Stinus Lindgreen

Research output

Research output per year 2006 2007 2008 2010 2012 2014 2016 2016

• 15 Journal article
• 1 Ph.D. thesis

Research output per year

Research output per year

Search results

• 2016

  AdapterRemoval v2: rapid adapter trimming, identification, and read merging

  Schubert, M., Lindgreen, S. & Orlando, L. A. A., 12 Feb 2016, In: BMC Research Notes. 9, 7 p., 88.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • structure-specific endonuclease I 100%
  • Datasets 72%
  • Amount 38%
  401 Citations (Scopus)

  145 Downloads (Pure)

• An evaluation of the accuracy and speed of metagenome analysis tools

  Lindgreen, S., Adair, K. L. & Gardner, P. P., 18 Jan 2016, In: Scientific Reports. 6, 14 p., 19233.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Metagenome 100%
  • Benchmarking 75%
  • Datasets 55%
  • Metagenomics 43%
  • Firearms 39%
  157 Citations (Scopus)

  125 Downloads (Pure)
• 2014

  Adaptable probabilistic mapping of short reads using position specific scoring matrices

  Kerpedjiev, P., Frellsen, J., Lindgreen, S. & Krogh, A., 9 Apr 2014, In: B M C Bioinformatics. 15, 17 p., 15:100.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Position-Specific Scoring Matrices 100%
  • Sequencing Method 93%
  • DNA Sequencing 77%
  • Scoring 74%
  • Error 46%
  31 Citations (Scopus)

  1550 Downloads (Pure)

• Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

  Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., Andersson, R., Jones, P. A., Hoover, C. A., Tikhonov, A., Prokhortchouk, E., Rubin, E. M., Sandelin, A. G., Gilbert, M. T. P., Krogh, A., Willerslev, E., & 1 othersOrlando, L. A. A., Mar 2014, In: Genome Research. 24, 3, p. 454-466 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Cytosine 100%
  • Nucleosomes 98%
  • Human Genome 88%
  • Methylation 76%
  • Epigenomics 73%
  90 Citations (Scopus)

  274 Downloads (Pure)

• Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling

  Lindgreen, S., Umu, S. U., Lai, A. S-W., Eldai, H., Liu, W., McGimpsey, S., Wheeler, N. E., Biggs, P. J., Thomson, N. R., Barquist, L., Poole, A. M. & Gardner, P. P., 1 Oct 2014, In: P L o S One. 10, 10, 10 p., e1003907.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • RNA 100%
  • non-coding RNA 95%
  • Untranslated RNA 93%
  • Phylogenetics 76%
  • Transcriptome 76%
  27 Citations (Scopus)

  704 Downloads (Pure)

• SNPest: a probabilistic graphical model for estimating genotypes

  Lindgreen, S., Krogh, A. & Pedersen, J. S., 2014, In: BMC Research Notes. 7, 12 p., 298.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Statistical Models 100%
  • Ancient DNA 94%
  • Error 66%
  • Diploidy 64%
  • Genotype 63%
  4 Citations (Scopus)

  296 Downloads (Pure)
• 2012

  AdapterRemoval: easy cleaning of next generation sequencing reads

  Lindgreen, S., 2012, In: BMC Research Notes. 5, 337, 7 p., 337.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • High-Throughput Nucleotide Sequencing 100%
  • Nucleotide 85%
  • Amount 44%
  • Single Nucleotide Polymorphism 43%
  • Nucleotides 42%
  318 Citations (Scopus)

  1179 Downloads (Pure)

• Improving ancient DNA read mapping against modern reference genomes

  Schubert, M., Ginolhac, A., Lindgreen, S., Thompson, J. F., Al-Rasheid, K. A. S., Willerslev, E., Krogh, A. & Orlando, L. A. A., 10 May 2012, In: BMC Genomics. 13, 15 p., 178.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Ancient DNA 100%
  • Genome 42%
  • Firearms 20%
  • DNA Damage 15%
  • Forensic Anthropology 11%
  133 Citations (Scopus)

