Duo Preservation String Mapping Problem. CoRR (2015)
Stefano Beretta, Mauro Castelli, Riccardo Dondi
Correcting gene tree by removal and modification: Tractability and approximability. J. Discrete Algorithms 33 (2015)
Stefano Beretta, Mario Cannataro, Riccardo Dondi
Workshop on Biomedical and Bioinformatics Challenges for Computer Science - BBC2015. ICCS (2015)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. Comput. J. 58 (7) (2015)
Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente
Further Steps in TANGO: improved taxonomic assignment in metagenomics. Bioinform. 30 (1) (2014)
Stefano Beretta, Riccardo Dondi
Gene Tree Correction by Leaf Removal and Modification: Tractability and Approximability. CiE (2014)
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi
Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs. J. Comput. Biol. 21 (1) (2014)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. LATA (2014)
Mauro Castelli, Stefano Beretta, Leonardo Vanneschi
A hybrid genetic algorithm for the repetition free longest common subsequence problem. Oper. Res. Lett. 41 (6) (2013)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. CoRR (2013)
Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova
Reconstructing isoform graphs from RNA-Seq data. BIBM (2012)
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi
Predicting Variants of Alternative Splicing from NGS data without the Genome CoRR (2011)