Publications - Working papers
Please find below working papers of our group. Currently, we list 58 working papers.
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Common Features in lncRNA Annotation and Classification: A survey
Christopher Klapproth, Rituparno Sen, Peter F. Stadler, Sven Findeiss, Jörg Fallmann
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Status: Accepted
Non-coding RNA
Abstract
Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene
expression. Their molecular functions range from miRNA sponging to chromatin-associated mecha-
nisms, leading to effects in disease progression and establishing them as diagnostic and therapeutic
targets. Still, only a few representatives of this diverse class of RNAs are well studied, while the vast
majority is poorly described beyond the existence of their transcripts. In this review we survey com-
mon in silico approaches for lncRNA annotation. We focus on the well-established sets of features
used for classification and discuss their specific advantages and weaknesses. While the available
tools perform very well for the task of distinguishing coding sequence from other RNAs, we find that
current methods are not well suited to distinguish lncRNAs or parts thereof from other non-protein-
coding input sequences. We conclude that the distinction of lncRNAs from intronic sequences and
untranslated regions of coding mRNAs remains a pressing research gap.
Keywords
lncRNA; feature extraction; machine learning; coding sequence; classification problems