Jan Gorodkin

Jan Gorodkin

Professor

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    1 - 151 out of 151Page size: 500
    1. 2024
    2. 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

    3. 2023
    4. 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 journal › Journal article › Research › peer-review

    5. 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 journal › Journal article › Research › peer-review

    6. 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 journal › Journal article › Research › peer-review

    7. Published

      Golgi fragmentation: One of the earliest organelle phenotypes in Alzheimer's disease neurons

      Haukedal, H., Corsi, G. I., Gadekar, V. P., Doncheva, N. T., Kedia, S., de Haan, N., Chandrasekaran, A., Jensen, P., Schiønning, P., Vallin, S., Marlet, F. R., Poon, A., Pires, C., Agha, F. K., Wandall, H. H., Cirera, S., Simonsen, A. H., Nielsen, T. T., Nielsen, J. E., Hyttel, P. & 7 others, Muddashetty, R., Aldana, Blanca, Gorodkin, Jan, Nair, D., Meyer, M., Larsen, M. R. & Freude, Kristine, 2023, In: Frontiers in Neuroscience. 17, 17 p., 1120086.

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

    8. 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

    9. 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

    10. 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

    11. 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

    12. 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

    13. 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

    14. 2022
    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

      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

    17. 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

    18. 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

    19. 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 journal › Review › Research › peer-review

    20. 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 journal › Journal article › Research › peer-review

    21. 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 journal › Journal article › Research › peer-review

    22. Published

      Massively targeted evaluation of therapeutic CRISPR off-targets in cells

      Pan, X., Qu, K., Yuan, H., Xiang, X., Anthon, C., Pashkova, L., Liang, X., Han, P., Corsi, G. I., Xu, F., Liu, P., Zhong, J., Zhou, Y., Ma, T., Jiang, H., Liu, J., Wang, J., Jessen, N., Bolund, L., Yang, H. & 5 others, Xu, X., Church, G. M., Gorodkin, Jan, Lin, L. & Luo, Y., 2022, In: Nature Communications. 13, 14 p., 4049.

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

    23. 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

    24. 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

    25. 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

    26. 2021
    27. 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 journal › Journal article › Research › peer-review

    28. 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

    29. 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 journal › Journal article › Research › peer-review

    30. 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 journal › Journal article › Research › peer-review

    31. 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 journal › Journal article › Research › peer-review

    32. Published

      Human pathways in animal models: possibilities and limitations

      Doncheva, Nadezhda Tsankova, Palasca, Oana, Yarani, R., Litman, Thomas, Anthon, Christian, Groenen, M. A. M., Stadler, P. F., Pociot, Flemming, Jensen, Lars Juhl & Gorodkin, Jan, 2021, In: Nucleic Acids Research. 49, 4, p. 1859-1871 13 p.

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

    33. Published

      Novel circRNA discovery in sheep shows evidence of high backsplice junction conservation

      Varela-Martínez, E., Corsi, G. I., Anthon, Christian, Gorodkin, Jan & Jugo, B. M., 2021, In: Scientific Reports. 11, 1, 11 p., 427.

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

    34. 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

    35. 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

    36. 2020
    37. Published

      Patient iPSC-Derived Neorons for Disease Modeling of Familiar Alzheimer's Disease with Mutations in Presenilin 1

      Haukedal, H., Poon, A. F., Jensen, P., Aldana, Blanca, Pires, C., Chandrasekaran, Abinaya, Christensen, S. K., Schiønning, P., Vallin, S., Simonsen, A. H., Nielsen, J., Dinnyes, A., Gorodkin, Jan, Ramakrishna, S., Muddashetty, R., Palakodeti, D., Hyttel, P., Waagepetersen, Helle S., Larsen, M. R. & Freude, Kristine, Oct 2020.

