Dynamic compression schemes for graph coloring. - Harun Mustafa; Ingo Schilken; Mikhail Karasikov; Carsten Eickhoff; Gunnar Rätsch; André Kahles (Bioinform., 2019)

Deep Multiple Instance Learning for Taxonomic Classification of Metagenomic read sets. - Andreas Georgiou; Vincent Fortuin; Harun Mustafa; Gunnar Rätsch (CoRR, 2019)

Communication-Efficient Jaccard similarity for High-Performance Distributed Genome Comparisons. - Maciej Besta; Raghavendra Kanakagiri; Harun Mustafa; Mikhail Karasikov; Gunnar Rätsch; Torsten Hoefler; Edgar Solomonik (IPDPS, 2020)

AStarix: Fast and Optimal Sequence-to-Graph Alignment. - Pesho Ivanov; Benjamin Bichsel; Harun Mustafa; André Kahles; Gunnar Rätsch; Martin T. Vechev (RECOMB, 2020)

Sparse Binary Relation Representations for Genome Graph Annotation. - Mikhail Karasikov; Harun Mustafa; Amir Joudaki; Sara Javadzadeh-No; Gunnar Rätsch; André Kahles (J. Comput. Biol., 2020)

Topology-based sparsification of graph annotations. - Daniel Danciu; Mikhail Karasikov; Harun Mustafa; André Kahles; Gunnar Rätsch (Bioinform., 2021)

GenStore: a high-performance in-storage processing system for genome sequence analysis. - Nika Mansouri-Ghiasi; Jisung Park 001; Harun Mustafa; Jeremie S. Kim; Ataberk Olgun; Arvid Gollwitzer; Damla Senol Cali; Can Firtina; Haiyu Mao; Nour Almadhoun Alserr; Rachata Ausavarungnirun; Nandita Vijaykumar; et al. (ASPLOS, 2022)

GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis. - Nika Mansouri-Ghiasi; Jisung Park 001; Harun Mustafa; Jeremie S. Kim; Ataberk Olgun; Arvid Gollwitzer; Damla Senol Cali; Can Firtina; Haiyu Mao; Nour Almadhoun Alserr; Rachata Ausavarungnirun; Nandita Vijaykumar; et al. (ISVLSI, 2022)

Lossless Indexing with Counting de Bruijn Graphs. - Mikhail Karasikov; Harun Mustafa; Gunnar Rätsch; André Kahles (RECOMB, 2022)

GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis. - Nika Mansouri-Ghiasi; Jisung Park 001; Harun Mustafa; Jeremie S. Kim; Ataberk Olgun; Arvid Gollwitzer; Damla Senol Cali; Can Firtina; Haiyu Mao; Nour Almadhoun Alserr; Rachata Ausavarungnirun; Nandita Vijaykumar; et al. (CoRR, 2022)

Algorithms for efficient sensitive search and sample comparison on petabase-scale genomics data. - Harun Mustafa (2022)

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 001; Onur Mutlu (CoRR, 2023)

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 001; Onur Mutlu (ISCA, 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)

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 001; Onur Mutlu (CoRR, 2025)