Related papers: Genome assembly, from practice to theory: safe, co…
In computational genomics, many analyses rely on efficient storage and traversal of $k$-mers, motivating compact representations such as spectrum-preserving string sets (SPSS), which store strings whose $k$-mer spectrum matches that of the…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
A path-covering problem on a directed acyclic graph (DAG) requires finding a set of source-to-sink paths that cover all the nodes, all the arcs, or subsets thereof, and additionally they are optimal with respect to some function. In this…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…
Complex networks have become increasingly popular for modeling various real-world phenomena. Realistic generative network models are important in this context as they avoid privacy concerns of real data and simplify complex network research…
Arising from structural graph theory, treewidth has become a focus of study in fixed-parameter tractable algorithms in various communities including combinatorics, integer-linear programming, and numerical analysis. Many NP-hard problems…
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the…
Control and characterization of networks is a paramount step for the development of many quantum technologies. Even for moderate-sized networks, this amounts to explore an extremely vast parameters space in search for the couplings defining…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Network flow is one of the most studied combinatorial optimization problems having innumerable applications. Any flow on a directed acyclic graph $G$ having $n$ vertices and $m$ edges can be decomposed into a set of $O(m)$ paths. In some…
Given a directed graph $G$ and a pair of nodes $s$ and $t$, an \emph{$s$-$t$ bridge} of $G$ is an edge whose removal breaks all $s$-$t$ paths of $G$ (and thus appears in all $s$-$t$ paths). Computing all $s$-$t$ bridges of $G$ is a basic…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Motivation: Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation or activity of…
Performing statistical analyses on collections of graphs is of import to many disciplines, but principled, scalable methods for multi-sample graph inference are few. Here we describe an "omnibus" embedding in which multiple graphs on the…
Motivation: As a fundamental task in bioinformatics, searching for massive short patterns over a long text is widely accelerated by various compressed full-text indexes. These indexes are able to provide similar searching functionalities to…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
The expected meeting time of two random walkers on an undirected graph of size $N$, where at each time step one walker moves and the process stops when they collide, satisfies a system of $\binom{N}{2}$ linear equations. Na\"{i}vely,…