Today we publish a comprehensive yet brief video tutorial on installation and usage of miRTrace – our quality control and taxonomic tracing software published in Genome Biology last year.
The number-loving computational biologist and smørrebrød master Marc Friedländer and his research group has recently discovered a way to tell what species tissue samples come from, by using microRNAs. Now they set out to revolutionize the field.
Read the full article at our host institute SciLifeLab: https://www.scilifelab.se/news/marc-friedlander-traces-origins-microrna/
miRTrace reveals the organismal origins of microRNA sequencing data
Software page: https://friedlanderlab.org/software/mirtrace/
We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurately (> 99%) assigns real and simulated data to 14 important animal and plant groups, sensitively detects parasitic infection in mammals, and discovers the primate origin of single cells. Applying our algorithm to over 700 public datasets, we find evidence that over 7% are cross-contaminated and present a novel solution to clean these computationally, even after sequencing has occurred. miRTrace is freely available at https://github.com/friedlanderlab/mirtrace.
The idea to do a retreat had been growing for some time already and we finally did it this August!
On a rainy Sunday eight members of the Friedländer group made their way to the Swedish isle of Gotland by ferry. Since three new members recently joined the group, the main focus of the retreat was to get to know each other by spending time together in Visby, the capital of Gotland.Read More …
Stockholm University announces two graduate student positions in Computational RNA Biology in the Friedländer group at the Department of Molecular Biosciences, The Wenner-Gren Institute (MBW).
More information: PhD in Computational RNA Biology : Stockholm, Sweden
Application deadline: April 24th, 2018.
Marc Friedländer’s research on miRNA functions in single cells has been awarded prestigious European Research Council (ERC) Starting Grant.
The ERC awarded research has been highlighted in News and Press:
After analyzing more than 800 public small RNA-Seq datasets, we found the exogenous miRNAs (xenomiRs), e.g. plant derived miRNAs, detected in human samples are more likely to originate from technical artifacts rather than dietary intake. We also performed carefully designed and controlled animal feeding studies, in which we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood.
Read the paper in RNA [Jan 2017].
Marc Friedländer has been awarded a research grant from Vetenskapsrådet for the period 2016-2019.