相关论文: Using sequencing coverage statistics to identify s…
Transcriptomic analysis are characterized by being not directly quantitative and only providing relative measurements of expression levels up to an unknown individual scaling factor. This difficulty is enhanced for differential expression…
Background. The large-scale pattern of distribution of genes on the chromosomes in the known animal genomes is not well characterized. We hypothesized that individual genes will be distributed on chromosomes in a mathematically ordered…
We present an alternative method for genome-wide association studies (GWAS) that is more powerful than the regular GWAS method for locus detection. The regular GWAS method suffers from a substantial multiple-testing burden because of the…
Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to policy development. An important and popular technique for…
Although bulk transcriptomic analyses have significantly contributed to an enhanced comprehension of multifaceted diseases, their exploration capacity is impeded by the heterogeneous compositions of biological samples. Indeed, by averaging…
In this paper, we provide a comprehensive analysis of periocular-based sex-prediction (commonly referred to as gender classification) using state-of-the-art machine learning techniques. In order to reflect a more challenging scenario where…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. For any prokaryotic taxon with at least three sequenced genomes, PanGeneHome provides (i) conservation level of genes, (ii) pangenome and core-genome…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach,…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
Cell type identification from single-cell transcriptomic data is a common goal of single-cell RNA sequencing (scRNAseq) data analysis. Neural networks have been employed to identify cell types from scRNAseq data with high performance.…
We present an approach to identify and track the evolution of niches in XCS that can be applied to any XCS model and any problem. It exploits the underlying principles of the evolutionary component of XCS, and therefore, it is independent…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
Selecting the top-$m$ variables with the $m$ largest population parameters from a larger set of candidates is a fundamental problem in statistics. In this paper, we propose a novel methodology called Sequential Correct Screening (SCS),…
Understanding the relationships between different properties of data, such as whether a connectome or genome has information about disease status, is becoming increasingly important in modern biological datasets. While existing approaches…
Upcoming wide-field spectroscopic surveys will observe galaxies in a range of cosmic web environments in and around galaxy clusters. In this paper, we test and quantify how successfully we will be able to identify the environment of…
Biclustering is a two way clustering approach involving simultaneous clustering along two dimensions of the data matrix. Finding biclusters of web objects (i.e. web users and web pages) is an emerging topic in the context of web usage…
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…