publications | Alberto Zeni, PhD

2026

MTIA 300: Meta’s First Training Chip with Built-in NICs and Collective Offloading Engines

MTIA Team

In International Symposium on Computer Architecture (ISCA), Jul 2026

Alberto Zeni is a member of the MTIA team that published this paper

Bib

@inproceedings{zeni2026mtia,
  title = {MTIA 300: Meta's First Training Chip with Built-in NICs and Collective Offloading Engines},
  author = {Team, MTIA},
  booktitle = {International Symposium on Computer Architecture (ISCA)},
  year = {2026},
  month = jul,
  note = {Alberto Zeni is a member of the MTIA team that published this paper}
}

2024

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, Jul 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}
}

Leveraging Difference Recurrence Relations for High-Performance GPU Genome Alignment

Alberto Zeni, Seth Onken, Marco D Santambrogio, and 1 more author

In 2024 33rd International Conference on Parallel Architectures and Compilation Techniques (PACT), Oct 2024

Bib

@inproceedings{zeni2024leveraging,
  title = {Leveraging Difference Recurrence Relations for High-Performance GPU Genome Alignment},
  author = {Zeni, Alberto and Onken, Seth and Santambrogio, Marco D and Samadi, Mehrzad},
  booktitle = {2024 33rd International Conference on Parallel Architectures and Compilation Techniques (PACT)},
  year = {2024},
  month = oct,
  organization = {IEEE}
}

The Genomic Computing Revolution: Defining the Next Decades of Accelerating Genomics

Harisankar Sadasivan, Artur Klauser, Juergen Hench, and 10 more authors

In 2024 IEEE High Performance Extreme Computing Conference (HPEC), Oct 2024

Bib

@inproceedings{sadasivan2024genomic,
  title = {The Genomic Computing Revolution: Defining the Next Decades of Accelerating Genomics},
  author = {Sadasivan, Harisankar and Klauser, Artur and Hench, Juergen and Turakhia, Yatish and Singh, Gagandeep and Zeni, Alberto and Beecroft, Sarah and Narayanasamy, Satish and Nivala, Jeff and Robey, Bob and Mutlu, Onur and Denolf, Kristof and Sitaraman, Sriranjani},
  booktitle = {2024 IEEE High Performance Extreme Computing Conference (HPEC)},
  year = {2024},
  organization = {IEEE}
}

2023

Methods for the alignment of sequence reads to non-acyclic genome graphs on heterogeneous computing systems

Guido Walter Di Donato, Alberto Zeni, Mirko Coggi, and 2 more authors

Oct 2023

Pub. No. WO2023170091A1

Bib

@article{di2022method,
  title = {Methods for the alignment of sequence reads to non-acyclic genome graphs on heterogeneous computing systems},
  author = {Di Donato, Guido Walter and Zeni, Alberto and Coggi, Mirko and Bruno, Guglielmo and Santambrogio, Marco Domenico},
  year = {2023},
  note = {Pub. No. WO2023170091A1}
}

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), Oct 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}
}

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), Oct 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}
}

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), Oct 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

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}
}

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}
}

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}
}

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}
}

2021

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}
}

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

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}
}

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

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}
}

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}
}

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}
}