Jan Gorodkin

Jan Gorodkin

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    1. Published

      RNA interactions in the 5' region of the HIV-1 genome

      Damgaard, C. K., Andersen, E. S., Knudsen, B., Gorodkin, Jan & Kjems, J., 2004, In: Journal of Molecular Biology. 336, 2, p. 369-379 11 p.

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

    2. Published

      RNA-Seq Study on the Longissimus thoracis Muscle of Italian Large White Pigs Fed Extruded Linseed with or without Antioxidants and Polyphenols

      Vegni, J., Sun, Y., Seemann, Ernst Stefan, Zappaterra, M., Davoli, R., Dall’Olio, S., Gorodkin, Jan & Zambonelli, P., 2023, In: Animals. 13, 7, 1187.

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

    3. Published

      RNAcentral: a hub of information for non-coding RNA sequences

      The RNAcentral Constortium , T., Gorodkin, Jan & Seemann, Ernst Stefan, 2019, In: Nucleic Acids Research. 47, D1, p. D221–D229

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

    4. Published

      RNAcentral 2021: Secondary structure integration, improved sequence search and new member databases

      Sweeney, B. A., Petrov, A. I., Ribas, C. E., Finn, R. D., Bateman, A., Szymanski, M., Karlowski, W. M., Seemann, S. E., Gorodkin, J., Cannone, J. J., Gutell, R. R., Kay, S., Marygold, S., Dos Santos, G., Frankish, A., Mudge, J. M., Barshir, R., Fishilevich, S., Chan, P. P., Lowe, T. M. & 26 others, Seal, R., Bruford, E., Panni, S., Porras, P., Karagkouni, D., Hatzigeorgiou, A. G., Ma, L., Zhang, Z., Volders, P. J., Mestdagh, P., Griffiths-Jones, S., Fromm, B., Peterson, K. J., Kalvari, I., Nawrocki, E. P., Petrov, A. S., Weng, S., Bouchard-Bourelle, P., Scott, M., Lui, L. M., Hoksza, D., Lovering, R. C., Kramarz, B., Mani, P., Ramachandran, S. & Weinberg, Z., 2021, In: Nucleic Acids Research. 49, D1, p. D212-D220

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

    5. Published

      RNAscClust: Clustering RNA sequences using structure conservation and graph based motifs

      Miladi, M., Junge, A., Costa, F., Seemann, Ernst Stefan, Havgaard, Jakob Hull, Gorodkin, Jan & Backofen, R., 2017, In: Bioinformatics. 33, 14, p. 2089-2096 8 p.

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

    6. Published

      RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs: efficient detection of local RNA secondary structure changes induced by SNPs

      Radhakrishnan, S., Tafer, H., Seemann, Ernst Stefan, Hofacker, I. L., Stadler, P. F. & Gorodkin, Jan, 2013, In: Human Mutation. 34, 4, p. 546-556 11 p.

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

    7. Published

      SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

      Panitz, F., Stengaard, H., Hornshøj, H., Gorodkin, J., Hedegaard, J., Cirera, S., Thomsen, B. S., Madsen, L. B., Høj, A., Vingborg, R., Zahn, B., Wang, X., Wang, X., Wernersson, R., Jørgensen, C. B., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T. & 5 others, Nielsen, B., Havgaard, Jakob Hull, Brunak, Søren, Fredholm, Merete & Bendixen, C., 2007, In: Bioinformatics. 23, 13, p. i387-91 5 p.

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

    8. 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

    9. Published

      SRPDB: Signal Recognition Particle Database

      Rosenblad, M. A., Gorodkin, Jan, Knudsen, B., Zwieb, C. & Samuelsson, T., 2003, In: Nucleic Acids Research. 31, 1, p. 363-364 2 p.

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

    10. Published

      Sandwich cortial lamination and single-cell analysis decodes the developing spatial processing system

      Liu, Y., Bergmann, T. B., Lee, J., Pfisterer, U. G., Handfield, L-F., Mori, Y., Asenjo Martinez, A., Lisa Vargas, I., Seemann, E. S., Lee, J. T. H., Patikis, N., Peralvo Vidal, J. M., Pihl, M., Kornum, B. R., Thomsen, P. D., Hyttel, P., Witter, M., Khodosevich, K., Gorodkin, J., Hemberg, M. & 2 others, Pers, Tune H & Hall, Vanessa Jane, 2019. 45 p.

