Giulia Guidi

PhD Student | University of California, Berkeley

ABOUT

I'm a first-year 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. I'm a member of PASSION Lab, BeBOp Group, and Performance and Algorithms Research (PAR) Group. I received both my M.Sc. in Biomedical Engineering and B.Sc. in Biomedical Engineering at Politecnico di Milano. Broadly, my research interests are Parallel Computing, Computational Genomics, and Applied Mathematics. Currently, I'm developing of a novel algorithm to de novo assemble genomes using long-read sequencing data, named Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (BELLA) and part of the ExaBiome Project.

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

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

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, 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, Marco D. Santambrogio

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

SELECTED Talks

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

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.

LOGAN

A high-performance x-drop long-read sequence alignment algorithm. Ongoing.

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.