Jan Gorodkin

Jan Gorodkin

Professor

Member of:


    1. 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 journalJournal articleResearchpeer-review

    2. Published
    3. Published
    4. 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 journalJournal articleResearchpeer-review

    5. Published

      De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences

      Ruzzo, W. L. & Gorodkin, Jan, 2014, RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin, J. & Ruzzo, W. L. (eds.). Vol. 1097. p. 303-18 16 p. (Methods in molecular biology (Clifton, N.J.)).

      Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

    6. Published

      A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: Identification of synteny breakpoints

      Lahbib-Mansais, Y., Karlskov-Mortensen, Peter, Mompart, F., Milan, D., Jørgensen, Claus Bøttcher, Cirera, Susanna, Gorodkin, Jan, Faraut, T., Yerle, M. & Fredholm, Merete, 2005, In: Genomics. 86, 4, p. 405-413 9 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    7. Published

      A non-enzymatic, isothermal strand displacement and amplification assay for rapid detection of SARS-CoV-2 RNA

      Mohammadniaei, M., Zhang, M., Ashley, J., Christensen, U. B., Friis-Hansen, L. J., Gregersen, R., Lisby, J. G., Benfield, Thomas, Nielsen, F. E., Henning Rasmussen, J., Pedersen, E. B., Olinger, A. C. R., Kolding, L. T., Naseri, M., Zheng, T., Wang, W., Gorodkin, Jan & Sun, Y., 2021, In: Nature Communications. 12, 5089.

      Research output: Contribution to journalJournal articleResearchpeer-review

    8. Published

      A splice-site variant in the lncRNA gene RP1-140A9.1 cosegregates in the large Volkmann cataract family

      Eiberg, Hans Rudolf Lytchoff, Mikkelsen, Annemette Friis, Bak, M., Tommerup, Niels, Lund, A. M., Wenzel, Anne, Sabarinathan, R., Gorodkin, Jan, Bang-Berthelsen, C. H. & Hansen, Lars, 2019, In: Molecular Vision. 25, p. 1-11 11 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    9. 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 journalJournal articleResearchpeer-review

    10. Published

      Adipocyte gene expression and DNA methylation patterns differ significantly between lean and obese pigs

      Jacobsen, M. J., Havgaard, Jakob Hull, Mentzel, Caroline M. Junker, Sørensen, P. M., Pundhir, Sachin, Anthon, Christian, Karlskov-Mortensen, Peter, Bruun, Camilla Vibeke Sichlau, Cirera, Susanna, Gorodkin, Jan, Jørgensen, Claus Bøttcher, Barrès, Romain & Fredholm, Merete, 9 Nov 2016, In: Journal of Animal Science. 94, Supplement 4, p. 46-47 2 p., P2019.

      Research output: Contribution to journalConference abstract in journalResearchpeer-review

    11. Published

      Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

      Kato, Y., Gorodkin, Jan & Havgaard, Jakob Hull, Dec 2017, In: BMC Genomics. 18, 1, 935.

      Research output: Contribution to journalJournal articleResearchpeer-review

    12. Published

      Alteration of microglial metabolism and inflammatory profile contributes to neurotoxicity in a hiPSC-derived microglia model of frontotemporal dementia 3

      Haukedal, H., Syshøj Lorenzen, S., Westi, Emil Winther, Corsi, G., Gadekar, V. P., McQuade, A., Davtyan, H., Doncheva, Nadezhda Tsankova, Schmid, B., Chandrasekaran, Abinaya, Seemann, Ernst Stefan, Cirera, Susanna, Blurton-Jones, M., Meyer, M., Gorodkin, Jan, Aldana, Blanca & Freude, Kristine, 2023, In: Brain, Behavior, and Immunity. 113, p. 353-373

