相关论文: Hypergraph covering problems motivated by genome a…
Motivated by problems of comparative genomics and paleogenomics, in [Chauve et al., 2009], the authors introduced the Gapped Consecutive-Ones Property Problem (k,delta)-C1P: given a binary matrix M and two integers k and delta, can the…
A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1's on each row are consecutive. A Minimal Conflicting Set is a set of rows that does not have the C1P, but every proper subset has…
A binary matrix $M$ has the consecutive ones property ($C1P$) for rows (resp. columns) if there is a permutation of its columns (resp. rows) that arranges the ones consecutively in all the rows (resp. columns). If $M$ has the $C1P$ for rows…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
A binary matrix satisfies the consecutive ones property (COP) if its columns can be permuted such that the ones in each row of the resulting matrix are consecutive. Equivalently, a family of sets F = {Q_1,..,Q_m}, where Q_i is subset of R…
A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1s on each row are consecutive. These matrices are used for DNA physical mapping and ancestral genome reconstruction in…
We present a dichotomy theorem on the parameterized complexity of the 3-uniform hypergraphicality problem. Given $0<c_1\le c_2 < 1$, the parameterized 3-uniform Hypergraphic Degree Sequence problem, $3uni-HDS_{c_1,c_2}$, considers degree…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
Inspired by notorious combinatorial optimization problems on graphs, in this paper we consider a series of related problems defined using a metric space and topology determined by a graph. Particularly, we present the Independent Set,…
A graph database is a digraph whose arcs are labeled with symbols from a fixed alphabet. A regular graph pattern (RGP) is a digraph whose edges are labeled with regular expressions over the alphabet. RGPs model navigational queries for…
Motivated by some problems in genome assembling, we investigate properties of spacings from absolutely continuous distributions. Several results on the asymptotic behavior of the maximal uniform and non-uniform $k$-spacings are presented.…
A $(0,1)$-matrix has the Consecutive Ones Property (C1P) for the rows if there is a permutation of its columns such that the ones in each row appear consecutively. We say a $(0, 1)$-matrix is nested if it has the consecutive ones property…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
Edge Constrained Vertex Coloring (ECVC) problems are defined on a finite multigraph, their solutions are characterized, and a linear time algorithm is given for solving $N$ ECVCs on the same underlying multigraph. Using ECVC problems we…
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…
The purpose of this article is to deal with the multiple values and uniqueness problem of meromorphic mappings from $\mathbb{C}^{m}$ into the complex projective space $\mathbb{P}^{n}(\mathbb{C})$ sharing fixed and moving hypersurfaces. We…
Constraint Satisfaction Problems (CSP) constitute a convenient way to capture many combinatorial problems. The general CSP is known to be NP-complete, but its complexity depends on a template, usually a set of relations, upon which they are…
A $(0,1)$-matrix has the consecutive-ones property (C1P) if its columns can be permuted to make the $1$'s in each row appear consecutively. This property was characterised in terms of forbidden submatrices by Tucker in 1972. Several graph…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…