Mohammed Alser

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 69

Top Topics

Massively Parallel

Sequence Analysis

Approximate String Matching

Energy Consumption

Top Venues

Publications

Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid Gollwitzer, Can Firtina, Julien Eudine, Haiyu Mao, Joël Lindegger, Meryem Banu Cavlak, Mohammed Alser, Jisung Park, Onur Mutlu
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. ISCA (2024)
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, Onur Mutlu
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis. ACM Trans. Archit. Code Optim. 21 (1) (2024)
Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid Gollwitzer, Can Firtina, Julien Eudine, Haiyu Mao, Joël Lindegger, Meryem Banu Cavlak, Mohammed Alser, Jisung Park, Onur Mutlu
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. CoRR (2024)
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, Nishil Talati, Onur Mutlu, Osman S. Unsal, Mateo Valero, Adrián Cristal
QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms. ISCA (2024)
Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. IEEE Trans. Computers 73 (5) (2024)
Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid Gollwitzer, Can Firtina, Julien Eudine, Haiyu Mao, Joël Lindegger, Meryem Banu Cavlak, Mohammed Alser, Jisung Park, Onur Mutlu
MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing. CoRR (2023)
Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joël Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu
MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation. CoRR (2023)
Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. Bioinform. 39 (5) (2023)
Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joël Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences. CoRR (2023)
Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu
GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping. CoRR (2023)
Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj
A framework for high-throughput sequence alignment using real processing-in-memory systems. Bioinform. 39 (5) (2023)
Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, Onur Mutlu
COVIDHunter: COVID-19 pandemic wave prediction and mitigation via seasonality-aware modeling. CoRR (2022)
Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, Said Hamdioui
Demeter: A Fast and Energy-Efficient Food Profiler using Hyperdimensional Computing in Memory. CoRR (2022)
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
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis. CoRR (2022)
Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj
High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory. CoRR (2022)
Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu
Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs. CoRR (2022)
Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. IPDPS Workshops (2022)
Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, Said Hamdioui
Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory. IEEE Access 10 (2022)
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
GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis. ISVLSI (2022)
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
GenStore: a high-performance in-storage processing system for genome sequence analysis. ASPLOS (2022)
Ivan Fernandez, Ricardo Quislant, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Eladio Gutiérrez, Oscar G. Plata, Onur Mutlu
Exploiting Near-Data Processing to Accelerate Time Series Analysis. ISVLSI (2022)
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, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities. CoRR (2022)
Gagandeep Singh, Mohammed Alser, Alireza Khodamoradi, Kristof Denolf, Can Firtina, Meryem Banu Cavlak, Henk Corporaal, Onur Mutlu
A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers. CoRR (2022)
Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj
High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory. IPDPS Workshops (2022)
João Dinis Ferreira, Gabriel Falcão, Juan Gómez-Luna, Mohammed Alser, Lois Orosa, Mohammad Sadrosadati, Jeremie S. Kim, Geraldo F. Oliveira, Taha Shahroodi, Anant Nori, Onur Mutlu
pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables. MICRO (2022)
Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. CoRR (2022)
Mohammed Alser, Joël Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gómez-Luna, Onur Mutlu
Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis. CoRR (2022)
Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. CoRR (2022)
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, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. CoRR (2022)
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering. CoRR (2022)
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, Onur Mutlu
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis. CoRR (2022)
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, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping. ISCA (2022)
Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj
A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems. CoRR (2022)
Ivan Fernandez, Ricardo Quislant, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Eladio Gutiérrez, Oscar G. Plata, Onur Mutlu
Exploiting Near-Data Processing to Accelerate Time Series Analysis. CoRR (2022)
Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. MICRO (2022)
Mohammed Alser, Julien Eudine, Onur Mutlu
Taming Large-Scale Genomic Analyses via Sparsified Genomics. CoRR (2022)
Jawad Haj-Yahya, Lois Orosa, Jeremie S. Kim, Juan Gómez-Luna, Abdullah Giray Yaglikçi, Mohammed Alser, Ivan Puddu, Onur Mutlu
IChannels: Exploiting Current Management Mechanisms to Create Covert Channels in Modern Processors. ISCA (2021)
João Dinis Ferreira, Gabriel Falcão, Juan Gómez-Luna, Mohammed Alser, Lois Orosa, Mohammad Sadrosadati, Jeremie S. Kim, Geraldo F. Oliveira, Taha Shahroodi, Anant Nori, Onur Mutlu
pLUTo: In-DRAM Lookup Tables to Enable Massively Parallel General-Purpose Computation. CoRR (2021)
Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs. Bioinform. 36 (22-23) (2021)
Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, Onur Mutlu
COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model. CoRR (2021)
Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira, Nika Mansouri-Ghiasi, Minesh Patel, Mohammed Alser, Saugata Ghose, Juan Gómez-Luna, Onur Mutlu
SIMDRAM: a framework for bit-serial SIMD processing using DRAM. ASPLOS (2021)
Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira, Nika Mansouri-Ghiasi, Minesh Patel, Mohammed Alser, Saugata Ghose, Juan Gómez-Luna, Onur Mutlu
SIMDRAM: An End-to-End Framework for Bit-Serial SIMD Computing in DRAM. CoRR (2021)
Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, Onur Mutlu
FPGA-based Near-Memory Acceleration of Modern Data-Intensive Applications. CoRR (2021)
Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, Onur Mutlu
FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications. IEEE Micro 41 (4) (2021)
Jawad Haj-Yahya, Jeremie S. Kim, Abdullah Giray Yaglikçi, Ivan Puddu, Lois Orosa, Juan Gómez-Luna, Mohammed Alser, Onur Mutlu
IChannels: Exploiting Current Management Mechanisms to Create Covert Channels in Modern Processors. CoRR (2021)
Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. IPDPS Workshops (2021)
Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. CoRR (2021)
Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Abdullah Giray Yaglikçi, Nandita Vijaykumar, Efraim Rotem, Onur Mutlu
SysScale: Exploiting Multi-domain Dynamic Voltage and Frequency Scaling for Energy Efficient Mobile Processors. ISCA (2020)
Ivan Fernandez, Ricardo Quislant, Eladio Gutiérrez, Oscar G. Plata, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu
NATSA: A Near-Data Processing Accelerator for Time Series Analysis. ICCD (2020)
Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira, Nika Mansouri-Ghiasi, Minesh Patel, Mohammed Alser, Saugata Ghose, Juan Gómez-Luna, Onur Mutlu
SIMDRAM: A Framework for Bit-Serial SIMD Processing Using DRAM. CoRR (2020)
Jawad Haj-Yahya, Yanos Sazeides, Mohammed Alser, Efraim Rotem, Onur Mutlu
Techniques for Reducing the Connected-Standby Energy Consumption of Mobile Devices. HPCA (2020)
Ivan Fernandez, Ricardo Quislant, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Eladio Gutiérrez, Oscar G. Plata, Onur Mutlu
NATSA: A Near-Data Processing Accelerator for Time Series Analysis. CoRR (2020)
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, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. CoRR (2020)
Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
Accelerating Genome Analysis: A Primer on an Ongoing Journey. CoRR (2020)
Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Abdullah Giray Yaglikçi, Nandita Vijaykumar, Efraim Rotem, Onur Mutlu
SysScale: Exploiting Multi-domain Dynamic Voltage and Frequency Scaling for Energy Efficient Mobile Processors. CoRR (2020)
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, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. MICRO (2020)
Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Lois Orosa, Efraim Rotem, Avi Mendelson, Anupam Chattopadhyay, Onur Mutlu
FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors. MICRO (2020)
Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
Accelerating Genome Analysis: A Primer on an Ongoing Journey. IEEE Micro 40 (5) (2020)
Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Lois Orosa, Efraim Rotem, Avi Mendelson, Anupam Chattopadhyay, Onur Mutlu
FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors. CoRR (2020)
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinform. 36 (12) (2020)
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm. CoRR (2019)
Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan
Shouji: a fast and efficient pre-alignment filter for sequence alignment. Bioinform. 35 (21) (2019)
Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs. CoRR (2019)
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. CoRR (2019)
Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan
SLIDER: Fast and Efficient Computation of Banded Sequence Alignment. CoRR (2018)
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC Genom. 19 (S2) (2018)
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies. CoRR (2017)
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Bioinform. 33 (21) (2017)
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
GateKeeper: Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture. CoRR (2016)
Mohammed Alser, Nour Almadhoun, Azita Nouri, Can Alkan, Erman Ayday
Can you Really Anonymize the Donors of Genomic Data in Today's Digital World? DPM/QASA@ESORICS (2015)