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Gene/pathway-based methods are drawing significant attention due to their usefulness in detecting rare and common variants that affect disease susceptibility. The biological mechanism of drug responses indicates that a gene-based analysis…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
Disease-gene association through Genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms (SNPs) that correlate with specific diseases needs statistical analysis of associations.…
One of the notable fields in studying the genetics of cancer is disease gene identification which affects disease treatment and drug discovery. Many researches have been done in this field. Genome-wide association studies (GWAS) are one of…
In the context of personalized medicine, text mining methods pose an interesting option for identifying disease-gene associations, as they can be used to generate novel links between diseases and genes which may complement knowledge from…
Understanding epistasis (genetic interaction) may shed some light on the genomic basis of common diseases, including disorders of maximum interest due to their high socioeconomic burden, like schizophrenia. Distance correlation is an…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
Motivated by genetic association studies of pleiotropy, we propose here a Bayesian latent variable approach to jointly study multiple outcomes or phenotypes. The proposed method models both continuous and binary phenotypes, and it accounts…
Motivation: Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in…
Advancement in sequencing technology enables the study of association between complex disorders and rare variants with low minor allele frequencies. One of the major challenges in rare variant testing is lack of statistical power of…
The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
Large language models (LLMs) have shown strong ability in generating rich representations across domains such as natural language processing and generation, computer vision, and multimodal learning. However, their application in biomedical…
Genetic improvement is a search technique that aims to improve a given acceptable solution to a problem. In this paper, we present the novel use of genetic improvement to find problem-specific optimized LLVM pass sequences. We develop a…
The identification of disease-associated genes has recently gathered much attention for uncovering disease complex mechanisms that could lead to new insights into the treatment of diseases. For exploring disease-susceptible genes, not only…
Feature embedding methods have been proposed in literature to represent sequences as numeric vectors to be used in some bioinformatics investigations, such as family classification and protein structure prediction. Recent theoretical…
Long-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…