Jan Gorodkin

Jan Gorodkin

Professor

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    1. Published

      CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters

      Alkan, F., Wenzel, Anne, Anthon, Christian, Havgaard, Jakob Hull & Gorodkin, Jan, 2018, In: Genome Biology. 19, 13 p., 177.

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

    2. Published

      RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets

      Alkan, F., Wenzel, Anne, Palasca, Oana, Kerpedjiev, P., Rudebeck, A. F., Stadler, P. F., Hofacker, I. L. & Gorodkin, Jan, 2017, In: Nucleic Acids Research. 45, 8, 13 p., e60.

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

    3. Published

      Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing

      Alquezar Planas, D. E., Mourier, T., Bruhn, C. A. W., Hansen, Anders Johannes, Vitcetz, S. N., Mørk, S., Gorodkin, Jan, Nielsen, H. A., Guo, Y., Sethuraman, A., Paxinos, E. E., Shan, T., Delwart, E. L. & Nielsen, L. P., 3 Sep 2013, In: Scientific Reports. 3, 10 p., 2468.

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

    4. Published

      The tmRDB and SRPDB resources

      Andersen, E. S., Rosenblad, M. A., Larsen, N., Westergaard, Jesper Cairo, Burks, J., Wower, I. K., Wower, J., Gorodkin, Jan, Samuelsson, T. & Zwieb, C., 2006, In: Nucleic Acids Research. 34, p. D163-D168 6 p.

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

    5. Published

      Semiautomated improvement of RNA alignments

      Andersen, E. S., Lind-Thomsen, A., Knudsen, B., Kristensen, S. E., Havgaard, Jakob Hull, Torarinsson, E., Larsen, N., Zwieb, C., Sestoft, P., Kjems, J. & Gorodkin, Jan, 2007, In: RNA: A publication of the RNA Society. 13, 11, p. 1850-1859 10 p.

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

    6. Published

      Structured RNAs and synteny regions in the pig genome

      Anthon, Christian, Tafer, H., Havgaard, Jakob Hull, Thomsen, B., Hedegaard, J., Seemann, Ernst Stefan, Pundhir, Sachin, Kehr, S., Bartschat, S., Nielsen, M., Nielsen, R. O., Fredholm, Merete, Stadler, P. F. & Gorodkin, Jan, 2014, In: BMC Genomics. 15, 27 p., 459.

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

    7. Published

      CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design

      Anthon, Christian, Corsi, G. I. & Gorodkin, Jan, 2022, In: Bioinformatics. 38, 24, p. 5437-5439 3 p.

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

    8. Published

      Comparative RNA genomics

      Backofen, R., Gorodkin, Jan, Hofacker, I. L. & Stadler, P. F., 2018, Comparative Genomics: Methods and Protocols. Humana Press, Vol. 1704. p. 363-400 38 p. (Methods in Molecular Biology, Vol. 1704).

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

    9. Published

      Production of human entorhinal stellate cell-like cells by forward programming shows an important role of Foxp1 in reprogramming

      Bergmann, T., Liu, Y., Skov, J., Mogus, L., Lee, J., Pfisterer, U., Handfield, L. F., Asenjo-Martinez, A., Lisa-Vargas, I., Seemann, S. E., Lee, J. T. H., Patikas, N., Kornum, B. R., Denham, M., Hyttel, P., Witter, M. P., Gorodkin, J., Pers, T. H., Hemberg, M., Khodosevich, K. & 1 others, Hall, Vanessa Jane, 2022, In: Frontiers in Cell and Developmental Biology. 10, 976549.

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

    10. Published

      The developing Entorhinal Cortex – a cellular map

      Bergmann, T. B., Liu, Y., Lee, J., Pfisterer, U. G., Asenjo Martinez, A., Seemann, Ernst Stefan, Pihl, M., Thomsen, Preben Dybdahl, Hyttel, P., witter, M., Khodosevich, Konstantin, Gorodkin, Jan, Pers, Tune H & Hall, Vanessa Jane, 2019.

