Publications

You can also find my articles on my Google Scholar profile.

* equal contribution

2026

GRAINS: Storage-Aware Algorithm-Architecture Co-Design Enabling High-Performance and Low-Cost Graph-Based Genome Analysis

N. Mansouri Ghiasi, H. Mustafa, T. Güloglu, R. Nadig, K. Koliogeorgi, S. R. Ruiz, M. Rautmann, F. Eris, M. Sadrosadati, J. Park, O. Mutlu

ACM/IEEE 53rd Annual International Symposium on Computer Architecture (ISCA), 4 August 2026

DOI Extended Paper

SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence Analysis

N. Mansouri Ghiasi, T. Güloglu, H. Mustafa, C. Firtina, K. Koliogeorgi, K. Kanellopoulos, H. Mao, R. Nadig, M. Sadrosadati, J. Park, O. Mutlu

IEEE International Symposium on High Performance Computer Architecture (HPCA), 4 March 2026

DOI Extended Paper

Rawsamble: Overlapping Raw Nanopore Signals using a Hash-based Seeding Mechanism

C. Firtina, M. Mordig, H. Mustafa, S. Goswami, N. Mansouri Ghiasi, S. Mercogliano, F. Eris, J. Lindegger, A. Kahles, O. Mutlu

Bioinformatics, 26 February 2026

DOI Extended Paper PubMed Code

2025

Efficient and accurate search in petabase-scale sequence repositories

M. Karasikov*, H. Mustafa*, D. Danciu, O. Kulkov, M. Zimmermann, C. Barber, G. Rätsch, A. Kahles

Nature, 8 October 2025

Swiss Institute of Bioinformatics (SIB) Remarkable Outputs 2025

DOI PubMed Code Website

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. Mao, J. Lindegger, M. B. Cavlak, M. Alser, J. Park, O. Mutlu

ACM/IEEE 51st Annual International Symposium on Computer Architecture (ISCA), 1 August 2024

DOI Extended Paper Code

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

H. Mustafa, M. Karasikov, N. Mansouri Ghiasi, G. Rätsch, A. Kahles

Bioinformatics, 28 June 2024

Conference version: Intelligent Systems for Molecular Biology (ISMB), 13 July 2024

DOI PubMed Code

2023

Aligning distant sequences to graphs using long seed sketches

A. Joudaki*, A. Meterez*, H. Mustafa, R. Groot Koerkamp, A. Kahles, G. Rätsch

Genome Research, 18 April 2023

Conference version: Research in Computational Molecular Biology (RECOMB), 2 April 2023

DOI PubMed Code

2022

Biosynthetic potential of the global ocean microbiome

L. Paoli, H. Ruscheweyh*, C. C. Forneris*, F. Hubrich*, S. Kautsar, A. Bhushan, A. Lotti, Q. Clayssen, G. Salazar, A. Milanese, …, H. Mustafa, et al.

Nature, 1 July 2022

Swiss Institute of Bioinformatics (SIB) Remarkable Outputs 2022

DOI PubMed Code

Lossless indexing with counting de Bruijn graphs

M. Karasikov, H. Mustafa, G. Rätsch, A. Kahles

Genome Research, 24 May 2022

Conference version: Research in Computational Molecular Biology (RECOMB), 29 April 2022

Swiss Institute of Bioinformatics (SIB) Remarkable Outputs 2022

DOI PubMed Code

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, O. Mutlu

27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), 22 February 2022

DOI Extended Paper Code

2021

Topology-based sparsification of graph annotations

D. Danciu*, M. Karasikov*, H. Mustafa, A. Kahles, G. Rätsch

Bioinformatics, 12 July 2021

Conference version: Intelligent Systems for Molecular Biology (ISMB), 25 July 2021

DOI PubMed Code

A global metagenomic map of urban microbiomes and antimicrobial resistance

D. Danko*, D. Bezdan*, E. E. Afshin, S. Ahsanuddin, C. Bhattacharya, D. J. Butler, K. R. Chng, D. Donnellan, J. Hecht, K. Jackson, …, H. Mustafa, et al.

Cell, 21 June 2021

DOI PubMed Code