Stinus Lindgreen

Research scientist
Systems Medicine

Phone +45 30 91 33 28


Research area
I have Ph.D and M.Sc in bioinformatics from University of Copenhagen and have worked as a researcher for many years at universities and in the private sector both in Denmark and abroad. I have a strong background in computer science, algorithmics and bioinformatics. All through my academic career I have been developing software and pipelines. In particular, a main focus for me has been to analyze large complex data sets primarily from next-generation sequencing projects. I have been involved in large, multidisciplinary research projects for years, most recently being involved in the Barley Genome Sequencing Consortium and heading an international collaboration investigating RNA-sequencing data from prokaryotes

My initial research focus was on the computational analysis of RNA, developing a method for aligning and predicting the structure of non-coding RNA sequences and being involved in the widely used Rfam database. However, my main focus over the years has been next-generation sequencing data, population genomics and ancient DNA, resulting in a joint first author paper in Nature, a Science paper and many other interesting studies. I have also focused extensively on transcription data (RNA-seq) and metagenomics.

Here at Steno, my main interest is large cross-disciplinary studies involving different data sets - genomics, transcriptomics, metabolomics, metagenomics etc. - and investigating the relevance in the clinic. Using my expertise to help patients and to broaden our understanding of diabetes is instrumental. I am always open to new collaborations so feel free to contact me if you need bioinformatics skills in your project.

Ongoing projects

Education (year, academic degree, institution – latest first)
2010: Ph.D in bioinformatics, University of Copenhagen, Denmark
2006: M.Sc. in bioinformatics, University of Copenhagen, Denmark
2003: B.Sc. in computer science, University of Copenhagen, Denmark

Latest positions
2015-2016: Research Scientist, Carlsberg Research Laboratory
2013-2015: Marie Curie Research Fellow, joint between University of Copenhagen, Denmark, and University of Canterbury, New Zealand
2012-2013: Post Doctoral Researcher, University of Canterbury, New Zealand
2010-2010: Post Doctoral Researcher, University of Copenhagen

Presentations the last 3 years 

Speaker: ”Effects of global change drivers on above and below ground systems”, ISME 15 Conference, Seoul, South Korea, August 2014
Poster presentation of Marie Curie research project at ESOF (European Science Open Forum) and Marie Sklodowska Curie conference, Copenhagen, June 2014
Invited speaker: “Heating significantly alters community composition and functioning both above and below ground”, University of Copenhagen, June 2014

Invited speaker: “Ancient DNA and Human Migration”, Bangor University, Wales, July 2013
Poster presentation: ISMB/ECCB, Berlin, Germany, 2013
Poster presentation: SMBE, Chicago, USA, 2013

Scientific publications 

Google scholar profile

Selected publications
N. Forsdick, S. Lindgreen, M. Massaro and M. L. Hale (2016): Isolation and characterisation of microsatellite loci for the Chatham Island black robin Petroica traversi, Conservation Genetics Resources (accepted)

M. Schubert, S. Lindgreen and L. Orlando (2016): AdapterRemoval v2: rapid adapter trimming, identification, and read merging, BMC Research Notes 9, 88

S. Lindgreen, K. L. Adair and P. P. Gardner (2016): An evaluation of the accuracy and speed of metagenome analysis tools, Scientific Reports 6, 19233

S. Lindgreen*, S. U. Umu*, A. S-W. Lai, H. Eldai, W. Liu, S. McGimpsey, N. Wheeler, P. J. Biggs, N. R. Thomson, L. Barquist, A. M. Poole, P. P. Gardner (2014): Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling, PLoS Computational Biology 10(10), e1003907

S. Lindgreen, A. Krogh, J. S. Pedersen (2014): SNPest: A probabilistic graphical model for estimating genotypes, BMC Research Notes, 7(1), 698

P. Kerpedjiev, J. Frellsen, S. Lindgreen, A. Krogh (2014): Adaptable probabilistic mapping of short reads using position specific scoring matrices, BMC Bioinformatics, 15(1), 100

