Stefan Seemann
I'm Assistant Professor in RNA bioinformatics at the Center for non-coding RNA in Technology and Health which is located at the Faculty for Health and Medical Sciences of the University of Copenhagen. Do you want to know more about my work? Then check out the BIOINF section.Blue mountains

Press release to the genome-wide screen for RNA structures - May 18, 2017

The vertebrate screen for conserved RNA structures (CRSs) has been accepted by Genome Research - May 4, 2017
In this work we looked for structure-based, rather than sequence-based, alignments of vertebrates in the UCSC 100-species tree. We further analyzed the ~520k identified human genomic regions for their functional implications, partly in human and mouse, through, e.g., expression studies (including a customized CaptureSeq experiment to characterize also noncoding RNAs lowly expressed in fetal brain), binding potentials, and structure probing. You can search for the predicted CRSs at

International Plant & Animal Genome Conference (PAG) in San Diego - 9th-13th January 2016
At this very exciting conference I have the great oportunity to give a talk about our work on the discovery of conserved RNA secondary structures in animals.

ELIXIR hackathon in Copenhagen - 23rd-25th September 2015
We have met with international collaborators for a two day hackathon in Frederiksberg for adding computational RNA tools to the Danish ELIXIR Node. See the latest statistics of the collected software.

BioZoom article - Monday, 29th June 2015
Our review article about Emerging tools for RNA structure analysis in polymorphic data is now published in the danish BioZoom magazine.

PETfold v2.0 and PETcofold v3.2 - Tuesday, 21 May 2013
PETcofold v3.2 comes together with PETfold v2.0 as C version using Vienna RNA Package library and Pfold library. PETfold increases the speed by a factor of 3 and PETcofold by a factor of 8 compared to the previous PERL-implementations. The web server is updated to PETfold v2.0 and PETcofold v3.2 too.

Malmö - Thursday 1 March 2012
Therese and I are going to live in Malmö at Nobelvägen for the next 1 and a half year. From the countryside to the city!

Postdoctorial Grant - Tuesday 20 December 2011
I get a postdoctorial grant for one year Australia in John Matticks group from the Carlbergfondet. YES - my research will be sponsored for one year by the danish beer industry!

2nd PETcofold paper is accepted - Monday 8 November 2010
Our paper describing the evaluation and application of PETcofold on known RNA-RNA interactions has been accepted by the journal Bioinformatics.

PhD defense - Friday 27 August 2010
I successfully defended my PhD thesis. The committee consisted of Elene Rivas, Joakim Lundeberg and Ole Winther. Afterwards we had a great barbecue party. Thanks to all my guests!

Start as Post Doc - Thursday 1 July 2010
I start a Post Doc position in Jan Gorodkins group for two more years.

RNA meeting in Seattle - Tuesday 22 June 2010
I am back in Seattle to participate on the RNA 2010 meeting at UW. I present a poster about PETcofold. I also use the chance to meet Derek, Greg and Sara again.

PhD thesis is handed in - Monday 7 June 2010
I handed in my PhD thesis with the title 'Prediction of structured non-coding RNAs, RNA-RNA interactions and their (co-)expression in the brain'.

PETcofold paper is accepted - Thursday 22 April 2010
The paper describing the algorithm of the PETfold extension for RNA cofolding structures including RNA-RNA interactions, PETcofold, has been accepted by Algorithms in Molecular Biology.

Hässleholm - Tuesday 1 September 2009
From today on, Therese and I officially live together in a 2 room apartment in Hässleholm, Skåne, Sweden.

Seattle - Tuesday 24 March 2009
Read this article if you like to know more about the Brain Institute where I'm working now - and don't get frightened off by the first picture: it's printed in the WIRED and not the WEIRD magazine!

Seattle - Saturday 6 January 2009
After 19.5 hours traveling I landed in rainy Seattle. I will stay for five month as visitor at UW and the Allen Institute for Brain Science.

PETfold paper is accepted - Saturday 9 August 2008
The paper describing our RNA secondary structure predictor PETfold has been accepted by Nucleic Acids Research today.

Hiking in Vietnam and Biking in Poland - Thursday 10 July 2008
Find some impressions about Hanoi, Halong Bay, Hue and Hoi An in Vietnam. I visited Therese there in March during her study about the application of antibiotics on piglets. Just two days ago, I came back from a short cycling tour in the north of poland.

Studieskolen - Tuesday 8 January 2008
Finally, I started a Danish language course at Studieskolen!

Frankfurt Marathon - Sunday 28 October 2007
I have run my 20th marathon in 2h 58min 35sec. It was my first marathon in under three hours!

Holland - Thursday 18 October 2007
The pictures of the Holland trip are online. Thanks a lot Carolina and her family for the warm and friendly hospitality!

New Website - Wednesday 17 October 2007
This website is based on Website Baker. This means more comfort for the administrator as well as more contents and updates for the reader! I hope you will enjoy my site :)