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
Our group analyzes vast datasets, designs novel methods and implements machine learning techniques to render the 100% of the genome informative and actionable.
Our lab has extensive experience in turning thousands of NGS experiments into unique resources, as well as in creating methods that are reliable and support innovation worldwide. Today, many of our implementations are considered as reference resources in non-coding RNA research.
We are extensively employing bulk, single cell, and spatial transcriptomic technologies to characterize cellular transcriptional programs and cell-cell communication, as well as how they are derailed in malignancies. This approach permits us to identify and prioritize novel biomarkers or therapeutic targets, regardless of their coding potential.
Publication List
https://scholar.google.com/citations?user=mhRFBnEAAAAJ&hl=en
Selected Publications
Prodromidou K*, Vlachos IS*, Gaitanou M, Kouroupi G, Hatzigeorgiou AG, Matsas R, (2020), MicroRNA-934 is a novel primate-specific small non-coding RNA with neurogenic function during early development, eLife 2020;9:e50561.
International Multiple Sclerosis Genetics Consortium, Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. Science 365, eaav7188 (2019).
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