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.
However, when a group of RNA enthusiasts assemble like this, a scientific program of substance (non-coding thou) is a crucial part of a retreat and each attendee had prepared one presentation on their main project and one on a scientific topic which was somewhat out of their comfort zone.
We were very lucky to find amazing facilities at our hotel, such as a atmospheric seminar room, comfortable rooms and even an indoor pool. The program had a great kick-off with our PI presenting his vision for the lab and the lab-members presenting their projects over the next days.
The weather cleared, and after long days of scientific talks we could relax with nice strolls in the beautiful medieval town of Visby.
In the afternoon of day two we rented a van and visited a nearby viewpoint and a astonishing beach. Motivated by the beautiful sights we discussed lab communication and outreach options late into the evening, after returning to the hotel.
In the morning of the third day we started early to drive to Ireviken were we met our guide Dr. Eliason from the Museum of Gotland who gave us an amazing geological and paleontological tour through the more than 400 million year old history of Gotland and its beautiful fossils (that all had microRNAs then!).
The program continued after a brief lunch with some great presentations outside the comfort zone and a couple of interesting discussions on promising grant project ideas for the months to come.
The day after most of the group took the ‘Indiana Jones Style’ way home with a very small airplane while knowing each other better than before, with new insights in own and outside-the-box topics and plenty of new ideas for our research, communication and grant writing.
With plenty of nice little restaurants, the nice surroundings and the quietness of after-season, Visby is a great place for a retreat!
We will be back.
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.