From BINF - Bioinformatics Centre
| Stinus Lindgreen|
University of Copenhagen
Ole Maaloes Vej 5
2200 Copenhagen N
phone: +45 3532 1287
I am a part of the Non-coding RNA group.
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.
- My CV can be found here.
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.
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.
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.
I like to read, and I like collecting books. I constantly have at least one book lying next to my bed.
- The last book I read was Don Rosa's The Life and Times of Scrooge McDuck and The Life and Times of Scrooge McDuck Companion
- And before that it was Christopher Hitchens: God Is Not Great: How Religion Poisons Everything
- And before that it was Ayaan Hirsi Ali: Infidel
- And before that it was Dennis Nørmark and Lars Andreassen: Det virkelige menneske - sjælens og kulturens naturhistorie (eng. The real man - the natural history of the soul and culture).
- And before that it was Sam Harris: The End of Faith
- And before that it was Richard Dawkins: The God Delusion
- And before that it was Irvine Welsh: Filth
- And before that it was Neil Gaiman: Stardust
- And before that it was Neil Gaiman and Ed Kramer (editors): The Sandman: Book of Dreams
- And before that it was Jørgen Leth: Det uperfekte menneske (sorry, only in Danish. The title means "The Imperfect Human")
- And before that it was Ian Fleming: The Man With The Golden Gun
- And before that it was Dan Brown: The Da Vinci Code
- And before that it was Paul Auster: Oracle Night
- And before that it was Yann Martel: Life of Pi
- And before that it was Neil Gaiman: Anansi Boys
- And before that it was Dan Brown: Angels and Demons
- And before that it was Paul Auster: The Book of Illusions
- And before that it was Ian Fleming: Thunderball
- And before that it was Umberto Eco: The Mysterious Flame of Queen Loana
- And before that it was Bret Easton Ellis: Lunar Park