Related papers: Suffix Arrays for Spaced-SNP Databases
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
An applied problem facing all areas of data science is harmonizing data sources. Joining data from multiple origins with unmapped and only partially overlapping features is a prerequisite to developing and testing robust, generalizable…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
Today's sequencing technology allows sequencing an individual genome within a few weeks for a fraction of the costs of the original Human Genome project. Genomics labs are faced with dozens of TB of data per week that have to be…
A computationally simple genome-wide association study (GWAS) algorithm for estimating the main and epistatic effects of markers or single nucleotide polymorphisms (SNPs) is proposed. It is based on the intuitive assumption that changes of…
It has been argued by Thom and Palm that sparsely-connected neural networks (SCNs) show improved performance over fully-connected networks (FCNs). Super-regular networks (SRNs) are neural networks composed of a set of stacked sparse layers…
Single-cell gene expression data are often characterized by large matrices, where the number of cells may be lower than the number of genes of interest. Factorization models have emerged as powerful tools to condense the available…
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such…
This paper introduces a speciation principle for neuroevolution where evolving networks are grouped into species based on the number of hidden neurons, which is indicative of the complexity of the search space. This speciation principle is…
Counting distinct permutations with replacement, especially when involving multiple subwords, is a longstanding challenge in combinatorial analysis, with critical applications in cryptography, bioinformatics, and statistical modeling. This…
Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are two kinds of commonly used markers in Y chromosome studies of forensic and population genetics. There has been increasing interest in the cost saving strategy by…
Numerous challenges persist that delay clinical interpretation of human genetic variants, to name a few: (1) un- structured PubMed articles are the most abundant source of evidence, yet their variant annotations are difficult to query…
In this paper, we address the problem of searching for semantically similar images from a large database. We present a compact coding approach, supervised quantization. Our approach simultaneously learns feature selection that linearly…
Small Ubiquitin-related modifier (SUMO) proteins are widely expressed in eukaryotic cells, which are reversibly coupled to their substrates by motif recognition, called sumoylation. Two interesting questions are 1) how many potential SUMO…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
Motivated by DNA-based storage, we study the noisy shuffling channel, which can be seen as the concatenation of a standard noisy channel (such as the BSC) and a shuffling channel, which breaks the data block into small pieces and shuffles…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…