Related papers: Conservation and losses of avian non-coding RNA lo…
Emerging high-throughput technologies have led to a deluge of putative non-coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology…
The subcellular localization of RNAs, including long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), microRNAs (miRNAs) and other smaller RNAs, plays a critical role in determining their biological functions. For instance, lncRNAs are…
Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames and which have been termed long non-coding RNAs (lncRNAs). Despite the existence of several well-characterized…
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to…
Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…
MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene expression. Identification of total number of miRNAs even in completely sequenced organisms is still an open problem. However, researchers have been using techniques that…
Biodiversity loss poses a significant threat to humanity, making wildlife monitoring essential for assessing ecosystem health. Avian species are ideal subjects for this due to their popularity and the ease of identifying them through their…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
Genomic datasets generated with massively parallel sequencing methods have the potential to propel systematics in new and exciting directions, but selecting appropriate markers and methods is not straightforward. We applied two approaches…
The ability to locate and annotate mitochondrial genes is an important practical issue, given the rapidly increasing number of mitogenomes appearing in the public databases. Unfortunately, tRNA genes in Metazoan mitochondria have proved to…
The majority of mammalian genomic transcripts do not directly code for proteins and it is currently believed that most of these are not under evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and its strong…
Comparative genomics methods are widely used to aid the functional annotation of non coding DNA regions. However, aligning non coding sequences requires new algorithms and strategies, in order to take into account extensive rearrangements…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the…
In the last decade, the discovery of noncoding RNA(ncRNA) has exploded. Classifying these ncRNA is critical todetermining their function. This thesis proposes a new methodemploying deep convolutional neural networks (CNNs) to classifyncRNA…
Research on long non-coding RNAs (lncRNAs) has garnered significant attention due to their critical roles in gene regulation and disease mechanisms. However, the complexity and diversity of lncRNA sequences, along with the limited knowledge…
Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA),…