Research Summary and Initiative Papers
Research Summary and Initiative Papers
Architecture for Health Initiative (Arch4Health): Computational Challenges in Health-Related Applications and the Role of Computer Architecture in Addressing Them
Nika Mansouri Ghiasi*, Konstantina Koliogeorgi*, and Onur Mutlu
to appear in ICS Workshops, 2026
Enabling Fast, Efficient, and Low-Cost Genomic and Metagenomic Analyses via Storage-Centric System Designs
Nika Mansouri Ghiasi, and Onur Mutlu
to appear in ICS Workshops, 2026
2026
GRAINS: Enabling High-Performance and Low-Cost Graph-Based Genome Analysis via Storage-Aware Algorithm-Architecture Co-Design
Nika Mansouri Ghiasi, Harun Mustafa, Talu Güloglu, Rakesh Nadig, Konstantina Koliogeorgi, Susana Rebolledo Ruiz, Marc Rautmann, Furkan Eris, Mohammad Sadrosadati, Jisung Park, Onur Mutlu
to appear in ISCA, 2026
RevaMp3D: Architecting the Processor Core and Caches for Systems with Monolithically-Integrated Logic and Memory
Nika Mansouri Ghiasi, Mohammad Sadrosadati, Geraldo F. Oliveira, Konstantinos Kanellopoulos, Rachata Ausavarungnirun, Juan Gómez Luna, João Ferreira, Jeremie S. Kim, Christina Giannoula, Nandita Vijaykumar, Jisung Park, Onur Mutlu
to appear in ACM TACO, 2026
Towards a decentralized future for open-science databases
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
in Nature Genetics Comment, 2026
Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism
Can Firtina, Maximilian Mordig, Harun Mustafa, Sayan Goswami, Nika Mansouri Ghiasi, Stefano Mercogliano, Furkan Eris, Joël Lindegger, Andre Kahles, Onur Mutlu
in Bioinformatics, 2026
SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Analysis
Nika Mansouri Ghiasi, Talu Güloglu, Harun Mustafa, Can Firtina, Konstantina Koliogeorgi, Konstantinos Kanellopoulos, Haiyu Mao, Rakesh Nadig, Mohammad Sadrosadati, Jisung Park, Onur Mutlu
in HPCA, 2026
Conduit: Programmer-Transparent Near-Data Processing Using Multiple Compute-Capable Resources in SSDs
Rakesh Nadig, Vamanan Arulchelvan, Mayank Kabra, Harshita Gupta, Rahul Bera, Nika Mansouri Ghiasi, Nanditha Rao, Qingcai Jiang, Andreas Kakolyris, Yu Lenny Liang, Mohammad Sadrosadati, Onur Mutlu
in HPCA, 2026
GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping
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
in HPCA, 2026
2025
REIS: A High-Performance and Energy-Efficient Retrieval System with In-Storage Processing
Kangqi Chen, Rakesh Nadig, Andreas Kosmas Kakolyris, Manos Frouzakis, Nika Mansouri Ghiasi, Yu Liang, Haiyu Mao, Jisung Park, Mohammad Sadrosadati, and Onur Mutlu
in ISCA, 2025
MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem
Melina Soysal, Konstantina Koliogeorgi, Can Firtina, Nika Mansouri Ghiasi, Rakesh Nadig, Haiyu Mao, Geraldo Francisco, Yu Liang, Klea Zambaku, Mohammad Sadrosadati, and Onur Mutlu
in ICS, 2025
Revisiting Main Memory-Based Covert and Side Channel Attacks in the Context of Processing-in-Memory
