Mohammed Alser

77 papers A* 12C 1Journal 57Unranked 6

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	AirLift: A Fast and Comprehensive Technique for Remapping Alignments Between Reference Genomes. IEEE Trans. Comput. Biol. Bioinform. Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, Onur Mutlu
2026	—	`ed.`	Computational Advances in Bio and Medical Sciences - 13th International Conference, ICCABS 2025, Atlanta, GA, USA, January 12-14, 2025, Revised Selected Papers ICCABS Mohammed Alser, Mukul S. Bansal, Yury Khudyakov, Serghei Mangul, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Shibu Yooseph, Alexander Zelikovsky
2026	J	`jnl`	FASTR: Reimagining FASTQ via Compact Image-inspired Representation. CoRR Adrian Tkachenko, Sepehr Salem, Ayotomiwa Ezekiel Adeniyi, Zülal Bingöl, Mohammed Nayeem Uddin, Akshat Prasanna, Alexander Zelikovsky, Serghei Mangul, Can Alkan, Mohammed Alser
2026	J	`jnl`	XMorph: Explainable Brain Tumor Analysis Via LLM-Assisted Hybrid Deep Intelligence. CoRR Sepehr Salem Ghahfarokhi, M. Moein Esfahani, Raj Sunderraman, Vince D. Calhoun, Mohammed Alser
2025	J	`jnl`	CiMBA: Accelerating Genome Sequencing Through On-Device Basecalling via Compute-in-Memory. IEEE Trans. Parallel Distributed Syst. William Andrew Simon, Irem Boybat, Riselda Kodra, Elena Ferro, Gagandeep Singh, Mohammed Alser, Shubham Jain, Hsinyu Tsai, Geoffrey W. Burr, Onur Mutlu, Abu Sebastian
2025	J	`jnl`	CiMBA: Accelerating Genome Sequencing through On-Device Basecalling via Compute-in-Memory. CoRR William Andrew Simon, Irem Boybat, Riselda Kodra, Elena Ferro, Gagandeep Singh, Mohammed Alser, Shubham Jain, Hsinyu Tsai, Geoffrey W. Burr, Onur Mutlu, Abu Sebastian
2024	J	`jnl`	ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis. ACM Trans. Archit. Code Optim. 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
2024	J	`jnl`	GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. IEEE Trans. Computers Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
2024	A*	`conf`	MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. ISCA 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
2024	J	`jnl`	MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. CoRR 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
2024	A*	`conf`	QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms. ISCA 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
2024	J	`jnl`	RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment. IEEE Access Joël Lindegger, Can Firtina, Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
2023	J	`jnl`	A framework for high-throughput sequence alignment using real processing-in-memory systems. Bioinform. Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj
2023	J	`jnl`	GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping. CoRR Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu
2023	J	`jnl`	MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation. CoRR Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joël Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu
2023	J	`jnl`	MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing. CoRR 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
2023	J	`jnl`	Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. Bioinform. Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu
2023	J	`jnl`	SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences. CoRR Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joël Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu
2022	J	`jnl`	A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers. CoRR Gagandeep Singh, Mohammed Alser, Alireza Khodamoradi, Kristof Denolf, Can Firtina, Meryem Banu Cavlak, Henk Corporaal, Onur Mutlu
2022	J	`jnl`	A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems. CoRR Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj
2022	—	`conf`	Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. IPDPS Workshops Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu
2022	J	`jnl`	Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. CoRR Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu
2022	J	`jnl`	ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis. CoRR 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
2022	J	`jnl`	COVIDHunter: COVID-19 pandemic wave prediction and mitigation via seasonality-aware modeling. CoRR Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, Onur Mutlu
2022	J	`jnl`	Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory. IEEE Access Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, Said Hamdioui
2022	J	`jnl`	Demeter: A Fast and Energy-Efficient Food Profiler using Hyperdimensional Computing in Memory. CoRR Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, Said Hamdioui
2022	—	`conf`	Exploiting Near-Data Processing to Accelerate Time Series Analysis. ISVLSI Ivan Fernandez, Ricardo Quislant, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Eladio Gutiérrez, Oscar G. Plata, Onur Mutlu
2022	J	`jnl`	Exploiting Near-Data Processing to Accelerate Time Series Analysis. CoRR Ivan Fernandez, Ricardo Quislant, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Eladio Gutiérrez, Oscar G. Plata, Onur Mutlu
2022	A*	`conf`	GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. MICRO Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
2022	J	`jnl`	GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. CoRR Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
2022	J	`jnl`	GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis. CoRR 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
2022	—	`conf`	GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis. ISVLSI 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
2022	A*	`conf`	GenStore: a high-performance in-storage processing system for genome sequence analysis. ASPLOS 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
2022	J	`jnl`	Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis. CoRR Mohammed Alser, Joël Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gómez-Luna, Onur Mutlu
2022	—	`conf`	High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory. IPDPS Workshops Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj
2022	J	`jnl`	High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory. CoRR Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj
2022	J	`jnl`	Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities. CoRR 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
