Harun Mustafa

According to our database, Harun Mustafa authored at least 15 papers between 2019 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

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

CoRR, April, 2025

2024

Label-guided seed-chain-extend alignment on annotated De Bruijn graphs.

Harun Mustafa, Mikhail Karasikov, Nika Mansouri-Ghiasi, Gunnar Rätsch, André Kahles

Bioinform., 2024

MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing.

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

Proceedings of the 51st ACM/IEEE Annual International Symposium on Computer Architecture, 2024

2023

MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing.

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

CoRR, 2023

2022

Algorithms for efficient sensitive search and sample comparison on petabase-scale genomics data.

Harun Mustafa

PhD thesis, 2022

GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis.

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

CoRR, 2022

Lossless Indexing with Counting de Bruijn Graphs.

Mikhail Karasikov, Harun Mustafa, Gunnar Rätsch, André Kahles

Proceedings of the Research in Computational Molecular Biology, 2022

GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis.

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

Proceedings of the IEEE Computer Society Annual Symposium on VLSI, 2022

GenStore: a high-performance in-storage processing system for genome sequence analysis.

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

Proceedings of the ASPLOS '22: 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems, Lausanne, Switzerland, 28 February 2022, 2022

2021

Topology-based sparsification of graph annotations.

Daniel Danciu, Mikhail Karasikov, Harun Mustafa, André Kahles, Gunnar Rätsch

Bioinform., 2021

2020

AStarix: Fast and Optimal Sequence-to-Graph Alignment.

Pesho Ivanov, Benjamin Bichsel, Harun Mustafa, André Kahles, Gunnar Rätsch, Martin T. Vechev

Proceedings of the Research in Computational Molecular Biology, 2020

Communication-Efficient Jaccard similarity for High-Performance Distributed Genome Comparisons.

Maciej Besta, Raghavendra Kanakagiri, Harun Mustafa, Mikhail Karasikov, Gunnar Rätsch, Torsten Hoefler, Edgar Solomonik

Proceedings of the 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2020

2019

Deep Multiple Instance Learning for Taxonomic Classification of Metagenomic read sets.

Andreas Georgiou, Vincent Fortuin, Harun Mustafa, Gunnar Rätsch

CoRR, 2019

Dynamic compression schemes for graph coloring.

Harun Mustafa, Ingo Schilken, Mikhail Karasikov, Carsten Eickhoff, Gunnar Rätsch, André Kahles

Bioinform., 2019

Sparse Binary Relation Representations for Genome Graph Annotation.

Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, André Kahles

Proceedings of the Research in Computational Molecular Biology, 2019