      Research output: Contribution to journalJournal articleResearchpeer-review

    13. Published

      Analyses of pig genomes provide insight into porcine demography and evolution

      Groenen, M. A., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H-J., Li, S., Larkin, D. M., Kim, H., Frantz, L. A. F., Caccamo, M., Ahn, H., Aken, B. L., Anselmo, A., Anthon, C., Auvil, L. & 116 others, Badaoui, B., Beattie, C. W., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Zhan, B., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S., Chow, W., Clark, R. C., Clee, C., Crooijmans, R. P. M. A., Dawson, H. D., Dehais, P., Sapio, F. D., Dibbits, B., Drou, N., Du, Z., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G. J., Fowler, K. E., Fredholm, Merete, Fritz, E., Gilbert, J. G. R., Giuffra, E., Gorodkin, Jan, Griffin, D. K., Harrow, J. L., Hayward, A., Howe, K., Hu, Z., Humphray, S. J., Hunt, T., Jensen, H. H., Jeon, J., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J., Kim, K., Kim, T., Larson, G., Lee, K., Lee, K., Leggett, R., Lewin, H. A., Li, Y., Liu, W., Loveland, J. E., Lu, Y., Lunney, J. K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M. P., Narayan, J., Nguyen, D. T., Ni, P., Oh, S., Onteru, S., Panitz, F., Park, E., Park, H., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J. M., Rodriguez-Zas, S., Rohrer, G. A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J. G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B. R., Sperber, G., Stadler, P., Sweedler, J. V., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerke, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C. & Schook, L. B., 2012, In: Nature. 491, 7424, p. 393-398 6 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    14. Published

      Assessing the miRNA sponge potential of RUNX1T1 in t(8;21) acute myeloid leukemia

      Junge, A., Zandi, R., Havgaard, Jakob Hull, Gorodkin, Jan & Cowland, J. B., 2017, In: Gene. 615, p. 35-40 6 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    15. Published

      Associating transcription factors and conserved RNA structures with gene regulation in the human brain

      Hecker, N., Seemann, Ernst Stefan, Silahtaroglu, Asli, Ruzzo, W. L. & Gorodkin, Jan, 2017, In: Scientific Reports. 7, 1, 16 p., 5776.

      Research output: Contribution to journalJournal articleResearchpeer-review

    16. 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 journalJournal articleResearchpeer-review

    17. Published

      Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

      Theis, C., Höner zu Siederdissen, C., Hofacker, I. L. & Gorodkin, Jan, 2013, In: Nucleic Acids Research. 41, 22, p. 9999-10009 11 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    18. Published

      Bsgatlas: A unified bacillus subtilis genome and transcriptome annotation atlas with enhanced information access

      Geissler, Adrian Sven, Anthon, Christian, Alkan, F., González-Tortuero, E., Poulsen, L. D., Kallehauge, T. B., Breüner, A., Seemann, Ernst Stefan, Vinther, Jeppe & Gorodkin, Jan, 2021, In: Microbial Genomics. 7, 2, 17 p., 000524.

      Research output: Contribution to journalJournal articleResearchpeer-review

    19. 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 journalJournal articleResearchpeer-review

    20. 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 journalJournal articleResearchpeer-review

    21. Published

      CRISPRi screen for enhancing heterologous alpha-amylase yield in Bacillus subtilis

      Geissler, Adrian Sven, Fehler, A. O., Poulsen, L. D., Gonzalez-Tortuero, E., Kallehauge, T. B., Alkan, F., Anthon, Christian, Seemann, Ernst Stefan, Rasmussen, M. D., Breuener, A., Hjort, C., Vinther, Jeppe & Gorodkin, Jan, 2023, In: Journal of Industrial Microbiology and Biotechnology. 50, 1, 16 p., kuac028.

      Research output: Contribution to journalJournal articleResearchpeer-review

    22. 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 journalJournal articleResearchpeer-review

    23. 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 journalJournal articleResearchpeer-review

    24. Published

      CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment

      Sundfeld, D., Havgaard, Jakob Hull, Gorodkin, Jan & De Melo, A. C. M. A., 2017, Proceedings: 2017 25th Euromicro International Conference on Parallel, Distributed and Network-Based Processing, PDP 2017. IEEE, p. 295-302 8 p. 7912663

      Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

    25. 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 proceedingBook chapterResearchpeer-review

    26. 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 journalJournal articleResearchpeer-review

    27. 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 journalJournal articleResearchpeer-review

    28. Published

      Comparing two K-category assignments by a K-category correlation coefficient

      Gorodkin, Jan, 2004, In: Computational Biology and Chemistry. 28, 5-6, p. 367-374 8 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    29. Published

      Computational approaches for predicting mutation effects on RNA Sstructure

      Radhakrishnan, S. & Gorodkin, Jan, 2014, Bioinformatics. Persson, B. (ed.). Elsevier, p. 111-121 11 p. (Comprehensive biomedical physics, Vol. 6).

      Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

    30. Published

      Concepts and introduction to RNA bioinformatics

      Gorodkin, Jan, Hofacker, I. L. & Ruzzo, W. L., 2014, In: Methods in molecular biology (Clifton, N.J.). 1097, p. 1-31 31 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    31. Published

      Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis

      Yarani, R., Palasca, Oana, Doncheva, Nadezhda Tsankova, Anthon, Christian, Pilecki, B., Svane, C. A. S., Mirza, A. H., Litman, Thomas, Holmskov, U., Bang-Berthelsen, C. H., Vilien, M., Jensen, Lars Juhl, Gorodkin, Jan & Pociot, Flemming, 2023, In: Frontiers in Molecular Biosciences. 9, 1081176.

      Research output: Contribution to journalJournal articleResearchpeer-review

    32. Published

      Cytoscape stringApp: Network analysis and visualization of proteomics data

      Doncheva, Nadezhda Tsankova, Morris, J., Gorodkin, Jan & Jensen, Lars Juhl, 2019, In: Journal of Proteome Research. 18, 2, p. 623-632

      Research output: Contribution to journalJournal articleResearchpeer-review

    33. 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 journalJournal articleResearchpeer-review

    34. Published

      Detection of RNA structures in porcine EST data and related mammals

      Seemann, Ernst Stefan, Gilchrist, M. J., Hofacker, I. L., Stadler, P. F. & Gorodkin, Jan, 2007, In: BMC Genomics. 8, 316, 17 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    35. Published

      Development of the entorhinal cortex occurs via parallel lamination during neurogenesis

      Liu, Y., Bergmann, T., Mori, Yuki, Peralvo Vidal, Juan Miguel, Pihl, M., Vasistha, Navneet A, Thomsen, Preben Dybdahl, Seemann, Ernst Stefan, Gorodkin, Jan, Hyttel, P., Khodosevich, Konstantin, Witter, M. P. & Hall, Vanessa Jane, 2021, In: Frontiers in Neuroanatomy. 15, 19 p., 663667.

      Research output: Contribution to journalJournal articleResearchpeer-review

    36. Published

      Differential and coherent processing patterns from small RNAs

      Pundhir, Sachin & Gorodkin, Jan, 13 Jul 2015, In: Scientific Reports. 5, 16 p., 12062.

      Research output: Contribution to journalJournal articleResearchpeer-review

    37. Published

      Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells: [Plus] Corrigendum

      Hölzer, M., Krähling, V., Amman, F., Barth, E., Bernhart, S. H., Carmelo, V. A. O., Collatz, M., Doose, G., Eggenhofer, F., Ewald, J., Fallmann, J., Feldhahn, L. M., Fricke, M., Gebauer, J., Gruber, A. J., Hufsky, F., Indrischek, H., Kanton, S., Linde, J., Mostajo, N. & 19 others, Ochsenreiter, R., Riege, K., Rivarola-Duarte, L., Sahyoun, A. H., Saunders, S. J., Seemann, Ernst Stefan, Tanzer, A., Vogel, B., Wehner, S., Wolfinger, M. T., Backofen, R., Gorodkin, Jan, Grosse, I., Hofacker, I., Hoffmann, S., Kaleta, C., Stadler, P. F., Becker, S. & Marz, M., 7 Oct 2016, In: Scientific Reports. 6, 16 p., 34589.

