Related papers: Whole Genome Phylogenetic Tree Reconstruction Usin…
We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…
The aim of this study is to investigate the relation that can be found between the phylogeny of a large set of complete chloroplast genomes, and the evolution of gene content inside these sequences. Core and pan genomes have been computed…
Graph-structured data arise ubiquitously in many application domains. A fundamental problem is to quantify their similarities. Graph kernels are often used for this purpose, which decompose graphs into substructures and compare these…
The Composition Vector Tree (CVTree) method, developed under the leadership of Professor Hao Bailin, is an alignment-free algorithm for constructing phylogenetic trees. Although initially designed for studying prokaryotic evolution based on…
Old photos preserve invaluable historical memories, making their restoration and colorization highly desirable. While existing restoration models can address some degradation issues like denoising and scratch removal, they often struggle…
In this article, we study directed graphs (digraphs) with a coloring constraint due to Von Neumann and related to Nim-type games. This is equivalent to the notion of kernels of digraphs, which appears in numerous fields of research such as…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
In Gaussian graphical model selection, noise-corrupted samples present significant challenges. It is known that even minimal amounts of noise can obscure the underlying structure, leading to fundamental identifiability issues. A recent line…
In this paper, we introduce flubbles, a new definition of "bubbles" corresponding to variants in a (pan)genome graph $G$. We then show a characterization for flubbles in terms of equivalence classes regarding cycles in an intermediate data…
The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…
We present practical algorithms for generating universal cycles uniformly at random. In particular, we consider universal cycles for shorthand permutations, subsets and multiset permutations, weak orders, and orientable sequences.…
Massively parallel DNA sequencing technologies are revolutionizing genomics research. Billions of short reads generated at low costs can be assembled for reconstructing the whole genomes. Unfortunately, the large memory footprint of the…
When two-dimensional atomic crystals are brought into close proximity to form a van der Waals heterostructure, neighbouring crystals can start influencing each others electronic properties. Of particular interest is the situation when the…
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…
The de Bruijn torus (or grid) problem looks to find an $n$-by-$m$ binary matrix in which every possible $j$-by-$k$ submatrix appears exactly once. The existence and construction of these binary matrices was determined in the 70's, with…
Decompilation aims to recover the source code form of a binary executable. It has many security applications, such as malware analysis, vulnerability detection, and code hardening. A prominent challenge in decompilation is to recover…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…