Ibrahim Numanagić
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SCALCE: boosting sequence compression algorithms using locally consistent encoding
F Hach, I Numanagić, C Alkan, SC Sahinalp
Bioinformatics 28 (23), 3051-3057, 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
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
DeeZ: reference-based compression by local assembly
F Hach, I Numanagić, SC Sahinalp
Nature Methods 11, 1082–1084, 2014
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
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
Statistical Binning for Barcoded Reads Improves Downstream Analyses
A Shajii, I Numanagić, C Whelan, B Berger
Cell Systems 7 (2), 219-226. e5, 2018
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
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
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
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
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
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
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
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
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
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, 2023
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
Efficient high throughput sequencing data compression and genotyping methods for clinical environments
I Numanagic
Simon Fraser University, 2016
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), 1-18, 2023
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