Harun Mustafa

20 papers A* 3A 1B 3Journal 11Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.
Bioinform.
Can Firtina, Maximilian Mordig, Harun Mustafa, Sayan Goswami, Nika Mansouri-Ghiasi, Stefano Mercogliano, Furkan Eris, Joël Lindegger, André Kahles, Onur Mutlu
2026 A* conf
SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence Analysis.
HPCA
Nika Mansouri-Ghiasi, Talu Güloglu, Harun Mustafa, Can Firtina, Konstantina Koliogeorgi, Konstantinos Kanellopoulos, Haiyu Mao, Rakesh Nadig, Mohammad Sadrosadati, Jisung Park, Onur Mutlu
2025 J jnl
SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Analysis.
CoRR
Nika Mansouri-Ghiasi, Talu Güloglu, Harun Mustafa, Can Firtina, Konstantina Koliogeorgi, Konstantinos Kanellopoulos, Haiyu Mao, Rakesh Nadig, Mohammad Sadrosadati, Jisung Park, Onur Mutlu
2024 J jnl
Label-guided seed-chain-extend alignment on annotated De Bruijn graphs.
Bioinform.
Harun Mustafa, Mikhail Karasikov, Nika Mansouri-Ghiasi, Gunnar Rätsch, André Kahles
2024 A* conf
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing.
ISCA
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
2024 J jnl
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing.
CoRR
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
2023 J jnl
MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing.
CoRR
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
2022 — —
Algorithms for efficient sensitive search and sample comparison on petabase-scale genomics data.
Harun Mustafa
2022 J jnl
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis.
CoRR
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
2022 — conf
GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis.
ISVLSI
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
2022 A* conf
GenStore: a high-performance in-storage processing system for genome sequence analysis.
ASPLOS
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
2022 B conf
Lossless Indexing with Counting de Bruijn Graphs.
RECOMB
Mikhail Karasikov, Harun Mustafa, Gunnar Rätsch, André Kahles
2021 J jnl
Topology-based sparsification of graph annotations.
Bioinform.
Daniel Danciu, Mikhail Karasikov, Harun Mustafa, André Kahles, Gunnar Rätsch
2020 B conf
AStarix: Fast and Optimal Sequence-to-Graph Alignment.
RECOMB
Pesho Ivanov, Benjamin Bichsel, Harun Mustafa, André Kahles, Gunnar Rätsch, Martin T. Vechev
2020 A conf
Communication-Efficient Jaccard similarity for High-Performance Distributed Genome Comparisons.
IPDPS
Maciej Besta, Raghavendra Kanakagiri, Harun Mustafa, Mikhail Karasikov, Gunnar Rätsch, Torsten Hoefler, Edgar Solomonik
2020 J jnl
Sparse Binary Relation Representations for Genome Graph Annotation.
J. Comput. Biol.
Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, André Kahles
2019 J jnl
Communication-Efficient Jaccard Similarity for High-Performance Distributed Genome Comparisons.
CoRR
Maciej Besta, Raghavendra Kanakagiri, Harun Mustafa, Mikhail Karasikov, Gunnar Rätsch, Torsten Hoefler, Edgar Solomonik
2019 J jnl
Deep Multiple Instance Learning for Taxonomic Classification of Metagenomic read sets.
CoRR
Andreas Georgiou, Vincent Fortuin, Harun Mustafa, Gunnar Rätsch
2019 J jnl
Dynamic compression schemes for graph coloring.
Bioinform.
Harun Mustafa, Ingo Schilken, Mikhail Karasikov, Carsten Eickhoff, Gunnar Rätsch, André Kahles
2019 B conf
Sparse Binary Relation Representations for Genome Graph Annotation.
RECOMB
Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, André Kahles