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

to appear 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

to appear 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