Genomics
Since the arrival of next-generation sequencing technologies the amount of genetic sequencing data has increased dramatically. This has has fueled an increase in human genetics research. At the same time, with the recent advent of…
Motivation: Exome or targeted sequencing data exerts analytical challenge to test single nucleotide polymorphisms (SNPs) with extremely small minor allele frequency (MAF). Various rare variant tests were proposed to increase power by…
A previous report claimed no evidence of transgenerational epigenetic inheritance in a mouse model of in utero environmental exposure, based on the observation that gene expression changes observed in the germ cells of G1 and G2 male fetus…
Down regulation of mRNA translation is an important problem in various bio-medical domains ranging from developing effective medicines for tumors and for viral diseases to developing attenuated virus strains that can be used for…
The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events -- choices of gene templates, base pair…
Indoor skin-contact surfaces of public fitness centers may serve as reservoirs of potential human transmission of methicillin-resistant Staphylococcus aureus (MRSA). We found a high prevalence of multi-drug resistant (MDR)-MRSA of CC59…
Methylation and hydroxylation of cytosines to form 5-methylcytosine (5mC) and 5-droxymethylcytosine (5hmC) belong to the most important epigenetic modifications and their vital role in the regulation of gene expression has been widely…
Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea. Here, we have analyzed RNA-seq data obtained from {\it…
Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a…
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce…
Variant detection from high-throughput sequencing data is an essential step in identification of alleles involved in complex diseases and cancer. To deal with these massive data, elaborated sequence analysis pipelines are employed. A core…
Motivated by a non-random but clustered distribution of SNPs, we introduce a phenomenological model to account for the clustering properties of SNPs in the human genome. The phenomenological model is based on a preferential mutation to the…
Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been…
Ancient mitochondrial DNA has been used in a wide variety of palaeontological and archaeological studies, ranging from population dynamics of extinct species to patterns of domestication. Most of these studies have traditionally been based…
The detection of rare variants is important for understanding the genetic heterogeneity in mixed samples. Recently, next-generation sequencing (NGS) technologies have enabled the identification of single nucleotide variants (SNVs) in mixed…
Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the genetic toolkit in Drosophila melanogaster. Despite their widespread use, the organization of balancer chromosomes has not been…
We propose a frame-based representation of k-mers for detecting sequencing errors and rare variants in next generation sequencing data obtained from populations of closely related genomes. Frames are sets of non-orthogonal basis functions,…
We studied the structuredness in a chloroplast genome of Siberian larch. The clusters in 63-dimensional space were identified with elastic map technique, where the objects to be clusterized are the different fragments of the genome. A…
Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be…
Efficient text indexing data structures have enabled large-scale genomic sequence analysis and are used to help solve problems ranging from assembly to read mapping. However, these data structures typically assume that the underlying…