Jan Gorodkin

Jan Gorodkin

Professor

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    Publication year:
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    101 - 125 out of 151Page size: 25
    1. 2012
    2. Published

      Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM

      Havgaard, Jakob Hull, Kaur, S. & Gorodkin, Jan, 2012, In: Current Protocols in Bioinformatics. 39, p. 12.11.1-12.11.15 5 p.

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

    3. Published

      DeepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns

      Langenberger, D., Pundhir, Sachin, Ekstrøm, Claus Thorn, Stadler, P. F., Hoffmann, S. & Gorodkin, Jan, 2012, In: Bioinformatics. 28, 1, p. 17-24 8 p.

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

    4. Published

      Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

      Croft, L. J., Szklarczyk, D., Jensen, Lars Juhl & Gorodkin, Jan, 2012, In: B M C Systems Biology. 6, 1, p. 90

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

    5. Published

      RILogo: visualising RNA-RNA interactions

      Menzel, K. P., Seemann, Ernst Stefan & Gorodkin, Jan, 2012, In: Bioinformatics. 28, 19, p. 2523-2526 4 p.

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

    6. Published

      RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model

      Wenzel, Anne, Akbasli, E. & Gorodkin, Jan, 2012, In: Bioinformatics. 28, 21, p. 2738-2746 9 p.

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

    7. Published

      Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain

      Seemann, Ernst Stefan, Sunkin, S. M., Hawrylycz, M. J., Ruzzo, W. L. & Gorodkin, Jan, 2012, In: BMC Genomics. 13, 1, p. 214-227 14 p.

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

    8. 2011
    9. Published

      Fast local fragment chaining using sum-of-pair gap costs

      Otto, C., Hoffmann, S., Gorodkin, Jan & Stadler, P. F., 2011, In: Algorithms for Molecular Biology. 6, 4

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

    10. Published

      From structure prediction to genomic screens for novel non-coding RNAs

      Gorodkin, Jan & Hofacker, I. L., 2011, In: PLoS Computational Biology. 7, 8, 13 p.

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

    11. Published

      Global microRNA analysis of the NCI-60 cancer cell panel

      Søkilde, R., Kaczkowski, B., Podolska, A., Cirera, Susanna, Gorodkin, Jan, Møller, S. & Litman, T., 2011, In: Molecular Cancer Therapeutics. 10, 3, p. 375-384 10 p.

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

    12. Published

      PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

      Seemann, Ernst Stefan, Richter, A. S., Gesell, T., Backofen, R. & Gorodkin, Jan, 2011, In: Bioinformatics. 27, 2, p. 211-219 9 p.

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

    13. Published

      The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

      Seemann, Ernst Stefan, Menzel, K. P., Backofen, R. & Gorodkin, Jan, 2011, In: Nucleic Acids Research. 39, Suppl. 2, p. W107-W111 5 p.

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

    14. Published

      maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences

      Menzel, K. P., Stadler, P. F. & Gorodkin, Jan, 2011, In: Bioinformatics. 27, 3, p. 317-325 9 p.

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

    15. 2010
    16. Published

      454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides

      Zagrobelny, Mika, Scheibye-Alsing, K., Jensen, N. B., Møller, Birger Lindberg, Gorodkin, Jan & Bak, Søren, 2010.

      Research output: Contribution to conference › Poster › Research

    17. Published

      454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides

      Zagrobelny, Mika, Scheibye-Alsing, K., Jensen, N. B., Møller, Birger Lindberg, Gorodkin, Jan & Bak, Søren, 2010.

      Research output: Contribution to conference › Poster › Research

    18. Published

      De novo prediction of structured RNAs from genomic sequences

      Gorodkin, Jan, Hofacker, I. L., Þórarinsson, E., Yao, Z., Havgaard, Jakob Hull & Ruzzo, W. L., 2010, In: Trends in Biotechnology. 28, 1, p. 9-19 11 p.

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

    19. Published

      A study of alternative splicing in the pig

      Hillig, A. N., Cirera, Susanna, Gilchrist, M. J., Gorodkin, Jan, Jørgensen, Claus Bøttcher & Fredholm, Merete, 2010, In: BMC Research Notes. 3, 123, 12 p.

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

    20. Published

      Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

      Seemann, Ernst Stefan, Richter, A. S., Gorodkin, Jan & Backofen, R., 2010, In: Algorithms for Molecular Biology. 5, 22, 13 p.

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

    21. 2009
    22. Published

      454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides

      Zagrobelny, Mika, Scheibye-Alsing, K., Jensen, N. B., Møller, Birger Lindberg, Gorodkin, Jan & Bak, Søren, 2009, In: BMC Genomics. 10, 574, 15 p.

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

    23. Published

      Genes involved in metabolism of cyanogenic glucosides in Zygaena filipendulae determined by 454 pyrosequencing

      Zagrobelny, Mika, Scheibye-Alsing, K., Jensen, N. B., Møller, Birger Lindberg, Gorodkin, Jan & Bak, Søren, 2009.

      Research output: Contribution to conference › Poster › Research

    24. Published

      Maximum likelihood estimation of weight matrices for targeted homology search

      Menzel, P., Gorodkin, Jan & Stadler, P. F., 2009, Proceedings of the German Conference on Bioinformatics 2009. Grosse, I., Neumann, S., Posch, S., Schreiber, F. & Stadler, P. (eds.). Gesellschaft für Informatik, p. 211-220 10 p. (Lecture Notes in Informatics).

      Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

    25. Published

      Sequence assembly

      Scheibye-Alsing, K., Hoffmann, S., Frankel, A. M., Jensen, P., Stadler, P. F., Mang, Y., Tommerup, Niels, Gilchrist, M. J., Hillig, A. N., Cirera, Susanna, Jørgensen, Claus Bøttcher, Fredholm, Merete & Gorodkin, Jan, 2009, In: Computational Biology and Chemistry. 33, 2, p. 121-136 16 p.

      Research output: Contribution to journal › Review › Research › peer-review

    26. Published

      Structural profiles of human miRNA families from pairwise clustering

      Kaczkowski, B., Þórarinsson, E., Reiche, K., Havgaard, Jakob Hull, Stadler, P. F. & Gorodkin, Jan, 2009, In: Bioinformatics. 25, 3, p. 291-294 4 p.

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

    27. Published

      The tedious task of finding homologous noncoding RNA genes

      Menzel, K. P., Gorodkin, Jan & Stadler, P. F., 2009, In: RNA: A publication of the RNA Society. 15, 12, p. 2075-2082 8 p.

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

    28. 2008
    29. Published

      Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

      Þórarinsson, E., Yao, Z., Wiklund, E. D., Bramsen, J. B., Hansen, C., Kjems, J., Tommerup, Niels, Ruzzo, W. L. & Gorodkin, Jan, 2008, In: Genome Research. 18, 2, p. 242-251 10 p.

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

    30. Published

      SNP-finding in pig mitochondrial ESTs

      Scheibye-Alsing, K., Cirera, Susanna, Gilchrist, M. J., Fredholm, Merete & Gorodkin, Jan, 2008, In: Animal Genetics. 39, 2, p. 193-195 3 p.

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

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