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LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns.

Oncotarget
Accumulating evidences suggest that long non-coding RNAs (lncRNAs) perform important functions. Genome-wide chromatin-states area rich source of information about cellular state, yielding insights beyond what is typically obtained by transcriptome pr...

Design of Knowledge Bases for Plant Gene Regulatory Networks.

Methods in molecular biology (Clifton, N.J.)
Developing a knowledge base that contains all the information necessary for the researcher studying gene regulation in a particular organism can be accomplished in four stages. This begins with defining the data scope. We describe here the necessary ...

TSSPlant: a new tool for prediction of plant Pol II promoters.

Nucleic acids research
Our current knowledge of eukaryotic promoters indicates their complex architecture that is often composed of numerous functional motifs. Most of known promoters include multiple and in some cases mutually exclusive transcription start sites (TSSs). M...