      Research output: Contribution to conference › Paper › Communication

    11. 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

    12. Published

      Sequence and expression analysis of gaps in human chromosome 20

      Minocherhomji, S., Seemann, Ernst Stefan, Mang, Y., Elschich, Z., Bak, M., Hansen, C., Papadopoulos, N., Josefsen, K., Nielsen, Henrik, Gorodkin, Jan, Tommerup, Niels & Silahtaroglu, Asli, Aug 2012, In: Nucleic Acids Research. 40, 14, p. 6660-6672 13 p.

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

    13. 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

    14. Published

      Simultaneous DNA and RNA mapping of somatic mitochondrial mutations across diverse human cancers

      Stewart, J. B., Alaei-Mahabadi, B., Radhakrishnan, S., Samuelsson, T., Gorodkin, Jan, Gustafsson, C. M. & Larsson, E., Jun 2015, In: P L o S Genetics. 11, 6, 15 p., e1005333.

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

    15. Published

      Single cell mapping the evolution of the spatial processing centre within the brain

      Ralbovszki, Dorottya Maria, Bertelsen, Mads Frost, Buchmann, Kurt, Mori, Yuki, Gorodkin, Jan, Hemberg, M., Seemann, Ernst Stefan, Khodosevich, Konstantin & Hall, Vanessa Jane, 1 May 2022.

      Research output: Contribution to conference › Poster › Communication

    16. Published

      Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project.

      Pundhir, Sachin, Hannibal, T. D., Bang-Berthelsen, C. H., Wegener, A. K., Pociot, Flemming, Holmberg, D. I. & Gorodkin, Jan, 2 May 2014, In: Gene. 545, 1, p. 80-87 8 p.

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

    17. Published

      Special issue: Computational analysis of RNA structure and function

      Gorodkin, Jan, 2019, In: Genes. 10, 1, 3 p., 55.

      Research output: Contribution to journal › Editorial › Research

    18. 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

    19. 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

    20. E-pub ahead of print

      Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease

      Velissari, R., Ilieva, M., Dao, J., Miller, H. E., Madsen, J. H., Gorodkin, Jan, Aikawa, M., Ishii, H. & Uchida, S., 2024, (E-pub ahead of print) In: Briefings in Functional Genomics.

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

    21. Published

      TISSUES 2.0: an integrative web resource on mammalian tissue expression

      Palasca, Oana, Santos, A., Stolte, C., Gorodkin, Jan & Jensen, Lars Juhl, 2018, In: Database: The Journal of Biological Databases and Curation. 2018, 1, p. 1-12

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

    22. Published

      The Bacillaceae-1 RNA motif comprises two distinct classes

      González-Tortuero, E., Anthon, Christian, Havgaard, Jakob Hull, Geissler, Adrian Sven, Breüner, A., Hjort, C., Gorodkin, Jan & Seemann, Ernst Stefan, 2022, In: Gene. 841, 146756.

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

    23. Published

      The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

      Havgaard, Jakob Hull, Lyngsø, R. B. & Gorodkin, Jan, 2005, In: Nucleic Acids Research. 33, p. W650-W653 4 p.

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

    24. 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

    25. Published

      The RNAsnp web server: predicting SNP effects on local RNA secondary structure

      Radhakrishnan, S., Tafer, H., Seemann, Ernst Stefan, Hofacker, I. L., Stadler, P. F. & Gorodkin, Jan, 2013, In: Nucleic Acids Research. 41, p. W475-W479 5 p.

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

    26. 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

    27. 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

    28. 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

    29. Published

      The identification and functional annotation of RNA structures conserved in vertebrates

      Seemann, Ernst Stefan, Mirza, A. H., Hansen, C., Bang-Berthelsen, C. H., Garde, C., Christensen-Dalsgaard, M., Torarinsson, E., Yao, Z., Workman, C. T., Pociot, Flemming, Nielsen, Henrik, Tommerup, Niels, Ruzzo, W. L. & Gorodkin, Jan, 2017, In: Genome Research. 27, p. 1371-1383 14 p.

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

    30. Published

      The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production

      Geissler, Adrian Sven, Poulsen, L. D., Doncheva, Nadezhda Tsankova, Anthon, Christian, Seemann, Ernst Stefan, González-Tortuero, E., Breüner, A., Jensen, Lars Juhl, Hjort, C., Vinther, Jeppe & Gorodkin, Jan, 2022, In: Frontiers in Microbiology. 13, 17 p., 909493.

