About me
I am a postdoctoral fellow in the Salzberg Lab at the Center for Computational Biology at Johns Hopkins University. My main research interests are in computational biology, genomics, and metagenomics.
I work primarily in the development and application of algorithms for large-scale sequence comparisons and analysis. This includes scalable methods for indexing and efficient algorithms for querying massive biological sequence databases, with applications in taxonomic profiling and antimicrobial resistance tracing. I also develop novel sequence alignment algorithms that better model complex genomic rearrangements, and allow for missing sequence imputation.
Brief History
I completed my Honours B.Sc. with High Distinction at the University of Toronto, dual majoring in computational biology and mathematics. Under the supervision of Michael Brudno, I developed methods for assembling the sequences of novel Alu insertions detected in second-generation sequencing data.
I completed my M.Sc. in computational biology at the ETH Zürich, where I developed a classification method for determining internal sites in proteins permissive to tag insertion under the joint supervision of Sven Panke and Jörg Stelling.
I joined the Biomedical Informatics Group in 2017 as a Ph.D. student, working with Gunnar Rätsch and André Kahles, and completed my Ph.D. at the end of 2022. I was subsequently a postdoctoral fellow in the same group from 2023 until 2025.
Since October 2025, I have been a postdoctoral fellow in the Salzberg Lab at Johns Hopkins University.
Selected Publications
* equal contribution
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
Swiss Institute of Bioinformatics (SIB) Remarkable Outputs 2025
Label-guided seed-chain-extend alignment on annotated De Bruijn graphs
H. Mustafa, M. Karasikov, N. Mansouri Ghiasi, G. Rätsch, A. Kahles
Dynamic compression schemes for graph coloring
H. Mustafa*, I. Schilken*, M. Karasikov, C. Eickhoff, G. Rätsch, A. Kahles
Lossless indexing with counting de Bruijn graphs
M. Karasikov, H. Mustafa, G. Rätsch, A. Kahles
Swiss Institute of Bioinformatics (SIB) Remarkable Outputs 2022
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
Communication-Efficient Jaccard similarity for High-Performance Distributed Genome Comparisons
M. Besta*, R. Kanakagiri*, H. Mustafa, M. Karasikov, G. Rätsch, T. Hoefler, E. Solomonik
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.
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.
Swiss Institute of Bioinformatics (SIB) Remarkable Outputs 2022
See the publications page for the full list.