Nisa Bostanci, Konstantinos Kanellopoulos, Ataberk Olgun, A. Giray Yaglikci, Ismail Emir Yuksel, Nika Mansouri Ghiasi, Zulal Bingol, Mohammad Sadrosadati, and Onur Mutlu
in DSN, 2025
Analysis of metagenomic data
S. Liu, J. S. Rodriguez, V. Munteanu, C. Ronkowski, N. Kumar Sharma, M. Alser, F. Andreace, R. Blekhman, D. Blaszczyk, R. Chikhi, K. A. Crandall, K. Della Libera, D. Francis, A. Frolova, A. Shahar Gancz, N. E. Huntley, P. Jaiswal, T. Kosciolek, P. P. Labaj, W. Labaj, T. Luan, Ch. Mason, A. M. Moustafa, H. Subrahmaniam Muralidharan, O. Mutlu, N. Mansouri Ghiasi, A. Rahnavard, F. Sun, S. Tian, B. T. Tierney, E. Van Syoc, R. Vicedomini, J. P. Zackular, A. Zelikovsky, K. Zieli´nska, E. Ganda, E. R. Davenport, M. Pop, D. Koslicki, S. Mangul
In Nature Reviews Methods Primers, 2025
Ariadne: Hotness-Aware and Size-Adaptive Compressed Swap Scheme for Mobile Devices
Y. Liang, A. Shen, C. J. Xue, R. Pan, H. Mao, N. Mansouri Ghiasi, Q. Jiang, R. Nadig, L. Li, R. Ausavarungnirun, M. Sadrosadati, O. Mutlu
in HPCA, 2025
2024
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing
N. Mansouri Ghiasi, M. Sadrosadati, H. Mustafa, A. Gollwitzer, C. Firtina, J. Eudine, H. Ma, J. Lindegger, M. Banu Cavlak, M. Alser, J. Park, O. Mutlu
In ISCA, 2024
Understanding and Modeling the Performance Landscape of Ultra-Dense 3D Memory Systems
N. Mansouri Ghiasi, O. Mutlu
In PACT ACM Student Research Competition, 2024
Label-Guided Seed-Chain-Extend Alignment on Annotated De Bruijn Graphs
H. Mustafa, M. Karasikov, N. Mansouri Ghiasi, G. Rätsch, A. Kahles
In ISMB, 2024
MATSA: An MRAM-Based Energy-Efficient Accelerator for Time Series Analysis
I. Fernandez, C. Giannoula, A. Manglik, R. Quislant, N. Mansouri Ghiasi, J. Gomez-Luna, E. Gutierrez, O. Plata, O. Mutlu
in IEEE Access, 2024
2023
Venice: Improving Solid-State Drive Parallelism at Low Cost via Conflict-Free Accesses
R. Nadig, M. Sadrosadati, H. Mao, N. Mansouri Ghiasi, A. Tavakkol, J. Park, H. Sarbazi-Azad, J. Luna, O. Mutlu
in ISCA, 2023
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes,
C. Firtina, N. Mansouri Ghiasi, J. Lindegger, G. Singh, M. Banu Cavlak, H. Mao, and O. Mutlu
in ISMB, 2023
Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs
J. Lindegger, D. Senol Cali, M. Alser, J. Gómez-Luna, N. Mansouri Ghiasi, O. Mutlu
in Bioinformatics, 2023
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
M. B. Cavlak, G. Singh, M. Alser, C. Firtina, J. Lindegger, M. Sadrosadati, N. Mansouri Ghiasi, C. Alkan, O. Mutlu
in APBC, 2023
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches
C. Firtina, J. Park, J. S. Kim, M. Alser, D. Senol Cali, T. Shahroodi, N. Mansouri Ghiasi, G. Singh, K. Kanellopoulos, C. Alkan, O. Mutlu
in NAR Genomics and Bioinformatics, 2023
2022
GenStore: A High-Performance In-Storage Processing System for Genome Sequence Analysis
