Related papers: Hidden breakpoints in genome alignments
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
This paper introduces a new way to define a genome rearrangement distance, using the concept of mean first passage time from probability theory. Crucially, this distance estimate provides a genuine metric on genome space. We develop the…
In the evolution of a genome, the gene sequence is sometimes rearranged, for example by transposition of two adjacent gene blocks. In biocombinatorics, one tries to reconstruct these rearrangement incidents from the resulting permutation.…
The detection of change-points in heterogeneous sequences is a statistical challenge with many applications in fields such as finance, signal analysis and biology. A wide variety of literature exists for finding an ideal set of…
We consider the problem of breakpoint detection in a regression modeling framework. To that end, we introduce a novel method, the max-EM algorithm which combines a constrained Hidden Markov Model with the Classification-EM (CEM) algorithm.…
Changepoint detection methods are used in many areas of science and engineering, e.g., in the analysis of copy number variation data, to detect abnormalities in copy numbers along the genome. Despite the broad array of available tools,…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Given a set of aligned sequences of independent noisy observations, we are concerned with detecting intervals where the mean values of the observations change simultaneously in a subset of the sequences. The intervals of changed means are…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
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…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
Genome-wide patterns of genetic divergence reveal mechanisms of adaptation under gene flow. Empirical data show that divergence is mostly concentrated in narrow genomic regions. This pattern may arise because differentiated loci protect…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
Sharing genome data in a privacy-preserving way stands as a major bottleneck in front of the scientific progress promised by the big data era in genomics. A community-driven protocol named genomic data-sharing beacon protocol has been…
An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
Very long and noisy sequence data arise from biological sciences to social science including high throughput data in genomics and stock prices in econometrics. Often such data are collected in order to identify and understand shifts in…