The Gram-positive bacterium Listeria monocytogenes is the causative agent of listeriosis, a severe food-borne infection characterised by abortion, septicaemia, or meningoencephalitis. L. monocytogenes causes outbreaks of febrile gastroenteritis and accounts for community-acquired bacterial meningitis in humans. Listeriosis has one of the highest mortality rates (up to 30%) of all food-borne inf...

MOTIVATION Over the past few years, experimental evidence has highlighted the role of microRNAs to human diseases. miRNAs are critical for the regulation of cellular processes, and, therefore, their aberration can be among the triggering causes of pathological phenomena. They are just one member of the large class of non-coding RNAs, which include transcribed ultra-conserved regions (T-UCRs), s...

sequencing technology has ushered in a new era in which unprecedented amount of genomic sequence and transcript sequence data with extraordinary detail can be generated at incredibly short time. As part of this advancement, the approaches that utilize the powerful next generation sequencing technology, such as RNA-Seq, may have dramatically changed the field of non-coding RNA (ncRNA) research. ...

MOTIVATION Non-coding RNAs (ncRNAs)-functional RNA molecules not coding for proteins-are grouped into hundreds of families of homologs. To find new members of an ncRNA gene family in a large genome database, covariance models (CMs) are a useful statistical tool, as they use both sequence and RNA secondary structure information. Unfortunately, CM searches are slow. Previously, we introduced 'rig...

The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments. The Drosophila chromatin remodeling ATPase ISWI plays evolutionarily conserved roles in chromatin organization. Interestingly, ISWI genetically interacts with the hsrω gene, encoding multiple non-coding RNAs (ncRNA) essential, among other functions, for ...

Noncoding RNAs (ncRNAs) play important roles in various cellular activities and diseases. In this paper, we presented a comprehensive review on computational methods for ncRNA prediction, which are generally grouped into four categories: (1) homology-based methods, that is, comparative methods involving evolutionarily conserved RNA sequences and structures, (2) de novo methods using RNA sequenc...

Recent large-scale transcriptome analyses have revealed a large number of transcripts with low protein-coding potential, known as non-coding RNAs (ncRNAs). Many studies revealed that several long ncRNAs are involved in the regulation of genome organization and gene expression, or in the structural components of functional domains in the nucleus. As regulation of mRNA decay in the cytoplasm is c...

Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three di...