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Mohammed Alser · SciRah

Researcher profile · Semantic Scholar

Mohammed Alser

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Mohammed Alser — researcher profile on SciRah

h-index: 29
Works: 82
Citations: 3,064

Most-cited papers

Critical Assessment of Metagenome Interpretation: the second round of challenges
Fernando Meyer, A. Fritz, Zhi-Luo Deng, David Koslicki +99 more
2021Nature Methods346 citations Open access
Semantic Scholar
SIMDRAM: a framework for bit-serial SIMD processing using DRAM
Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira +6 more
2021International Conference on Architectural Support for Programming Languages and Operating Systems230 citations Open access
Semantic Scholar
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 +6 more
2017BMC Genomics213 citations Open access
Semantic Scholar
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis
Damla Senol Cali, G. Kalsi, Zülal Bingöl, Can Firtina +12 more
2020Micro159 citations Open access
Semantic Scholar
Technology dictates algorithms: recent developments in read alignment
Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, K. Taraszka +13 more
2020Genome Biology136 citations Open access
Semantic Scholar
GateKeeper: a new hardware architecture for accelerating pre‐alignment in DNA short read mapping
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oğuz Ergin +2 more
2016Bioinform.127 citations Open access
Semantic Scholar
Accelerating Genome Analysis: A Primer on an Ongoing Journey
Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim +3 more
2020IEEE Micro108 citations Open access
Semantic Scholar
FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications
Gagandeep Singh, Mohammed Alser, Damla Senol Cali, D. Diamantopoulos +3 more
2021IEEE Micro105 citations Open access
Semantic Scholar
Shouji: a fast and efficient pre-alignment filter for sequence alignment
Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu +1 more
2018Bioinform.104 citations Open access
Semantic Scholar
GenStore: a high-performance in-storage processing system for genome sequence analysis
Harun Mustafa, Ataberk Olgun, Arvid E. Gollwitzer, Rachata Ausavarungnirun +3 more
2022International Conference on Architectural Support for Programming Languages and Operating Systems97 citations
Semantic Scholar
NATSA: A Near-Data Processing Accelerator for Time Series Analysis
Ivan Fernandez, Ricardo Quislant, Christina Giannoula, Mohammed Alser +4 more
2020ICCD91 citations Open access
Semantic Scholar
pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables
João Dinis Ferreira, Gabriel Falcão, Juan Gómez-Luna, Mohammed Alser +7 more
2021Micro84 citations Open access
Semantic Scholar
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, C. Alkan +1 more
2019Bioinform.81 citations Open access
Semantic Scholar
SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping
Damla Senol Cali, K. Kanellopoulos, Joel Lindegger, Zülal Bingöl +14 more
2022International Symposium on Computer Architecture72 citations
Semantic Scholar
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
Mohammed Alser, Joel Lindegger, Can Firtina, Nour Almadhoun +4 more
2022Computational and Structural Biotechnology Journal70 citations Open access
Semantic Scholar
A framework for high-throughput sequence alignment using real processing-in-memory systems
Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan G'omez-Luna +2 more
2022Bioinform.70 citations Open access
Semantic Scholar
Metalign: efficient alignment-based metagenomic profiling via containment min hash
N. Lapierre, Mohammed Alser, E. Eskin, D. Koslicki +1 more
2020Genome Biology69 citations Open access
Semantic Scholar
Analysis of metagenomic data
Shaopeng Liu, Judith S. Rodríguez, Viorel Munteanu, C. Ronkowski +36 more
2025Nature Reviews Methods Primers68 citations Open access
Semantic Scholar
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali +3 more
2019Bioinform.55 citations Open access
Semantic Scholar
SysScale: Exploiting Multi-domain Dynamic Voltage and Frequency Scaling for Energy Efficient Mobile Processors
Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, A. G. Yağlıkçı +3 more
2020International Symposium on Computer Architecture50 citations Open access
Semantic Scholar
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping
Hai-Yu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina +5 more
2022Micro49 citations Open access
Semantic Scholar
MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
N. Lapierre, S. Mangul, Mohammed Alser, Igor Mandric +3 more
2018BMC Genomics47 citations Open access
Semantic Scholar
MAGNET: Understanding and Improving the Accuracy of Genome Pre-Alignment Filtering
Mohammed Alser, Onur Mutlu, C. Alkan
201747 citations
Semantic Scholar
BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
Can Firtina, Jisung Park, Mohammed Alser, Jeremie S. Kim +7 more
2021bioRxiv44 citations Open access
Semantic Scholar
pLUTo: In-DRAM Lookup Tables to Enable Massively Parallel General-Purpose Computation
João Dinis Ferreira, Gabriel Falcão, Juan Gómez-Luna, Mohammed Alser +7 more
2021arXiv.org41 citations
Semantic Scholar
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis
Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim +10 more
2022arXiv.org37 citations
Semantic Scholar
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing
Nika Mansouri Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid E. Gollwitzer +8 more
2024International Symposium on Computer Architecture31 citations Open access
