publications

Publications in reversed chronological order. Please refer to the project page for papers' PDFs and other materials, such as slides and videos. Generated by jekyll-scholar.

2023

  1. Designing Efficient SIMD Kernels for High-Performance Sequence Alignment
    Popovici, Doru Thom, Awan, Muaaz Gul, Guidi, Giulia, Egan, Rob, Hofmeyr, Steven, Oliker, Leonid, and Yelick, Katherine
    In 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) 2023

2022

  1. Extreme-Scale Many-Against-Many Protein Similarity Search
    Selvitopi, Oguz, Ekanayake, Saliya, Guidi, Giulia, Awan, Muaaz, Pavlopoulos, Georgios, Azad, Ariful, Kyrpides, Nikos, Oliker, Leonid, Yelick, Katherine, and Buluç, Aydın
    International Conference for High Performance Computing, Networking, Storage, and Analysis (SC’22) 2022
  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

2021

  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. BuDDI: A Declarative Bloom Language for CALM Programming
    Garcia, Rolando, and Guidi, Giulia
    2021
  3. BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper
    Guidi, Giulia, Ellis, Marquita, Rokhsar, Daniel, Yelick, Katherine, and Buluç, Aydın
    In SIAM Conference on Applied and Computational Discrete Algorithms (ACDA21) 2021
  4. 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

2020

  1. The parallelism motifs of genomic data analysis
    Yelick, Katherine, Buluç, Aydın, Awan, Muaaz, Azad, Ariful, Brock, Benjamin, Egan, Rob, Ekanayake, Saliya, Ellis, Marquita, Georganas, Evangelos, Guidi, Giulia, and others,
    Philosophical Transactions of the Royal Society A 2020
  2. Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices
    Selvitopi, Oguz, Ekanayake, Saliya, Guidi, Giulia, Pavlopoulos, Georgios, Azad, Ariful, and Buluç, Aydın
    International Conference for High Performance Computing, Networking, Storage, and Analysis (SC’20) 2020
  3. LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment
    Zeni, Alberto, Guidi, Giulia, Ellis, Marquita, Ding, Nan, Santambrogio, Marco D., Hofmeyr, Steven, Buluç, Aydın, Oliker, Leonid, and Yelick, Katherine
    In International Parallel and Distributed Processing Symposium (IPDPS) 2020

2019

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

2017

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

2016

  1. On How to Improve FPGA-Based Systems Design Productivity via SDAccel
    Guidi, Giulia, Reggiani, Enrico, Di Tucci, Lorenzo, Durelli, Gianluca, Blott, Michaela, and Santambrogio, Marco D.
    In 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) 2016
  2. ProFAX: a Hardware Acceleration of a Protein Folding Algorithm
    Guidi, Giulia, Di Tucci, Lorenzo, and Santambrogio, Marco D.
    In 2016 IEEE 2nd International Forum on Research and Technologies for Society and Industry Leveraging a better tomorrow (RTSI) 2016