| 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 | 306* | 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 | 254 | 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 | 202 | 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 | 90 | 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 Alignment P 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: Memory-efficient taxonomic classification and abundance estimation for metagenomics with deep learning 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 |