| SCALCE: boosting sequence compression algorithms using locally consistent encoding F Hach, I Numanagić, C Alkan, SC Sahinalp Bioinformatics 28 (23), 3051-3057, 2012 | 188 | 2012 |
| Comparison of high-throughput sequencing data compression tools I Numanagić, JK Bonfield, F Hach, J Voges, J Ostermann, C Alberti, ... nature methods 13 (12), 1005-1008, 2016 | 131 | 2016 |
| Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes I Numanagić, S Malikić, M Ford, X Qin, L Toji, M Radovich, TC Skaar, ... Nature Communications 9 (1), 828, 2018 | 108 | 2018 |
| Fast characterization of segmental duplications in genome assemblies I Numanagić, AS Gökkaya, L Zhang, B Berger, C Alkan, F Hach Bioinformatics 34 (17), i706-i714, 2018 | 95 | 2018 |
| DeeZ: reference-based compression by local assembly F Hach, I Numanagić, SC Sahinalp Nature Methods 11, 1082–1084, 2014 | 71 | 2014 |
| An efficient genotyper and star-allele caller for pharmacogenomics A Hari, Q Zhou, N Gonzaludo, J Harting, SA Scott, X Qin, S Scherer, ... Genome Research 33 (1), 61-70, 2023 | 61 | 2023 |
| Statistical Binning for Barcoded Reads Improves Downstream Analyses A Shajii, I Numanagić, C Whelan, B Berger Cell Systems 7 (2), 219-226. e5, 2018 | 53* | 2018 |
| Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data I Numanagić, S Malikić, VM Pratt, TC Skaar, DA Flockhart, SC Sahinalp Bioinformatics 31 (12), i27-i34, 2015 | 53 | 2015 |
| Fast characterization of segmental duplication structure in multiple genome assemblies H Išerić, C Alkan, F Hach, I Numanagić Algorithms for Molecular Biology 17 (1), 4, 2022 | 51 | 2022 |
| Discovery and genotyping of novel sequence insertions in many sequenced individuals P Kavak, YY Lin, I Numanagić, H Asghari, T Güngör, C Alkan, F Hach Bioinformatics 33 (14), i161-i169, 2017 | 44 | 2017 |
| CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project A Gaedigk, EC Boone, SE Scherer, S Lee, I Numanagić, C Sahinalp, ... The Journal of Molecular Diagnostics 24 (4), 337-350, 2022 | 42 | 2022 |
| Codon: A Compiler for High-Performance Pythonic Applications and DSLs A Shajii, G Ramirez, H Smajlović, J Ray, B Berger, S Amarasinghe, ... Proceedings of the 32nd ACM SIGPLAN International Conference on Compiler …, 2023 | 40 | 2023 |
| Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing H Smajlović, A Shajii, B Berger, H Cho, I Numanagić Genome Biology 24 (1), 5, 2023 | 34* | 2023 |
| A Python-based programming language for high-performance computational genomics A Shajii, I Numanagić, AT Leighton, H Greenyer, S Amarasinghe, ... Nature Biotechnology 39 (9), 1062-1064, 2021 | 33* | 2021 |
| Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets E Berger, D Yorukoglu, L Zhang, SK Nyquist, AK Shalek, M Kellis, ... Nature Communications 11 (1), 1-9, 2020 | 31 | 2020 |
| Optimal compressed representation of high throughput sequence data via light assembly AA Ginart, J Hui, K Zhu, I Numanagić, TA Courtade, SC Sahinalp, ... Nature communications 9 (1), 566, 2018 | 29 | 2018 |
| Seq: a high-performance language for bioinformatics A Shajii, I Numanagić, R Baghdadi, B Berger, S Amarasinghe Proceedings of the ACM on Programming Languages 3 (OOPSLA), 125, 2019 | 24 | 2019 |
| ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms P Dao, I Numanagić, YY Lin, F Hach, E Karakoc, N Donmez, C Collins, ... Bioinformatics 30 (5), 644-651, 2014 | 22 | 2014 |
| Analytical Validation of a Computational Method for Pharmacogenetic Genotyping from Clinical Whole Exome Sequencing RC Ly, T Shugg, R Ratcliff, W Osei, TC Lynnes, VM Pratt, BP Schneider, ... The Journal of Molecular Diagnostics, 2022 | 15 | 2022 |
| Computational identification of micro-structural variations and their proteogenomic consequences in cancer YY Lin, A Gawronski, F Hach, S Li, I Numanagić, I Sarrafi, S Mishra, ... Bioinformatics 34 (10), 1672-1681, 2017 | 14 | 2017 |
S. Cenk SahinalpCancer Data Science Labotatory, National Cancer Institute, NIHVerified email at nih.gov
