Giulia Guidi

PhD Student | University of California, Berkeley

ABOUT

Giulia 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 and a member of PASSION Lab, BeBOp Group, and Performance and Algorithms Research (PAR) Group. She received both my M.Sc. in Biomedical Engineering and B.Sc. in Biomedical Engineering at Politecnico di Milano. Giulia's research is focused on the development of a novel algorithm to de novo assemble genomes in distributed memory using long-read sequencing data as part of the ExaBiome Project. Giulia is interested in the intersection of High-Performance Computing (HPC) and Computational Biology as enabling technology for faster, high-quality bioinformatics and biomedical research.

CONTACT: GGUIDI at BERKELEY dot EDU | GGUIDI at LBL dot GOV

Social & News

Inspiring Quotes

Jump, and you will find out how to unfold your wings as you fall. —Ray Bradbury

You know, sometimes all you need is twenty seconds of insane courage. Just literally twenty seconds of just embarrassing bravery. And I promise you, something great will come of it. —Benjamin Mee, We Bought a Zoo

What is important is to keep learning, to enjoy challenge, and to tolerate ambiguity. In the end there are no certain answers. —Martina Horner

Software

Distributed memory version of BELLA based on MPI and using CombBLAS library. diBELLA uses BELLA's overlapping methodology and completes it adding a transitive reduction step performed through algebraic operations, a repeat resolution step, and a scaffolding step to obtain an end-to-end distributed memory long-read assembler.

Distributed memory protein sequence aligner based on MPI and using CombBLAS library.

The first high-performance GPU-based implementation of the popular x-drop alignment algorithm.

A computationally efficient and highly accurate long-read to long-read aligner and overlapper. BELLA is written in C++ and it is currently implemented in shared-memory, single node using OpenMP.

SELECTED PUBLICATIONS

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly | PDF

Giulia Guidi, Oguz Selvitopi, Marquita Ellis, Leonid Oliker, Katherine Yelick, Aydın Buluç

arXiv:2010.10055 [cs.DC]

Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices | PDF

Oguz Selvitopi , Saliya Ekanayake , Giulia Guidi, Georgios A. Pavlopoulos , Ariful Azad, Aydın Buluç

International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'20)

The Parallelism Motifs of Genomic Data Analysis | PDF

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

Philosophical Transactions of the Royal Society A

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment | PDF

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, and Katherine Yelick

International Parallel and Distributed Processing Symposium (IPDPS 2020)

diBELLA: Distributed Long Read to Long Read Alignment | PDF

Marquita Ellis, Giulia Guidi, Aydın Buluç, Leonid Oliker and Katherine Yelick

48th International Conference on Parallel Processing (ICPP 2019)

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper | PDF

Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick and Aydın Buluç

bioRxiv, doi: https://doi.org/10.1101/464420

On How to Improve FPGA-based Systems Design Productivity via SDAccel PDF

Giulia Guidi, Enrico Reggiani, Lorenzo Di Tucci, Gianluca Durelli, Michaela Blott, and Marco D. Santambrogio

2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)

ProFAX: a Hardware Acceleration of a Protein Folding Algorithm | PDF

Giulia Guidi, Lorenzo Di Tucci, and Marco D. Santambrogio

2016 IEEE 2nd International Forum on Research and Technologies for Society and Industry Leveraging a better tomorrow (RTSI)

SELECTED Talks

Redesigning Genomics Overlap Detection Through the Lens of Linear Algebra

CS Seminar, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 2020.

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper

Biological Data Science Meeting, Cold Spring Harbor Laboratory. New York, NY, USA. 2018.

Northern California Computational Biology Conference, UCSF. San Francisco, CA, USA. 2018.

ProFAX: a Hardware Acceleration of a Protein Folding Algorithm

Xilinx Ireland. Saggart, County Dublin, Ireland. 2016.

Swarm Lab at UC Berkeley. Berkeley, CA, USA. 2016.

Selected projects

Untangling the Performance Gap between HPC and Cloud Systems: A Case Study

Computational sciences, such as computational cosmology, provide an important pool of first-class, large-scale problems. Scientists have historically resorted to the massive computing resources of High-Performance Computing (HPC) systems to run their software. In the past decade, however, cloud computing has been gaining increasing popularity among scientists as an alternative to HPC. Despite the prolific literature comparing HPC and cloud systems and promising results, the question of whether cloud computing can match HPC performance fora wide range of scientific applications is still open. Ongoing.

diBELLA: Distributed Long-Read to Long-Read Alignment

A distributed memory parallelization of BELLA. Ongoing.

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper

A computationally efficient and highly accurate long-read to long-read aligner and overlapper. Distributed long-read assembler-to-be. Ongoing.

Optimizing X-Drop Alignment via Adaptive Band and Instruction-Level Parallelism

A high-performance adaptive banded and vectorized pairwise alignment . Ongoing.

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

A high-performance GPU-based x-drop long-read sequence alignment algorithm. Last update: Fall 2019.

Toward a Guide for Noisy Sequence Alignment

Exploration of noisy, long-read data features of that could facilitate the separation of overlapping sequences from non-overlapping ones in the context of the de novo genome assembly using linear support vector machine, gradient-boosting classifier, and random forest classifier. Last update: Fall 2018.

ProFAX: a Hardware Acceleration of a Protein Folding Algorithm

FPGA-based implementation of a protein folding algorithm. Last update: Fall 2016.