Sigillvm Vniversitatis Hafniensis (The faculty of Science) The Bioinformatics Centre University of Copenhagen

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Contact info

http://www.djaevlebryg.dk/billeder/banner-2.jpg

Stinus looking for the monster in Loch Ness Stinus Lindgreen
Bioinformatics Centre
University of Copenhagen
Ole Maaloes Vej 5
2200 Copenhagen N
Denmark

mail: stinus@binf.ku.dk
phone: +45 3532 1287

Research interests

I am a part of the Non-coding RNA group.

  • RNA structure prediction
  • Multiple alignment
  • Phylogenetic inference
  • Algorithmics in general

Prediction of rRNA secondary structure

I am currently working on a project concerning simultaneous multiple alignment and structure prediction of RNA sequences. The method is based on Markov chain Monte Carlo in a simulated annealing framework. An initial random alignment is iteratively improved, and the common secondary structure is predicted. I score the structural alignment using a combination of entropy, basepairing probabilities and covariation.

I attended the conference Evolution of Biomolecular Structure 2006 in Vienna where I presented a poster describing my structural alignment method. I also presented my work at the Bioinformatics 2006 conference in Aarhus. I took part in the RNA workshop Computational approaches to functional and regulatory RNAs held in Benasque, Spain, in July 2006. Anders Krogh (University of Copenhagen) and Paul Gardner (Wellcome Trust Sanger Institute) are my supervisors.

I have been organizing and teaching the course Introduction to bioinformatics for biology and biochemistry students together with Morten Lindow.

  • My CV can be found here.

Publications

P.P. Gardner, J. Daub, J.G. Tate, E.P. Nawrocki, D.L. Kolbe, S. Lindgreen, A.C. Wilkinson, R.D. Finn, S. Griffiths-Jones, S.R. Eddy and A. Bateman (2008). Rfam: updates to the RNA families database, Nucleic Acids Research

E. Torarinsson and S. Lindgreen* (2008). WAR: Webserver for aligning structural RNAs, Nucleic Acids Research, doi:10.1093/nar/gkn275
*The two authors should be considered as joint first author
The webserver can be found here.

S. Lindgreen, P.P. Gardner and A. Krogh (2007). MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing, Bioinformatics, 23(24):3304-11

S. Lindgreen, P.P. Gardner and Anders Krogh (2007). Multiple alignment and structure prediction of non-coding RNA sequences, BMC Bioinformatics, 8(Suppl 8):P8 from the Third ISCB Student Council Symposium at the Fifteenth Annual International ISMB Conference

S. Lindgreen, P.P. Gardner and A. Krogh (2006). Measuring covariation in RNA alignments: Physical realism improves information measures, Bioinformatics, 22(24):2988-2995 - Supplementary material

B. K. Nielsen, S. Lindgreen, P. Winter, and M. Zachariasen (2005). Deferred path heuristic for phylogenetic trees revisited. In M.-F. Sagot and K.S. Guimarães (eds.), CompBioNets 2005: Algorithmics and Computational Methods for Biochemical and Evolutionary Networks, volume 5 of Texts in Algorithmics, 75-92, Kings' College London, Strand, London, 2005. College Publications.

You can download some of my scripts and programs as well as the data I have used from this page.

Other info

My best advice to anyone who wants to raise a happy, mentally healthy child is: Keep him or her as far away from church as you can.
Frank Zappa

A few facts about me:

  • I completed my B.Sc. in computer science in the summer 2003 from the Department of Computer Science, University of Copenhagen. I wrote about simultaneous multiple alignment and phylogenetic inference using sequence graphs. The method is known as the deferred path heuristic. Ass.prof. Pawel Winter was my supervisor.
  • I got my M.Sc. in bioinformatics in January 2006 (on Friday the 13th!). My thesis "Simultaneous Multiple Alignment and Structure Prediction of RNA Sequences" was written under supervision from Anders Krogh and Paul Gardner.
  • I constitute 25 percent of the forces behind the microbrewery Bryggeriet Djævlebryg Aps..
  • Do you have a computational biology problem? Then visit BioGeeks.
  • I am a big fan of whisky (single malt in particular), beer, the occasional cigar, James Bond, Nietzsche, Georg Brandes, and the scientific method. I am very skeptical by nature and a great believer in nothing.
  • I highly recommend reading Preacher, Sin City and Sandman.
  • Of music, I like listening to Strapping Young Lad, Frank Zappa and Meshuggah - and of course classics like Iron Maiden, Led Zeppelin, Megadeth, Pink Floyd, Tori Amos and King Diamond.

Open letter (in Danish) to the Danish Parliament regarding the threat from "intelligent design" and other creationist ideas.

Reading

I like to read, and I like collecting books. I constantly have at least one book lying next to my bed.

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