Semantic Scholar
RUBICON: a framework for designing efficient deep learning-based genomic basecallers
Gagandeep Singh, Mohammed Alser, K. Denolf, Can Firtina +4 more
2022Genome Biology31 citations Open access
Semantic Scholar
Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory
Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser +3 more
2022IEEE Access31 citations Open access
Semantic Scholar
GRIM-filter: fast seed filtering in read mapping using emerging memory technologies
Jeremie S. Kim, Damla Şenol, Hongyi Xin, Donghyuk Lee +6 more
201729 citations
Semantic Scholar
High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory
Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez Luna +2 more
2022IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum28 citations Open access
Semantic Scholar
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping
Zülal Bingöl, Mohammed Alser, Onur Mutlu, O. Ozturk +1 more
2021IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum27 citations Open access
Semantic Scholar
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs
Joel Lindegger, Damla Senol Cali, Mohammed Alser, Juan G'omez-Luna +2 more
2022Bioinform.24 citations Open access
Semantic Scholar
TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina +5 more
2022bioRxiv22 citations Open access
Semantic Scholar
SIMDRAM: An End-to-End Framework for Bit-Serial SIMD Computing in DRAM
Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira +6 more
2021arXiv.org22 citations
Semantic Scholar
Techniques for Reducing the Connected-Standby Energy Consumption of Mobile Devices
Jawad Haj-Yahya, Yanos Sazeides, Mohammed Alser, Efraim Rotem +1 more
2020International Symposium on High-Performance Computer Architecture22 citations
Semantic Scholar
IChannels: Exploiting Current Management Mechanisms to Create Covert Channels in Modern Processors
Jawad Haj-Yahya, Jeremie S. Kim, A. G. Yağlıkçı, Ivan Puddu +4 more
2021International Symposium on Computer Architecture21 citations Open access
Semantic Scholar
Packaging and containerization of computational methods
Mohammed Alser, Brendan Lawlor, Richard J. Abdill, Sharon Waymost +16 more
2024Nature Protocols20 citations
Semantic Scholar
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
Joel Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati +2 more
2023IEEE Access19 citations Open access
Semantic Scholar
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis
Can Firtina, Kamlesh R. Pillai, G. Kalsi, Bharathwaj Suresh +9 more
2022ACM Transactions on Architecture and Code Optimization (TACO)18 citations Open access
Semantic Scholar
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali +4 more
2019bioRxiv14 citations Open access
Semantic Scholar
FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors
Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, L. Orosa +4 more
2020Micro12 citations Open access
Semantic Scholar
CiMBA: Accelerating Genome Sequencing Through On-Device Basecalling via Compute-in-Memory
W. Simon, I. Boybat, Riselda Kodra, E. Ferro +7 more
2025IEEE Transactions on Parallel and Distributed Systems10 citations Open access
Semantic Scholar
A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers
Gagandeep Singh, Mohammed Alser, K. Denolf, Can Firtina +4 more
2023bioRxiv10 citations Open access
Semantic Scholar
Taming large-scale genomic analyses via sparsified genomics
Mohammed Alser, Julien Eudine, O. Mutlu
2025Nature Communications7 citations Open access
Semantic Scholar
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm
Joel Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna +1 more
2022IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum7 citations Open access
Semantic Scholar
AirLift: A Fast and Comprehensive Technique for Translating Alignments between Reference Genomes
Jeremie S. Kim, Can Firtina, Damla Senol Cali, Mohammed Alser +3 more
20197 citations
Semantic Scholar
Can you Really Anonymize the Donors of Genomic Data in Today's Digital World?
Mohammed Alser, Nour Almadhoun, Azita Nouri, C. Alkan +1 more
2015DPM/QASA@ESORICS7 citations
Semantic Scholar
QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms
Julián Pavón, Iván Vargas Valdivieso, Carlos Rojas, César Hernández +13 more
2024International Symposium on Computer Architecture6 citations Open access
Semantic Scholar
COVIDHunter: COVID-19 Pandemic Wave Prediction and Mitigation via Seasonality Aware Modeling
Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell +1 more
2022Frontiers in Public Health5 citations Open access
Semantic Scholar

Frequent co-authors

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Onur Mutlu×32
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Onur Mutlu — researcher profile on SciRah
Jeremie S. Kim×17
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C. Alkan×17
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Can Firtina×17
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Damla Senol Cali

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Joel Lindegger×9

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Joel Lindegger — researcher profile on SciRah

Saugata Ghose×7

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Meryem Banu Cavlak×7

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S. Mangul — researcher profile on SciRah

Nika Mansouri Ghiasi×6

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Nika Mansouri Ghiasi — researcher profile on SciRah

Juan Gómez-Luna×6

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Juan Gómez-Luna — researcher profile on SciRah