MAIN
RESEARCH
MEMBERS
PUBLICATIONS
SERVICES
COURSES
CONFERENCES
EMPLOYMENT
JOURNALS
MEETINGS
CONTACT
TOOLS
Single motif
Composite motif
Promoter fetcher
Compo
genePI
PriorsEditor
DATASETS
LOGIN
Last Update:
September 27, 2017
PROJECTS
MicroRNAs & ncRNAs
Regulatory mechanisms and interactions of non-protein-coding RNAs
Non-protein-coding RNAs (ncRNA) have been shown to be involved in important aspects of gene regulation, including chromatin silencing, alternative splicing, RNA editing, mRNA cleavage and translational suppression. This project will try to elucidate regulatory mechanisms involving ncRNA molecules, and in particular microRNA (miRNA), by using a combination of bioinformatic and experimental approaches. Zebrafish will be used as a model system for testing predictions from bioinformatic analyses This is a collaborative project between NTNU and the Sars International Centre for Marine Molecular Biology and the Computational Biology Unit at the University of Bergen (UoB). Here at NTNU, we will focus on developing novel computational algorithms for miRNA gene and target prediction as well as for general ncRNA gene discovery. Our methods include robust machine learning algorithms such as boosting and support vector machines.
The roles of microRNAs and transcription factors in gene regulation and tissue specific expression
MicroRNAs (miRNAs) are important genes that regulate many aspects of animal development, including cell growth, cell differentiation, and cell death, and aberrant miRNA expression levels characterize many diseases, ranging from various cancers to heart disorders and mental illnesses. Many miRNAs seem to have tissue-specific expression patterns, which suggest that together with transcription factors, miRNAs may be crucial for establishing and maintaining tissue specific gene regulation. These mechanisms are currently poorly understood, however. By combining bioinformatic and experimental approaches, this project will try to elucidate how miRNAs and transcription factors coordinately regulate genes. The project will focus on three problems: cell-cycle regulation, cell-type specific gene expression in rat brains, and aberrant miRNA expression during virus infections.
Tools
References
| MicroRNAs |
| (2007) "Robust Machine Learning Algorithms Predict MicroRNA Genes and Targets" Saetrom, P.; Snove, O.J. Methods Enzymol 427c():25-49 view article |
| (2007) "Epigenetics and microRNAs" Saetrom, P.; Snove, O.J.; Rossi, J.J. Pediatric research 61(5 Pt 2):17r-23r view article |
| (2007) "MicroRNAs in Disease and Potential Therapeutic Applications" Soifer, HS.; Rossi, JJ.; Saetrom, P. Molecular Therapy 15(12):2070-2079 view article |
| MicroRNA targeting |
| (2007) "Distance constraints between microRNA target sites dictate efficacy and cooperativity" Saetrom, P.; Heale, B.S.E.; Snove, O.J.; Aagaard, L.; Alluin, J.; Rossi, J.J. Nucleic acids research 35(7):2333-2342 view article |
| (2005) "Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms" Saetrom, O.; Snove, O.J.; Saetrom, P. RNA (New York, N.Y.) 11(7):995-1003 view article tool |
| MicroRNA genes |
| (2007) "Reliable prediction of Drosha processing sites improves microRNA gene prediction" Helvik, S.A.; Snove, O.J.; Saetrom, P. Bioinformatics (Oxford, England) 23(2):142-149 view article tool |
| (2006) "Conserved microRNA characteristics in mammals" Saetrom, P.; Snove, O.; Nedland, M.; Grunfeld, T.B.; Lin, Y.; Bass, M.B.; Canon, J.R. Oligonucleotides 16(2):115-144 view article |
| Non-coding RNAs |
| (2005) "Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming" Saetrom, P.; Sneve, R.; Kristiansen, K.I.; Snove, O.J.; Grunfeld, T.; Rognes, T.; Seeberg, E. Nucleic acids research 33(10):3263-3270 view article |
Bioinformatics & Gene RegulationDepartment of Cancer Research and Molecular Medicine
Norwegian University of Science and Technology
Trondheim, Norway