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Mohammed Alser
I am a Senior Researcher and Lecturer of bioinformatics and computer architecture at D-INFK and D-ITET, ETH Zürich.
My primary research incorporates several aspects of bioinformatics, metagenomics, computational genomics, and computer architecture. I am particularly interested in rethinking the complete compute stack, starting from the way we handle input data and algorithms, to the underlying hardware architecture for efficiently analyzing genomic data on existing and unconventional (e.g., non-von Neumann) computing technologies. I am focusing on incorporating efficient genomic analyses into clinical practice for rapid surveillance of disease outbreaks, diagnosis of genetic disorders, and identification of pathogens and microbiomes around us. I am interested in transforming ideas into innovation and providing consultation services to companies and communities. I closely advise and mentor several graduate and undergraduate students (>40 overall) at ETH Zürich, CMU, and Bilkent University.
I received several international awards for innovation and academic achievements. I received the ETH Zürich Exceptional Performance Award for two consecutive years, the IEEE Turkey Doctoral Dissertation Award, the Yasser Arafat award, the prestigious TÜBITAK doctoral fellowship, and the HiPEAC Collaboration Grant. I was named the Best Palestinian PhD Student in Turkey. I earned my PhD in Computer Engineering from Bilkent University, Turkey, where I work with Can Alkan and Onur Mutlu on my doctoral thesis, “Accelerating the Understanding of Life's Code Through Better Algorithms and Hardware Design”. I was previously working at ZarLab (UCLA), CfAED (TU Dresden), and PETRONAS.
News
- May 2023: A reviewer for Switzerland's Research Partnership Grants.
- April 2023: A panelist & session chair at RECOMB 2023 to discuss hardware acceleration for omics analyses, Istanbul Marriott Hotel Sisli, Turkey.
- April 2023: Invited to deliver two talks about Sparsified Genomics and Filtering Before Parsing at BIO-Arch workshop, Istanbul Technical University, Turkey.
- March 2023: Delivered a talk about Genome-on-Diet at the workshop of Data Structures in Bioinformatics (DSB) 2023, TU Delft, Netherlands.
- Feb 2023: Invited to serve on the Program Committee of the International Society for Computational Biology & European Conference on Computational Biology (ISMB/ECCB) 2023, Lyon, France. Welcome to submit!
- Feb 2023: Invited to serve on the Program Committee of the 22nd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2023), Florida, USA. Welcome to submit! Deadline: January 21, 2023
- Jan 2023: Invited to serve on the Program Committee of the 23rd IEEE/ACM CCGRID 2023. Welcome to submit!
- Nov 2022: Invited by the Arab-German Young Academy of Sciences and Humanities (AGYA) to deliver a talk and share experiences on starting graduate programs in Bioinformatics in the Arab region.
- July 2022: Delivered a talk on Genome-on-Diet, GenStore, and SeGraM at the International Genome Graph Symposium (IGGSy) 2022.
- July 2022: Presented our Technology dictates algorithms work at the Intelligent Systems for Molecular Biology (ISMB) 2022.
- May 2022: Delivered a talk at EFCL/CSNOW to attract women into the fields of computer science and computer engineering.
- May 2022: Awarded TUBITAK UBYT 2022.
- April 2022: Our work on Critical Assessment of Metagenome Interpretation: the second round of challenges is published in Nature Methods, 2022.
- Feb 2022: Invited to deliver the first talk of the System-on-Chip Lab speaker series at Khalifa University, UAE, on "Analyzing Genomes via Efficient HW/SW Co-Design".
- Jan 2022: Nominated to represent ETH Zürich at the prestigious Global Young Scientists Summit 2022 for Nobel laureates
- Dec 2021: Member of the BioPIM project funded by the European Innovation Council’s Pathfinder program for accelerating genome analysis.
- Dec 2021: Invited to serve on the Program Committee of the 30th Conference on Intelligent Systems for Molecular Biology (ISMB 2022), USA. Welcome to submit! Deadline: January 13, 2022
- Nov 2021: Invited to serve on the Program Committee of the 7th High-Performance Computing Conference (BASARIM 2022), Turkey. Welcome to submit! Deadline: February 7, 2022
- Oct 2021: Elected as a member of the Higher Council for Innovation & Excellence (HCIE Diaspora), Palestine
- Oct 2021: Invited to serve on the Program Committee of the 21st IEEE International Workshop on High Performance Computational Biology (HiCOMB 2022), France. Welcome to submit! Deadline: January 22, 2022
- Oct 2021: Invited to serve as an external PhD examiner to the School of Engineering, Newcastle University.
