OM
Onur Mutlu
cs.ARcs.DCcs.CRq-bio.GNcs.LGcs.PFcs.AIq-bio.QMSoftwarecs.DS
On Valency
published · living versionsW_92jh5vez·v1 · currentpublished
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping
with Hongyi Xin, Richard Zhu, Sunny Nahar, John Emmons +3
1 version
Preprints & journals
336 papers in the corpus · 2009–2026CertiFlash: A Formal Verification Framework for Flash Translation Layers in Computational Solid State Drives2609.10347v1 · Harshita Gupta, Mayank Kabra, Rakesh Nadig et al.2026 · 0 citationsarXiv
DCC: Data-Centric Compilation of Machine Learning Kernels for Processing-In-Memory Architectures2511.15503v5 · Peiming Yang, Sankeerth Durvasula, Ivan Fernandez et al.2025 · 0 citationsarXiv
FLINT: Efficiently Leveraging High Bandwidth Flash for Capacity-Scalable LLM Inference Acceleration2608.25062v1 · Geraldo F. Oliveira, Arash Tavakkol, Xiangyu Zhu et al.2026 · 0 citationsarXiv
De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.42632028 · Bingöl, Zülal, Şahin, Berkan, Zambaku, Klea et al.2026 · 0 citationsBriefings in bioinformatics. 2026;27(4)
RevaMp3D: Architecting the Processor Core and Cache Hierarchy for Systems with Monolithically-Integrated Logic and Memory2210.08508v4 · Nika Mansouri Ghiasi, Mohammad Sadrosadati, Geraldo F. Oliveira et al.2022 · 1 citationarXiv
Exploring High-Bandwidth Flash for Modern LLM Inference: Opportunities and Challenges2608.13868v1 · Dowon Son, Yonggon Park, Hyunuk Cho et al.2026 · 1 citationarXiv
Experimental Study on System-Level Performance Impact of Read Disturbance in Modern SSDs2608.14073v1 · Yonggon Park, Hyunuk Cho, Onur Mutlu et al.2026 · 0 citationsarXiv
Towards a decentralized future for open-science databases.42156561 · Sharma, Gaurav, Munteanu, Viorel, Ghiasi, Nika Mansouri et al.2026 · 1 citationNature genetics. 2026;58(7):1451-1455
Valinor: Architectural Support for Fast, Energy-Efficient and Programmable Physical Memory Allocation2607.14789v1 · Konstantinos Kanellopoulos, Spiros Galanopoulos, Konstantinos Sgouras et al.2026 · 0 citationsarXiv
Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.41746292 · Firtina, Can, Mordig, Maximilian, Mustafa, Harun et al.2026 · 3 citationsBioinformatics (Oxford, England). 2026;42(3)
Systems Biology and Network Analysis: From Multi-omics Integration to Biological Mechanisms.41758182 · Bebek, Gurkan, Mutlu, Onur, Hajirasouliha, Iman et al.2026 · 0 citationsPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2026;31:752-754
Enabling Fast, Efficient, and Low-Cost Genomic and Metagenomic Analyses via Storage-Centric System Designs2607.02552v1 · Nika Mansouri Ghiasi, Onur Mutlu2026 · 1 citationarXiv
COSM: A Cooperative Scheduling Framework for Concurrent PIM and CPU Execution on Mobile Devices2606.30553v2 · Yilong Zhao, Fangxin Liu, Onur Mutlu et al.2026 · 0 citationsarXiv
Revelator: Rapid Data Fetching via System-Software-Guided Hash-based Speculative Address Translation2508.02007v2 · Konstantinos Kanellopoulos, Konstantinos Sgouras, Harsh Songara et al.2025 · 0 citationsarXiv
GRAINS: Storage-Aware Algorithm-Architecture Co-Design Enabling High-Performance and Low-Cost Graph-Based Genome Analysis2606.26468v1 · Nika Mansouri Ghiasi, Harun Mustafa, Talu Guloglu et al.2026 · 0 citationsarXiv
