Giulia Guidi, PhD

Project Scientist in the Applied Math and Computational Sciences Division at Lawrence Berkeley National Laboratory | she/her

584-2

Soda Hall, UC Berkeley

Berkeley, CA, USA 94720

I will be starting as an Assistant Professor of Computer Science at Cornell University in Spring 2023.

I work on challenges at the intersection of large-scale computational biology and the algorithms and software infrastructures. I leverage high-performance computing techniques and computer systems and architectures to make genomics data processing faster and more flexible for the community, and to enable higher-quality bioinformatics and biomedical research. Another important focus of my work is developing software to make cloud infrastructures more accessible for high-performance scientific computing.

I am recruiting PhD students with some background in parallel programming and interest in high-performance computing for computational sciences. If you are a prospective PhD student, please read the students page.

I received my PhD in Computer Science from UC Berkeley in August 2022 under the supervision of Aydın Buluç and Kathy Yelick and my dissertation is titled “Parallel Algorithms for De Novo Long Read Genome Assembly via Sparse Linear Algebra”. You can read about it here and watch the defense recording here.

I received a 2020 SIGHPC Computational & Data Science Fellowship and work as a Project Scientist in the Applied Math and Computational Sciences Division at Lawrence Berkeley National Laboratory.

Here are a recent CV and the Tl;dr version of my Research Statement.

The best way to contact me is by email: gg434 at cornell dot edu.

news

Sep 26, 2022 In Spring 2023, I will be teaching CS5220 at Cornell University.
Sep 16, 2022 I’m very pleased to have been invited to give a talk at the minisymposium on Combinatorial Scientific Computing at the SIAM conference on Computational Science and Engineering (CSE) 2023. Looking forward to being in Amsterdam next February!
Jul 30, 2022 I’m very happy I have been invited to give a seminar on parallel algorithms for genomic analysis at SRI International (Menlo Park, CA) on August 4, 2022.
Jul 29, 2022 On August 4, 2022, I’ll be a panelist for the OpenACC panel on “Current and Future Approaches to Parallel Programming”.
Jul 5, 2022 I’m very excited to announce our paper titled “Extreme-Scale Many-Against-Many Protein Similarity Search” has been selected as a finalist for the 2022 ACM Gordon Bell Prize.
Jun 16, 2022 I’m happy to announce our paper titled “Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly” has been accepted for publication at the 51st International Conference on Parallel Processing (ICPP) 2022.
Apr 12, 2022 I will be joining Cornell as an Assistant Professor in the Department of Computer Science Cornell Bowers CIS in Spring 2023!
Mar 23, 2022 I’m honored to receive the 2022 Outstanding Graduate Student Instructor Award from the UC Berkeley GSI Teaching and Resource Center. I truly enjoyed my time as TA (GSI) for Applications of Parallel Computers!

selected publications

  1. 10 Years Later: Cloud Computing is Closing the Performance Gap
    Guidi, Giulia, Ellis, Marquita, Buluç, Aydın, Yelick, Katherine, and Culler, David
    4th Workshop on Hot Topics in Cloud Computing Performance at the International Conference on Performance Engineering (ICPE) 2021. 2021
  2. Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly
    Guidi, Giulia, Raulet, Gabriel, Rokhsar, Daniel, Oliker, Leonid, Yelick, Katherine, and Buluç, Aydın
    In 51th International Conference on Parallel Processing (ICPP) 2022
  3. Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly
    Guidi, Giulia, Selvitopi, Oguz, Ellis, Marquita, Oliker, Leonid, Yelick, Katherine, and Buluç, Aydın
    In International Parallel and Distributed Processing Symposium (IPDPS) 2021