Computational and RNA Biology

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  1. Published

    CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

    Pan, X., Ma, Z., Sun, X., Li, H., Zhang, T., Zhao, C., Wang, N., Heller, Rasmus, Hung Wong, W., Wang, W., Jiang, Y. & Wang, Y., 2023, In: Genomics, Proteomics and Bioinformatics. 21, 3, p. 632-648 17 p.

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

  2. Published

    CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties

    Lillestøl, R. K., Shah, S. A., Brügger, K., Redder, P., Phan, Safir Hien, Christiansen, Jan & Garrett, Roger Antony, 2009, In: Molecular Microbiology. 72, 1, p. 259-272

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

  3. Published

    CRISPR-Cas adaptive immune systems of the sulfolobales: unravelling their complexity and diversity

    Garrett, Roger Antony, Shah, S. A., Erdmann, S., Guannan, L., Mousaei, M., León Sobrino, C., Peng, W., Islin, S. R., Deng, Ling, Vestergaard, G., Peng, Xu & She, Q., 2015, In: Life. 5, 1, p. 783-817 35 p.

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

  4. 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

  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

    CTCF-KDM4A complex correlates with histone modifications that negatively regulate CHD5 gene expression in cancer cell lines

    Guerra-Calderas, L., González-Barrios, R., Patiño, C. C., Alcaraz, N., Salgado-Albarrán, M., de León, D. C., Hernández, C. C., Sánchez-Pérez, Y., Maldonado-Martínez, H. A., De la Rosa-Velazquez, I. A., Vargas-Romero, F., Herrera, L. A., García-Carrancá, A. & Soto-Reyes, E., 2018, In: OncoTarget. 9, 24, p. 17028-17042 15 p.

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

  7. Published

    CTLs' repertoire shaping in the thymus: a Monte Carlo simulation

    Castiglione, F., Santoni, D. & Rapin, N. P. J., 2011, In: Autoimmunity. 44, 4, p. 261-270 10 p.

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

  8. Published

    Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data

    Korneliussen, Thorfinn Sand, Moltke, Ida, Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: B M C Bioinformatics. 14, 14 p., 289.

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

  9. Published

    Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

    Stovgaard, K., Andreetta, C., Ferkinghoff-Borg, J. & Hamelryck, Thomas Wim, 1 Jan 2010, In: B M C Bioinformatics. 11, p. 429

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

  10. Published

    Calibrated uncertainty for molecular property prediction using ensembles of message passing neural networks

    Busk, J., Jørgensen, P. B., Bhowmik, A., Schmidt, M. N., Winther, Ole & Vegge, T., 2022, In: Machine Learning: Science and Technology. 3, 1, 12 p., 015012.

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

  11. Published

    Can large language models reason about medical questions?

    Liévin, V., Hother, C. E., Motzfeldt, A. G. & Winther, Ole, 2024, In: Patterns. 5, 3, 12 p., 100943.

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

  12. Published

    Can small wildlife conservancies maintain genetically stable populations of large mammals? Evidence for increased genetic drift in geographically restricted populations of Cape buffalo in East Africa

    Heller, Rasmus, Okello, J. B. A. & Siegismund, Hans Redlef, 2010, In: Molecular Ecology. 19, 7, p. 1324-34 10 p.

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

  13. Published

    Cancer Cell Acid Adaptation Gene Expression Response is Correlated to Tumor-Specific Tissue Expression Profiles and Patient Survival

    Yao, Jiayi, Czaplinska, D., Ialchina, Renata, Schnipper, J., Liu, B., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2020, In: Cancers. 12, 8, 27 p., 2183.

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

  14. Published

    Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa

    Enroth, S., Rada-Iglesisas, A., Andersson, Robin, Wallerman, O., Wanders, A., Påhlman, L., Komorowski, J. & Wadelius, C., 2011, In: B M C Cancer. 11, 13 p., 450.

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

  15. Published

    Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin

    Vikeså, J., Møller, A. K. H., Kaczkowski, B., Helweg-Larsen, R. B., Winther, Ole, Henao Giraldo, R., Krogh, Anders, Perell, K., Jensen, F., Daugaard, G. & Nielsen, Finn Cilius, 2015, In: B M C Cancer. 15, 14 p., 151.

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

  16. Published

    Cape buffalo mitogenomics reveals a holocene shift in the African human-megafauna dynamics

    Heller, Rasmus, Brüniche-Olsen, A. & Siegismund, Hans Redlef, 2012, In: Molecular Ecology. 21, 16, p. 3947-3959 13 p.

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

  17. Published

    Cardiovascular Autonomic Neuropathy in Type 1 Diabetes Is Associated With Disturbances in TCA, Lipid, and Glucose Metabolism

    Hansen, C. S., Suvitaival, T., Theilade, Karen Simone, Mattila, I., Lajer, M., Trošt, K., Ahonen, L., Hansen, T. W., Legido-Quigley, C., Rossing, Peter & Ahluwalia, Tarun Veer Singh, 2022, In: Frontiers in Endocrinology. 13, 831793.

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

  18. Published

    Cardiovascular autonomic neuropathy and the impact on progression of diabetic kidney disease in type 1 diabetes

    Bjerre-Christensen, T., Winther, S. A., Tofte, N., Theilade, S., Ahluwalia, Tarun Veer Singh, Lajer, M., Hansen, T. W., Rossing, Peter & Hansen, C. S., 2021, In: B M J Open Diabetes Research & Care. 9, 1, 9 p., e002289.

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

  19. Published

    Catalytic residues Lys197 and Arg199 of Bacillus subtilis phosphoribosyl diphosphate synthase. Alanine-scanning mutagenesis of the flexible catalytic loop.

    Hove-Jensen, B., Bentsen, A. K. & Harlow, K. W., 2005, In: FEBS Journal. 272, 14, p. 3631-9 8 p.

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

  20. Published

    Catchment properties and the photosynthetic trait composition of freshwater plant communities

    Iversen, L. L., Winkel, A., Baastrup-Spohr, L., Hinke, A. B., Alahuhta, J., Baattrup-Pedersen, A., Birk, S., Brodersen, P., Chambers, P. A., Ecke, F., Feldmann, T., Gebler, D., Heino, J., Jespersen, T. S., Moe, S. J., Riis, T., Sass, L., Vestergaard, O., Maberly, S. C., Sand-jensen, K. & 1 others, Pedersen, Ole, 2019, In: Science. 366, 6467, p. 878-881 4 p.

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

  21. Published

    Cellular inhibitor of apoptosis protein 2 controls human colonic epithelial restitution, migration, and Rac1 activation

    Seidelin, Jakob Benedict, Larsen, S., Linnemann, D., Vainer, B., Coskun, M., Troelsen, J. T. & Nielsen, Ole Haagen, Jan 2015, In: American Journal of Physiology: Gastrointestinal and Liver Physiology. 308, 2, p. G92-G99 8 p.

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

  22. Published

    Cellular origin of prognostic chromosomal aberrations in AML patients

    Mora-Jensen, H., Jendholm, L. J., Rapin, N. P. J., Andersen, M. K., Roug, A. S., Bagger, F. O., Bullinger, L., Winther, Ole, Borregaard, N., Porse, Bo Torben & Theilgaard-Mønch, Kim, 11 Feb 2015, In: Leukemia. 29, p. 1785-1789 5 p.

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

  23. Published

    Challenges for serology-based characterization of foot-and-mouth disease outbreaks in endemic areas; identification of two separate lineages of serotype O FMDV in Uganda in 2011

    Namatovu, A., Belsham, G. J., Ayebazibwe, C., Dhikusooka, M. T., Wekesa, S. N., Siegismund, Hans Redlef, Muwanika, V. B. & Tjørnehøj, K., 2015, In: Transboundary and Emerging Diseases. 62, 5, p. 522-534 13 p.

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

  24. Published

    Characterisation of recent foot-and-mouth disease viruses from African buffalo ( Syncerus caffer ) and cattle in Kenya is consistent with independent virus populations

    Wekesa, S., Sangula, A., Belsham, G. J., Tjornehoj, K., Muwanika, V. B., Gakuya, F., Mijele, D. & Siegismund, Hans Redlef, 2015, In: B M C Veterinary Research. 11, 17.

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

  25. Published

    Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways

    Thieffry, A., Vigh, Maria Louisa, Lange, Jette Bornholdt, Ivanov, M., Brodersen, Peter & Sandelin, Albin Gustav, 2020, In: The Plant Cell. 32, 6, p. 1845-1867 23 p.

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

  26. Published

    Characterization of different crystal forms of the a-glucosidase MalA from Sulfolobus solfataricus

    Ernst, H. A., Willemoës, Martin, Lo Leggio, Leila, Leonard, G., Blum, P. & Larsen, Sine, 2005, In: Acta Crystallographica Section F. 61, p. 1039-1042

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

  27. Published

    Characterization of different crystal forms of the alpha-glucosidase MalA from Sulfolobus solfataricus

    Ernst, H. A., Willemoës, Martin, Lo Leggio, Leila, Leonard, G., Blum, P. & Larsen, Sine, 2005, In: Acta Crystallographica. Section F : Structural Biology and Crystallization Communications. 61, Pt 12, p. 1039-42 3 p.

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

  28. Published

    Characterization of foot-and-mouth disease viruses (FMDVs) from Ugandan cattle outbreaks during 2012-2013: evidence for circulation of multiple serotypes

    Namatovu, A., Tjørnehøj, K., Belsham, G. J., Dhikusooka, M. T., Wekesa, S. N., Muwanika, V. B., Siegismund, Hans Redlef & Ayebazibwe, C., 2015, In: PloS one. 10, 2, 17 p., e0114811.

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

  29. Published

    Characterization of industrially-produced Lacticaseibacillus rhamnosus GG and Lactobacillus acidophilus LA-5: Analysis of genomic integrity, transcriptome and phenotypes

    Strickertsson, Marianne Stage, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 206 p.

    Research output: Book/Report › Ph.D. thesis › Research

  30. Published

    Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

    Boyd, M., Thodberg, M., Vitezic, M., Lange, J. B., Vitting-Seerup, K., Chen, Y., Coskun, M., Li, Y., Lo, B. Z. S., Klausen, P., Schweiger, P., Pedersen, A. G., Rapin, N. P. J-P., Skovgaard, K., Dahlgaard, K., Andersson, R., Terkelsen, T. B., Lilje, B., Troelsen, J. T., Petersen, A. M. & 7 others, Jensen, Kim Bak, Gögenur, Ismail, Thielsen, P., Seidelin, Jakob Benedict, Nielsen, Ole Haagen, Bjerrum, Jakob Tveiten & Sandelin, Albin Gustav, 2018, In: Nature Communications. 9, 19 p., 1661.

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

  31. Published

    Characterization of the human RFX transcription factor family by regulatory and target gene analysis

    Sugiaman-Trapman, D., Vitezic, M., Jouhilahti, E., Mathelier, A., Lauter, G., Misra, S., Daub, C. O., Kere, J. & Swoboda, P., 2018, In: BMC Genomics. 19, 15 p., 181.

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

  32. Published

    Characterizing glucokinase variant mechanisms using a multiplexed abundance assay

    Gersing, S., Schulze, Thea Klarsø, Cagiada, Matteo, Stein, Amelie, Roth, F. P., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2024, In: Genome Biology. 25, 1, 22 p., 98.

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

  33. Published

    Characterizing leader sequences of CRISPR loci

    Alkhnbashi, O., Shah, S. A., Garrett, Roger Antony, Saunders, S. J., Costa, F. & Backofen, R., 2016, In: Bioinformatics. 32, 17, p. i576-i585 10 p.

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

  34. Published

    Chimpanzee genomic diversity reveals ancient admixture with bonobos

    de Manuel, M., Kuhlwilm, M., Frandsen, P., Sousa, V. C., Desai, T., Prado-Martinez, J., Hernandez-Rodriguez, J., Dupanloup, I., Lao, O., Hallast, P., Schmidt, J. M., Heredia-Genestar, J. M., Benazzo, A., Barbujani, G., Peter, B. M., Kuderna, L. F. K., Casals, F., Angedakin, S., Arandjelovic, M., Boesch, C. & 17 others, Kühl, H., Vigilant, L., Langergraber, K., Novembre, J., Gut, M., Gut, I., Navarro, A., Carlsen, F., Andrés, A. M., Siegismund, Hans Redlef, Scally, A., Excoffier, L., Tyler-Smith, C., Castellano, S., Xue, Y., Hvilsom, C. & Marques-Bonet, T., 2016, In: Science. 354, 6311, p. 477-481 5 p.

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

  35. Published

    Chirality in microbial biofilms is mediated by close interactions between the cell surface and the substratum

    Jauffred, Liselotte, Vejborg, R. M., Korolev, K. S., Brown, Stanley & Oddershede, L. B., 14 Apr 2017, In: I S M E Journal. 11, 7, p. 1688-1701

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

  36. Published

    Chlorosomes: The light-harvesting complexes of green bacteria

    Vassilieva, E. V., Frigaard, Niels-Ulrik & Bryant, D. A., 2000, In: The Spectrum. 13, p. 7-13

    Research output: Contribution to journal › Journal article › Research

  37. Published

    Chromatin image-driven modelling

    Kadlof, M., Banecki, K., Chilinski, Mateusz & Plewczynski, D., 2024, In: Methods. 226, p. 54-60 7 p.

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

  38. Published

    Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression

    Garland, W., Müller, I., Wu, M., Schmid, M., Imamura, K., Rib, Leonor, Sandelin, Albin Gustav, Helin, K. & Jensen, T. H., 2022, In: Molecular Cell. 82, 9, p. 1691-1707.e8

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

  39. Published

    Chromosomal gene inactivation in the green sulfur bacterium Chlorobium tepidum by natural transformation

    Frigaard, Niels-Ulrik & Bryant, D. A., 2001, In: Applied and Environmental Microbiology. 67, 6, p. 2538-2544 6 p.

