- Published
Cross-species ChIP-seq studies provide insights into regulatory strategies of PPAR¿ in adipocytes
Schmidt, S. F., Jørgensen, M., Sandelin, Albin Gustav & Mandrup, S., 2012, In: Transcription. 3, 1, p. 19-24 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Crosstalk between tumor acidosis, p53 and extracellular matrix regulates pancreatic cancer aggressiveness
Czaplinska, D., Ialchina, Renata, Andersen, Henriette Berg, Yao, Jiayi, Stigliani, Arnaud, Dannesboe, Johs, Flinck, M., Chen, X., Mitrega, J., Gnosa, S. P., Dmytriyeva, O., Alves, F., Napp, J., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2023, In: International Journal of Cancer. 152, 6, p. 1210-1225 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Current and emerging approaches to define intestinal epithelium-specific transcriptional networks
Olsen, A. K., Boyd, M., Danielsen, E. T. & Troelsen, J. T., Feb 2012, In: American Journal of Physiology: Gastrointestinal and Liver Physiology. 302, 3, p. G277-86Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Current challenges in understanding the role of enhancers in disease
Zaugg, J. B., Sahlén, P., Andersson, Robin, Alberich-Jorda, M., de Laat, W., Deplancke, B., Ferrer, J., Mandrup, S., Natoli, G., Plewczynski, D., Rada-Iglesias, A. & Spicuglia, S., 2022, In: Nature Structural and Molecular Biology. 29, 12, p. 1148-1158 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cytoplasmic mRNPs revisited: Singletons and condensates
Mateu-Regue, A., Nielsen, Finn Cilius & Christiansen, Jan, 2020, In: BioEssays. 42, 12, 13 p., 2000097.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DGCR8 HITS-CLIP reveals novel functions for the microprocessor
Macias, S., Plass, M., Stajuda, A., Michlewski, G., Eyras, E. & Cáceres, J. F., 2012, In: Nature Structural and Molecular Biology. 19, 8Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DGCR8 acts as an adaptor for the exosome complex to degrade double-stranded structured RNAs
Macias, S., Cordiner, R. A., Gautier, P., Plass, M. & Caceres, J. F., 2015, In: Molecular Cell. 60, 6, p. 873-885 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DNA metabarcoding illuminates the contribution of small and very small prey taxa to the diet of lions
Groen, K., Beekenkamp, S., de Iongh, H. H., Lesilau, F., Chege, M., Narisha, L., Veldhuis, M., Bertola, Laura, van Bodegom, P. M. & Trimbos, K. B., 2023, In: Environmental DNA. 5, 6, p. 1321-1331 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch
Norregaard, K., Andersson, M., Sneppen, Kim, Nielsen, Peter E., Brown, Stanley & Oddershede, L. B., 22 Oct 2013, In: Proceedings of the National Academy of Sciences USA (PNAS). 110, 43, p. 17386-91 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Daily estimates of clinical severity of symptoms in bipolar disorder from smartphone-based self-assessments
Busk, J., Faurholt-Jepsen, M., Frost, M., Bardram, J. E., Kessing, Lars Vedel & Winther, Ole, 2020, In: Translational Psychiatry. 10, 12 p., 194.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage
Hanghøj, Kristian Ebbesen, Renaud, Gabriel, Albrechtsen, Anders & Orlando, L., 2019, In: GigaScience. 8, 4, 6 p., giz025.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Darwinian and demographic forces affecting human protein coding genes.
Nielsen, Rasmus, Hubisz, M. J., Hellmann, I., Torgerson, D., Andres, A. M., Albrechtsen, Anders, Gutenkunst, R., Adams, M. D., Cargill, M., Boyko, A., Indap, A., Bustamante, C. D. & Clark, A. G., 2009, In: Genome Research. 19, 5, p. 838-49 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
Li, M., Sun, C., Xu, N., Bian, P., Tian, X., Wang, X., Wang, Y., Jia, X., Heller, R., Wang, M., Wang, F., Dai, X., Luo, R., Guo, Y., Wang, X., Yang, P., Hu, D., Liu, Z., Fu, W., Zhang, S. & 10 others, , 2022, In: Molecular Biology and Evolution. 39, 4, 16 p., msac066.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
De Novo Pathway Enrichment with KeyPathwayMiner
Alcaraz, N., Hartebrodt, A. & List, M., 2020, Protein-Protein Interaction Networks: Methods and Protocols. Canzar, S. & Ringeling, F. R. (eds.). Humana Press, p. 181-199 19 p. (Methods in Molecular Biology, Vol. 2074).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
De Novo Pathway-Based Classification of Breast Cancer Subtypes
List, M., Alcaraz, N. & Batra, R., 2020, Protein-Protein Interaction Networks: Methods and Protocols. Canzar, S. & Ringeling, F. R. (eds.). Humana Press, p. 201-213 13 p. (Methods in Molecular Biology, Vol. 2074).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Deciphering Transcriptional Regulation: Computational Approaches
Valen, E., 2010, Museum Tusculanum. 97 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Deciphering regulatory mechanisms underlying gene co-activity
van Duin, Lucas, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 131 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data