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

    38. 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

    39. 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

    40. 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

    41. 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

    42. 2019
    43. 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

    44. Published

      Patient iPSC-Derived Neurons for Disease Modeling of Familiar Alzheier's Disease with Mutations in Presenilin 1

      Haukedal, H., Poon, A. F., Jensen, P., Aldana, Blanca, Pires, C., Chandrasekaran, Abinaya, Christensen, S. K., Schiønning, P., Vallin, S., Simonsen, A. H., Nielsen, J., Dinnyes, A., Gorodkin, Jan, Ramakrishna, S., Muddashetty, R., Palakodeti, D., Hyttel, P., Waagepetersen, Helle S., Larsen, M. R. & Freude, Kristine, 26 Mar 2019.

      Research output: Contribution to conference › Poster › Communication

    45. 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 journal › Journal article › Research › peer-review

    46. 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 journal › Journal article › Research › peer-review

    47. 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 journal › Journal article › Research › peer-review

    48. Published

      Inferring disease-associated long non-coding RNAs using genome - wide tissue expression profiles

      Pan, X., Jensen, Lars Juhl & Gorodkin, Jan, 2019, In: Bioinformatics. 35, 9, p. 1494-1502 9 p.

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

    49. Published

      Production of stellate cells from induced pluripotent stem cells to study Alzheimer's disease pathology

      Mogus, L., 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, 2019. 1 p.

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

    50. 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

    51. 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

    52. 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

    53. 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

    54. 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

    55. 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

    56. 2018
    57. Published

      Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures

      Sabarinathan, R., Anthon, Christian, Gorodkin, Jan & Seemann, Ernst Stefan, 4 Dec 2018, In: Genes. 9, 12, 17 p., 604.

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

    58. 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

    59. 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

    60. 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

    61. 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

    62. Published

      Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

      Pan, X., Wenzel, Anne, Jensen, Lars Juhl & Gorodkin, Jan, 2018, In: PLoS ONE. 13, 8, 15 p., e0202369.

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

    63. 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

    64. Published

      Identification and characterization of novel conserved RNA structures in Drosophila

      Kirsch, Rebecca, Seemann, Ernst Stefan, Ruzzo, W. L., Cohen, S. M., Stadler, P. F. & Gorodkin, Jan, 2018, In: BMC Genomics. 19, 20 p., 899.

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

    65. 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

    66. 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

    67. 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

    68. 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

    69. 2017
    70. 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 journal › Journal article › Research › peer-review

    71. 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 journal › Journal article › Research › peer-review

    72. 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 journal › Journal article › Research › peer-review

    73. 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 proceeding › Article in proceedings › Research › peer-review

    74. Published

      RAIN: RNA-protein Association and Interaction Networks

      Junge, A., Refsgaard, J. C., Garde, C., Pan, X., Santos, A., Alkan, F., Anthon, Christian, von Mering, C., Workman, C. T., Jensen, Lars Juhl & Gorodkin, Jan, 2017, In: Database: The Journal of Biological Databases and Curation. 2017, 9 p., baw167.

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

    75. 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

    76. 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

    77. 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

    78. 2016
    79. Published

      Joint profiling of miRNAs and mRNAs reveals miRNA mediated gene regulation in the Göttingen minipig obesity model

      Mentzel, Caroline M. Junker, Alkan, F., Keinicke, H., Jacobsen, M. J., Gorodkin, Jan, Fredholm, Merete & Cirera, Susanna, 30 Nov 2016, In: P L o S One. 11, 11, 16 p., e0167285.

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

    80. 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 journal › Conference abstract in journal › Research › peer-review

    81. 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 journal › Journal article › Research › peer-review

    82. 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 journal › Journal article › Research › peer-review

    83. 2015
    84. Published

      Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

      Sükösd, Z., Andersen, E. S., Seemann, Ernst Stefan, Jensen, M. K., Hansen, M., Gorodkin, Jan & Kjems, J., 2 Dec 2015, In: Nucleic Acids Research. 43, 21, p. 10168-79 12 p.

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

    85. Published

      Gender and obesity specific MicroRNA expression in adipose tissue from lean and obese pigs

      Mentzel, Caroline M. Junker, Anthon, Christian, Jacobsen, M. J., Karlskov-Mortensen, Peter, Bruun, Camilla Vibeke Sichlau, Jørgensen, Claus Bøttcher, Gorodkin, Jan, Cirera, Susanna & Fredholm, Merete, 29 Jul 2015, In: P L o S One. 10, 7, 19 p., e0131650.

