Genomics
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…
Motivated by the need for fast and accurate classification of unlabeled nucleotide sequences on a large scale, we developed NASCUP, a new classification method that captures statistical structures of nucleotide sequences by compact…
In the post-genome era, biologists have sought to measure the complete complement of proteins, termed proteomics. Currently, the most effective method to measure the proteome is with shotgun, or bottom-up, proteomics, in which the proteome…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture…
Heart failure is a major cause for premature death. Given heterogeneity of the heart failure syndrome, identifying genetic determinants of cardiac function and structure may provide greater insights into heart failure. Despite progress in…
It is important to study on genes affecting to growing environment of main crops. Especially the recognition problem of promoter region, which is the problem to predict whether DNA sequences contain promoter regions or not, is prior to find…
Taking advantages of high-throughput genotyping technology of single nucleotide polymorphism (SNP), large genome-wide association studies (GWASs) have been considered as the promise to unravel the complex relationships between genotypes and…
Drug resistance is still a major challenge in cancer therapy. Drug combination is expected to overcome drug resistance. However, the number of possible drug combinations is enormous, and thus it is infeasible to experimentally screen all…
Among the different biomarkers of aging based on omics and clinical data, DNA methylation clocks stand apart providing unmatched accuracy in assessing the biological age of both humans and animal models of aging. Here, we discuss robustness…
The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm,…
Repeated exposure to low-level blast may initiate a range of adverse health problem such as traumatic brain injury (TBI). Although many studies successfully identified genes associated with TBI, yet the cellular mechanisms underpinning TBI…
CpG islands (CGI) marked by bivalent chromatin in stem cells are believed to be more prone to aberrant DNA methylation in tumor cells. The robustness and genome-wide extent of this instructive program in different cancer types remain to be…
Parental allele-specific expression of imprinted genes is mediated by imprinting control regions (ICRs) that are constitutively marked by DNA methylation imprints on the maternal or paternal allele. Mono-allelic DNA methylation is strictly…
Motivation: Identifying genomic variants is an essential step for connecting genotype and phenotype. The usual approach consists of statistical inference of variants from alignments of sequencing reads. State-of-the-art variant callers can…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
The Kolmogorov-Arnold stochasticity parameter technique is applied for the first time to the study of cancer genome sequencing, to reveal mutations. Using data generated by next generation sequencing technologies, we have analyzed the exome…
Next-generation sequencing technology enables routine detection of bacterial pathogens for clinical diagnostics and genetic research. Whole genome sequencing has been of importance in the epidemiologic analysis of bacterial pathogens.…
Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid…