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Items: 4

1.

A space and time-efficient index for the compacted colored de Bruijn graph.

Almodaresi F, Sarkar H, Srivastava A, Patro R.

Bioinformatics. 2018 Jul 1;34(13):i169-i177. doi: 10.1093/bioinformatics/bty292.

2.

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.

Pandey P, Almodaresi F, Bender MA, Ferdman M, Johnson R, Patro R.

Cell Syst. 2018 Aug 22;7(2):201-207.e4. doi: 10.1016/j.cels.2018.05.021. Epub 2018 Jun 20.

3.

Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis.

Malik L, Almodaresi F, Patro R.

Bioinformatics. 2018 Oct 1;34(19):3265-3272. doi: 10.1093/bioinformatics/bty378.

PMID:
29746620
4.

Improved data-driven likelihood factorizations for transcript abundance estimation.

Zakeri M, Srivastava A, Almodaresi F, Patro R.

Bioinformatics. 2017 Jul 15;33(14):i142-i151. doi: 10.1093/bioinformatics/btx262.

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