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

    86. 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 journal › Journal article › Research › peer-review

    87. 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

    88. 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 journal › Journal article › Research › peer-review

    89. 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

    90. 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 journal › Journal article › Communication

    91. Published

      Optimizing RNA structures by sequence extensions using RNAcop

      Hecker, N., Christensen-Dalsgaard, M., Seemann, Ernst Stefan, Havgaard, Jakob Hull, Stadler, P. F., Hofacker, I. L., Nielsen, Henrik & Gorodkin, Jan, 2015, In: Nucleic Acids Research. 43, 17, p. 8135-8145 11 p.

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

    92. Published

      Quality Assessment of Domesticated Animal Genome Assemblies

      Seemann, Ernst Stefan, Anthon, Christian, Palasca, Oana & Gorodkin, Jan, 2015, In: Bioinformatics and Biology Insights. 9, Suppl 4, p. 49-58 10 p.

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

    93. Published

      RNA 3D modules in genome-wide predictions of RNA 2D structure

      Theis, C., Zirbel, C. L., Zu Siederdissen, C. H., Anthon, Christian, Hofacker, I. L., Nielsen, Henrik & Gorodkin, Jan, 2015, In: PLOS ONE. 10, 10, 13 p., e0139900.

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

    94. 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

    95. 2014
    96. 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

    97. 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 proceeding › Book chapter › Research › peer-review

    98. 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 proceeding › Book chapter › Research › peer-review

    99. 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 journal › Journal article › Research › peer-review

    100. Published

      Protein-driven inference of miRNA-disease associations

      Mørk, S., Pletscher-Frankild, S., Palleja, A., Gorodkin, Jan & Jensen, Lars Juhl, 2014, In: Bioinformatics (Oxford, England). 30, 3, p. 392-397 6 p.

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

    101. Published

      RNA Structural Alignments, Part I: Sankoff-Based Approaches for Structural Alignments

      Havgaard, Jakob Hull & Gorodkin, Jan, 2014, RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Gorodkin, J. & Ruzzo, W. L. (eds.). p. 275-90 16 p. (Methods in molecular biology (Clifton, N.J.)).

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

    102. 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

    103. 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

    104. 2013
    105. 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

    106. 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 journal › Journal article › Research › peer-review

    107. Published

      Global Analysis of Genetic and Epigenetic differences associated with Obesity

      Jacobsen, M. J., Mentzel, Caroline M. Junker, Kogelman, L., Mark, T., Karlskov-Mortensen, Peter, Bruun, Camilla Vibeke Sichlau, Cirera, Susanna, Gorodkin, Jan, Kadarmideen, H., Barrès, Romain, Jørgensen, Claus Bøttcher & Fredholm, Merete, 2013.

      Research output: Contribution to conference › Poster › Research › peer-review

    108. 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

    109. 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

    110. 2012
    111. Published

      Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae

      Podolska, A., Anthon, Christian, Bak, M., Tommerup, Niels, Skovgaard, K., Heegaard, P. M., Gorodkin, Jan, Cirera, S. & Fredholm, Merete, Sep 2012, In: B M C Genomics. 13, 1, p. 459

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

    112. 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

    113. 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 journal › Journal article › Research › peer-review

    114. 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

    115. 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

    116. 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

    117. 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

    118. 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

    119. 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

    120. 2011
    121. 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

    122. 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

    123. 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

    124. 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

    125. 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

    126. 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

    127. 2010
    128. Published

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

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

      Research output: Contribution to conference › Poster › Research

    129. Published

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

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

      Research output: Contribution to conference › Poster › Research

    130. 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

    131. 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

    132. 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

    133. 2009
    134. Published

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

      Zagrobelny, M., 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

    135. Published

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

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

      Research output: Contribution to conference › Poster › Research

    136. 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

    137. 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

    138. 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

    139. 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

    140. 2008
    141. 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

    142. 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

    143. 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

    144. 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

    145. 2007
    146. 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 journal › Journal article › Research › peer-review

    147. 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 journal › Journal article › Research › peer-review

    148. 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 journal › Journal article › Research › peer-review

    149. Published

      Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

      Karlskov-Mortensen, Peter, Hu, Z. L., Gorodkin, Jan, Reecy, J. M. & Fredholm, Merete, 2007, In: Animal Genetics. 38, 4, p. 401-405 5 p.

