Damla Senol Cali

Damla Senol Cali

Staff Software Engineer,
Hardware Acceleration

Bionano Genomics

Biography

I am a Staff Software Engineer, Hardware Acceleration at Bionano Genomics. I received my Ph.D. degree in Computer Engineering from the SAFARI Research Group at Carnegie Mellon University, where I was advised by Prof. Onur Mutlu and Prof. Saugata Ghose. My research focuses on hardware/software co-design for accelerating bioinformatics applications and genomic data analysis. I am also excited about memory systems and processing-in-memory. During my Ph.D., I also interned at Intel Labs in 2018 and 2020. I obtained my M.S. in Computer Engineering from Carnegie Mellon University in 2019, and my B.S. in Computer Engineering from Bilkent University in 2015.

Interests

  • Bioinformatics
  • Genomics
  • Hardware/Software Co-Design
  • Hardware Acceleration
  • Memory Systems
  • Processing-in-Memory

Education

  • Ph.D. in Computer Engineering, 2021

    Carnegie Mellon University

  • M.Sc. in Computer Engineering, 2019

    Carnegie Mellon University

  • B.Sc. in Computer Engineering, 2015

    Bilkent University

News

December 22, 2021

I am excited to share my video interview for the SAFARI Research Group's December'21 newsletter.

November 7, 2021

I have presented my Ph.D. dissertation on "Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design" in SAFARI Seminar Series.

November 2, 2021

My Ph.D. dissertation on "Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design" is online now.

October 11, 2021

I have joined Bionano Genomics as a "Staff Software Engineer, Hardware Acceleration".
I am very excited to continue working on accelerating genomic data analysis and being part of the amazing mission of Bionano Genomics to improve human well-being!

August 27, 2021

Today marks my last day at the SAFARI Research Group and Carnegie Mellon University!
I would like to thank my advisors Onur Mutlu and Saugata Ghose, my committee members Can Alkan and James Hoe, my industry mentors Gurpreet Singh Kalsi, Sreenivas Subramoney and Lavanya Subramanian, my friends and colleagues from SAFARI Research Group, ARCANA, and Bilkent CompGen, my family and friends, and my parents - Mine and Sinan, my sister - Irmak, and my husband - Tunca. I am very grateful to everyone who supported and helped me during this amazing journey!

July 15, 2021

I am very excited to share that I have successfully defended my Ph.D. thesis on "Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design".

June 27, 2021

I am excited to share my research summary talk: "Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design".

January 6, 2021

I am excited to share my video interview for the SAFARI Research Group's January'21 newsletter.

Publications

GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping

SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping

GenStore: A High-Performance In-Storage Processing System for Genome Sequence Analysis

FPGA-based Near-Memory Acceleration of Modern Data-Intensive Applications

GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis

Accelerating Genome Analysis: A Primer on an Ongoing Journey

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

Demystifying Workload–DRAM Interactions: An Experimental Study

GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies

Talks and Posters

Accelerating Genome Sequence Analysis via Efficient Hardware-Algorithm Co-Design

GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis

GenGraph: A Hardware Acceleration Framework for Sequence-to-Graph Mapping

GenASM: A Low-Power, Memory-Efficient Approximate String Matching Acceleration Framework for Genome Sequence Analysis

BitMAC: An In-Memory Accelerator for Bitvector-Based Sequence Alignment of Both Short and Long Genomic Reads

Top 10 Best Student Presenter Award

Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions

Accelerating Approximate Pattern Matching with Processing-In-Memory (PIM) and Single-Instruction Multiple-Data (SIMD) Programing

Best Poster Award

Experience

 
 
 
 
 

Staff Software Engineer, Hardware Acceleration

Bionano Genomics

October 2021 – Current San Diego, CA
 
 
 
 
 

Research Intern

Intel Labs

May 2020 – December 2020 Portland, OR
 
 
 
 
 

Research Intern

Intel Labs

May 2018 – August 2018 Santa Clara, CA
 
 
 
 
 

Graduate Research and Teaching Assistant

Carnegie Mellon University

August 2015 – August 2021 Pittsburgh, PA
 
 
 
 
 

Undergraduate Research and Teaching Assistant

Bilkent University

February 2013 – June 2015 Ankara, Turkey