publications

2024

1. Starlight: A kernel optimizer for GPU processing

   Alberto Zeni, Emanuele Del Sozzo, Eleonora D’Arnese, and 2 more authors

   Journal of Parallel and Distributed Computing, 2024

   Bib

   @article{zeni2024starlight,
     title = {Starlight: A kernel optimizer for GPU processing},
     author = {Zeni, Alberto and Del Sozzo, Emanuele and D'Arnese, Eleonora and Conficconi, Davide and Santambrogio, Marco D},
     journal = {Journal of Parallel and Distributed Computing},
     pages = {104832},
     year = {2024},
     publisher = {Elsevier}
   }

2023

1. New Solution For a (Scaff) Old Problem: an FPGA Approach

   Alberto Zeni, Emanuele Del Sozzo, Beatrice Branchini, and 2 more authors

   In 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2023

   Bib

   @inproceedings{zeni2023new,
     title = {New Solution For a (Scaff) Old Problem: an FPGA Approach},
     author = {Zeni, Alberto and Del Sozzo, Emanuele and Branchini, Beatrice and Di Tucci, Lorenzo and Santambrogio, Marco D},
     booktitle = {2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
     pages = {75--78},
     year = {2023},
     organization = {IEEE}
   }

2. On the Genome Sequence Alignment FPGA Acceleration via KSW2z

   Alberto Zeni, Guido Walter Di Donato, Alessia Della Valle, and 2 more authors

   In 2023 IEEE International Symposium on Circuits and Systems (ISCAS), 2023

   Bib

   @inproceedings{zeni2023genome,
     title = {On the Genome Sequence Alignment FPGA Acceleration via KSW2z},
     author = {Zeni, Alberto and Di Donato, Guido Walter and Della Valle, Alessia and Carloni, Filippo and Santambrogio, Marco D},
     booktitle = {2023 IEEE International Symposium on Circuits and Systems (ISCAS)},
     pages = {1--5},
     year = {2023},
     organization = {IEEE}
   }

3. TSUNAMI: a GPU implementation of the WFA algorithm

   Giulia Gerometta, Alberto Zeni, and Marco D Santambrogio

   In 2023 32nd International Conference on Parallel Architectures and Compilation Techniques (PACT), 2023

   Bib

   @inproceedings{gerometta2023tsunami,
     title = {TSUNAMI: a GPU implementation of the WFA algorithm},
     author = {Gerometta, Giulia and Zeni, Alberto and Santambrogio, Marco D},
     booktitle = {2023 32nd International Conference on Parallel Architectures and Compilation Techniques (PACT)},
     pages = {150--161},
     year = {2023},
     organization = {IEEE}
   }

2022

1. Method of aligning strings of characters representing genomic data and related hardware device

   ZENI Alberto, Matteo Crespi, Lorenzo Di Tucci, and 2 more authors

   Apr 2022

   US Patent App. 17/594,585

   Bib

   @misc{alberto2022method,
     title = {Method of aligning strings of characters representing genomic data and related hardware device},
     author = {Alberto, ZENI and Crespi, Matteo and Di Tucci, Lorenzo and Santambrogio, Marco Domenico and Pizzato, Fabio},
     year = {2022},
     month = apr,
     note = {US Patent App. 17/594,585}
   }

2. Pushing the level of abstraction of digital system design: A survey on how to program FPGAs

   Emanuele Del Sozzo, Davide Conficconi, Alberto Zeni, and 3 more authors

   ACM Computing Surveys, Apr 2022

   Bib

   @article{sozzo2022pushing,
     author = {Sozzo, Emanuele Del and Conficconi, Davide and Zeni, Alberto and Salaris, Mirko and Sciuto, Donatella and Santambrogio, Marco D},
     journal = {ACM Computing Surveys},
     volume = {55},
     number = {5},
     pages = {1--48},
     year = {2022},
     publisher = {ACM New York, NY}
   }

3. Fast Genome Analysis Leveraging Exact String Matching

   Beatrice Branchini, Sofia Breschi, Alberto Zeni, and 1 more author

   In 2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Apr 2022

   Bib

   @inproceedings{branchini2022fast,
     title = {Fast Genome Analysis Leveraging Exact String Matching},
     author = {Branchini, Beatrice and Breschi, Sofia and Zeni, Alberto and Santambrogio, Marco D},
     booktitle = {2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
     pages = {136--139},
     year = {2022},
     organization = {IEEE}
   }

4. Surfing the Wavefront of Genome Alignment

   Beatrice Branchini, Giulia Gerometta, Luisa Cicolini, and 3 more authors

   In 2022 IEEE International Symposium on Circuits and Systems (ISCAS), Apr 2022

   Bib

   @inproceedings{branchini2022surfing,
     title = {Surfing the Wavefront of Genome Alignment},
     author = {Branchini, Beatrice and Gerometta, Giulia and Cicolini, Luisa and Zeni, Alberto and Del Sozzo, Emanuele and Santambrogio, Marco D},
     booktitle = {2022 IEEE International Symposium on Circuits and Systems (ISCAS)},
     pages = {1754--1758},
     year = {2022},
     organization = {IEEE}
   }