      Research output: Contribution to conference › Conference abstract for conference › Research

    11. Published

      Uncovering the anatomical and molecular landscape of the starting point of Alzheimer’s disease in the brain

      Bergmann, T. B., Liu, Y., Lee, J., Pfisterer, U. G., Asenjo Martinez, A., Seemann, Ernst Stefan, Pihl, M., Thomsen, Preben Dybdahl, Hyttel, P., witter, M., Khodosevich, Konstantin, Gorodkin, Jan, Pers, Tune H & Hall, Vanessa Jane, 2019.

      Research output: Contribution to conference › Conference abstract for conference › Research

    12. Published

      The developing Entorhinal cortex - a cellular map

      Bergmann, T. B., Liu, Y., Lee, J., Pfisterer, U. G., Handfield, L., Asenjo Martinez, A., Seemann, Ernst Stefan, Witter, M., Khodosevich, Konstantin, Gorodkin, Jan, Hemberg, M., Pers, Tune H & Hall, Vanessa Jane, 25 Nov 2019. 1 p.

      Research output: Contribution to conference › Conference abstract for conference › Communication

    13. Published

      The developmental neurogenic niche of the Entorhinal cortex revealed by single-cell transcriptomics.

      Bergmann, T. B., Liu, Y., Lee, J., Peralvo Vidal, Juan Miguel, Mori, Yuki, Seemann, Ernst Stefan, Pihl, M., Thomsen, Preben Dybdahl, Hyttel, P., witter, M., Gorodkin, Jan, Hall, Vanessa Jane & Pers, Tune H, 2018.

      Research output: Contribution to conference › Conference abstract for conference › Research

    14. Published

      Profiling of Ribose Methylations in RNA by High-Throughput Sequencing

      Birkedal, U., Christensen-Dalsgaard, M., Krogh, Nicolai, Radhakrishnan, S., Gorodkin, Jan & Nielsen, Henrik, 7 Jan 2015, In: Angewandte Chemie (International ed. in English). 54, 2, p. 451-455 5 p.

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

    15. Published

      IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs

      Brogaard, L., Larsen, Lars, Heegaard, P. M. H., Anthon, Christian, Gorodkin, Jan, Dürrwald, R. & Skovgaard, K., 2018, In: PLOS ONE. 13, 4, 23 p., e0194765.

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

    16. Published

      Utilizing directed evolution to interrogate and optimize CRISPR/Cas guide RNA scaffolds

      Bush, K., Corsi, G. I., Yan, A. C., Haynes, K., Layzer, J. M., Zhou, J. H., Llanga, T., Gorodkin, Jan & Sullenger, B. A., 2023, In: Cell Chemical Biology. 30, 8, p. 879-892.e5

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

    17. Published

      Progress and harmonization of gene editing to treat human diseases: Proceeding of COST Action CA21113 GenE-HumDi

      Cavazza, A., Hendel, A., Bak, R. O., Rio, P., Güell, M., Lainšček, D., Arechavala-Gomeza, V., Peng, L., Hapil, F. Z., Harvey, J., Ortega, F. G., Gonzalez-Martinez, C., Lederer, C. W., Mikkelsen, K., Gasiunas, G., Kalter, N., Gonçalves, M. A. F. V., Petersen, J., Garanto, A., Montoliu, L. & 20 others, Maresca, M., Seemann, Ernst Stefan, Gorodkin, Jan, Mazini, L., Sanchez, R., Rodriguez-Madoz, J. R., Maldonado-Pérez, N., Laura, T., Schmueck-Henneresse, M., Maccalli, C., Grünewald, J., Carmona, G., Kachamakova-Trojanowska, N., Miccio, A., Martin, F., Turchiano, G., Cathomen, T., Luo, Y., Tsai, S. Q. & Benabdellah, K., 2023, In: Molecular Therapy Nucleic Acids. 34, 14 p., 102066.

