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Mohammed Alser
Mohammed H. Alser – Mohammed H. K. Alser
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2020 – today
- 2024
- [j15]Can Firtina
, Kamlesh R. Pillai
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis. ACM Trans. Archit. Code Optim. 21(1): 19:1-19:29 (2024) - [j14]Zülal Bingöl
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. IEEE Trans. Computers 73(5): 1206-1218 (2024) - [c19]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: 597-612 - [c18]Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. ISCA 2024: 660-677 - [i40]Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. CoRR abs/2406.19113 (2024) - 2023
- [j13]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) - [j12]Joël Lindegger
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. Bioinform. 39(5) (2023) - [i39]Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu:
GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping. CoRR abs/2309.17063 (2023) - [i38]Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences. CoRR abs/2310.16908 (2023) - [i37]Arvid E. Gollwitzer
MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation. CoRR abs/2311.02029 (2023) - [i36]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 abs/2311.12527 (2023) - 2022
- [j11]Taha Shahroodi
Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory. IEEE Access 10: 82493-82510 (2022) - [c17]Nika Mansouri-Ghiasi, Jisung Park
GenStore: a high-performance in-storage processing system for genome sequence analysis. ASPLOS 2022: 635-654 - [c16]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu:
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. IPDPS Workshops 2022: 162 - [c15]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: 163 - [c14]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: 638-655 - [c13]Ivan Fernandez, Ricardo Quislant
Exploiting Near-Data Processing to Accelerate Time Series Analysis. ISVLSI 2022: 279-282 - [c12]Nika Mansouri-Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim, Ataberk Olgun, Arvid Gollwitzer
GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis. ISVLSI 2022: 283-287 - [c11]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: 710-726 - [c10]João Dinis Ferreira, Gabriel Falcão
pLUTo: Enabling Massively Parallel Computation in DRAM via Lookup Tables. MICRO 2022: 900-919 - [d1]João Dinis Ferreira
pLUTo: Enabling Massively Parallel Computation In DRAM via Lookup Tables. Zenodo, 2022 - [i35]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 abs/2202.10400 (2022) - [i34]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu:
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. CoRR abs/2203.15561 (2022) - [i33]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 abs/2203.16261 (2022) - [i32]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 abs/2204.02085 (2022) - [i31]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 abs/2205.05883 (2022) - [i30]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 abs/2205.07957 (2022) - [i29]Ivan Fernandez, Ricardo Quislant
Exploiting Near-Data Processing to Accelerate Time Series Analysis. CoRR abs/2206.00938 (2022) - [i28]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 abs/2206.01932 (2022) - [i27]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 abs/2206.06692 (2022) - [i26]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 abs/2207.09765 (2022) - [i25]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 abs/2208.01243 (2022) - [i24]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 abs/2208.09985 (2022) - [i23]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 abs/2209.08600 (2022) - [i22]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 abs/2211.03079 (2022) - [i21]Mohammed Alser, Julien Eudine, Onur Mutlu:
Taming Large-Scale Genomic Analyses via Sparsified Genomics. CoRR abs/2211.08157 (2022) - [i20]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 abs/2212.04953 (2022) - 2021
- [j10]Mohammed Alser
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs. Bioinform. 36(22-23): 5282-5290 (2021) - [j9]Gagandeep Singh
FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications. IEEE Micro 41(4): 39-48 (2021) - [c9]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: 329-345 - [c8]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: 209 - [c7]Jawad Haj-Yahya, Lois Orosa, Jeremie S. Kim, Juan Gómez-Luna, Abdullah Giray Yaglikçi, Mohammed Alser, Ivan Puddu
IChannels: Exploiting Current Management Mechanisms to Create Covert Channels in Modern Processors. ISCA 2021: 985-998 - [i19]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 abs/2102.03667 (2021) - [i18]Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan:
