An FPGA-based design and implementation of an all-digital serializer for inter module communication in SoC. - Maher Assaad; Mohammed H. Alser (IEICE Electron. Express, 2011)

Design of an All-Digital Synchronized Frequency Multiplier Based on a Dual-Loop (D/FLL) Architecture. - Maher Assaad; Mohammed H. Alser (VLSI Design, 2012)

Design and Characterization of Low Power and Low Noise Truly All-Digital Clock and Data Recovery Circuit for SERDES Devices. - Maher Assaad; Mohammed H. Alser; Amine Bermak (J. Low Power Electron., 2013)

Can you Really Anonymize the Donors of Genomic Data in Today's Digital World? - Mohammed Alser; Nour Almadhoun; Azita Nouri; Can Alkan; Erman Ayday (DPM/QASA@ESORICS, 2015)

GateKeeper: Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture. - Mohammed Alser; Hasan Hassan; Hongyi Xin; Oguz Ergin; Onur Mutlu; Can Alkan (CoRR, 2016)

GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. - Mohammed Alser; Hasan Hassan; Hongyi Xin; Oguz Ergin; Onur Mutlu; Can Alkan (Bioinform., 2017)

GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. - Jeremie S. Kim; Damla Senol Cali; Hongyi Xin; Donghyuk Lee; Saugata Ghose; Mohammed Alser; Hasan Hassan; Oguz Ergin; Can Alkan; Onur Mutlu (BMC Genom., 2018)

SLIDER: Fast and Efficient Computation of Banded Sequence Alignment. - Mohammed Alser; Hasan Hassan; Akash Kumar 001; Onur Mutlu; Can Alkan (CoRR, 2018)

Accelerating the understanding of life 's code through better algorithms and hardware design (Yaşamın kodunu anlamayı daha iyi algoritmalar ve donanım tasarımlarıyla hızlandırmak) - Mohammed H. K. Alser (2018)

Shouji: a fast and efficient pre-alignment filter for sequence alignment. - Mohammed Alser; Hasan Hassan; Akash Kumar 001; Onur Mutlu; Can Alkan (Bioinform., 2019)

Accelerating the Understanding of Life's Code Through Better Algorithms and Hardware Design. - Mohammed H. K. Alser (CoRR, 2019)

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. - Jeremie S. Kim; Can Firtina; Meryem Banu Cavlak; Damla Senol Cali; Mohammed Alser; Nastaran Hajinazar; Can Alkan; Onur Mutlu (CoRR, 2019)

Techniques for Reducing the Connected-Standby Energy Consumption of Mobile Devices. - Jawad Haj-Yahya; Yanos Sazeides; Mohammed Alser; Efraim Rotem; Onur Mutlu (HPCA, 2020)

NATSA: A Near-Data Processing Accelerator for Time Series Analysis. - Ivan Fernandez; Ricardo Quislant; Eladio Gutiérrez; Oscar G. Plata; Christina Giannoula; Mohammed Alser; Juan Gómez-Luna; Onur Mutlu (ICCD, 2020)

SysScale: Exploiting Multi-domain Dynamic Voltage and Frequency Scaling for Energy Efficient Mobile Processors. - Jawad Haj-Yahya; Mohammed Alser; Jeremie S. Kim; Abdullah Giray Yaglikçi; Nandita Vijaykumar; Efraim Rotem; Onur Mutlu (ISCA, 2020)

GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. - Damla Senol Cali; Gurpreet S. Kalsi; Zülal Bingöl; Can Firtina; Lavanya Subramanian; Jeremie S. Kim; Rachata Ausavarungnirun; Mohammed Alser; Juan Gómez-Luna; Amirali Boroumand; Anant Nori; Allison Scibisz; et al. (MICRO, 2020)

FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors. - Jawad Haj-Yahya; Mohammed Alser; Jeremie S. Kim; Lois Orosa 001; Efraim Rotem; Avi Mendelson; Anupam Chattopadhyay; Onur Mutlu (MICRO, 2020)

Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. - Can Firtina; Jeremie S. Kim; Mohammed Alser; Damla Senol Cali; A. Ercüment Çiçek; Can Alkan; Onur Mutlu (Bioinform., 2020)

Accelerating Genome Analysis: A Primer on an Ongoing Journey. - Mohammed Alser; Zülal Bingöl; Damla Senol Cali; Jeremie S. Kim; Saugata Ghose; Can Alkan; Onur Mutlu (IEEE Micro, 2020)

SIMDRAM: a framework for bit-serial SIMD processing using DRAM. - Nastaran Hajinazar; Geraldo F. Oliveira; Sven Gregorio; João Dinis Ferreira; Nika Mansouri-Ghiasi; Minesh Patel; Mohammed Alser; Saugata Ghose; Juan Gómez-Luna; Onur Mutlu (ASPLOS, 2021)

