Call for Participation:

AACBB 2022

We welcome you to take part in the 4th Accelerator Architecture in Computational Biology and Bioinformatics workshop (AACBB-2022) In conjunction with 49th IEEE International Symposium on Computer Architecture

June 18th 2022
New York City, New York, USA
Featuring invited talks by

  • Lisa Wu Willis, Duke
  • Onur Mutlu, ETH Zurich and CMU
  • Tajana Rosing, UCSD

Workshop website:

Accepted papers:

  1. Alireza Mohammadidoost, Kyle Smith and Yatish Turakhia: GPU Acceleration of Pairwise Sequence Alignment Using Wavefront Skipping
  2. Miquel Moreto and Santiago Marco-Sola: Accelerating the Wavefront Alignment Algorithm on CPUs, GPUs and FPGAs
  3. Elena Espinosa, Ivan Fernandez, Rafael Larrosa Jiménez and Oscar Plata: Whole-Genome Assembly: An Experimental Study of Computational Costs and Architectural Opportunities
  4. Damla Senol Cali, Saugata Ghose and Onur Mutlu: Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design
  5. Zheming Jin: Performance Portability of Epistasis Detection using SYCL on a GPU
  6. Yuhao Fang, Aman Sinha and Bo-Cheng Lai: REAL-GSM: Re-programmable Engines for Acceleration on LPDDR4x-based Stacked DRAM to support Genomic String Matching
  7. Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa, Jeremie Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser and Onur Mutlu: GenStore: A High-Performance In-Storage Processing System for Genome Sequence Analysis
  8. Esteban Garzón, Roman Golman, Zuher Jahshan, Robert Hanhan, Natan Vinshtok-Melnik, Marco Lanuzza, Adam Teman, Leonid Yavits: Hamming Distance vs. Edit Distance for Approximate Associative Genomic Processing

List of Topics

This workshop focuses on architecture and design of hardware and software accelerators for computational biology and bioinformatics problems. Topics of interest include, but are not limited to the following:

Hardware and software algorithms/applications in the fields of computational biology, such as (but not limited to):

  • Bioinformatics
  • Genomics
  • Proteomics
  • Protein structure prediction
  • Covid-19 pandemic

Bioinformatics and computational biology accelerator architecture and design based on (but not limited to):

  • 3D memory-logic stack
  • Near-data (in-memory) processing
  • In-data processing
  • FPGAs
  • Reconfigurable architectures
  • Emerging memory technologies and their impact on bioinformatics and computational biology
  • Impact of bioinformatics and biology applications on computer architecture research
  • Bioinformatics and computational biology-inspired hardware/software trade-offs


Program Committee

  • Ananth Kalyanaraman, WSU
  • Can Alkan, Bilkent University
  • Engin Ipek, University of Rochester
  • Jason Cong, UCLA
  • Mattan Erez, UT Austin
  • Mircea Stan, UVA
  • Onur Mutlu, ETH/CMU
  • Ran Ginosar, Technion
  • Ronnie Ronen, Technion
  • Yuan Xie, UCSB

Organizing committee

* Department of Engineering, Bar Ilan University ^ Department of Electrical and Computer Engineering, University of California, San Diego


All questions about submissions should be emailed to Leonid Yavits (