A global metagenomic map of urban microbiomes and antimicrobial resistance D Danko, D Bezdan, EE Afshin, S Ahsanuddin, C Bhattacharya, DJ Butler, ...
Cell 184 (13), 3376-3393. e17, 2021
304 * 2021 Biosynthetic potential of the global ocean microbiome L Paoli, HJ Ruscheweyh, CC Forneris, F Hubrich, S Kautsar, A Bhushan, ...
Nature 607 (7917), 111-118, 2022
255 2022 Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment KR Chng, C Li, D Bertrand, AHQ Ng, JS Kwah, HM Low, C Tong, ...
Nature medicine 26 (6), 941-951, 2020
203 2020 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, ...
Proceedings of the 27th ACM International Conference on Architectural …, 2022
95 * 2022 Communication-efficient jaccard similarity for high-performance distributed genome comparisons M Besta, R Kanakagiri, H Mustafa, M Karasikov, G Rätsch, T Hoefler, ...
2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS …, 2020
89 2020 Indexing all life’s known biological sequences M Karasikov, H Mustafa, D Danciu, M Zimmermann, C Barber, G Rätsch, ...
bioRxiv, 2024
71 * 2024 AStarix : Fast and Optimal Sequence-to-Graph AlignmentP Ivanov, B Bichsel, H Mustafa, A Kahles, G Rätsch, M Vechev
International Conference on Research in Computational Molecular Biology, 104-119, 2020
35 2020 Dynamic compression schemes for graph coloring H Mustafa, I Schilken, M Karasikov, C Eickhoff, G Rätsch, A Kahles
Bioinformatics 35 (3), 407-414, 2019
34 * 2019 Lossless indexing with counting de bruijn graphs M Karasikov, H Mustafa, G Rätsch, A Kahles
Genome Research 32 (9), 1754-1764, 2022
27 2022 Sparse binary relation representations for genome graph annotation M Karasikov, H Mustafa, A Joudaki, S Javadzadeh-No, G Rätsch, ...
Journal of Computational Biology, 2020
26 2020 Detecting Alu insertions from high-throughput sequencing data M David, H Mustafa, M Brudno
Nucleic acids research 41 (17), e169-e169, 2013
24 2013 Sequence-based prediction of permissive stretches for internal protein tagging and knockdown S Oesterle, TM Roberts, LA Widmer, H Mustafa, S Panke, S Billerbeck
BMC biology 15, 1-17, 2017
16 2017 META A Georgiou, V Fortuin, H Mustafa, G Rätsch
arXiv preprint arXiv:1909.13146, 2019
13 * 2019 Aligning distant sequences to graphs using long seed sketches A Joudaki, A Meterez, H Mustafa, RG Koerkamp, A Kahles, G Rätsch
Genome Research, gr. 277659.123, 2023
10 2023 Topology-based sparsification of graph annotations D Danciu, M Karasikov, H Mustafa, A Kahles, G Rätsch
Bioinformatics 37 (Supplement_1), i169-i176, 2021
7 * 2021 Label-guided seed-chain-extend alignment on annotated De Bruijn graphs H Mustafa, M Karasikov, N Mansouri Ghiasi, G Rätsch, A Kahles
Bioinformatics 40 (Supplement_1), i337-i346, 2024
5 * 2024 Assembly and characterization of novel Alu inserts detected from next-generation sequencing data H Mustafa, M David, M Brudno
Mobile genetic elements 4 (5), 1-7, 2014
4 2014 MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing NM Ghiasi, M Sadrosadati, H Mustafa, A Gollwitzer, C Firtina, J Eudine, ...
2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture …, 2024
2 2024 Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism C Firtina, M Mordig, H Mustafa, S Goswami, NM Ghiasi, S Mercogliano, ...
arXiv preprint arXiv:2410.17801, 2024
2024 Algorithms for efficient sensitive search and sample comparison on petabase-scale genomics data H Mustafa
ETH Zurich, 2022
2022