Solon P. Pissis

Linear-Time Superbubble Identification Algorithm.

2015 · arXiv (Cornell University)

DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce masses of …

Internal Shortest Absent Word Queries

2021 · DROPS (Schloss Dagstuhl – Leibniz Center for Informatics)

Given a string T of length n over an alphabet Σ ⊂ {1,2,…,n^{𝒪(1)}} of size σ, we are to preprocess T so that given a range [i,j], we can return a representation of a shortest …

Utility-Oriented String Mining

2024 · Society for Industrial and Applied Mathematics eBooks

A string is often provided with numerical scores (utilities) which quantify the importance, interest, profit, or risk of the letters occurring at every position of the string. For example, every DNA fragment produced by modern …

Minimizing the Minimizers via Alphabet Reordering

2024 · arXiv (Cornell University)

Minimizers sampling is one of the most widely-used mechanisms for sampling strings [Roberts et al., Bioinformatics 2004]. Let $S=S[1]\ldots S[n]$ be a string over a totally ordered alphabet $Σ$. Further let $w\geq 2$ and $k\geq …