Kinalis, S., Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2019, In: BMC Bioinformatics. 20, 9 p., 379.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Deep Learning for Diagnostic Binary Classification of Multiple-Lesion Skin Diseases
Thomsen, K., Christensen, A. L., Iversen, L., Lomholt, H. B. & Winther, Ole, 2020, In: Frontiers in Medicine. 7, 7 p., 574329.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Deep Recurrent Conditional Random Field Network for Protein Secondary Prediction
Johansen, A. R., Sønderby, C. K., Sønderby, S. K. & Winther, O., 2017, ACM-BCB '17: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. p. 73-78 6 p.Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
Deep integrative models for large-scale human genomics
Sigurdsson, Arnór Ingi, Louloudis, Ioannis, Banasik, Karina, Westergaard, David, Winther, Ole, Lund, O., Ostrowski, Sisse Rye, Erikstrup, C., Pedersen, Ole Birger Vesterager, Nyegaard, Mette, Brunak, Søren, Vilhjálmsson, B. & Rasmussen, Simon, 2023, In: Nucleic Acids Symposium Series. 51, 12, 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
Fort, A., Hashimoto, K., Yamada, D., Salimullah, M., Keya, C. A., Saxena, A., Bonetti, A., Voineagu, I., Bertin, N., Kratz, A., Noro, Y., Wong, C-H., de Hoon, M., Andersson, R., Sandelin, A. G., Suzuki, H., Wei, C-L., Koseki, H., Hasegawa, Y., Forrest, A. R. R. & 2 others, , 2014, In: Nature Genetics. 46, 6, p. 558-566 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load
INSIGHT START Study Group, I. S. S. G., 2023, In: PLOS Computational Biology. 19, 1, 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DeepLoc: prediction of protein subcellular localization using deep learning
Almagro Armenteros, J. J., Sønderby, C. K., Sønderby, S. K., Nielsen, H. & Winther, Ole, 1 Nov 2017, In: Bioinformatics. 33, 21, p. 3387-3395 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models
Thumuluri, V., Almagro Armenteros, J. J., Johansen, A. R., Nielsen, H. & Winther, Ole, 2022, In: Nucleic Acids Research. 50, W1, p. W228-W234Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning
Wang, Jun, Horlacher, M., Cheng, L. & Winther, Ole, 2024, In: Bioinformatics. 40, 2, 10 p., btae065.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DeepPeptide predicts cleaved peptides in proteins using conditional random fields
Teufel, Felix Georg, Refsgaard, J. C., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, Ole & Madsen, D., 2023, In: Bioinformatics (Oxford, England). 39, 10, 6 p., btad616.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Demographic inferences from large-scale NGS data
Pedersen, C. T., 2017, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
Deorphanizing Peptides Using Structure Prediction
Teufel, Felix Georg, Refsgaard, J. C., Kasimova, M. A., Deibler, K., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, Ole & Madsen, D., 2023, In: Journal of Chemical Information and Modeling. 63, 9, 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DermX: An end-to-end framework for explainable automated dermatological diagnosis
Jalaboi, R., Faye, F., Orbes-Arteaga, M., Jørgensen, D., Winther, Ole & Galimzianova, A., 2023, In: Medical Image Analysis. 83, 12 p., 102647.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Design of association studies with pooled or un-pooled next-generation sequencing data
Kim, S. Y., Li, Y., Guo, Y., Li, R., Holmkvist, J., Hansen, Torben, Pedersen, Oluf Borbye, Wang, J. & Nielsen, Rasmus, 2010, In: Genetic Epidemiology. 34, 5, p. 479-491 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detecting host responses to microbial stimulation using primary epithelial organoids
Lange, Jette Bornholdt, Müller, C. V., Nielsen, M. J., Strickertsson, J., Rago, D., Chen, Y., Maciag, Grzegorz Jerzy, Skov, Jonathan, Wellejus, A., Schweiger, P. J., Hansen, Stine Lind, Broholm, C., Gögenur, Ismail, Maimets, Martti, Sloth, S., Hendel, J., Baker, A., Sandelin, Albin Gustav & Jensen, Kim Bak, 2023, In: Gut Microbes. 15, 2, 16 p., 2281012.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detecting selection in low-coverage high-throughput sequencing data using principal component analysis
Meisner, Jonas, Albrechtsen, Anders & Hanghøj, Kristian Ebbesen, 2021, In: BMC Bioinformatics. 22, 13 p., 470.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detecting sequence signals in targeting peptides using deep learning
Almagro Armenteros, J. J., Salvatore, Marco, Emanuelsson, O., Winther, Ole, von Heijne, G., Elofsson, A. & Nielsen, H., 2019, In: Life Science Alliance. 2, 5, 14 p., 201900429.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detection of Active Matriptase using a Biotinylated Chloromethyl Ketone Peptide
Godiksen, S., Soendergaard, C., Friis, S., Jensen, J. K., Lange, Jette Bornholdt, Sales, K. U., Huang, M., Bugge, T. H. & Vogel, Lotte, 2013, In: P L o S One. 8, 10, 10 p., e77146.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detection of Viable and Total Bacterial Community in the Pit Mud of Chinese Strong-Flavor Liquor Using Propidium Monoazide Combined With Quantitative PCR and 16S rRNA Gene Sequencing
