publications

Publications in reversed chronological order. Generated by jekyll-scholar.

2021

  1. 10 years later: cloud computing is closing the performance gap
    Guidi, Giulia, Ellis, Marquita, Buluç, Aydın, Yelick, Katherine, and Culler, David
    Companion of the 2021 ACM/SPEC International Conference on Performance Engineering (ICPE21 Companion) 2021
  2. 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
    2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS) 2021

2020

  1. BELLA: berkeley efficient long-read to long-read aligner and overlapper
    Guidi, Giulia, Ellis, Marquita, Rokhsar, Daniel, Yelick, Katherine, and Buluç, Aydın
    bioRxiv 2020
  2. 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
  3. LOGAN: high-performance GPU-based x-drop long-read alignment
    Zeni, Alberto, Guidi, Giulia, Ellis, Marquita, Ding, Nan, Santambrogio, Marco Domenico, Hofmeyr, Steven, Buluç, Aydın, Oliker, Leonid, and Yelick, Katherine
    In 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS) 2020
  4. 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

2019

  1. diBELLA: distributed long read to long read alignment
    Ellis, Marquita, Guidi, Giulia, Buluç, Aydın, Oliker, Leonid, and Yelick, Katherine
    In Proceedings of the 48th International Conference on Parallel Processing 2019

2017

  1. HUGenomics: a support to personalized medicine research
    Di Tucci, Lorenzo, Guidi, Giulia, Notargiacomo, Sara, Cerina, Luca, Scolari, Alberto, and Santambrogio, Marco Domenico
    In 2017 IEEE 3rd International Forum on Research and Technologies for Society and Industry (RTSI) 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 Domenico
    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 Domenico
    In 2016 IEEE 2nd International Forum on Research and Technologies for Society and Industry Leveraging a better tomorrow (RTSI) 2016