  3285 Downloads (Pure)
• 2011

  An Aboriginal Australian genome reveals separate human dispersals into Asia

  Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando, L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K., Avila Arcos, M. D. C., & 38 othersMoreno Mayar, J. V., Muller, C., Dortch, J., Gilbert, T., Lund, O., Wesolowska, A., Karmin, M., Weinert, L. A., Wang, B., Li, J., Tai, S., Xiao, F., Hanihara, T., van Driem, G., Jha, A. R., Ricaut, F-X., de Knijff, P., Migliano, A. B., Gallego Romero, I., Kristiansen, K., Lambert, D. M., Brunak, S., Forster, P., Brinkmann, B., Nehlich, O., Bunce, M., Richards, M., Gupta, R., Bustamante, C. D., Krogh, A., Foley, R. A., Lahr, M. M., Balloux, F., Sicheritz-Pontén, T., Villems, R., Nielsen, R., Wang, J. & Willerslev, E., 7 Oct 2011, In: Science. 334, 6052, p. 94-98 5 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Oceanic Ancestry Group 100%
  • Genome 46%
  • Gene Flow 34%
  • Western Australia 29%
  • North American Indians 27%
  412 Citations (Scopus)
• 2010

  Ancient human genome sequence of an extinct Palaeo-Eskimo

  Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, T., Wang, Y., Raghavan, M., Campos, P., Kamp, H. L. M., Wilson, A. S., Gledhill, A., Tridico, S., & 32 othersBunce, M., Lorenzen, E., Binladen, J. K. M. A., Guo, X., Zhao, J., Zhang, X., Zhang, H., Li, Z., Chen, M., Orlando, L. A. A., Kristiansen, K., Bak, M., Tommerup, N., Bendixen, C., Pierre, T. L., Grønnow, B., Meldgaard, M., Andreasen, C., Fedorova, S. A., Osipova, L. P., Higham, T. F. G., Ramsey, C. B., Hansen, T. V. O., Nielsen, F. C., Crawford, M. H., Brunak, S., Sicheritz-Pontén, T., Villems, R., Nielsen, R., Krogh, A., Wang, J. & Willerslev, E., 11 Feb 2010, In: Nature. 463, 7282, p. 757-762 6 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Inuits 100%
  • Human Genome 70%
  • Single Nucleotide Polymorphism 56%
  • Genome 45%
  • Permafrost 41%
  485 Citations (Scopus)

• Bioinformatical approaches to RNA structure prediction & Sequencing of an ancient human genome

  Lindgreen, S., 2010, Biologisk Institut: Museum Tusculanum. 111 p.

  Research output: Book/Report › Ph.D. thesis

  • Ancient DNA 100%
  • Human Genome 65%
  • Base Pairing 64%
  • Research Personnel 43%
  • RNA 43%
• 2008

  Rfam: updates to the RNA families database

  Gardner, P. P., Daub, J., Tate, J. G., Nawrocki, E. P., Kolbe, D. L., Lindgreen, S., Wilkinson, A. C., Finn, R. D., Griffiths-Jones, S., Eddy, S. R. & Bateman, A., 2008, In: Nucleic Acids Research.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Nucleic Acid Databases 100%
  • Small Nucleolar RNA 61%
  • Sequence Alignment 51%
  • Transfer RNA 46%
  • MicroRNAs 35%
  625 Citations (Scopus)

• WAR: webserver for aligning structural RNAs

  Þórarinsson, E. & Lindgreen, S., 2008, In: Nucleic Acids Research. 36, Suppl. 2, p. W79-W84 6 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Untranslated RNA 100%
  • RNA 61%
  36 Citations (Scopus)

  665 Downloads (Pure)
• 2007

  MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.

  Lindgreen, S., Gardner, P. P. & Krogh, A., 2007, In: Bioinformatics. 23, 24, p. 3304-11 7 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Structure Prediction 100%
  • RNA 75%
  • Simulated Annealing 75%
  • Alignment 72%
  • Untranslated RNA 70%
  57 Citations (Scopus)

• Multiple alignment and structure prediction of non-coding RNA sequences

  Lindgreen, S., Gardner, P. P. & Krogh, A., 20 Nov 2007, In: BMC Bioinformatics. 8, SUPPL. 8, P8.

  Research output: Contribution to journal › Journal article › Research › peer-review

  1 Citation (Scopus)
• 2006

  Measuring covariation in RNA alignments: Physical realism improves information measures

  Lindgreen, S., Gardner, P. P. & Krogh, A., 2006, In: Bioinformatics. 22, 24, p. 2988-2995 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Information Measure 100%
  • RNA 93%
  • Alignment 89%
  • Untranslated RNA 88%
  • Computational Biology 73%
  39 Citations (Scopus)