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. CoRR abs/2103.14978 (2021) - [i17]João Dinis Ferreira
pLUTo: In-DRAM Lookup Tables to Enable Massively Parallel General-Purpose Computation. CoRR abs/2104.07699 (2021) - [i16]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 abs/2105.12839 (2021) - [i15]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 abs/2106.05050 (2021) - [i14]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 abs/2106.06433 (2021) - 2020
- [j8]Can Firtina
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinform. 36(12): 3669-3679 (2020) - [j7]Mohammed Alser, Zülal Bingöl, Damla Senol Cali
Accelerating Genome Analysis: A Primer on an Ongoing Journey. IEEE Micro 40(5): 65-75 (2020) - [c6]Jawad Haj-Yahya, Yanos Sazeides, Mohammed Alser, Efraim Rotem, Onur Mutlu:
Techniques for Reducing the Connected-Standby Energy Consumption of Mobile Devices. HPCA 2020: 623-636 - [c5]Ivan Fernandez, Ricardo Quislant
NATSA: A Near-Data Processing Accelerator for Time Series Analysis. ICCD 2020: 120-129 - [c4]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: 227-240 - [c3]Damla Senol Cali
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. MICRO 2020: 951-966 - [c2]Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Lois Orosa
FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors. MICRO 2020: 1051-1066 - [i13]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 abs/2005.07613 (2020) - [i12]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 abs/2008.00961 (2020) - [i11]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 abs/2009.07692 (2020) - [i10]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 abs/2009.09094 (2020) - [i9]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 abs/2010.02079 (2020) - [i8]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 abs/2012.11890 (2020)
2010 – 2019
- 2019
- [j6]Mohammed Alser, Hasan Hassan, Akash Kumar
Shouji: a fast and efficient pre-alignment filter for sequence alignment. Bioinform. 35(21): 4255-4263 (2019) - [i7]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 abs/1902.04341 (2019) - [i6]Mohammed H. K. Alser:
Accelerating the Understanding of Life's Code Through Better Algorithms and Hardware Design. CoRR abs/1910.03936 (2019) - [i5]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 abs/1910.09020 (2019) - [i4]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 abs/1912.08735 (2019) - 2018
- [b1]Mohammed H. K. Alser:
Accelerating the understanding of life\'s code through better algorithms and hardware design (Yaşamın kodunu anlamayı daha iyi algoritmalar ve donanım tasarımlarıyla hızlandırmak). İhsan Doğramacı Bilkent University, Turkey, 2018 - [j5]Jeremie S. Kim, Damla Senol Cali
GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC Genom. 19(S2) (2018) - [i3]Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan:
SLIDER: Fast and Efficient Computation of Banded Sequence Alignment. CoRR abs/1809.07858 (2018) - 2017
- [j4]Mohammed Alser, Hasan Hassan, Hongyi Xin
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Bioinform. 33(21): 3355-3363 (2017) - [i2]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 abs/1711.01177 (2017) - 2016
- [i1]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 abs/1604.01789 (2016) - 2015
- [c1]Mohammed Alser, Nour Almadhoun, Azita Nouri, Can Alkan
Can you Really Anonymize the Donors of Genomic Data in Today's Digital World? DPM/QASA@ESORICS 2015: 237-244 - 2013
- [j3]Maher Assaad
Design and Characterization of Low Power and Low Noise Truly All-Digital Clock and Data Recovery Circuit for SERDES Devices. J. Low Power Electron. 9(1): 63-72 (2013) - 2012
- [j2]Maher Assaad
Design of an All-Digital Synchronized Frequency Multiplier Based on a Dual-Loop (D/FLL) Architecture. VLSI Design 2012: 546212:1-546212:7 (2012) - 2011
- [j1]Maher Assaad
An FPGA-based design and implementation of an all-digital serializer for inter module communication in SoC. IEICE Electron. Express 8(23): 2017-2023 (2011)
Coauthor Index
Nour Almadhoun
aka: Nour Almadhoun Alserr
aka: Nour Almadhoun Alserr
[j15] [j14] [c19] [c18] [i40] [j13] [j12] [i39] [i38] [i37] [i36] [j11] [c17] [c16] [c15] [c14] [c13] [c12] [c11] [c10] [d1] [i35] [i34] [i33] [i32] [i31] [i30] [i29] [i28] [i27] [i26] [i25] [i24] [i23] [i22] [i21] [i20] [j10] [j9] [c9] [c8] [c7] [i19] [i18] [i17] [i16] [i15] [i14] [j8] [j7] [c6] [c5] [c4] [c3] [c2] [i13] [i12] [i11] [i10] [i9] [i8] [j6] [i7] [i5] [i4] [j5] [i3] [j4] [i2] [i1]
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