Related papers: Indexing Finite Language Representation of Populat…
Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language…
The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…
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…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
Locating recombination hotspots in genomic data is an important but difficult task. Current methods frequently rely on estimating complicated models at high computational cost. In this paper we develop an extremely fast, scalable method for…
We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT.…
Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model…
We present an automated method of identifying communities of functionally related genes from the biomedical literature. These communities encapsulate human gene and protein interactions and identify groups of genes that are complementary in…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
What is a population? This review considers how a population may be defined in terms of understanding the structure of the underlying genetics of the individuals involved. The main approach is to consider statistically identifiable groups…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
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…
A precise estimate of allele and haplotype polymorphism is of great interest in theoretical population genetics, but also has practical applications, such as bone marrow registries management. Allele polymorphism is driven mainly by point…
We present a general framework based on weighted finite automata and weighted finite-state transducers for describing and implementing speech recognizers. The framework allows us to represent uniformly the information sources and data…
The search of information in large text repositories has been plagued by the so-called document-query vocabulary gap, i.e. the semantic discordance between the contents in the stored document entities on the one hand and the human query on…
For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each gene) and structure (order…
In population genetics, there is often interest in inferring selection coefficients. This task becomes more challenging if multiple linked selected loci are considered simultaneously. For such a situation, we propose a novel generalized…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
BACKGROUND: One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode of protein function assignment is mostly…