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Performance and Algorithms Research

Giulia Guidi

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Giulia Guidi
Graduate Student Research Assistant
LBNL Office: 59-4026A

About

Giulia Guidi is a Ph.D. student in Computer Science at UC Berkeley and a graduate research assistant at the Computational Research Division of Lawrence Berkeley National Laboratory advised by Aydın Buluç and Kathy Yelick. Giulia is a 2020 SIGHPC Computational & Data Science Fellow. Giulia received both her Master's in Biomedical Engineering (2018) and her Bachelor's in Biomedical Engineering (2016) at Politecnico di MilanoHer work is in the area of computer systems research, including cloud and parallel computing, and she is interested in building a collaborative interdisciplinary research program. Giulia is currently working on the challenges of large-scale computational biology, as well as the algorithms and software infrastructures that meet the usability and performance demand of this community. Currently, she is developing a novel algorithm for de novo assembly of genomes in distributed memory using long-read sequencing data and sparse matrix abstraction as part of the ExaBiome project. Giulia is also working on how to make cloud computing more accessible for high-performance scientific computing.

Current Project

Software

Journal Articles

Katherine Yelick, Aydın Buluç, Muaaz Awan, Ariful Azad, Benjamin Brock, Rob Egan, Saliya Ekanayake, Marquita Ellis, Evangelos Georganas, Giulia Guidi, Steven Hofmeyr, Oguz Selvitopi, Cristina Teodoropol, Leonid Oliker, "The parallelism motifs of genomic data analysis", Philosophical Transactions of The Royal Society A: Mathematical, Physical and Engineering Sciences, 2020,

Conference Papers

Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick, Aydın Buluç, "BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper", SIAM Conference on Applied and Computational Discrete Algorithms (ACDA21), 2021, doi: 10.1101/464420

Giulia Guidi, Marquita Ellis, Aydin Buluc, Katherine Yelick, David Culler, "10 Years Later: Cloud Computing is Closing the Performance Gap", 4th Workshop on Hot Topics in Cloud Computing Performance (HotCloudPerf 2021) at the International Conference on Performance Engineering (ICPE) 2021., February 10, 2021,

Giulia Guidi, Oguz Selvitopi, Marquita Ellis, Leonid Oliker, Katherine Yelick, Aydin Buluc, "Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly", Proceedings of the IPDPS, 2021., October 20, 2020,

Oguz Selvitopi*, Saliya Ekanayake*, Giulia Guidi, Georgios Pavlopoulos, Ariful Azad, Aydın Buluç, "Distributed Many-to-Many Protein Sequence Alignment Using Sparse Matrices", Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis (SC’20)., 2020,

(*:joint first authors)

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick, "LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment", 34th IEEE International Parallel and Distributed Processing Symposium (IPDPS20), 2020, doi: 10.1109/IPDPS47924.2020.00055

Marquita Ellis, Giulia Guidi, Aydın Buluç, Leonid Oliker, Katherine Yelick, "diBELLA: Distributed Long Read to Long Read Alignment", 48th International Conference on Parallel Processing (ICPP), June 25, 2019,

Lorenzo Di Tucci, Giulia Guidi, Sara Notargiacomo, Luca Cerina, Alberto Scolari, Marco D. Santambrogio, "HUGenomics: A Support to Personalized Medicine Research", 2017 IEEE 3rd International Forum on Research and Technologies for Society and Industry (RTSI), October 12, 2017,

Giulia Guidi, Lorenzo Di Tucci, Marco D. Santambrogio, "ProFAX: a Hardware Acceleration of a Protein Folding Algorithm", 2016 IEEE 2nd International Forum on Research and Technologies for Society and Industry Leveraging a better tomorrow (RTSI), November 14, 2016,

Giulia Guidi, Enrico Reggiani, Lorenzo Di Tucci, Gianluca Durelli, Michaela Blott, Marco D. Santambrogio, "On How to Improve FPGA-Based Systems Design Productivity via SDAccel", 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), August 4, 2016,