Stefano Beretta

38 papers C 6Misc 3Journal 20Unranked 5
YearRankTypeTitle / Venue / Authors
2020 J jnl
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites.
Bioinform.
Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini
2019 — ch.
Algorithms for Strings and Sequences: Pairwise Alignment.
Encyclopedia of Bioinformatics and Computational Biology (1)
Stefano Beretta
2019 — conf
Comparing Deep and Machine Learning Approaches in Bioinformatics: A miRNA-Target Prediction Case Study.
ICCS (3)
Valentina Giansanti, Mauro Castelli, Stefano Beretta, Ivan Merelli
2019 — ch.
Graph Theory and Definitions.
Encyclopedia of Bioinformatics and Computational Biology (1)
Stefano Beretta, Luca Denti, Marco Previtali
2019 — ch.
Network Properties.
Encyclopedia of Bioinformatics and Computational Biology (1)
Stefano Beretta, Luca Denti, Marco Previtali
2019 J jnl
Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era.
Quant. Biol.
Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni
2019 C conf
Parallel Computing in Deep Learning: Bioinformatics Case Studiesa.
PDP
Valentina Giansanti, Stefano Beretta, Daniele Cesini, Daniele D'Agostino, Ivan Merelli
2018 J jnl
A Scalable Genetic Programming Approach to Integrate miRNA-Target Predictions: Comparing Different Parallel Implementations of M3GP.
Complex.
Stefano Beretta, Mauro Castelli, Luis Muñoz, Leonardo Trujillo, Yuliana Martínez, Ales Popovic, Luciano Milanesi, Ivan Merelli
2018 J jnl
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.
BMC Bioinform.
Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni
2018 C conf
Computing Empirical P-Values for Estimating Gene-Gene Interactions in Genome-Wide Association Studies: A Parallel Computing Approach.
PDP
Valentina Giansanti, Daniele D'Agostino, Carlo Maj, Stefano Beretta, Ivan Merelli
2018 J jnl
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads.
BMC Bioinform.
Stefano Beretta, Murray Patterson, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni
2018 J jnl
Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: A Logistic Model Tree Solution.
J. Comput. Biol.
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Kel, Valentina Giansanti, Ivan Merelli
2018 J jnl
Learning the Structure of Bayesian Networks: A Quantitative Assessment of the Effect of Different Algorithmic Schemes.
Complex.
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Roberto Henriques, Daniele Ramazzotti
2017 J jnl
A quantitative assessment of the effect of different algorithmic schemes to the task of learning the structure of Bayesian Networks.
CoRR
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Daniele Ramazzotti
2017 J jnl
Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks.
CoRR
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Merelli, Daniele Ramazzotti
2017 C conf
Low-Power Architectures for miRNA-Target Genome Wide Analysis.
PDP
Stefano Beretta, Lucia Morganti, Elena Corni, Andrea Ferraro, Daniele Cesini, Daniele D'Agostino, Luciano Milanesi, Ivan Merelli
2017 — conf
Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext.
AlCoB
Stefano Beretta, Paola Bonizzoni, Luca Denti, Marco Previtali, Raffaella Rizzi
2017 Misc conf
Rank miRNA: a web tool for identifying polymorphisms altering miRNA target sites.
ICCS
Stefano Beretta, Carlo Maj, Ivan Merelli
2017 J jnl
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.
BMC Bioinform.
Giulio Spinozzi, Andrea Calabria, Stefano Brasca, Stefano Beretta, Ivan Merelli, Luciano Milanesi, Eugenio Montini
2016 Misc conf
9
ICCS
Stefano Beretta, Mario Cannataro, Mauro Castelli
2016 C conf
A Machine Learning Approach for the Integration of miRNA-Target Predictions.
PDP
Stefano Beretta, Mauro Castelli, Yuliana Martínez, Luis Muñoz, Sara Silva, Leonardo Trujillo, Luciano Milanesi, Ivan Merelli
2016 — conf
Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks.
IJCCI (ECTA)
Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Merelli, Daniele Ramazzotti
2016 J jnl
Corrigendum to "Parameterized tractability of the maximum-duo preservation string mapping problem" [Theoret. Comput. Sci. 646(2016) 16-25].
Theor. Comput. Sci.
Stefano Beretta, Mauro Castelli, Riccardo Dondi
2016 J jnl
Parameterized tractability of the maximum-duo preservation string mapping problem.
Theor. Comput. Sci.
Stefano Beretta, Mauro Castelli, Riccardo Dondi
2015 Misc conf
8
ICCS
Stefano Beretta, Mario Cannataro, Riccardo Dondi
2015 — conf
Correcting Gene Trees by Leaf Insertions: Complexity and Approximation.
ICTCS
Stefano Beretta, Riccardo Dondi
2015 J jnl
Correcting gene tree by removal and modification: Tractability and approximability.
J. Discrete Algorithms
Stefano Beretta, Mauro Castelli, Riccardo Dondi
2015 J jnl
Covering Pairs in Directed Acyclic Graphs.
Comput. J.
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
2015 J jnl
Parameterized Tractability of the Maximum-Duo Preservation String Mapping Problem.
CoRR
Stefano Beretta, Mauro Castelli, Riccardo Dondi
2014 C conf
Covering Pairs in Directed Acyclic Graphs.
LATA
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
2014 J jnl
Further Steps in TANGO: improved taxonomic assignment in metagenomics.
Bioinform.
Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente
2014 C conf
Gene Tree Correction by Leaf Removal and Modification: Tractability and Approximability.
CiE
Stefano Beretta, Riccardo Dondi
2014 J jnl
Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs.
J. Comput. Biol.
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi
2013 J jnl
A hybrid genetic algorithm for the repetition free longest common subsequence problem.
Oper. Res. Lett.
Mauro Castelli, Stefano Beretta, Leonardo Vanneschi
2013 — —
Algorithms for next generation sequencing data analysis.
Stefano Beretta
2013 J jnl
Covering Pairs in Directed Acyclic Graphs.
CoRR
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
2012 — conf
Reconstructing isoform graphs from RNA-Seq data.
BIBM
Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova
2011 J jnl
Predicting Variants of Alternative Splicing from NGS data without the Genome
CoRR
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi