Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genome

The central dogma of molecular biology states that the genetic information flows from DNA to RNA to protein. This dogma has exerted a substantial influence on our understanding of the genetic activities in the cells. Under this influence, the prevailing assumption until the recent past was that genes are basically repositories for protein coding information, and proteins are responsible for most of the important biological functions in all cells. In the meanwhile, the importance of RNAs has remained rather obscure, and RNA was mainly viewed as a passive intermediary that bridges the gap between DNA and protein. Except for classic examples such as tRNAs (transfer RNAs) and rRNAs (ribosomal RNAs), functional noncoding RNAs were considered to be rare. However, this view has experienced a dramatic change during the last decade, as systematic screening of various genomes identified myriads of noncoding RNAs (ncRNAs), which are RNA molecules that function without being translated into proteins [11], [40]. It has been realized that many ncRNAs play important roles in various biological processes. As RNAs can interact with other RNAs and DNAs in a sequence-specific manner, they are especially useful in tasks that require highly specific nucleotide recognition [11]. Good examples are the miRNAs (microRNAs) that regulate gene expression by targeting mRNAs (messenger RNAs) [4], [20], and the siRNAs (small interfering RNAs) that take part in the RNAi (RNA interference) pathways for gene silencing [29], [30]. Recent developments show that ncRNAs are extensively involved in many gene regulatory mechanisms [14], [17]. The roles of ncRNAs known to this day are truly diverse. These include transcription and translation control, chromosome replication, RNA processing and modification, and protein degradation and translocation [40], just to name a few. These days, it is even claimed that ncRNAs dominate the genomic output of the higher organisms such as mammals, and it is being suggested that the greater portion of their genome (which does not encode proteins) is dedicated to the control and regulation of cell development [27]. As more and more evidence piles up, greater attention is paid to ncRNAs, which have been neglected for a long time. Researchers began to realize that the vast majority of the genome that was regarded as “junk,” mainly because it was not well understood, may indeed hold the key for the best kept secrets in life, such as the mechanism of alternative splicing, the control of epigenetic variations and so forth [27]. The complete range and extent of the role of ncRNAs are not so obvious at this point, but it is certain that a comprehensive understanding of cellular processes is not possible without understanding the functions of ncRNAs [47]

Towards Robustness in Parsing - Fuzzifying Context-Free Language Recognition

We discuss the concept of robustness with respect to parsing a context-free language. Our approach is based on the notions of fuzzy language, (generalized) fuzzy context-free grammar and parser / recognizer for fuzzy languages. As concrete examples we consider a robust version of Cocke-Younger-Kasami's algorithm and a robust kind of recursive descent recognizer

Data-Oriented Language Processing. An Overview

During the last few years, a new approach to language processing has started to emerge, which has become known under various labels such as "data-oriented parsing", "corpus-based interpretation", and "tree-bank grammar" (cf. van den Berg et al. 1994; Bod 1992-96; Bod et al. 1996a/b; Bonnema 1996; Charniak 1996a/b; Goodman 1996; Kaplan 1996; Rajman 1995a/b; Scha 1990-92; Sekine & Grishman 1995; Sima'an et al. 1994; Sima'an 1995-96; Tugwell 1995). This approach, which we will call "data-oriented processing" or "DOP", embodies the assumption that human language perception and production works with representations of concrete past language experiences, rather than with abstract linguistic rules. The models that instantiate this approach therefore maintain large corpora of linguistic representations of previously occurring utterances. When processing a new input utterance, analyses of this utterance are constructed by combining fragments from the corpus; the occurrence-frequencies of the fragments are used to estimate which analysis is the most probable one. In this paper we give an in-depth discussion of a data-oriented processing model which employs a corpus of labelled phrase-structure trees. Then we review some other models that instantiate the DOP approach. Many of these models also employ labelled phrase-structure trees, but use different criteria for extracting fragments from the corpus or employ different disambiguation strategies (Bod 1996b; Charniak 1996a/b; Goodman 1996; Rajman 1995a/b; Sekine & Grishman 1995; Sima'an 1995-96); other models use richer formalisms for their corpus annotations (van den Berg et al. 1994; Bod et al., 1996a/b; Bonnema 1996; Kaplan 1996; Tugwell 1995).Comment: 34 pages, Postscrip