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

    18. Published

      Mutation in FTD3 CHMP2B causes impaired autography and distorted energy metabolism cumulating in reactive astrocyte phenotypes

      Chandrasekaran, A., Dittlau, K. S., Corsi, G., Haukedal, H., Doncheva, N. T., Ramakrishna, S., Ambardar, S., Salcedo, C., Schmidt, S. I., Cirera, S., Pihl, M., Schmid, B., Nielsen, T. T., Nielsen, J., Kolko, M., Kobolak, J., Dinnyes, A., Hyttel, P., Palakodeti, D., Gorodkin, J. & 4 others, Muddashetty, R., Meyer, M., Aldana, Blanca & Freude, Kristine, 2020.

      Research output: Contribution to conference › Conference abstract for conference › Research

    19. Published

      Astrocytic reactivity triggered by defective autophagy and metabolic failure causes neurotoxicity in frontotemporal dementia type 3

      Chandrasekaran, A., Dittlau, K. S., Corsi, G. I., Haukedal, H., Doncheva, N. T., Ramakrishna, S., Ambardar, S., Salcedo, C., Schmidt, S. I., Zhang, Y., Cirera, S., Pihl, M., Schmid, B., Nielsen, T. T., Nielsen, J. E., Kolko, M., Kobolák, J., Dinnyés, A., Hyttel, P., Palakodeti, D. & 5 others, Gorodkin, Jan, Muddashetty, R. S., Meyer, M., Aldana, Blanca & Freude, Kristine, 2021, In: Stem Cell Reports. 16, 11, p. 2736-2751

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

    20. Published

      Mutations in FTD3 CHMP2B causes impaired autophagy and distorted energy metabolism cumulating in reactive astrocyte phenotypes

      Chandrasekaran, A., Dittlau, K. S., Corsi, G., Doncheva, N. T., Haukedal, H., Ramakrishna, S., Ambardar, S., Salcedo, C., Schmidt, S. I., Cirera, S., Pihl, M., Schmid, B., Nielsen, T. T., Nielsen, J., Kolko, M., Kobolak, J., Dinnyes, A., Hyttel, P., Palakodeti, D., Gorodkin, J. & 4 others, Muddashetty, R., Meyer, M., Aldana, Blanca & Freude, Kristine, 2020.

      Research output: Contribution to conference › Poster › Research

    21. Published

      CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context

      Corsi, G. I., Qu, Kunli, Alkan, F., Pan, Xiaoguang, Luo, Y. & Gorodkin, Jan, 2022, In: Nature Communications. 13, 14 p., 3006.

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

    22. Published

      CRISPRroots: On-and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells

      Corsi, G. I., Gadekar, V. P., Gorodkin, Jan & Seemann, Ernst Stefan, 2022, In: Nucleic Acids Research. 50, 4, 12 p., E20.

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

    23. Published

      The transcriptomic landscape of neurons carrying PSEN1 mutations reveals changes in extracellular matrix components and non-coding gene expression

      Corsi, G. I., Gadekar, V. P., Haukedal, H., Doncheva, Nadezhda Tsankova, Anthon, Christian, Ambardar, S., Palakodeti, D., Hyttel, P., Freude, Kristine, Seemann, Ernst Stefan & Gorodkin, Jan, 2023, In: Neurobiology of Disease. 178, 17 p., 105980.

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

    24. Published

      Letter to the editor: Testing on external independent datasets is necessary to corroborate machine learning model improvement

      Corsi, G. I., Anthon, Christian & Gorodkin, Jan, 2023, In: Bioinformatics. 39, 6, btad327.

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

    25. Published

      Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a

      Creutzburg, S. C. A., Wu, W. Y., Mohanraju, P., Swartjes, T., Alkan, F., Gorodkin, Jan, Staals, R. H. J. & van der Oost, J., 2020, In: Nucleic Acids Research. 48, 6, p. 3228-3243 16 p.

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

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