65 citations · 376 across the 32 of their papers we have counts for
6 papers · 1 filter
Genome-on-Diet: Taming Large-Scale Genomic Analyses via Sparsified Genomics
Mohammed Alser, Julien Eudine, Onur Mutlu
Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational…
RUBICON: A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers
Gagandeep Singh, Mohammed Alser, Kristof Denolf +5
Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The a…
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping
Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati +6
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore seq…
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
Can Firtina, Kamlesh Pillai, Gurpreet S. Kalsi +10
Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequen…
COVIDHunter: COVID-19 pandemic wave prediction and mitigation via seasonality-aware modeling
Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr +2
Early detection and isolation of COVID-19 patients are essential for successful implementation of mitigation strategies and eventually curbing the disease spread. With a limited nu…
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities
Mohammed Alser, Sharon Waymost, Ram Ayyala +17
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on t…