| Building large updatable colored de Bruijn graphs via merging MD Muggli, B Alipanahi, C Boucher Bioinformatics 35 (14), i51-i60, 2019 | 54 | 2019 |
| Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences SM Lakin, A Kuhnle, B Alipanahi, NR Noyes, C Dean, M Muggli, ... Communications biology 2 (1), 294, 2019 | 46 | 2019 |
| Cancer treatment monitoring using cell-free DNA fragmentomes I van’t Erve, B Alipanahi, K Lumbard, ZL Skidmore, L Rinaldi, LK Millberg, ... Nature communications 15 (1), 8801, 2024 | 26 | 2024 |
| Metagenome SNP calling via read-colored de Bruijn graphs B Alipanahi, MD Muggli, M Jundi, NR Noyes, C Boucher Bioinformatics 36 (22-23), 5275-5281, 2020 | 22* | 2020 |
| Succinct dynamic de Bruijn graphs B Alipanahi, A Kuhnle, SJ Puglisi, L Salmela, C Boucher Bioinformatics 37 (14), 1946-1952, 2021 | 21 | 2021 |
| Buffering updates enables efficient dynamic de bruijn graphs J Alanko, B Alipanahi, J Settle, C Boucher, T Gagie Computational and structural biotechnology journal 19, 4067-4078, 2021 | 14 | 2021 |
| Recoloring the colored de Bruijn graph B Alipanahi, A Kuhnle, C Boucher International Symposium on String Processing and Information Retrieval, 1-11, 2018 | 11 | 2018 |
| Disentangled long-read de Bruijn graphs via optical maps B Alipanahi, L Salmela, SJ Puglisi, M Muggli, C Boucher bioRxiv, 094235, 2016 | 11 | 2016 |
| Aligning optical maps to de Bruijn graphs K Mukherjee, B Alipanahi, T Kahveci, L Salmela, C Boucher Bioinformatics 35 (18), 3250-3256, 2019 | 10 | 2019 |
| Hierarchical hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences. Commun Biol 2: 294 SM Lakin, A Kuhnle, B Alipanahi, NR Noyes, C Dean, M Muggli, ... | 9 | 2019 |
| Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer C Hruban, DC Bruhm, IM Chen, S Koul, AV Annapragada, NA Vulpescu, ... Science Advances 11 (21), eads5002, 2025 | 7 | 2025 |
| Cell-free DNA fragmentation profiling for therapeutic response monitoring in metastatic colorectal cancer. ZL Skidmore, I van't Erve, K Lumbard, B Alipanahi, L Keefer, L Rinaldi, ... Journal of Clinical Oncology 41 (16_suppl), e15664-e15664, 2023 | 3 | 2023 |
| Leveraging the cfDNA fragmentome to predict immunotherapy response N Niknafs, L Sivapalan, B Alipanahi, D Rabizadeh, M Najjar, ZL Skidmore, ... Cancer Research 85 (8_Supplement_1), 3772-3772, 2025 | 2 | 2025 |
| Longitudinal cell-free tumor load dynamics represent an early endpoint for immunotherapy response in non-small cell lung cancer L Sivapalan, B Alipanahi, A Balan, JE Medina, N Niknafs, E Peters, ... Cancer Research 84 (6_Supplement), 6557-6557, 2024 | 2 | 2024 |
| Cell-free DNA fragmentation profiling for monitoring therapeutic response in metastatic colorectal cancer B Alipanahi, I van't Erve, K Lumbard, LK Millberg, Z Skidmore, L Rinaldi, ... Cancer Research 83 (7_Supplement), 5714-5714, 2023 | 2 | 2023 |
| Abstract B025: Monitoring response to immunotherapy in lung cancer using cell-free DNA fragmentomes L Sivapalan, B Alipanahi, JE Medina, B Tripp, ZL Skidmore, P Ghanem, ... Clinical Cancer Research 30 (21_Supplement), B025-B025, 2024 | 1 | 2024 |
| Dissecting small cell lung cancer subtypes with cell-free DNA fragmentomes. L Rinaldi, ZL Skidmore, B Alipanahi, G Graham, B Chesnick, N Takahashi, ... Journal of Clinical Oncology 41 (16_suppl), 8592-8592, 2023 | 1 | 2023 |
| Variants and Applications of Colored De Bruijn Graphs B Alipanahi University of Florida, 2020 | 1 | 2020 |
| Combining cell-free DNA fragmentomes and total tumour volume improves prognostication and tumour response evaluation in patients with colorectal cancer liver metastases N Crnovrsanin, JM Zeeuw, M Ali, R Kemna, B Alipanahi, K Lumbard, ... EBioMedicine 123, 2026 | | 2026 |
| 34 Monitoring response to immunotherapy in lung cancer using cell-free DNA fragmentomes B Alipanahi, L Sivapalan, JE Medina, B Tripp, ZL Skidmore, P Ghanem, ... Journal for ImmunoTherapy of Cancer 12 (Suppl 2), 2024 | | 2024 |