5. Method for the alignment of sequence reads to cyclic genome graphs on heterogeneous computing systems

   GW Di Donato, A Zeni, M Coggi, and 3 more authors

   Apr 2022

   Bib

   @article{di2022method,
     title = {Method for the alignment of sequence reads to cyclic genome graphs on heterogeneous computing systems},
     author = {Di Donato, GW and Zeni, A and Coggi, M and Bruno, G and Santambrogio, MD and others},
     year = {2022}
   }

2021

1. The importance of being x-drop: High performance genome alignment on reconfigurable hardware

   Alberto Zeni, Guido Walter Di Donato, Lorenzo Di Tucci, and 2 more authors

   In 2021 IEEE 29th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), Apr 2021

   Bib

   @inproceedings{zeni2021importance,
     title = {The importance of being x-drop: High performance genome alignment on reconfigurable hardware},
     author = {Zeni, Alberto and Di Donato, Guido Walter and Di Tucci, Lorenzo and Rabozzi, Marco and Santambrogio, Marco D},
     booktitle = {2021 IEEE 29th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM)},
     pages = {133--141},
     year = {2021},
     organization = {IEEE}
   }

2. Optimized implementation of the hpcg benchmark on reconfigurable hardware

   Alberto Zeni, Kenneth O’Brien, Michaela Blott, and 1 more author

   In Euro-Par 2021: Parallel Processing: 27th International Conference on Parallel and Distributed Computing, Lisbon, Portugal, September 1–3, 2021, Proceedings 27, Apr 2021

   Bib

   @inproceedings{zeni2021optimized,
     title = {Optimized implementation of the hpcg benchmark on reconfigurable hardware},
     author = {Zeni, Alberto and O’Brien, Kenneth and Blott, Michaela and Santambrogio, Marco D},
     booktitle = {Euro-Par 2021: Parallel Processing: 27th International Conference on Parallel and Distributed Computing, Lisbon, Portugal, September 1--3, 2021, Proceedings 27},
     pages = {616--630},
     year = {2021},
     organization = {Springer International Publishing}
   }

2020

1. Leveraging Succinct Data Structures for DNA Sequence Mapping on FPGA

   Guido Walter Di Donato, Alberto Zeni, Lorenzo Di Tucci, and 1 more author

   In 2020 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Apr 2020

   Bib

   @inproceedings{di2020leveraging,
     title = {Leveraging Succinct Data Structures for DNA Sequence Mapping on FPGA},
     author = {Di Donato, Guido Walter and Zeni, Alberto and Di Tucci, Lorenzo and Santambrogio, Marco D},
     booktitle = {2020 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
     pages = {1--4},
     year = {2020},
     organization = {IEEE}
   }

2. Logan: High-performance gpu-based x-drop long-read alignment

   Alberto Zeni, Giulia Guidi, Marquita Ellis, and 6 more authors

   In 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS), Apr 2020

   Bib

   @inproceedings{zeni2020logan,
     title = {Logan: High-performance gpu-based x-drop long-read alignment},
     author = {Zeni, Alberto and Guidi, Giulia and Ellis, Marquita and Ding, Nan and Santambrogio, Marco D and Hofmeyr, Steven and Bulu{\c{c}}, Ayd{\i}n and Oliker, Leonid and Yelick, Katherine},
     booktitle = {2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS)},
     pages = {462--471},
     year = {2020},
     organization = {IEEE}
   }

2019

1. Metodo di allineamento di stringhe di caratteri che rappresentano dati genomici e relativo dispositivo hardware

   A Zeni, M Crespi, L Di Tucci, and 2 more authors

   Apr 2019

   Bib

   @article{zeni2019metodo,
     title = {Metodo di allineamento di stringhe di caratteri che rappresentano dati genomici e relativo dispositivo hardware},
     author = {Zeni, A and Crespi, M and Di Tucci, L and Santambrogio, M and Pizzato, F},
     year = {2019}
   }

2. An FPGA-based computing infrastructure tailored to efficiently scaffold genome sequences

   Alberto Zeni, Matteo Crespi, Lorenzo Di Tucci, and 1 more author

   In 2019 IEEE 27th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), Apr 2019

   Bib

   @inproceedings{zeni2019fpga,
     title = {An FPGA-based computing infrastructure tailored to efficiently scaffold genome sequences},
     author = {Zeni, Alberto and Crespi, Matteo and Di Tucci, Lorenzo and Santambrogio, Marco D},
     booktitle = {2019 IEEE 27th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM)},
     pages = {333--333},
     year = {2019},
     organization = {IEEE}
   }

3. circFA: a FPGA-based circular RNA aligner

   Alberto Zeni, Francesco Peverelli, Enrico Cabri, and 3 more authors

   In 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI), Apr 2019

   Bib

   @inproceedings{zeni2019circfa,
     title = {circFA: a FPGA-based circular RNA aligner},
     author = {Zeni, Alberto and Peverelli, Francesco and Cabri, Enrico and Di Tucci, Lorenzo and Cerina, Luca and Santambrogio, Marco D},
     booktitle = {2019 IEEE EMBS International Conference on Biomedical \& Health Informatics (BHI)},
     pages = {1--4},
     year = {2019},
     organization = {IEEE}
   }