J. S. Pedersen, E. Valen, A. M. V. Velazquez, B. J. Parker, M. Rasmussen, S. Lindgreen, B. Lilje, D. J. Tobin, T. K. Kelly, S. Vang, R. Andersson, P. A. Jones, C. A. Hoover, A. Tikhonov, E. Prokhortchouk, E. M. Rubin, A. Sandelin, M. T. P. Gilbert, A. Krogh, E. Willerslev, L. Orlando (2014): Genome Research, 24(3), 454-466

S. Lindgreen (2012): Codon evolution: Mechanisms and Models (Book review). Trends In Evolutionary Biology, 4(1), e8. doi:10.4081/eb.2012.e8

S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation Sequencing Reads, BMC Research Notes, 5:337

M. Schubert, A. Ginolhac, S. Lindgreen, J. F. Thompson, K. AS. Al-Rasheid, E. Willerslev, A. Krogh and L. Orlando (2012): Improving ancient DNA read mapping against modern reference genomes, BMC Genomics, 13(1), 178

M. Rasmussen, X. Guo, Y. Wang, K. E. Lohmueller, S. Rasmussen, A. Albrechtsen, L. Skotte, S. Lindgreen, M. Metspalu, T. Jombart, T. Kivisild, W. Zhai, A. Eriksson, A. Manica, L. Orlando, M. Francisco, S. Tridico, E. Metspalu, K. Nielsen, María. C. Ávila-Arcos, J. Víc. Moreno-Mayar, C. Muller, J. Dortch, M. T. P. Gilbert, O. Lund, A. Wesolowska, M. Karmin, L. A. Weinert, B. Wang, J. Li, S. Tai, F. Xiao, T. Hanihara, G. v. Driem, A. R. Jha, François-X. Ricaut, P. d. Knijff, A. B. Migliano, I. G. Romero, K. Kristiansen, D. M. Lambert, S. Brunak, P. Forster, B. Brinkmann, O. Nehlich, M. Bunce, M. Richards, R. Gupta, C. D. Bustamante, A. Krogh, R. A. Foley, M. M. Lahr, F. Balloux, T. Sicheritz-Pontén, R. Villems, R. Nielsen, J. Wang and E. Willerslev (2011): An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia, Science, 334(6052), 94-98

M. Rasmussen*, Y. Li*, S. Lindgreen*, J.S. Pedersen, A. Albrechtsen, I. Moltke, M. Metspalu, E. Metspalu, T. Kivisild, R. Gupta, M. Bertalan, K. Nielsen, M.T.P. Gilbert, Y. Wang, M. Raghavan, P.F. Campos, H. Munkholm Kamp, A.S. Wilson, A. Gledhill, S. Tridico, M. Bunce, E.D. Lorenzen, J. Binladen, X. Guo, J. Zhao, X. Zhang, H. Zhang, Z. Li, M. Chen, L. Orlando, K. Kristiansen, M. Bak, N. Tommerup, C. Bendixen, T.L. Pierre, B. Grønnow, M. Meldgaard, C. Andreasen, S.A. Fedorova, L.P. Osipova, T.F.G. Higham, C.B. Ramsey, T.v.O. Hansen, F.C. Nielsen, M.H. Crawford, S. Brunak, T. Sicheritz-Pontén, R. Villems, R. Nielsen, A. Krogh, J. Wang and E. Willerslev (2010): Ancient human genome sequence of an extinct Palaeo-Eskimo, Nature, 463(7282), 757-762.

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 (2009): Rfam: updates to the RNA families database, Nucleic Acids Research (Database issue), 37 (suppl. 1), D136-D140

E. Torarinsson* and S. Lindgreen* (2008): WAR: Webserver for aligning structural RNAs, Nucleic Acids Research (Webserver issue), 36 (suppl. 2), W79-W84.

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):3304-3311

S. Lindgreen, P.P. Gardner and A. Krogh (2007): Multiple alignment and structure prediction of non-coding RNA sequences (poster abstract), 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

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, King’s College London, Strand, London

Sidst opdateret 12-01-2017