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Nika Mansouri Ghiasi, Harun Mustafa, Talu Güloglu, Rakesh Nadig, Konstantina Koliogeorgi, Susana Rebolledo Ruiz, Marc Rautmann, Furkan Eris, Mohammad Sadrosadati, Jisung Park, Onur Mutlu
GRAINS: Enabling High-Performance and Low-Cost Graph-Based Genome Analysis via Storage-Aware Algorithm-Architecture Co-Design
In International Symposium on Computer Architecture (ISCA), 2026
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Nika Mansouri Ghiasi, Talu Güloglu, Harun Mustafa, Can Firtina, Konstantina Koliogeorgi, Konstantinos Kanellopoulos, Haiyu Mao, Rakesh Nadig, Mohammad Sadrosadati, Jisung Park, Onur Mutlu
SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence Analysis
In International Symposium on High-Performance Computer Architecture (HPCA), 2026
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Nika Mansouri Ghiasi, Mohammad Sadrosadati, Geraldo F. Oliveira, Konstantinos Kanellopoulos, Rachata Ausavarungnirun, Juan Gómez-Luna, João Dinis Ferreira, Jeremie S. Kim, Christina Giannoula, Nandita Vijaykumar, Jisung Park, Onur Mutlu
RevaMp3D: Architecting the Processor Core and Cache Hierarchy for Systems with Monolithically-Integrated Logic and Memory
In ACM Transactions on Architecture and Code Optimization (TACO), 2026
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Gaurav Sharma, Viorel Munteanu, Nika Mansouri Ghiasi, Utkarsha Mahanta, Jineta Banerjee, Susheel Varma, Luca Foschini, Kyle Ellrott, Onur Mutlu, Dumitru Ciorbă, Roel A. Ophoff, Viorel Bostan, Jason H. Moore, Despoina Sousoni, Arunkumar Krishnan, Alexander G. Lucaci, Alba Tull, Christopher E. Mason, Mihai Dimian, Gustavo Stolovitzky, Fabio G. Liberante, Taras K. Oleksyk, Serghei Mangul
Towards a decentralized future for open-science databases
In Nature Genetics, 2026
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Can Firtina, Maximilian Mordig, Harun Mustafa, Sayan Goswami, Nika Mansouri Ghiasi, Stefano Mercogliano, Furkan Eris, Joël Lindegger, André Kahles, Onur Mutlu
Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism
In Bioinformatics, 2026
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Rakesh Nadig, Vamanan Arulchelvan, Mayank Kabra, Harshita Gupta, Rahul Bera, Nika Mansouri Ghiasi, Nanditha Rao, Qingcai Jiang, Andreas Kosmas Kakolyris, Yu Liang, Mohammad Sadrosadati, Onur Mutlu
Conduit: Programmer-Transparent Near-Data Processing Using Multiple Compute-Capable Resources in SSDs
In International Symposium on High-Performance Computer Architecture (HPCA), 2026
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Julien Eudine, Chu Li, Zhuo Cheng, Renzo Andri, Can Firtina, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Konstantina Koliogeorgi, Anirban Nag, Arash Tavakkol, Haiyu Mao, Onur Mutlu, Shai Bergman, Ji Zhang
GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping
In International Symposium on High-Performance Computer Architecture (HPCA), 2026
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Kangqi Chen, Rakesh Nadig, Andreas Kosmas Kakolyris, Manos Frouzakis, Nika Mansouri Ghiasi, Yu Liang, Haiyu Mao, Jisung Park, Mohammad Sadrosadati, Onur Mutlu
REIS: A High-Performance and Energy-Efficient Retrieval System with In-Storage Processing
In International Symposium on Computer Architecture (ISCA), 2025
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Melina Soysal, Konstantina Koliogeorgi, Can Firtina, Nika Mansouri Ghiasi, Rakesh Nadig, Haiyu Mao, Geraldo F. Oliveira, Yu Liang, Klea Zambaku, Mohammad Sadrosadati, Onur Mutlu
MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem
In ACM International Conference on Supercomputing (ICS), 2025
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Nisa Bostanci, Konstantinos Kanellopoulos, Ataberk Olgun, Abdullah Giray Yaglikci, Ismail Emir Yuksel, Nika Mansouri Ghiasi, Zulal Bingol, Mohammad Sadrosadati, Onur Mutlu
Revisiting Main Memory-Based Covert and Side Channel Attacks in the Context of Processing-in-Memory
In Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN), 2025
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Shaopeng Liu, Judith S. Rodriguez, Viorel Munteanu, Cynthia Ronkowski, Nitesh Kumar Sharma, Mohammed Alser, Francesco Andreace, Ran Blekhman, Dagmara Błaszczyk, Rayan Chikhi, Keith A. Crandall, Katja Della Libera, Dallace Francis, Alina Frolova, Abigail Shahar Gancz, Naomi E. Huntley, Pooja Jaiswal, Tomasz Kosciolek, Pawel P. Łabaj, Wojciech Łabaj, Tu Luan, Christopher Mason, Ahmed M. Moustafa, Harihara Subrahmaniam Muralidharan, Onur Mutlu, Nika Mansouri Ghiasi, Ali Rahnavard, Fengzhu Sun, Shuchang Tian, Braden T. Tierney, Emily Van Syoc, Riccardo Vicedomini, Joseph P. Zackular, Alex Zelikovsky, Kinga Zielińska, Erika Ganda, Emily R. Davenport, Mihai Pop, David Koslicki, Serghei Mangul
Analysis of metagenomic data
In Nature Reviews Methods Primers, 2025