IChannels: Exploiting Current Management Mechanisms to Create Covert Channels in Modern Processors. - Jawad Haj-Yahya; Lois Orosa 001; Jeremie S. Kim; Juan Gómez-Luna; Abdullah Giray Yaglikçi; Mohammed Alser; Ivan Puddu; Onur Mutlu (ISCA, 2021)

SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs. - Mohammed Alser; Taha Shahroodi; Juan Gómez-Luna; Can Alkan; Onur Mutlu (Bioinform., 2021)

COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model. - Mohammed Alser; Jeremie S. Kim; Nour Almadhoun Alserr; Stefan W. Tell; Onur Mutlu (CoRR, 2021)

pLUTo: In-DRAM Lookup Tables to Enable Massively Parallel General-Purpose Computation. - João Dinis Ferreira; Gabriel Falcão 001; Juan Gómez-Luna; Mohammed Alser; Lois Orosa 001; Mohammad Sadrosadati; Jeremie S. Kim; Geraldo F. Oliveira; Taha Shahroodi; Anant Nori; Onur Mutlu (CoRR, 2021)

SIMDRAM: An End-to-End Framework for Bit-Serial SIMD Computing in DRAM. - Nastaran Hajinazar; Geraldo F. Oliveira; Sven Gregorio; João Dinis Ferreira; Nika Mansouri-Ghiasi; Minesh Patel; Mohammed Alser; Saugata Ghose; Juan Gómez-Luna; Onur Mutlu (CoRR, 2021)

FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications. - Gagandeep Singh 002; Mohammed Alser; Damla Senol Cali; Dionysios Diamantopoulos; Juan Gómez-Luna; Henk Corporaal; Onur Mutlu (IEEE Micro, 2021)

GenStore: a high-performance in-storage processing system for genome sequence analysis. - Nika Mansouri-Ghiasi; Jisung Park 001; Harun Mustafa; Jeremie S. Kim; Ataberk Olgun; Arvid Gollwitzer; Damla Senol Cali; Can Firtina; Haiyu Mao; Nour Almadhoun Alserr; Rachata Ausavarungnirun; Nandita Vijaykumar; et al. (ASPLOS, 2022)

High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory. - Safaa Diab; Amir Nassereldine; Mohammed Alser; Juan Gómez-Luna; Onur Mutlu; Izzat El Hajj (IPDPS Workshops, 2022)

Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. - Joël Lindegger; Damla Senol Cali; Mohammed Alser; Juan Gómez-Luna; Onur Mutlu (IPDPS Workshops, 2022)

SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping. - Damla Senol Cali; Konstantinos Kanellopoulos; Joël Lindegger; Zülal Bingöl; Gurpreet S. Kalsi; Ziyi Zuo; Can Firtina; Meryem Banu Cavlak; Jeremie S. Kim; Nika Mansouri-Ghiasi; Gagandeep Singh 002; Juan Gómez-Luna; et al. (ISCA, 2022)

Exploiting Near-Data Processing to Accelerate Time Series Analysis. - Ivan Fernandez; Ricardo Quislant; Christina Giannoula; Mohammed Alser; Juan Gómez-Luna; Eladio Gutiérrez; Oscar G. Plata; Onur Mutlu (ISVLSI, 2022)

GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis. - Nika Mansouri-Ghiasi; Jisung Park 001; Harun Mustafa; Jeremie S. Kim; Ataberk Olgun; Arvid Gollwitzer; Damla Senol Cali; Can Firtina; Haiyu Mao; Nour Almadhoun Alserr; Rachata Ausavarungnirun; Nandita Vijaykumar; et al. (ISVLSI, 2022)

pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables. - João Dinis Ferreira; Gabriel Falcão 001; Juan Gómez-Luna; Mohammed Alser; Lois Orosa 001; Mohammad Sadrosadati; Jeremie S. Kim; Geraldo F. Oliveira; Taha Shahroodi; Anant Nori; Onur Mutlu (MICRO, 2022)

GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. - Haiyu Mao; Mohammed Alser; Mohammad Sadrosadati; Can Firtina; Akanksha Baranwal; Damla Senol Cali; Aditya Manglik; Nour Almadhoun Alserr; Onur Mutlu (MICRO, 2022)

Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory. - Taha Shahroodi; Mahdi Zahedi; Can Firtina; Mohammed Alser; Stephan Wong; Onur Mutlu; Said Hamdioui (IEEE Access, 2022)

GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis. - Nika Mansouri-Ghiasi; Jisung Park 001; Harun Mustafa; Jeremie S. Kim; Ataberk Olgun; Arvid Gollwitzer; Damla Senol Cali; Can Firtina; Haiyu Mao; Nour Almadhoun Alserr; Rachata Ausavarungnirun; Nandita Vijaykumar; et al. (CoRR, 2022)

Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities. - Mohammed Alser; Sharon Waymost; Ram Ayyala; Brendan Lawlor; Richard J. Abdill; Neha Rajkumar; Nathan LaPierre; Jaqueline J. Brito; Andre M. Ribeiro-dos-Santos; Can Firtina; Nour Almadhoun; Varuni Sarwal; et al. (CoRR, 2022)

Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis. - Mohammed Alser; Joël Lindegger; Can Firtina; Nour Almadhoun; Haiyu Mao; Gagandeep Singh 002; Juan Gómez-Luna; Onur Mutlu (CoRR, 2022)

COVIDHunter: COVID-19 pandemic wave prediction and mitigation via seasonality-aware modeling. - Mohammed Alser; Jeremie S. Kim; Nour Almadhoun Alserr; Stefan W. Tell; Onur Mutlu (CoRR, 2022)

A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers. - Gagandeep Singh 002; Mohammed Alser; Alireza Khodamoradi; Kristof Denolf; Can Firtina; Meryem Banu Cavlak; Henk Corporaal; Onur Mutlu (CoRR, 2022)

Taming Large-Scale Genomic Analyses via Sparsified Genomics. - Mohammed Alser; Julien Eudine; Onur Mutlu (CoRR, 2022)

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering. - Meryem Banu Cavlak; Gagandeep Singh 002; Mohammed Alser; Can Firtina; Joël Lindegger; Mohammad Sadrosadati; Nika Mansouri-Ghiasi; Can Alkan; Onur Mutlu (CoRR, 2022)

pLUTo: Enabling Massively Parallel Computation In DRAM via Lookup Tables. - João Dinis Ferreira; Gabriel Falcão 001; Juan Gómez-Luna; Mohammed Alser; Lois Orosa 001; Mohammad Sadrosadati; Jeremie S. Kim; Geraldo F. Oliveira; Taha Shahroodi; Anant Nori; Onur Mutlu (Zenodo, 2022)

GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping. - Julien Eudine; Mohammed Alser; Gagandeep Singh 002; Can Alkan; Onur Mutlu (CoRR, 2023)

SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences. - Maximilian-David Rumpf; Mohammed Alser; Arvid E. Gollwitzer; Joël Lindegger; Nour Almadhoun; Can Firtina; Serghei Mangul; Onur Mutlu (CoRR, 2023)

MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation. - Arvid E. Gollwitzer; Mohammed Alser; Joel Bergtholdt; Joël Lindegger; Maximilian-David Rumpf; Can Firtina; Serghei Mangul; Onur Mutlu (CoRR, 2023)

MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing. - Nika Mansouri-Ghiasi; Mohammad Sadrosadati; Harun Mustafa; Arvid Gollwitzer; Can Firtina; Julien Eudine; Haiyu Mao; Joël Lindegger; Meryem Banu Cavlak; Mohammed Alser; Jisung Park 001; Onur Mutlu (CoRR, 2023)

A framework for high-throughput sequence alignment using real processing-in-memory systems. - Safaa Diab; Amir Nassereldine; Mohammed Alser; Juan Gómez-Luna; Onur Mutlu; Izzat El Hajj (Bioinform., 2023)

Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. - Joël Lindegger; Damla Senol Cali; Mohammed Alser; Juan Gómez-Luna; Nika Mansouri-Ghiasi; Onur Mutlu (Bioinform., 2023)

MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. - Nika Mansouri-Ghiasi; Mohammad Sadrosadati; Harun Mustafa; Arvid Gollwitzer; Can Firtina; Julien Eudine; Haiyu Mao; Joël Lindegger; Meryem Banu Cavlak; Mohammed Alser; Jisung Park 001; Onur Mutlu (ISCA, 2024)

QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms. - Julian Pavon; Iván Vargas Valdivieso; Carlos Rojas; César Hernández; Mehmet Aslan; Roger Figueras; Yichao Yuan; Joël Lindegger; Mohammed Alser; Francesc Moll; Santiago Marco-Sola; Oguz Ergin; et al. (ISCA, 2024)

RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment. - Joël Lindegger; Can Firtina; Nika Mansouri-Ghiasi; Mohammad Sadrosadati; Mohammed Alser; Onur Mutlu (IEEE Access, 2024)

ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis. - Can Firtina; Kamlesh R. Pillai; Gurpreet S. Kalsi; Bharathwaj Suresh; Damla Senol Cali; Jeremie S. Kim; Taha Shahroodi; Meryem Banu Cavlak; Joël Lindegger; Mohammed Alser; Juan Gómez-Luna; Sreenivas Subramoney; et al. (ACM Trans. Archit. Code Optim., 2024)

GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. - Zülal Bingöl; Mohammed Alser; Onur Mutlu; Ozcan Ozturk 001; Can Alkan (IEEE Trans. Computers, 2024)

CiMBA: Accelerating Genome Sequencing Through On-Device Basecalling via Compute-in-Memory. - William Andrew Simon; Irem Boybat; Riselda Kodra; Elena Ferro; Gagandeep Singh 002; Mohammed Alser; Shubham Jain; Hsinyu Tsai; Geoffrey W. Burr; Onur Mutlu; Abu Sebastian (IEEE Trans. Parallel Distributed Syst., 2025)