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

May 30, 2022

Our work, "SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping", is accepted in ISCA 2022.

December 22, 2021

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

SAFARI 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.

Slides (PDF) Slides (PPTX)

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".

Slides (PDF) Slides (PPTX) SAFARI News

June 27, 2021

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

Slides (PDF) Slides (PPTX)

January 6, 2021

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

Interview Transcript SAFARI January'21 Newsletter

Publications

Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
October 2022 In Proceedings of the 55th IEEE/ACM International Symposium on Microarchitecture (MICRO)

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

Paper
Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger, Zulal Bingol, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri Ghiasi, Gagandeep Singh, Juan Gomez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
June 2022 In Proceedings of the 49th International Symposium on Computer Architecture (ISCA)

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

Paper Source Code & Datasets ISCA'22 Talk and Q/A Video (22 minutes) Talk Slides (PDF) Talk Slides (PPTX)
Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, Onur Mutlu
February 2022 In Proceedings of the 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS)

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

Paper
Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gomez-Luna, Henk Corporaal, Onur Mutlu
July 2021 IEEE Micro

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

Paper
Damla Senol Cali, Gurpreet S. Kalsi, Zulal Bingol, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
October 2020 In Proceedings of the 53rd International Symposium on Microarchitecture (MICRO)

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

Paper Source Code Talk Video (18 minutes) Talk Slides (PDF) Talk Slides (PPTX) Live Talk and Q/A Video (15 minutes) Short Talk Video (6 minutes) Short Talk Slides (PDF) Short Talk Slides (PPTX) Lightning Talk Video (90 seconds) Lightning Talk Slides (PDF) Lightning Talk Slides (PPTX) Lecture Video (37 minutes) Lecture Slides (PDF) Lecture Talk Slides (PPTX)
Mohammed Alser, Zulal Bingol, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
September 2020 IEEE Micro

Accelerating Genome Analysis: A Primer on an Ongoing Journey

Paper
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercument Cicek, Can Alkan, Onur Mutlu
March 2020 Bioinformatics

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

Paper
Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu
July 2019 In Proceedings of the ACM International Conference on Measurement and Modeling of Computer Systems (SIGMETRICS)

Demystifying Workload–DRAM Interactions: An Experimental Study

Paper
Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
April 2018 Briefings in Bioinformatics

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

Paper arXiv Version AACBB 2019 Talk Video Slides (PDF) Slides (PPTX)
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
January 2018 BMC Genomics

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

Paper

Talks and Posters

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

June 18, 2022 • 4th HPCA Workshop on Accelerator Architecture in Computational Biology and Bioinformatics (AACBB), New York City, NY
Slides (PDF) Slides (PPTX)

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

May 24, 2022 RECOMB 2022 Poster Session, San Diego, CA
Poster (PDF) Poster (PPTX)

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

Sep 14, 2021 TECHCON 2021 (Virtual)
Talk Video Slides (PDF) Slides (PPTX)

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

Sep 10, 2020 ARM Research Summit 2020 (Virtual)
Talk Video Short Talk Video and Q&A Slides (PDF) Slides (PPTX)

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

Top 10 Best Student Presenter Award
Sep 10, 2019 TECHCON 2019, Austin, TX

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

Feb 16, 2019 2nd HPCA Workshop on Accelerator Architecture in Computational Biology and Bioinformatics (AACBB), Washington, DC
Talk Video Slides (PDF) Slides (PPTX)

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

Best Poster Award
Apr 21, 2018 RECOMB-Seq 2018, Paris, France

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