Related papers: Identifying DNA motifs based on match and mismatch…
Name disambiguation is a key and also a very tough problem in many online systems such as social search and academic search. Despite considerable research, a critical issue that has not been systematically studied is disambiguation on the…
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Given a (machine learning) classifier and a collection of unlabeled data, how can we efficiently identify misclassification patterns presented in this dataset? To address this problem, we propose a human-machine collaborative framework that…
The problem of generalized function matching can be defined as follows: given a pattern $p=p_1 \cdots p_m$ and a text $t=t_1 \cdots t_n$, find a mapping $f:\Sigma_p\rightarrow\Sigma_t^{*}$ and all text locations $i$ such that $f(p_1) f(p_2)…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
Genetic programming and artificial life systems commonly employ tag-matching schemes to determine interactions between model components. However, the implications of criteria used to determine affinity between tags with respect to…
A flood of reliable seismic data will soon arrive. The migration to larger telescopes on the ground may free up 4-m class instruments for multi-site campaigns, and several forthcoming satellite missions promise to yield nearly uninterrupted…
RNA motifs typically consist of short, modular patterns that include base pairs formed within and between modules. Estimating the abundance of these patterns is of fundamental importance for assessing the statistical significance of matches…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
Matching for causal inference is a well-studied problem, but standard methods fail when the units to match are text documents: the high-dimensional and rich nature of the data renders exact matching infeasible, causes propensity scores to…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
In this paper, we describe the problem of cognate identification and its relation to phylogenetic inference. We introduce subsequence based features for discriminating cognates from non-cognates. We show that subsequence based features…
Efficient pattern matching is fundamental for practical term rewrite engines. By preprocessing the given patterns into a finite deterministic automaton the matching patterns can be decided in a single traversal of the relevant parts of the…
Background: DNA, RNA, and protein sequence motifs can be recognition sites for biological functions such as regulation, DNA base modification, and molecular binding in general. The gain and loss of such motifs can carry important…
A new method for determining whether or not a mitrochondrial DNA (mtDNA) sequence belongs to a vertebrate is described and tested. This method only needs the mtDNA sequence of the organism in question, and unlike alignment based methods, it…
DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA…
This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and…
We develop statistically based methods to detect single nucleotide DNA mutations in next generation sequencing data. Sequencing generates counts of the number of times each base was observed at hundreds of thousands to billions of genome…