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Items: 8

1.

PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.

Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC.

Genome Res. 2019 Nov;29(11):1860-1877. doi: 10.1101/gr.234435.118. Epub 2019 Oct 18.

2.

Collaborative intra-tumor heterogeneity detection.

Khakabimamaghani S, Malikic S, Tang J, Ding D, Morin R, Chindelevitch L, Ester M.

Bioinformatics. 2019 Jul 15;35(14):i379-i388. doi: 10.1093/bioinformatics/btz355.

3.

A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression.

Karpov N, Malikic S, Rahman MK, Sahinalp SC.

Algorithms Mol Biol. 2019 Jul 27;14:17. doi: 10.1186/s13015-019-0152-9. eCollection 2019.

4.

Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data.

Malikic S, Jahn K, Kuipers J, Sahinalp SC, Beerenwinkel N.

Nat Commun. 2019 Jun 21;10(1):2750. doi: 10.1038/s41467-019-10737-5.

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.

Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data.

Donmez N, Malikic S, Wyatt AW, Gleave ME, Collins CC, Sahinalp SC.

J Comput Biol. 2017 Jun;24(6):515-523. doi: 10.1089/cmb.2016.0148. Epub 2017 Jan 5.

PMID:
28056180
7.

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.

8.

Clonality inference in multiple tumor samples using phylogeny.

Malikic S, McPherson AW, Donmez N, Sahinalp CS.

Bioinformatics. 2015 May 1;31(9):1349-56. doi: 10.1093/bioinformatics/btv003. Epub 2015 Jan 6.

PMID:
25568283

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