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

    150. Published

      Multiple structural alignment and clustering of RNA sequences: sequence analysis

      Torarinsson, E., Havgaard, Jakob Hull & Gorodkin, Jan, 2007, In: Bioinformatics. 23, 8, p. 926-32 7 p.

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

    151. Published

      Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

      Gorodkin, J., Cirera, S., Hedegaard, J., Gilchrist, M. J., Panitz, F., Jørgensen, C., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T., Nielsen, B., Havgaard, J. H., Rosenkilde, C., Wang, J., Li, H., Li, R., Liu, B., Hu, S., Dong, W. & 16 others, Li, W., Yu, J., Wang, J., Staefeldt, H., Wernersson, R., Madsen, L. B., Thomsen, B. S., Hornshøj, H., Bujie, Z., Wang, X., Wang, X., Bolund, L., Brunak, Søren, Yang, H., Bendixen, C. & Fredholm, Merete, 2007, In: Genome Biology. 8, R45, p. R45 16 p.

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

    152. Published

      Principles and limitations of computational microRNA gene and target finding

      Lindow, M. & Gorodkin, Jan, 2007, In: DNA and Cell Biology. 26, 5, p. 339-351 13 p.

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

    153. 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

    154. 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

    155. 2006
    156. Published

      Linkage mapping of gene-associated SNPs to pig chromosome 11

      Sawera, M., Cirera, Susanna, Jørgensen, Claus Bøttcher, Gorodkin, Jan & Fredholm, Merete, 2006, In: Animal Genetics. 37, 3, p. 199-204 6 p.

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

    157. Published

      MicroRNA sequence motifs reveal asymmetry between the stem arms

      Gorodkin, Jan, Havgaard, Jakob Hull, Ensterö, M., Sawera, M., Jensen, P., Öhman, M. & Fredholm, Merete, 2006, In: Computational Biology and Chemistry. 30, 4, p. 249-254 6 p.

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

    158. 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

    159. 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

    160. 2005
    161. 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 journal › Journal article › Research › peer-review

    162. Published

      Mapping and expression studies of the mir17-92 cluster on pig chromosome 11

      Sawera, M., Gorodkin, Jan, Cirera, Susanna & Fredholm, Merete, 2005, In: Mammalian Genome. 16, 8, p. 594-598 5 p.

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

    163. Published

      Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

      Havgaard, Jakob Hull, Lyngsø, R. B., Stormo, G. D. & Gorodkin, Jan, 2005, In: Bioinformatics. 21, 9, p. 1815-1824 10 p.

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

    164. Published

      Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing

      Wernersson, R., Schierup, M. H., Jørgensen, F. G., Gorodkin, J., Panitz, F., Stærfeldt, H-H., Christensen, O. F., Mailund, T., Hornshøj, H., Klein, A., Wang, J., Liu, B., Hu, S., Dong, W., Li, W., Wong, G. K. S., Yu, J., Wang, J., Bendixen, C., Fredholm, M. & 3 others, Brunak, S., Yang, H. & Bolund, L., 2005, In: BMC Genomics. 70, 6, p. 1-7 7 p.

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

    165. Published

      Pigs in sequence space: a 0.66X coverage Sino-Danish pig genome survey

      Rasmus, W., Schierup, M. H., Jørgensen, F. G., Gorodkin, Jan, Panitz, F., Stærfeldt, H., Christensen, O. F., Mailund, T., Hornshøj, H., Klein, A., Wang, J., Wong, G. K. S., Yu, J., Wang, J., Bendixen, C., Fredholm, Merete, Brunak, S., Yang, H. & Bolund, L., 2005. 1 p.

      Research output: Contribution to conference › Poster › Research

    166. 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

    167. 2004
    168. 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 journal › Journal article › Research › peer-review

    169. 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 journal › Journal article › Research › peer-review

    170. 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

    171. 2003
    172. 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

    173. 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

    ID: 4356276