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Mohammed Alser
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GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies
JS Kim, D Senol Cali, H Xin, D Lee, S Ghose, M Alser, H Hassan, O Ergin, ...
BMC genomics 19 (2), 23-40, 2018
1272018
GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping
M Alser, H Hassan, H Xin, O Ergin, O Mutlu, C Alkan
Bioinformatics, 2017
922017
Genasm: A high-performance, low-power approximate string matching acceleration framework for genome sequence analysis
DS Cali, GS Kalsi, Z Bingöl, C Firtina, L Subramanian, JS Kim, ...
2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture …, 2020
582020
SIMDRAM: a framework for bit-serial SIMD processing using DRAM
N Hajinazar, GF Oliveira, S Gregorio, JD Ferreira, NM Ghiasi, M Patel, ...
Proceedings of the 26th ACM International Conference on Architectural …, 2021
53*2021
Shouji: a fast and efficient pre-alignment filter for sequence alignment
M Alser, H Hassan, A Kumar, O Mutlu, C Alkan
Bioinformatics 35 (21), 4255-4263, 2019
522019
Natsa: A near-data processing accelerator for time series analysis
I Fernandez, R Quislant, E Gutiérrez, O Plata, C Giannoula, M Alser, ...
2020 IEEE 38th International Conference on Computer Design (ICCD), 120-129, 2020
472020
Accelerating genome analysis: A primer on an ongoing journey
M Alser, Z Bingöl, DS Cali, J Kim, S Ghose, C Alkan, O Mutlu
IEEE Micro 40 (5), 65-75, 2020
412020
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs
M Alser, T Shahroodi, J Gómez-Luna, C Alkan, O Mutlu
Bioinformatics 36 (22-23), 5282-5290, 2020
352020
Critical Assessment of Metagenome Interpretation: the second round of challenges
F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ...
Nature methods 19 (4), 429-440, 2022
312022
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
C Firtina, JS Kim, M Alser, D Senol Cali, AE Cicek, C Alkan, O Mutlu
Bioinformatics 36 (12), 3669-3679, 2020
312020
Technology dictates algorithms: recent developments in read alignment
M Alser, J Rotman, D Deshpande, K Taraszka, H Shi, PI Baykal, HT Yang, ...
Genome biology 22 (1), 1-34, 2021
282021
Fpga-based near-memory acceleration of modern data-intensive applications
G Singh, M Alser, DS Cali, D Diamantopoulos, J Gómez-Luna, ...
IEEE Micro 41 (4), 39-48, 2021
282021
MAGNET: understanding and improving the accuracy of genome pre-alignment filtering
M Alser, O Mutlu, C Alkan
arXiv preprint arXiv:1707.01631, 2017
272017
Metalign: efficient alignment-based metagenomic profiling via containment min hash
N LaPierre, M Alser, E Eskin, D Koslicki, S Mangul
Genome biology 21 (1), 1-15, 2020
252020
pluto: In-dram lookup tables to enable massively parallel general-purpose computation
JD Ferreira, G Falcao, J Gómez-Luna, M Alser, L Orosa, M Sadrosadati, ...
arXiv preprint arXiv:2104.07699, 2021
202021
SysScale: Exploiting multi-domain dynamic voltage and frequency scaling for energy efficient mobile processors
J Haj-Yahya, M Alser, J Kim, AG Yağlıkçı, N Vijaykumar, E Rotem, O Mutlu
2020 ACM/IEEE 47th Annual International Symposium on Computer Architecture …, 2020
202020
Techniques for reducing the connected-standby energy consumption of mobile devices
J Haj-Yahya, Y Sazeides, M Alser, E Rotem, O Mutlu
2020 IEEE International Symposium on High Performance Computer Architecture …, 2020
192020
GRIM-Filter: fast seed filtering in read mapping using emerging memory technologies
JS Kim, D Senol, H Xin, D Lee, S Ghose, M Alser, H Hassan, O Ergin, ...
arXiv preprint arXiv:1708.04329, 2017
172017
MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
N LaPierre, S Mangul, M Alser, I Mandric, NC Wu, D Koslicki, E Eskin
BMC genomics 20 (5), 1-10, 2019
162019
Can you Really Anonymize the Donors of Genomic Data in Today’s Digital World?
M Alser, N Almadhoun, A Nouri, C Alkan, E Ayday
Data Privacy Management, and Security Assurance, 237-244, 2015
11*2015
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Articles 1–20