      Research output: Contribution to journalJournal articleResearchpeer-review

    38. Published

      Differentially Expressed miRNAs in Ulcerative Colitis and Crohn's Disease

      Yarani, R., Shojaeian, A., Palasca, Oana, Doncheva, Nadezhda Tsankova, Jensen, Lars Juhl, Gorodkin, Jan & Pociot, Flemming, 2022, In: Frontiers in Immunology. 13, 21 p., 865777.

      Research output: Contribution to journalReviewResearchpeer-review

    39. 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 journalJournal articleResearchpeer-review

    40. Published

      Does rapid sequence divergence preclude RNA structure conservation in vertebrates?

      Seemann, Ernst Stefan, Mirza, A. H., Bang-Berthelsen, C. H., Garde, C., Christensen-Dalsgaard, M., Workman, C. T., Pociot, Flemming, Tommerup, Niels, Gorodkin, Jan & Ruzzo, W. L., 2022, In: Nucleic Acids Research. 50, 5, p. 2452-2463 12 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    41. Published

      EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues

      Scheibye-Alsing, K., Cirera, Susanna, Gilchrist, M. J., Fredholm, Merete & Gorodkin, Jan, 2007, In: BMC Genomics. 8, 367, 13 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    42. Published

      Emerging applications of read profiles towards the functional annotation of the genome

      Pundhir, Sachin, Poirazi, P. & Gorodkin, Jan, 19 May 2015, In: Frontiers in Genetics. 6, 11 p., 188.

      Research output: Contribution to journalJournal articleResearchpeer-review

    43. Published

      Emerging tools for RNA structure analysis in polymorphic data

      Radhakrishnan, S., Seemann, Ernst Stefan & Gorodkin, Jan, 2015, In: Biozoom. 2, p. 10-13 4 p.

      Research output: Contribution to journalJournal articleCommunication

    44. Published

      Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

      Xiang, X., Corsi, G. I., Anthon, C., Qu, K., Pan, X., Liang, X., Han, P., Dong, Z., Liu, L., Zhong, J., Ma, T., Wang, J., Zhang, X., Jiang, H., Xu, F., Liu, X., Xu, X., Wang, J., Yang, H., Bolund, L. & 4 others, Church, G. M., Lin, L., Gorodkin, Jan & Luo, Y., 2021, In: Nature Communications. 12, 1, 9 p., 3238.

      Research output: Contribution to journalJournal articleResearchpeer-review

    45. Published

      Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism

      Jacobsen, M. J., Havgaard, Jakob Hull, Anthon, Christian, Mentzel, Caroline M. Junker, Cirera, Susanna, Krogh, P. M., Pundhir, Sachin, Karlskov-Mortensen, Peter, Bruun, C. S., Lesnik, P., Guerin, M., Gorodkin, Jan, Jørgensen, Claus Bøttcher, Fredholm, Merete & Barrès, Romain, 2019, In: Frontiers in Genetics. 10, 13 p., 1268.

      Research output: Contribution to journalJournal articleResearchpeer-review

    46. Published

      Evolutionary rate variation and RNA secondary structure prediction

      Knudsen, B., Andersen, E. S., Damgaard, C., Kjems, J. & Gorodkin, Jan, 2004, In: Computational Biology and Chemistry. 28, 3, p. 219-226 8 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    47. 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 journalJournal articleResearchpeer-review

    48. Published

      Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

      Havgaard, Jakob Hull, Torarinsson, E. & Gorodkin, Jan, 2007, In: PLoS Computational Biology. 3, 10, p. 1896-1908 13 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

    49. Published

      Flagella disruption in Bacillus subtilis increases amylase production yield

      Fehler, A. O., Kallehauge, T. B., Geissler, Adrian Sven, González-Tortuero, E., Seemann, Ernst Stefan, Gorodkin, Jan & Vinther, Jeppe, 2022, In: Microbial Cell Factories. 21, 11 p., 131.

      Research output: Contribution to journalJournal articleResearchpeer-review

    50. Published

      Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

      Sundfeld, D., Havgaard, Jakob Hull, de Melo, A. C. M. A. & Gorodkin, Jan, 2016, In: Bioinformatics. 32, 8, p. 1238-1240 3 p.

      Research output: Contribution to journalJournal articleResearchpeer-review

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