Numanagić I - Search Results

1

Computational pharmacogenotype extraction from clinical next-generation sequencing.

Shugg T, Ly RC, Osei W, Rowe EJ, Granfield CA, Lynnes TC, Medeiros EB, Hodge JC, Breman AM, Schneider BP, Sahinalp SC, Numanagić I, Salisbury BA, Bray SM, Ratcliff R, Skaar TC. Shugg T, et al. Among authors: numanagic i. Front Oncol. 2023 Jul 4;13:1199741. doi: 10.3389/fonc.2023.1199741. eCollection 2023. Front Oncol. 2023. PMID: 37469403 Free PMC article.

2

Analytical Validation of a Computational Method for Pharmacogenetic Genotyping from Clinical Whole Exome Sequencing.

Ly RC, Shugg T, Ratcliff R, Osei W, Lynnes TC, Pratt VM, Schneider BP, Radovich M, Bray SM, Salisbury BA, Parikh B, Sahinalp SC, Numanagić I, Skaar TC. Ly RC, et al. Among authors: numanagic i. J Mol Diagn. 2022 Jun;24(6):576-585. doi: 10.1016/j.jmoldx.2022.03.008. Epub 2022 Apr 20. J Mol Diagn. 2022. PMID: 35452844 Free PMC article.

3

Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data.

Numanagić I, Malikić S, Pratt VM, Skaar TC, Flockhart DA, Sahinalp SC. Numanagić I, et al. Bioinformatics. 2015 Jun 15;31(12):i27-34. doi: 10.1093/bioinformatics/btv232. Bioinformatics. 2015. PMID: 26072492 Free PMC article.

4

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes.

Numanagić I, Malikić S, Ford M, Qin X, Toji L, Radovich M, Skaar TC, Pratt VM, Berger B, Scherer S, Sahinalp SC. Numanagić I, et al. Nat Commun. 2018 Feb 26;9(1):828. doi: 10.1038/s41467-018-03273-1. Nat Commun. 2018. PMID: 29483503 Free PMC article.

5

An efficient genotyper and star-allele caller for pharmacogenomics.

Hari A, Zhou Q, Gonzaludo N, Harting J, Scott SA, Qin X, Scherer S, Sahinalp SC, Numanagić I. Hari A, et al. Among authors: numanagic i. Genome Res. 2023 Jan;33(1):61-70. doi: 10.1101/gr.277075.122. Epub 2023 Jan 19. Genome Res. 2023. PMID: 36657977 Free PMC article.

6

DeeZ: reference-based compression by local assembly.

Hach F, Numanagić I, Sahinalp SC. Hach F, et al. Among authors: numanagic i. Nat Methods. 2014 Nov;11(11):1082-4. doi: 10.1038/nmeth.3133. Nat Methods. 2014. PMID: 25357237 No abstract available.

7

Computational identification of micro-structural variations and their proteogenomic consequences in cancer.

Lin YY, Gawronski A, Hach F, Li S, Numanagic I, Sarrafi I, Mishra S, McPherson A, Collins CC, Radovich M, Tang H, Sahinalp SC. Lin YY, et al. Among authors: numanagic i. Bioinformatics. 2018 May 15;34(10):1672-1681. doi: 10.1093/bioinformatics/btx807. Bioinformatics. 2018. PMID: 29267878 Free PMC article.

8

Comparison of high-throughput sequencing data compression tools.

Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J, Alberti C, Mattavelli M, Sahinalp SC. Numanagić I, et al. Nat Methods. 2016 Dec;13(12):1005-1008. doi: 10.1038/nmeth.4037. Epub 2016 Oct 24. Nat Methods. 2016. PMID: 27776113

9

Optimal compressed representation of high throughput sequence data via light assembly.

Ginart AA, Hui J, Zhu K, Numanagić I, Courtade TA, Sahinalp SC, Tse DN. Ginart AA, et al. Among authors: numanagic i. Nat Commun. 2018 Feb 8;9(1):566. doi: 10.1038/s41467-017-02480-6. Nat Commun. 2018. PMID: 29422526 Free PMC article.

10

ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

Dao P, Numanagić I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC. Dao P, et al. Among authors: numanagic i. Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15. Bioinformatics. 2014. PMID: 24130305

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