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Nature Communications|January 21, 2025
Taming large-scale genomic analyses via sparsified genomicsMohammed Alser, Julien Eudine, Onur Mutlu
Bioinformatics (Oxford, England)|March 30, 2019
Shouji: a fast and efficient pre-alignment filter for sequence alignmentMohammed Alser, Hasan Hassan, Akash Kumar, et al.
Bioinformatics (Oxford, England)|December 14, 2020
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAsMohammed Alser, Taha Shahroodi, Juan Gómez-Luna, et al.
Bioinformatics (Oxford, England)|June 3, 2017
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mappingMohammed Alser, Hasan Hassan, Hongyi Xin, et al.
Frontiers in Public Health|July 5, 2022
COVIDHunter: COVID-19 Pandemic Wave Prediction and Mitigation via Seasonality Aware ModelingMohammed Alser, Jeremie S Kim, Nour Almadhoun Alserr, et al.
Bioinformatics (Oxford, England)|March 27, 2023
A framework for high-throughput sequence alignment using real processing-in-memory systemsSafaa Diab, Amir Nassereldine, Mohammed Alser, et al.
Bioinformatics (Oxford, England)|March 24, 2023
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICsJoël Lindegger, Damla Senol Cali, Mohammed Alser, et al.
Computational and Structural Biotechnology Journal|September 12, 2022
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architecturesMohammed Alser, Joel Lindegger, Can Firtina, et al.
Bioinformatics (Oxford, England)|March 14, 2020
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithmCan Firtina, Jeremie S Kim, Mohammed Alser, et al.
Genome Biology|February 16, 2024
RUBICON: a framework for designing efficient deep learning-based genomic basecallersGagandeep Singh, Mohammed Alser, Kristof Denolf, et al.
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