The purpose of our group is to apply state-of-the-art computational and genomic methods to address fundamental questions in RNA biology. The focus is on quantitatively describing and functionally characterizing animal transcriptomes, and methods include next-generation sequencing of single and pooled cells, as well as development of source code and custom wet-lab protocols.

Of particular interest to us is the biogenesis and function of microRNAs (miRNAs). These are 22 nucleotide RNAs which down-regulate the expression of target protein coding genes. miRNAs are found in all animals studied, in numbers which largely correlate with organismal complexity. For instance, nematodes have around 200 miRNA genes, while humans have more than 3000. Mutant animals which are deficient in miRNAs generally exhibit gross developmental defects or embryonic lethality, underlining the importance of these regulators. Given that most animal mRNAs are likely targets, it is not surprising that miRNAs are involved in numerous biological processes, ranging from formation of cell identity to development and human disease. Even though miRNAs have been systematically studied for more than ten years, fundamental questions regarding their biogenesis and function remain unanswered (see Research Projects).

The group is part of the Department of Molecular Biosciences, Wenner-Gren Institute of Stockholm University, but is located at the SciLifeLab genomics institute. The group will consist of equal parts computational and wet-lab biologists, working in close collaboration to pursue individual projects.

 

Key words

Computational biology, genomics, single-cell transcriptomics, miRNA biogenesis and function

 

Selected Publications

Kang W, Bang-Berthelsen CH, Holm A, Houben AJ, Müller AH, Thymann T, Pociot F, Estivill X, Friedländer MR (2017), ‘Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts’, RNA, 23(4):433-445.

Friedländer MR, Lizano E, Houben A, Bezdan D, Bañez-Coronel M, Kudla G, Mateu-Huertas E, Kagerbauer B, González J, Chen KC, LeProust EM, Martí E, Estivill X. (2014), Evidence for the biogenesis of more than 1,000 novel human microRNAs, Genome Biology, advance access, 15:R57.

Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET. (2013), Transcriptome and genome sequencing uncovers functional variation in human populations, Nature, 501(7468):506-11.

Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. (2012), miRDeep2 accurately identifies known and hundreds of novel miRNAs in seven animal clades, Nucleic Acids Research, 40(1):37-52.

Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. (2008), 'Discovering microRNAs from deep sequencing data using miRDeep', Nature Biotechnology, 26(4):407-15.