N. Mansouri Ghiasi, J. Park, H. Mustafa, J. Kim, A. Olgun, A. Gollwitzer, D. Senol Cali, C. Firtina, H. Mao, N. Almadhoun Alserr, R. Ausavarungnirun, N. Vijaykumar, M. Alser, and O. Mutlu
in ASPLOS, 2022
ALP: Alleviating CPU-Memory Data Movement Overheads in Memory-Centric Systems
N. Mansouri Ghiasi, N. Vijaykumar, G. F Oliveira, L. Orosa, I. Fernandez, M. Sadrosadati, K. Kanellopoulos, N. Hajinazar, J. Gómez Luna, O. Mutlu
in IEEE TETC, 2022
RevaMp3D: Architecting the Processor Core and Cache Hierarchy for Systems with Monolithically-Integrated Logic and Memory
N. Mansouri Ghiasi, M. Sadrosadati, G. F Oliveira, K. Kanellopoulos, R. Ausavarungnirun, J. Gómez Luna, A. Manglik, J. Ferreira, J. S Kim, C. Giannoula, N. Vijaykumar, J. Park, O. Mutlu
in arXiv, 2022
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping
D. Senol Cali, K. Kanellopoulos, J. Lindegger, Z. Bingol, G. S. Kalsi, Z. Zuo, C. Firtina, M. B. Cavlak, J. Kim, N. Mansouri Ghiasi, G. Singh, J. Gomez-Luna, N. Almadhoun Alserr, M. Alser, S. Subramoney, C. Alkan, S. Ghose, and O. Mutlu
in ISCA, 2022
2021
CODIC: A Low-Cost Substrate for Enabling Custom In-DRAM Functionalities and Optimizations
L. Orosa, Y. Wang, M. Sadrosadati, J. S. Kim, M. Patel, I. Puddu, H. Luo, K. Razavi, J. Gómez-Luna, H. Hassan, N. Mansouri Ghiasi, S. Ghose, and O. Mutlu
in ISCA, 2021
SIMDRAM: A Framework for Bit-Serial SIMD Processing Using DRAM
N. Hajinazar, G. F. Oliveira, S. Gregorio, J. Dinis Ferreira, N. Mansouri Ghiasi, M. Patel, M. Alser, S. Ghose, J. Gómez-Luna, O. Mutlu
in ASPLOS, 2021
2020
FIGARO: Improving System Performance via Fine-Grained In-DRAM Data Relocation and Caching
Y. Wang, L. Orosa, X. Peng, Y. Guo, S. Ghose, M. Patel, J. S. Kim, J. Gómez-Luna, M. Sadrosadati, N. Mansouri Ghiasi, O. Mutlu
in MICRO, 2020
2019
SMASH: Co-designing Software Compression and Hardware-Accelerated Indexing for Efficient Sparse Matrix Operations
K. Kanellopoulos, N. Vijaykumar, C. Giannoula, R. Azizi Barzoki, S. Koppula, N. Mansouri Ghiasi, T. Shahroodi, J. Gómez-Luna, O. Mutlu
in MICRO, 2019
CROW: A Low-Overhead Substrate for Improving DRAM Performance and Energy-Efficiency
H. Hassan, M. Patel, J. S. Kim, A. G. Yaglikci, N. Vijaykumar, N. Mansouri Ghiasi, S. Ghose, O. Mutlu
in ISCA, 2019
2018
Reducing DRAM Latency via Charge-Level-Aware Look-Ahead Partial Restoration
Y. Wang, A. Tavakkol, L. Orosa, S. Ghose, N. Mansouri Ghiasi, M. Patel, J. S. Kim, H. Hassan, M. Sadrosadati, O. Mutlu
in MICRO, 2018
FLIN: Enabling Fairness and Enhancing Performance in Modern NVMe Solid State Drives
A. Tavakkol, M. Sadrosadati, S. Ghose, J. S. Kim, Y. Luo, Y. Wang, N. Mansouri Ghiasi, L. Orosa, J. Gómez-Luna, O. Mutlu
in ISCA, 2018
2017
Efficient Critical Path Identification Based on Viability Analysis Method Considering Process Variations
S. Abolmaali, N. Mansouri Ghiasi, M. Kamal, A. Afzali-Kusha, M. Pedram
in IEEE TVLSI, September 2017