- Sept 2021: Awarded ETH Zürich Performance Bonus, a recognition of exceptional performance.
- August 2021: Speaking at RECOMB 2021 about the urgent need for accelerating genome analysis
- July 2021: Presented COVIDHunter at ISMB/ECCB 2021, Virtually, 29 July 2021. Talk Video, Slides (pptx) (pdf).
- April 2021: Invited to deliver the keynote speech at The 9th International Conference on Computer, Control, Informatics and its Applications (IC3INA 2021). Welcome to submit!
- March 2021: Awarded TUBITAK UBYT 2021.
- Feb 2021: Invited to serve on the Program Committee of the ISMB/ECCB 2021. Welcome to submit!
- Jan 2021: Invited to serve on the Program Committee of the HiCOMB 2021. Welcome to submit!
- Jan 2021: My interview with SAFARI on my recent and future work is now featuring the January 2021 issue of the SAFARI Newsletter.
- Dec 2020: Our latest work, SneakySnake, is now available on Bioinformatics, arXiv, and GitHub.
- Oct 2020: Our work, GenASM, on accelerating pre-alignment filtering and sequence alignment is accepted in MICRO 2020.
- Sept 2020: Awarded ETH Zürich Performance Bonus, a recognition of exceptional performance.
- Aug 2020: Our work with UCLA, Metalign, efficient alignment-based metagenomic profiling via containment min hash is published in Genome Biology
- July 2020: Delivered the keynote speech at the ICITB 2020 on Enabling Intelligent Data Analysis.
- Dec 2019: Honored to accept the invitation of the University of Tokyo to give talks and lectures on accelerating genome analysis, in Japan.
- March 2019: Joined the kickoff meeting of the first Swiss Genome Center and Swiss Health2030 assembly, Geneva, Switzerland
- Feb 2019: Delivered a talk at Microsoft Swiss Joint Research Center Workshop 2019, Zürich, Switzerland
Selected Publications
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Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, Serghei Mangul,
"Technology dictates algorithms: Recent developments in read alignment"
Genome Biology , August 2021.
[arXiv preprint]
[Source Code and Data] -
Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, and Onur Mutlu,
"FPGA-based Near-Memory Acceleration of Modern Data-Intensive Applications"
IEEE Micro (IEEE MICRO), 2021.
[Extended arXiv preprint]
[Invited Talk Video by Mohammed Alser: A Roadmap for Fast and Efficient Genome Analysis]
[Invited Talk Video by Mohammed Alser: Accelerating Genome Analysis Using New Algorithms and Hardware Designs]
[Slides (pptx)(pdf)]
[Talk Video (1 hour 2 minutes)] -
Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, and Onur Mutlu,
"COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model" Preprint in arXiv and medRxiv, 6 February 2021.
[medRxiv preprint]
[arXiv preprint]
[COVIDHunter Source Code and Data]
[Switzerland Case Study]
[Talk Video (7 minutes)]
[ISMB/ECCB 2021 Poster (pptx) (pdf)]
[ISMB/ECCB 2021 Short Talk Slides (pptx) (pdf)] -
Mohammed Alser, Taha Shahroodi, Juan-Gomez Luna, Can Alkan, and Onur Mutlu,
"SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs"
Bioinformatics, 2020.
[Source Code]
[Online link at Bioinformatics Journal]
Poster presentation at the Swiss Genomics Forum 2019, Geneva, 27 Sept 2019.
[Poster (pptx) (pdf)]
Poster presentation at ISMB/ECCB 2019, Basel, Switzerland July 21 - July 25.
[Poster (pptx) (pdf)] -
Mohammed Alser, Zulal Bingol, Damla Senol Cali, Jeremie Kim, Saugata Ghose, Can Alkan, and Onur Mutlu,
"Accelerating Genome Analysis: A Primer on an Ongoing Journey"
IEEE Micro (IEEE MICRO), Vol. 40, No. 5, pages 65-75, September/October 2020.
[Invited Talk Video by Mohammed Alser: A Roadmap for Fast and Efficient Genome Analysis]
[Invited Talk Video by Mohammed Alser: Accelerating Genome Analysis Using New Algorithms and Hardware Designs]
[Slides (pptx)(pdf)]
[Talk Video (1 hour 2 minutes)]