Meryem Banu Cavlak

17 papers A* 3Journal 14
YearRankTypeTitle / 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
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 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 J jnl
RowPress Vulnerability in Modern DRAM Chips.
CoRR
Haocong Luo, Ataberk Olgun, A. Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, Onur Mutlu
2024 J jnl
RowPress Vulnerability in Modern DRAM Chips.
IEEE Micro
Haocong Luo, Ataberk Olgun, Abdullah Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, 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
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes.
Bioinform.
Can Firtina, Nika Mansouri-Ghiasi, Joël Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu
2023 A* conf
RowPress: Amplifying Read Disturbance in Modern DRAM Chips.
ISCA
Haocong Luo, Ataberk Olgun, Abdullah Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, Onur Mutlu
2023 J jnl
RowPress: Amplifying Read Disturbance in Modern DRAM Chips.
CoRR
Haocong Luo, Ataberk Olgun, Abdullah Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, 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
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
FastRemap: a tool for quickly remapping reads between genome assemblies.
Bioinform.
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, 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
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
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