Talks and Presentations

Sequence analysis at scale: Accurate algorithms for indexing, comparing, and decontaminating the world's biological sequence data

Seminars in the Computer Engineering Department, 9 October 2026

Invited talk at Bilkent University

Efficient, accurate, petabyte-scale indexing and query of biological sequences

Arch4Health, 31 January 2026

Invited workshop talk at the 32nd IEEE International Symposium on High-Performance Computer Architecture (HPCA)

Video

Large-scale multi-genome representation and microbiome analysis with the MetaGraph framework

Algorithms and Data Structures for Population Scale Genomics (261-5112-00L), 11 December 2024

Lecture at ETH Zurich

Analyzing Petabase-scale Genomics Data with Annotated de Bruijn Graphs

Algorithms and Data Structures for Population Scale Genomics (261-5112-00L), 13 December 2023

Lecture at ETH Zurich

The Computational Side of Computational Biology

The Undergraduate Artificial Intelligence Day (UAID), 7 October 2013

Workshop talk at the University of Toronto

Efficient, accurate, SRA-scale indexing and query

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

Cold Spring Harbor Laboratory Meeting: Genome Informatics (CSHL-GI), 6 November 2025

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

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

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

Video

Large-scale multi-genome representation and microbiome analysis with the MetaGraph framework

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

International Genome Graph Symposium (IGGSy), 3 July 2024

A modular framework for label-guided alignment to sequence graph databases

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

Cold Spring Harbor Laboratory Meeting: Biological Data Science (CSHL-BDS), 12 November 2022

MetaGraph-MLA: a Novel Algorithm for Multi-label Alignment of Sequences to Annotated de Bruijn Graphs

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

International Genome Graph Symposium (IGGSy), 5 July 2022

META²: Memory-efficient taxonomic classification and abundance estimation for metagenomics with deep learning

A. Georgiou, V. Fortuin*, H. Mustafa*⁺, G. Rätsch

Intelligent Systems for Molecular Biology (ISMB), 15 July 2020

Sparse Binary Relation Representations for Genome Graph Annotation

M. Karasikov, H. Mustafa⁺, A. Joudaki, S. Javadzadeh-no, G. Rätsch, A. Kahles

Research in Computational Molecular Biology (RECOMB), 7 July 2019

Slides

Can we accurately align two entire human genomes?

H. Mustafa⁺, H. J. Ji, C. Hoh, N. Mansouri Ghiasi, S. L. Salzberg

Intelligent Systems for Molecular Biology (ISMB), 2026

Code

MetaGraph-MLA: a novel algorithm for multi-label alignment of sequences to annotated de Bruijn graphs

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

Research in Computational Molecular Biology (RECOMB), 2023

Metagraph: a versatile framework for scalable annotated de Bruijn graphs

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

Intelligent Systems for Molecular Biology (ISMB), 2019

F1000 Best Poster Award