Related papers: Suffix Arrays for Spaced-SNP Databases
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…
Despite much progress over the past decade, current Single Nucleotide Polymorphism (SNP) genotyping technologies still offer an insufficient degree of multiplexing when required to handle user-selected sets of SNPs. In this paper we propose…
By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
In biological evolution complex neural structures grow from a handful of cellular ingredients. As genomes in nature are bounded in size, this complexity is achieved by a growth process where cells communicate locally to decide whether to…
Brain function results from communication between neurons connected by complex synaptic networks. Synapses are themselves highly complex and diverse signaling machines, containing protein products of hundreds of different genes, some in…
Extracting an understanding of the underlying system from high dimensional data is a growing problem in science. Discovering informative and meaningful features is crucial for clustering, classification, and low dimensional data embedding.…
There exists many complicated $k$-noncrossing pseudoknot RNA structures in nature based on some special conditions. The special characteristic of RNA structures gives us great challenges in researching the enumeration, prediction and the…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
The suffix array is the key to efficient solutions for myriads of string processing problems in different applications domains, like data compression, data mining, or Bioinformatics. With the rapid growth of available data, suffix array…
Recent studies have shown that single-stranded viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison it has been suggested that wild-type…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
Differential Privacy (DP) considers a scenario in which an adversary has almost complete information about the entries of a database. This worst-case assumption is likely to overestimate the privacy threat faced by an individual in…
The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
A novel mechanism for sympatric speciation that takes into account complex bio-processes within each individual organism is proposed. According to dynamical systems theory, organisms with identical genotypes can possess differentiated…
The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci and the genome-wide patterns of polymorphism show signatures consistent with…