Ramulator 2.1: A Composable Memory System Simulator for Modern DRAM Systems2606.13844v2 · Haocong Luo, F. Nisa Bostanc\i, Ataberk Olgun et al.2026 · 0 citationsarXiv
Memory-Centric Computing: Security Benefits and Challenges of Processing-in-DRAM2606.20786v1 · Ismail Emir Yuksel, F. Nisa Bostanci, Ataberk Olgun et al.2026 · 0 citationsarXiv
Architecture for Health Initiative (Arch4Health): Computational Challenges in Health-Related Applications and the Role of Computer Architecture in Addressing Them2606.22685v1 · Nika Mansouri Ghiasi, Konstantina Koliogeorgi, Onur Mutlu2026 · 0 citationsarXiv
Clutch: High Performance Vector-Scalar Comparison using DRAM via Chunked Temporal Coding2606.22812v1 · Daichi Tokuda, Tatsuya Kubo, Ismail Emir Yuksel et al.2026 · 2 citationsarXiv
ScaleDisturb: Exploiting Temporal Asymmetry to Amplify Read Disturbance in Modern DRAM Chips2606.07761v1 · Jikun Wang, Haocong Luo, Ataberk Olgun et al.2026 · 1 citationarXiv
Hermes: Accelerating Long-Latency Load Requests via Perceptron-Based Off-Chip Load Prediction2209.00188v4 · Rahul Bera, Konstantinos Kanellopoulos, Shankar Balachandran et al.2022 · 37 citationsarXiv
A decentralized future for the open-science databases.41040803 · Sharma, Gaurav, Munteanu, Viorel, Ghiasi, Nika Mansouri et al.2026 · 0 citationsArXiv. 2025
Taking Cryptography Out of the Data Path via Near-Memory Processing in DRAM2605.20047v1 · Nicola Barcarolo, Brahmaiah Gandham, Mohammad Sadrosadati et al.2026 · 0 citationsarXiv
HE-PIM: Demystifying Homomorphic Operations on a Real-world Processing-in-Memory System2605.12841v1 · Harshita Gupta, Mayank Kabra, Jaewoo Park et al.2026 · 0 citationsarXiv
Cleaning up the Mess: Re-Evaluating the Real-System Modeling Accuracy of Ramulator 2.02510.15744v4 · F. Nisa Bostanci, Haocong Luo, Ataberk Olgun et al.2025 · 5 citationsarXiv
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes1912.08735v5 · Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak et al.2019 · 7 citationsIEEE Transactions on Computational Biology and Bioinformatics, 23 (2): 589-597, 2026
Demystifying Chains, Trees, and Graphs of Thoughts2401.14295v6 · Maciej Besta, Florim Memedi, Zhenyu Zhang et al.2024 · 19 citationsIEEE Transactions on Pattern Analysis and Machine Intelligence, Volume 47, Issue 12, pages 10967-10989 (December 2025)
Accelerating Triangle Counting with Real Processing-in-Memory Systems2505.04269v2 · Lorenzo Asquini, Manos Frouzakis, Juan G'omez-Luna et al.2025 · 2 citationsProc. IPDPS Workshop on Graphs, Architectures, Programming, and Learning (GrAPL), 2025
Machine Learning-Driven Intelligent Memory System Design: From On-Chip Caches to Storage2603.14583v1 · Rahul Bera, Rakesh Nadig, Onur Mutlu2026 · 0 citationsarXiv
DiscoRD: An Experimental Methodology for Quickly Discovering the Reliable Read Disturbance Threshold of Real DRAM Chips2603.12435v1 · Ataberk Olgun, F. Nisa Bostanci, Ismail Emir Yuksel et al.2026 · 0 citationsarXiv
Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism2410.17801v3 · Can Firtina, Maximilian Mordig, Harun Mustafa et al.2024 · 0 citationsarXiv
ALPHA-PIM: Analysis of Linear Algebraic Processing for High-Performance Graph Applications on a Real Processing-In-Memory System2602.09174v1 · Marzieh Barkhordar, Alireza Tabatabaeian, Mohammad Sadrosadati et al.2026 · 3 citationsIEEE International Symposium on Workload Characterization (2025) 257-271
GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping2601.19384v1 · Julien Eudine, Chu Li, Zhuo Cheng et al.2026 · 2 citationsarXiv
Artificial Intelligence for Objective Assessment of Pediatric Uroflowmetry Curves.40816601 · Yücel, Ömer Barış, Tekin, Ali, Tiryaki, Sibel et al.2025 · 7 citationsUrology. 2025;206:125-130
REIS: A High-Performance and Energy-Efficient Retrieval System with In-Storage Processing2506.16444v2 · Kangqi Chen, Andreas Kosmas Kakolyris, Rakesh Nadig et al.2025 · 14 citationsarXiv
In-DRAM True Random Number Generation Using Simultaneous Multiple-Row Activation: An Experimental Study of Real DRAM Chips2510.20269v1 · Ismail Emir Yuksel, Ataberk Olgun, F. Nisa Bostanci et al.2025 · 4 citationsarXiv
DRAM Bender: An Extensible and Versatile FPGA-based Infrastructure to Easily Test State-of-the-art DRAM Chips2211.05838v6 · Ataberk Olgun, Hasan Hassan, A. Giray Yagl\ikc\i et al.2022 · 60 citationsarXiv
ColumnDisturb: Understanding Column-based Read Disturbance in Real DRAM Chips and Implications for Future Systems2510.14750v2 · \.Ismail Emir Yuksel, Ataberk Olgun, F. Nisa Bostanc\i et al.2025 · 15 citationsarXiv
Understanding and Mitigating Covert Channel and Side Channel Vulnerabilities Introduced by RowHammer Defenses2503.17891v3 · F. Nisa Bostanc\i, Oguzhan Canpolat, Ataberk Olgun et al.2025 · 8 citationsarXiv
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques2510.03629v1 · Furkan Eris, Ulysse McConnell, Can Firtina et al.2025 · 1 citationarXiv
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques10.1101/2025.10.04.680405v1 · Eris, F., McConnell, U., Firtina, C. et al.2025 · 1 citationbioRxiv
A decentralized future for the open-science databases2509.19206v1 · Gaurav Sharma, Viorel Munteanu, Nika Mansouri Ghiasi et al.2025 · 0 citationsarXiv
Chronus: Understanding and Securing the Cutting-Edge Industry Solutions to DRAM Read Disturbance2502.12650v2 · Oguzhan Canpolat, A. Giray Yagl\ikc\i, Geraldo F. Oliveira et al.2025 · 22 citationsarXiv
Self-Managing DRAM: A Low-Cost Framework for Enabling Autonomous and Efficient in-DRAM Operations2207.13358v9 · Hasan Hassan, Ataberk Olgun, A. Giray Yaglikci et al.2022 · 2 citationsarXiv
Analysis of metagenomic data.40688383 · Liu, Shaopeng, Rodriguez, Judith S, Munteanu, Viorel et al.2025 · 84 citationsNature reviews. Methods primers. 2025;5
MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem2506.10931v2 · Melina Soysal, Konstantina Koliogeorgi, Can Firtina et al.2025 · 8 citationsarXiv
PuDHammer: Experimental Analysis of Read Disturbance Effects of Processing-using-DRAM in Real DRAM Chips2506.12947v1 · Ismail Emir Yuksel, Akash Sood, Ataberk Olgun et al.2025 · 6 citationsarXiv
Revisiting Main Memory-Based Covert and Side Channel Attacks in the Context of Processing-in-Memory2404.11284v4 · F. Nisa Bostanci, Konstantinos Kanellopoulos, Ataberk Olgun et al.2024 · 5 citationsarXiv
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering2212.04953v3 · Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser et al.2022 · 16 citationsFrontiers in Genetics, 15: 1429306, 2024
PIM Is All You Need: A CXL-Enabled GPU-Free System for Large Language Model Inference2502.07578v3 · Yufeng Gu, Alireza Khadem, Sumanth Umesh et al.2025 · 43 citationsarXiv
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