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

  40. Published

    Chromosome evolution and the genetic basis of agronomically important traits in greater yam

    Bredeson, J. V., Lyons, J. B., Oniyinde, I. O., Okereke, N. R., Kolade, O., Nnabue, I., Nwadili, C. O., Hřibová, E., Parker, M., Nwogha, J., Shu, S., Carlson, J., Kariba, R., Muthemba, S., Knop, K., Barton, G. J., Sherwood, A. V., Lopez-Montes, A., Asiedu, R., Jamnadass, R. & 13 others, Muchugi, A., Goodstein, D., Egesi, C. N., Featherston, J., Asfaw, A., Simpson, G. G., Doležel, J., Hendre, P. S., Van Deynze, A., Kumar, P. L., Obidiegwu, J. E., Bhattacharjee, R. & Rokhsar, D. S., 2022, In: Nature Communications. 13, 16 p., 2001.

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

  41. Published

    Chromosome-scale haplotype-resolved pangenomics

    Garg, S., Balboa, Renzo Fidel Ferdinando & Kuja, J., 2022, In: Trends in Genetics. 38, 11, p. 1103-1107 5 p.

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

  42. Published

    Chronic acidosis rewires cancer cell metabolism through PPARα signaling

    Rolver, M. G., Holland, L. K. K., Ponniah, M., Prasad, N. S., Yao, Jiayi, Schnipper, J., Kramer, S., Elingaard-Larsen, L., Pedraz-Cuesta, E., Liu, B., Pardo, L. A., Maeda, K., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2023, In: International Journal of Cancer. 152, 8, 17 p.

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

  43. Published

    Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs

    Lv, W., Pan, X., Han, P., Wang, Z., Feng, W., Xing, X., Wang, Q., Qu, K., Zeng, Y., Zhang, C., Xu, Z., Li, Y., Zheng, T., Lin, L., Liu, C., Liu, X., Li, H., Henriksen, R. A., Bolund, L., Lin, L. & 7 others, Jin, X., Yang, H., Zhang, X., Yin, T., Regenberg, Birgitte, He, F. & Luo, Y., 2022, In: Clinical and Translational Medicine. 12, 4, 16 p., e817.

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

  44. Published

    Circular DNA elements of chromosomal origin are common in healthy human somatic tissue

    Møller, H. D., Mohiyuddin, M., Prada Luengo, Inigo, Sailani, M. R., Halling, Jens Frey, Plomgaard, Peter Stendahl, Maretty, L., Hansen, Anders Johannes, Snyder, M. P., Pilegaard, Henriette, Lam, H. Y. K. & Regenberg, Birgitte, 1 Dec 2018, In: Nature Communications. 9, 12 p., 1069.

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

  45. Published

    Circulating Free Fatty Acid and Phospholipid Signature Predicts Early Rapid Kidney Function Decline in Patients With Type 1 Diabetes

    Afshinnia, F., Rajendiran, T. M., He, C., Byun, J., Montemayor, D., Darshi, M., Tumova, J., Kim, J., Limonte, C. P., Miller, R. G., Costacou, T., Orchard, T. J., Ahluwalia, Tarun Veer Singh, Rossing, Peter, Snell-Bergeon, J. K., de Boer, I. H., Natarajan, L., Michailidis, G., Sharma, K. & Pennathur, S., 2021, In: Diabetes Care. 44, 9, p. 2098-2106 9 p.

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

  46. Published

    Circulating cytokines and cytokine receptors in infliximab treatment failure due to TNF-α independent Crohn disease

    Steenholdt, Casper, Coskun, M., Buhl, S., Bendtzen, K., Ainsworth, M. A., Brynskov, J. & Nielsen, Ole Haagen, 2016, In: Medicine (Baltimore). 95, 16, 8 p., e3417.

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

  47. Published

    Class II recombinant phosphoribosyl diphosphate synthase from spinach. Phosphate independence and diphosphoryl donor specificity.

    Krath, B. N. & Hove-Jensen, B., 2001, In: Journal of Biological Chemistry. 276, 21, p. 17851-6 5 p.

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

  48. Published

    Classifying disease-associated variants using measures of protein activity and stability

    Jepsen, M. M., Fowler, D. M., Hartmann-Petersen, Rasmus, Stein, Amelie & Lindorff-Larsen, Kresten, 2020, Protein Homeostasis Diseases: Mechanisms and Novel Therapies. Pey, A. L. (ed.). Elsevier, p. 91-107

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

  49. Published

    Climate change and human colonization triggered habitat loss and fragmentation in Madagascar

    Salmona, J., Heller, Rasmus, Quéméré, E. & Chikhi, L., Oct 2017, In: Molecular Ecology. 26, 19, p. 5203-5222 20 p.

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

  50. Published

    Clinical application of high-throughput sequencing technology in prenatal screening and diagnosis of birth defects

    ZENG, F., 2022, Department of Biology, Faculty of Science, University of Copenhagen. 118 p.

    Research output: Book/Report › Ph.D. thesis › Research

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