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Yu Liang, Aofeng Shen, Chun Jason Xue, Riwei Pan, Haiyu Mao, Nika Mansouri Ghiasi, Qingcai Jiang, Rakesh Nadig, Lei Li, Rachata Ausavarungnirun, Mohammad Sadrosadati, Onur Mutlu
Ariadne: Hotness-Aware and Size-Adaptive Compressed Swap Scheme for Mobile Devices
In International Symposium on High-Performance Computer Architecture (HPCA), 2025
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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
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing
In International Symposium on Computer Architecture (ISCA), 2024
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Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
In IEEE Access, 2024
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Harun Mustafa, Mikhail Karasikov, Nika Mansouri Ghiasi, Gunnar Rätsch, André Kahles
Label-Guided Seed-Chain-Extend Alignment on Annotated De Bruijn Graphs
In Annual Conference on Intelligent Systems for Molecular Biology (ISMB), 2024
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Ivan Fernandez, Christina Giannoula, Aditya Manglik, Ricardo Quislant, Nika Mansouri Ghiasi, Juan Gómez-Luna, Eladio Gutierrez, Oscar Plata, Onur Mutlu
MATSA: An MRAM-Based Energy-Efficient Accelerator for Time Series Analysis
In IEEE Access, 2024
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Nika Mansouri Ghiasi, Onur Mutlu
Understanding and Modeling the Performance Landscape of Ultra-Dense 3D Memory Systems
In ACM Student Research Competition at the International Conference on Parallel Architectures and Compilation Techniques (PACT SRC), 2024
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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
In Bioinformatics, 2023
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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
In Asia Pacific Bioinformatics Conference (APBC), 2023
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Rakesh Nadig, Mohammad Sadrosadati, Haiyu Mao, Nika Mansouri Ghiasi, Arash Tavakkol, Jisung Park, Hamid Sarbazi-Azad, Juan Gómez-Luna, Onur Mutlu
Venice: Improving Solid-State Drive Parallelism at Low Cost via Conflict-Free Accesses
In International Symposium on Computer Architecture (ISCA), 2023
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Can Firtina, Nika Mansouri Ghiasi, Joël Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
In Annual Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB), 2023
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Can Firtina, Jisung Park, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, Taha Shahroodi, Nika Mansouri Ghiasi, Gagandeep Singh, Konstantinos Kanellopoulos, Can Alkan, Onur Mutlu
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches
In NAR Genomics and Bioinformatics, 2023
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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 In-Storage Processing System for Genome Sequence Analysis
In International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), 2022
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Nika Mansouri Ghiasi, Nandita Vijaykumar, Geraldo F. Oliveira, Lois Orosa, Ivan Fernandez, Mohammad Sadrosadati, Konstantinos Kanellopoulos, Nastaran Hajinazar, Juan Gómez-Luna, Onur Mutlu
ALP: Alleviating CPU-Memory Data Movement Overheads in Memory-Centric Systems
In IEEE Transactions on Emerging Topics in Computing (IEEE TETC), 2022
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Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zulal Bingol, 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
In International Symposium on Computer Architecture (ISCA), 2022
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Lois Orosa, Yaohua Wang, Mohammad Sadrosadati, Jeremie S. Kim, Minesh Patel, Ivan Puddu, Haocong Luo, Kaveh Razavi, Juan Gómez-Luna, Hasan Hassan, Nika Mansouri Ghiasi, Saugata Ghose, Onur Mutlu
CODIC: A Low-Cost Substrate for Enabling Custom In-DRAM Functionalities and Optimizations
In International Symposium on Computer Architecture (ISCA), 2021
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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
In International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), 2021
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Yaohua Wang, Arash Tavakkol, Lois Orosa, Saugata Ghose, Nika Mansouri Ghiasi, Minesh Patel, Jeremie S. Kim, Hasan Hassan, Mohammad Sadrosadati, Onur Mutlu
Reducing DRAM Latency via Charge-Level-Aware Look-Ahead Partial Restoration
In International Symposium on Microarchitecture (MICRO), 2018
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Arash Tavakkol, Mohammad Sadrosadati, Saugata Ghose, Jeremie S. Kim, Yixin Luo, Yaohua Wang, Nika Mansouri Ghiasi, Lois Orosa, Juan Gómez-Luna, Onur Mutlu
FLIN: Enabling Fairness and Enhancing Performance in Modern NVMe Solid State Drives
In International Symposium on Computer Architecture (ISCA), 2018