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Items: 13

1.

Fast characterization of segmental duplications in genome assemblies.

Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F.

Bioinformatics. 2018 Sep 1;34(17):i706-i714. doi: 10.1093/bioinformatics/bty586.

2.

Statistical Binning for Barcoded Reads Improves Downstream Analyses.

Shajii A, Numanagić I, Whelan C, Berger B.

Cell Syst. 2018 Aug 22;7(2):219-226.e5. doi: 10.1016/j.cels.2018.07.005.

3.

Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses.

Shajii A, Numanagić I, Berger B.

Res Comput Mol Biol. 2018 Apr;10812:280-282. No abstract available.

4.

Publisher Correction: 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.

Nat Commun. 2018 Apr 26;9(1):1755. doi: 10.1038/s41467-018-03711-0.

5.

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.

Nat Commun. 2018 Feb 26;9(1):828. doi: 10.1038/s41467-018-03273-1.

6.

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.

Nat Commun. 2018 Feb 8;9(1):566. doi: 10.1038/s41467-017-02480-6. Erratum in: Nat Commun. 2018 Apr 26;9(1):1755.

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.

Bioinformatics. 2018 May 15;34(10):1672-1681. doi: 10.1093/bioinformatics/btx807.

8.

Discovery and genotyping of novel sequence insertions in many sequenced individuals.

Kavak P, Lin YY, Numanagic I, Asghari H, Güngör T, Alkan C, Hach F.

Bioinformatics. 2017 Jul 15;33(14):i161-i169. doi: 10.1093/bioinformatics/btx254.

9.

Comparison of high-throughput sequencing data compression tools.

Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J, Alberti C, Mattavelli M, Sahinalp SC.

Nat Methods. 2016 Dec;13(12):1005-1008. doi: 10.1038/nmeth.4037. Epub 2016 Oct 24.

PMID:
27776113
10.

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

Numanagić I, Malikić S, Pratt VM, Skaar TC, Flockhart DA, Sahinalp SC.

Bioinformatics. 2015 Jun 15;31(12):i27-34. doi: 10.1093/bioinformatics/btv232.

11.

DeeZ: reference-based compression by local assembly.

Hach F, Numanagić I, Sahinalp SC.

Nat Methods. 2014 Nov;11(11):1082-4. doi: 10.1038/nmeth.3133. No abstract available.

PMID:
25357237
12.

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.

Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15.

PMID:
24130305
13.

SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Hach F, Numanagic I, Alkan C, Sahinalp SC.

Bioinformatics. 2012 Dec 1;28(23):3051-7. doi: 10.1093/bioinformatics/bts593. Epub 2012 Oct 9.

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