Tan, G., Zhou, R., Zhang, W., Hu, Y., Ruan, Z., Li, J., Zhang, C., Shen, D., Peng, N., Liang, Y. & Zhao, S., 2020, In: Frontiers in Microbiology. 11, 9 p., 896.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing
Enroth, Christel Hougård, Poulsen, L. D., Iversen, S., Kirpekar, F., Albrechtsen, Anders & Vinther, Jeppe, 2019, In: Nucleic Acids Research. 47, 20, 13 p., e126.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing
Kielpinski, L. J., Boyd, M., Sandelin, Albin Gustav & Vinther, Jeppe, 2013, In: Methods in molecular biology (Clifton, N.J.). 1038, p. 213-31 19 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detection of slicer activity by immunopurified plant ARGONAUTE1
Arribas Hernandez, Laura, Vigh, Maria Louisa & Brodersen, Peter, 2019, Plant MicroRNAs: Methods and Protocols. Folter, S. D. (ed.). Humana Press, p. 295-316 22 p. (Methods in Molecular Biology, Vol. 1932).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Determinants of enhancer and promoter activities of regulatory elements
Andersson, Robin & Sandelin, Albin Gustav, 2020, In: Nature Reviews Genetics. 21, 2, p. 71-87 17 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA
Dehasque, M., Chrzanová Pecnerová, Patrícia, Kempe Lagerholm, V., Ersmark, E., Danilov, G. K., Mortensen, P., Vartanyan, S. & Dalén, L., 2022, In: Genes. 13, 4, 16 p., 687.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Diabetes in population isolates: lessons from Greenland
Grarup, Niels, Moltke, Ida, Albrechtsen, Anders & Hansen, Torben, 2015, In: The Review of Diabetic Studies. 12, 3-4, p. 320-329 10 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Differential expression of cellular microRNAs in HPV 11, -16, and -45 transfected cells
Dreher, A., Rossing, M., Kaczkowski, B., Andersen, D. K., Larsen, T. J., Christophersen, M. K., Nielsen, Finn Cilius & Norrild, B., 2011, In: Biochemical and Biophysical Research Communications. 412, 1, p. 20-5 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Differential expression of cellular microRNAs in HPV-11 transfected cells. An analysis by three different array platforms and qRT-PCR
Dreher, A., Rossing, M., Kaczkowski, B., Nielsen, Finn Cilius & Norrild, B., 17 Dec 2010, In: Biochemical and Biophysical Research Communications. 403, 3-4, p. 357-62 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Differential gene expression in the otic capsule and the middle ear-an annotation of bone-related signaling genes
Nielsen, M. C., Martin-Bertelsen, T., Friis, M., Winther, Ole, Friis-Hansen, Lennart Jan, Rye-Jørgensen, N., Bloch, S. & Sørensen, Mads Sølvsten, 2015, In: Otology & Neurotology. 36, 4, p. 727-732 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations
Høie, M. H., Gade, F. S., Johansen, J., Würtzen, C., Winther, Ole, Nielsen, M. & Marcatili, P., 2024, In: Frontiers in Immunology. 15, 12 p., 1322712.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discovering novel hydrolases from hot environments
Wohlgemuth, R., Littlechild, J., Monti, D., Schnorr, K., van Rossum, T., Siebers, B., Menzel, P., Kublanov, I. V., Rike, A. G., Skretas, G., Szabo, Z., Peng, Xu & Young, M. J., 2018, In: Biotechnology Advances. 36, 8, p. 2077-2100Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I., Aitken, S. & 31 others, , 2021, In: Nature Communications. 12, 18 p., 3297.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale
Danish Pan Genome Consortium, D. P. G. C., Belling, K. G. & Rasmussen, Simon, 2015, In: GigaScience. 4, 13 p., 64.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discrete structural dynamics of pseudo-palindromic motifs control DNA binding of bacterial toxin-antitoxin complexes
Brodersen, D. E., Bendtsen, K. L., Xu, K., Luckmann, M., Winther, K. S., Shah, S. A. & Pedersen, C. N. S., 2017, In: F A S E B Journal. 31, S1, 1 p., 777.2.Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
Most downloads
-
6190
downloads
Reconstructing genome evolution in historic samples of the Irish potato famine pathogen
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
5481
downloads
Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
5253
downloads
True single-molecule DNA sequencing of a pleistocene horse bone
Research output: Contribution to journal › Journal article › Research › peer-review
Published
Latest publications
MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch
Research output: Contribution to journal › Journal article › Research › peer-review
Genetic diversity of lion populations in Kenya: Evaluating past management practices and recommendations for future conservation actions
Research output: Contribution to journal › Journal article › Research › peer-review
Characterizing glucokinase variant mechanisms using a multiplexed abundance assay
Research output: Contribution to journal › Journal article › Research › peer-review