Ioannis Vlachos Non-coding Research Lab

Turning Junk DNA into an RNA Goldmine

Research

Let’s Focus on the 98%!
For the lifetime of our species, it’s only yesterday that we found out that the earth is not flat, and a few seconds away that there are thousands of non-coding RNAs with a multitude of functional roles. Until recently, biomedical research was mostly focused on the 2% of the human genome that encodes for proteins. It is currently re-inventing itself in order to understand and harness these fascinating regulatory newcomers.

The Revolution
The RNA revolution has turned junk-DNA into a non-coding RNA (ncRNA) goldmine. Recent breakthroughs have shown how ncRNAs, such as microRNAs (miRNAs) or long non-coding RNAs (lncRNAs), can play important regulatory roles in numerous physiological or pathological processes.

The Challenge
Unfortunately, the lack of functional characterization for most non-coding genomic regions and transcripts impedes their incorporation into translational research.

Our Approach
To this end, we analyze vast datasets, design novel methods and implement algorithms that identify non-coding elements as potential biomarkers and therapeutic targets, as well as facilitate the prioritization of non-coding variants associated with monogenic or complex polygenic traits.

Selected Publications

Paraskevopoulou MD, Karagkouni D, Vlachos IS, Tastsoglou S, Hatzigeorgiou AG. (2018), microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions. Nature Communications 9(1): 3601.

Kouroupi G, Taoufik E, Vlachos IS, Tsioras K, Antoniou N, Papastefanaki F, Chroni-Tzartou D, Wrasidlo W, Bohl D, Stellas D, Politis PK, Vekrellis K, Papadimitriou D, Stefanis L, Bregestovski P, Hatzigeorgiou AG, Masliah E, Matsas R. (2017), Defective synaptic connectivity and axonal neuropathology in a human iPSC-based model of familial Parkinson’s disease. Proceedings of the National Academy of Sciences of the United States of America 114(18):E3679-E3688.

Vlachos, IS, Vergoulis, T, Paraskevopoulou MD., Lykokanellos F, Georgakilas G, Georgiou P, Chatzopoulos S, Karagkouni D, Christodoulou F, Dalamagas T, Hatzigeorgiou AG. (2016), DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. Nucleic Acids Research 44: W128-34.

Vlachos IS, Zagganas K, Paraskevopoulou MD, Georgakilas G, Karagkouni D, Vergoulis T, Dalamagas T, Hatzigeorgiou AG. (2015), DIANA-miRPath v3.0: Deciphering microRNA function with experimental support. Nucleic Acids Research 43: W460-466.

Vlachos IS, Paraskevopoulou MD, Karagkouni D, Georgakilas G, Vergoulis T, Kanellos I, Anastasopoulos IL, Maniou S, Karathanou K, Kalfakakou D, Fevgas A, Dalamagas T, Hatzigeorgiou AG. (2015), DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Research 43: D153-159.

Georgakilas G, Vlachos IS, Paraskevopoulou MD, Yang P, Zhang Y, Economides AN, Hatzigeorgiou AG. (2014), microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nature Communications 5: 5700.

Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, Zagganas K, Tsanakas P, Floros E, Dalamagas T, Hatzigeorgiou AG. (2015), DIANA-LncBase v2: Indexing microRNA targets on non-coding transcripts. Nucleic Acids Research 44: D231-238.

Georgakilas G*, Vlachos IS*, Zagganas K, Vergoulis T, Paraskevopoulou MD, Kanellos I, Tsanakas P, Dellis D, Fevgas A, Dalamagas T, Hatzigeorgiou AG. (2015), DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Nucleic Acids Research 44: D190-195.

Paraskevopoulou MD, Vlachos IS, Athanasiadis E, Spyrou G. (2013), BiDaS: a web-based Monte Carlo BioData Simulator based on sequence/feature characteristics. Nucleic acids research 41: W582-586.

Vlachos IS, Kostoulas N, Vergoulis T, Georgakilas G, Reczko M, Maragkakis M, Paraskevopoulou MD, Prionidis K, Dalamagas T, Hatzigeorgiou AG. (2012), DIANA miRPath v.2.0: Investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Research 40: W498-W504.

Vergoulis T*, Vlachos IS*, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Theodore D, Hatzigeorgiou AG. (2012), TarBase 6.0: Capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Research 40: D222-D229.

Complete Publication List

https://scholar.google.com/citations?user=mhRFBnEAAAAJ&hl=en