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

    31. 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

    32. 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

    33. 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

    34. Published

      Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

      Torarinsson, E., Sawera, M., Havgaard, Jakob Hull, Fredholm, Merete & Gorodkin, Jan, 2006, In: Genome Research. 16, 7, p. 885-889 5 p.

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

    35. Published

      Transcriptome landscape of protein-coding genes and long noncoding RNAs in the colon and blood of DSS-induced mouse model of Acute ulcerative colitis

      Yarani, R., Palasca, Oana, Doncheva, Nadezhda Tsankova, Anthon, Christian, Pilecki, B., Litman, Thomas, Holmskov, U., Jensen, Lars Juhl, Gorodkin, Jan & Pociot, Flemming, 2019, In: Journal of Crohn's and Colitis. 13, p. S129-S130

      Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

    36. Published

      Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites

      Radhakrishnan, S., Wenzel, Anne, Novotny, P., Tang, X., Kalari, K. R. & Gorodkin, Jan, 2014, In: P L o S One. 9, 1, 16 p., e82699.

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

    37. Published

      Transcriptomic landscape of lncRNAs in inflammatory bowel disease

      Mirza, A. H., Bang-Berthelsen, C. H., Seemann, Ernst Stefan, Pan, X., Frederiksen, K. S., Vilien, M., Gorodkin, Jan & Pociot, Flemming, 2015, In: Genome Medicine. 7, 22 p., 39.

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

    38. 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

    39. Published

      Translational co-regulation of a ligand and inhibitor by a conserved RNA element

      Zaucker, A., Nagorska, A., Kumari, P., Hecker, N., Wang, Y., Huang, S., Cooper, L., Sivashanmugam, L., VijayKumar, S., Brosens, J., Gorodkin, Jan & Sampath, K., Jan 2018, In: Nucleic Acids Research. 46, 1, p. 104–119

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

    40. Published

      Translational control of furina by an RNA regulon is important for left-right patterning, heart morphogenesis and cardiac valve function

      Nagorska, A., Zaucker, A., Lambert, F., Inman, A., Toral-Perez, S., Gorodkin, Jan, Wan, Y., Smutny, M. & Sampath, K., 2023, In: Development (Cambridge). 150, 23, 15 p., 201657.

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

    41. Published

      Uncovering the anatomical and molecular landscape of the developing entorhinal cortex.

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

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

    42. 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

    43. Published

      Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

      Seemann, Ernst Stefan, Gorodkin, Jan & Backofen, R., 2008, In: Nucleic Acids Research. 36, 20, p. 6355-6362 8 p.

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

    44. Published

      Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities

      Sundfeld, D., Teodoro, G., Havgaard, Jakob Hull, Gorodkin, Jan & Melo, A. C. M. A., 2020, In: Concurrency Computation. 32, 10, e5468.

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

    45. Published

      Utilization of ESTs from Cassava: Progress on Development of EST-SSR Markers and an Oligo DNA Microarray

      Ingelbrecht, I. L., Jørgensen, Kirsten, Bak, Søren, Gorodkin, Jan, Raji, A., Winter, S., Lokko, Y., Gedil, M., Anderson, J. V. & Møller, Birger Lindberg, 2008.

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

    46. 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

    47. Published

      Warburg Effect Metabolism Drives Neoplasia in a Drosophila Genetic Model of Epithelial Cancer

      Eichenlaub, T., Villadsen, René, Freitas, F. C. P., Andrejeva, Diana, Aldana, Blanca, Nguyen, H. T., Petersen, Ole William, Gorodkin, Jan, Herranz, Hector & Cohen, S. M., 2018, In: Current Biology. 28, 20, p. 3220-3228.e6

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

    48. Published

      WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.

      Pan, X., Xiong, K., Anthon, Christian, Hyttel, P., Freude, Kristine, Jensen, Lars Juhl & Gorodkin, Jan, 6 Nov 2018, In: Genes. 9, 11, 11 p., 536.

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

    49. Published

      iPSC-derived Microglia for Disease Modeling of Frontotemporal Dementia 3

      Haukedal, H., Freude, Kristine, Garcia, B. A., Corsi, G., Gadekar, V. & Gorodkin, Jan, 2021, In: Glia. 69, S1, p. E480-E481 T14-066D.

      Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

    50. 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

    51. Published

      tmRDB (tmRNA database)

      Zwieb, C., Gorodkin, Jan, Knudsen, B., Burks, J. & Wower, J., 2003, In: Nucleic Acids Research. 31, 1, p. 446-447 2 p.

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

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