Related papers: Genomic Problems Involving Copy Number Profiles: C…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
Given two genomes with duplicate genes, \textsc{Zero Exemplar Distance} is the problem of deciding whether the two genomes can be reduced to the same genome without duplicate genes by deleting all but one copy of each gene in each genome.…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
We call change-point problem (CPP) the identification of changes in the probabilistic behavior of a sequence of observations. Solving the CPP involves detecting the number and position of such changes. In genetics the study of how and what…
In this paper, we study a generalization of the classical minimum cut prob- lem, called Connectivity Preserving Minimum Cut (CPMC) problem, which seeks a minimum cut to separate a pair (or pairs) of source and destination nodes and…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
Parameterized complexity enables the practical solution of generally intractable NP-hard problems when certain parameters are small, making it particularly useful in real-world applications. The study of string problems in this framework…
Many practical problems in almost all scientific and technological disciplines have been classified as computationally hard (NP-hard or even NP-complete). In life sciences, combinatorial optimization problems frequently arise in molecular…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
We consider the problem of finding a minimum common partition of two strings (MCSP). The problem has its application in genome comparison. MCSP problem is proved to be NP-hard. In this paper, we develop an Integer Programming (IP)…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…