2022	J	`jnl`	Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs. CoRR Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu
2022	J	`jnl`	SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. CoRR 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
2022	A*	`conf`	SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping. ISCA 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
2022	J	`jnl`	Taming Large-Scale Genomic Analyses via Sparsified Genomics. CoRR Mohammed Alser, Julien Eudine, Onur Mutlu
2022	J	`jnl`	TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering. CoRR Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu
2022	A*	`conf`	pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables. MICRO 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
2021	J	`jnl`	COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model. CoRR Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, Onur Mutlu
2021	J	`jnl`	FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications. IEEE Micro Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, Onur Mutlu
2021	J	`jnl`	FPGA-based Near-Memory Acceleration of Modern Data-Intensive Applications. CoRR Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, Onur Mutlu
2021	—	`conf`	GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. IPDPS Workshops Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
2021	J	`jnl`	GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. CoRR Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
2021	A*	`conf`	IChannels: Exploiting Current Management Mechanisms to Create Covert Channels in Modern Processors. ISCA Jawad Haj-Yahya, Lois Orosa, Jeremie S. Kim, Juan Gómez-Luna, Abdullah Giray Yaglikçi, Mohammed Alser, Ivan Puddu, Onur Mutlu
2021	J	`jnl`	IChannels: Exploiting Current Management Mechanisms to Create Covert Channels in Modern Processors. CoRR Jawad Haj-Yahya, Jeremie S. Kim, Abdullah Giray Yaglikçi, Ivan Puddu, Lois Orosa, Juan Gómez-Luna, Mohammed Alser, Onur Mutlu
2021	J	`jnl`	SIMDRAM: An End-to-End Framework for Bit-Serial SIMD Computing in DRAM. CoRR Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira, Nika Mansouri-Ghiasi, Minesh Patel, Mohammed Alser, Saugata Ghose, Juan Gómez-Luna, Onur Mutlu
2021	A*	`conf`	SIMDRAM: a framework for bit-serial SIMD processing using DRAM. ASPLOS Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira, Nika Mansouri-Ghiasi, Minesh Patel, Mohammed Alser, Saugata Ghose, Juan Gómez-Luna, Onur Mutlu
2021	J	`jnl`	SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs. Bioinform. Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu
2021	J	`jnl`	pLUTo: In-DRAM Lookup Tables to Enable Massively Parallel General-Purpose Computation. CoRR 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
2020	J	`jnl`	Accelerating Genome Analysis: A Primer on an Ongoing Journey. CoRR Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
2020	J	`jnl`	Accelerating Genome Analysis: A Primer on an Ongoing Journey. IEEE Micro Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
2020	J	`jnl`	Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinform. Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2020	A*	`conf`	FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors. MICRO Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Lois Orosa, Efraim Rotem, Avi Mendelson, Anupam Chattopadhyay, Onur Mutlu
2020	J	`jnl`	FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors. CoRR Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Lois Orosa, Efraim Rotem, Avi Mendelson, Anupam Chattopadhyay, Onur Mutlu
2020	A*	`conf`	GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. MICRO 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
2020	J	`jnl`	GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. CoRR 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
2020	C	`conf`	NATSA: A Near-Data Processing Accelerator for Time Series Analysis. ICCD Ivan Fernandez, Ricardo Quislant, Eladio Gutiérrez, Oscar G. Plata, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu
2020	J	`jnl`	NATSA: A Near-Data Processing Accelerator for Time Series Analysis. CoRR Ivan Fernandez, Ricardo Quislant, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Eladio Gutiérrez, Oscar G. Plata, Onur Mutlu
2020	J	`jnl`	SIMDRAM: A Framework for Bit-Serial SIMD Processing Using DRAM. CoRR Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira, Nika Mansouri-Ghiasi, Minesh Patel, Mohammed Alser, Saugata Ghose, Juan Gómez-Luna, Onur Mutlu
2020	A*	`conf`	SysScale: Exploiting Multi-domain Dynamic Voltage and Frequency Scaling for Energy Efficient Mobile Processors. ISCA Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Abdullah Giray Yaglikçi, Nandita Vijaykumar, Efraim Rotem, Onur Mutlu
2020	J	`jnl`	SysScale: Exploiting Multi-domain Dynamic Voltage and Frequency Scaling for Energy Efficient Mobile Processors. CoRR Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Abdullah Giray Yaglikçi, Nandita Vijaykumar, Efraim Rotem, Onur Mutlu
2020	A*	`conf`	Techniques for Reducing the Connected-Standby Energy Consumption of Mobile Devices. HPCA Jawad Haj-Yahya, Yanos Sazeides, Mohammed Alser, Efraim Rotem, Onur Mutlu
2019	J	`jnl`	AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. CoRR Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu
2019	J	`jnl`	Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm. CoRR Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2019	J	`jnl`	Shouji: a fast and efficient pre-alignment filter for sequence alignment. Bioinform. Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan
2019	J	`jnl`	SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs. CoRR Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu
2018	J	`jnl`	GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC Genom. Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
2018	J	`jnl`	SLIDER: Fast and Efficient Computation of Banded Sequence Alignment. CoRR Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan
2017	J	`jnl`	GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies. CoRR Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
2017	J	`jnl`	GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Bioinform. Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
2016	J	`jnl`	GateKeeper: Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture. CoRR Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
2015	—	`conf`	Can you Really Anonymize the Donors of Genomic Data in Today's Digital World? DPM/QASA@ESORICS Mohammed Alser, Nour Almadhoun, Azita Nouri, Can Alkan, Erman Ayday