Maximal haplotype blocks with unknowns and pangenome SNPs

We are extending recent progress on the problem of finding maximal perfect haplotype blocks from a set of SNP-resolved haplotypes to include unknown data and to work in a pangenomic setting.

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Network flow decomposition with application to RNA assembly

We are extending a flow network model of RNA short read data to account for errors in the data collection process and developing algorithms to use this model to determine RNA transcripts and their abundances.

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Shape reconstruction using topological descriptors

We are developing algorithms to reconstruct shapes from topological descriptors such as persistence diagrams and Euler characteristic curves.

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