- 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
- Published
Disease-linked mutations cause exposure of a protein quality control degron
Kampmeyer, Caroline, Larsen-Ledet, Sven, Wagnkilde, M. R., Michelsen, M., Iversen, Henriette Kring Mangor, Nielsen, S. V., Lindemose, Søren, Caregnato, A., Ravid, T., Stein, Amelie, Teilum, Kaare, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2022, In: Structure. 30, 9, p. 1245-1253.e5Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Disorder in a two-domain neuronal Ca2+-binding protein regulates domain stability and dynamics using ligand mimicry
Staby, L., Kemplen, K. R., Stein, Amelie, Ploug, Michael, Clarke, J., Skriver, Karen, Heidarsson, P. O. & Kragelund, Birthe Brandt, 2021, In: Cellular and molecular life sciences : CMLS. 78, p. 2263-2278 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Dispersal mediated coexistence of mud snails (Hydrobiidae) in an estuary
Siegismund, Hans Redlef & Hylleberg, J., 1987, In: Marine Biology. 94, p. 395-402Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Dissecting the target specificity of RNase H recruiting oligonucleotides using massively parallel reporter analysis of short RNA motifs
Rukov, J. L., Hagedorn, P. H., Høy, I. B., Feng, Y., Lindow, M. & Vinther, Jeppe, 2015, In: Nucleic Acids Research. 43, 17, p. 8476-8487 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DivA: detection of non-homologous and very divergent regions in protein sequence alignments
Zepeda Mendoza, M. L., Nygaard, S. & Rodrigues da Fonseca, Rute Andreia, 2014, In: BMC Research Notes. 7, 806, 6 p., 806.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Diverse bacterial genomes encode an operon of two genes, one of which is a unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons
Baranov, P., Vestergaard, Bente, Hamelryck, Thomas Wim, Gesteland, Nyborg, J. & Atking, J., 2006, In: Biology Direct. 13, p. 1-28 28 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Diversity and transboundary mobility of serotype O foot-and-mouth disease virus in East Africa: implications for vaccination policies
Balinda, S., Sangula, A. K., Heller, Rasmus, Muwanika, V. B., Belsham, G., Masembe, C. & Siegismund, Hans Redlef, 1 Oct 2010, In: Infection, Genetics and Evolution. 10, 7, p. 1058-65 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Diversity of nature's assembly lines - recent discoveries in non-ribosomal peptide synthesis
Payne, J. A. E., Schoppet, M., Hansen, M. H. & Cryle, M. J., 2017, In: Molecular BioSystems. 13, 1, p. 9-22 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Dominance of a clonal green sulfur bacterial population in a stratified lake
Gregersen, Lea Haarup, Habicht, K. S., Peduzzi, S., Tonolla, M., Canfield, D. E., Miller, M., Cox, R. P. & Frigaard, Niels-Ulrik, 2009, In: FEMS Microbiology Ecology. 70, 1, p. 30-41 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Down-regulation of miR-129-5p and the let-7 family in neuroendocrine tumors and metastases leads to up-regulation of their targets Egr1, G3bp1, Hmga2 and Bach1
Døssing, K. B. V., Binderup, Tina, Kaczkowski, B., Jacobsen, A. M. B., Rossing, M., Winther, O., Federspiel, B., Knigge, Ulrich, Kjær, Andreas & Friis-Hansen, L., 2015, In: Genes. 6, 1, p. 1-21 21 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Down-regulation of microRNAs controlling tumourigenic factors in follicular thyroid carcinoma
Rossing, M., Helweg-Larsen, R. B., Henao Giraldo, R., Winther, Ole, Vikeså, J., Niazi, O., Godballe, C., Krogdahl, A., Glud, M., Sørensen, C. H., Kiss, K., Bennedbæk, F. N. & Nielsen, Finn Cilius, 2012, In: Journal of Molecular Endocrinology. 48, 1, p. 11-23 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DoxoDB: A Database for the Expression Analysis of Doxorubicin-Induced lncRNA Genes
Distefano, R., Ilieva, M., Madsen, J. H., Rennie, Sarah & Uchida, S., 2023, In: Non-coding RNA. 9, 4, 24 p., 39.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Drosha regulates gene expression independently of RNA cleavage function
Gromak, N., Dienstbier, M., Macias, S., Plass, M., Eyras, E., Cáceres, J. F. & Proudfoot, N. J., 2013, In: Cell Reports. 5, 6, p. 1499-510 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Dwarfism and impaired gut development in insulin-like growth factor II mRNA-binding protein 1-deficient mice
Hansen, Thomas van Overeem, Hammer, N. A., Nielsen, J., Madsen, Mette, Dalbaeck, C., Wewer, Ulla M., Christiansen, Jan & Nielsen, Finn Cilius, 2004, In: Molecular and Cellular Biology. 24, 10, p. 4448-64 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
ERG Controls B Cell Development by Promoting Igh V-to-DJ Recombination
Søndergaard, E., Rauch, A., Michaut, Magali, Rapin, N., Rehn, M., Wilhelmson, Anna, Camponeschi, A., Hasemann, M. S., Bagger, F. O., Jendholm, J., Knudsen, K. J., Mandrup, S., Mårtensson, I. L. & Porse, Bo Torben, 26 Nov 2019, In: Cell Reports. 29, 9, p. 2756-2769.e6 21 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation
Knudsen, K. J., Rehn, M. C., Hasemann, M. S., Rapin, N. P. J., Bagger, F. O., Ohlsson, E. K., Willer, A., Frank, Anne-Katrine, Søndergaard, E., Jendholm, L. J., Thorén, L. A. M., Lee, J., Rak, J., Theilgaard-Mønch, Kim & Porse, Bo Torben, 2015, In: Genes & Development. 29, p. 1915-1929 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas
Mohammad, F., Weissmann, S., Leblanc, B. O., Pandey, D. P., Højfeldt, J. W., Comet, I., Zheng, C., Johansen, Jens Vilstrup, Rapin, N. P. J., Porse, Bo Torben, Tvardovskiy, A., Jensen, O. N., Olaciregui, N. G., Lavarino, C., Suñol, M., de Torres, C., Mora, J., Carcaboso, A. M. & Helin, K., Apr 2017, In: Nature Medicine. 23, 4, p. 483-492 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance
Larsen, T. S. & Krogh, Anders, 2003, In: BMC Bioinformatics. 4(1), p. 21Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Editorial: Long-read sequencing—Pitfalls, benefits and success stories
Wohlers, I., Garg, S. & Hehir-Kwa, J. Y., 2023, In: Frontiers in Genetics. 13, 3 p., 1114542.Research output: Contribution to journal › Editorial › Research › peer-review
- Published
Effect of alkaline treatment on bacteriochlorophyll a, quinones, and energy transfer in chlorosomes from Chlorobium tepidum and Chlorobium phaeobacteroides
van Walree, C. A., Sakuragi, Y., Steensgaard, D. B., Bösinger, C. S., Frigaard, Niels-Ulrik, Cox, R. P., Holzwarth, A. R. & Miller, M., 1999, In: Photochemistry and Photobiology. 69, p. 322-328 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Effect of chronic uremia on the transcriptional profile of the calcified aorta analyzed by RNA sequencing
Rukov, J. L., Gravesen, Eva, Mace, M. L., Hofman-Bang, J., Vinther, Jeppe, Andersen, C. B., Lewin, E. & Ølgaard, Klaus, 2016, In: American Journal of Physiology: Renal Physiology. 310, 6, p. F477-F491 18 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Effect of ecological and anthropogenic factors on grouping patterns in African lions across Kenya
Chege, M., Bertola, Laura, De Snoo, G. R., Ngene, S., Otieno, T., Amoke, I., van 't Zelfde, M., Dolrenry, S., Broekhuis, F., Tamis, W., De Iongh, H. H. & Elliot, N. B., 2024, In: Ecology and Evolution. 14, 2, 14 p., e10982.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Effect of energy metabolism on protein motility in the bacterial outer membrane
Ryder, T. W., Xu, L., Berg-Sørensen, K., Brown, Stanley & Oddershede, L. B., 2009, In: Biophysical Journal. 97, 5, p. 1305-1312 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Effect of supercoiling on the λ switch
Norregaard, K., Andersson, M., Sneppen, Kim, Nielsen, Peter E., Brown, Stanley & Oddershede, L. B., 1 Jan 2014, In: Bacteriophage. 4, 2, p. 1-5 5 p., e27517.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades
Hansen, S., Krishna, S., Semsey, S. & Svenningsen, Sine Lo, 17 Jul 2015, In: Scientific Reports. 5, 12186.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model
Thygesen, Christian Bahne, Al-Sibahi, A. S., Steenmanns, C. S., Sanz Moreta, Lys, Sørensen, A. B. & Hamelryck, Thomas Wim, 2021, International Conference on Machine Learning, 18-24 July 2021, Virtual. PMLR, p. 10258-10267 (Proceedings of Machine Learning Research, Vol. 139).Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
Efficient approaches for large-scale GWAS with genotype uncertainty
Jørsboe, E. & Albrechtsen, Anders, 2022, In: G3: Genes, Genomes, Genetics (Bethesda). 12, 1, 9 p., jkab385.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Efficient statistical and computational methods for large scale sequencing data
Li, Zilong, 2024, Department of Biology, Faculty of Science, University of Copenhagen. 149 p.Research output: Book/Report › Doctoral thesis › Research
- Published
Efficient, non-disruptive local moves for Monte Carlo sampling of proteins
Bottaro, S., Boomsma, Wouter, Johansson, Kristoffer Enøe, Andreetta, C., Hamelryck, Thomas Wim & Ferkinghoff-Borg, J., 2011, Next Generation Statistics in Biosciences: Proceedings of the 30th Leeds Annual Statistical Research (LASR) Workshop. Mardia, K. V., Gusnanto, A., Riley, A. D. & Voss, J. (eds.). University of Leeds, p. 127 1 p.Research output: Chapter in Book/Report/Conference proceeding › Conference abstract in proceedings › Research
- Published
Eight millennia of matrilineal genetic continuity in the South Caucasus
Margaryan, Ashot, Derenko, M., Hovhannisyan, H., Malyarchuk, B., Heller, Rasmus, Khachatryan, Z., Avetisyan, P., Badalyan, R., Bobokhyan, A., Melikyan, V., Sargsyan, G., Piliposyan, A., Simonyan, H., Mkrtchyan, R., Denisova, G., Yepiskoposyan, L., Willerslev, Eske & Allentoft, Morten Erik, 10 Jul 2017, In: Current Biology. 27, 13, p. 2023-2028 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Electronic energy transfer involving carotenoid pigments in chlorosomes of two green bacteria: Chlorobium tepidum and Chloroflexus aurantiacus
Melø, T. B., Frigaard, Niels-Ulrik, Matsuura, K. & Razi Naqvi, K., 2000, In: Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 56, 10, p. 2001-2010 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Embryonic expression of Drosophila IMP in the developing CNS and PNS
Adolph, S. K., Delotto, R., Nielsen, Finn Cilius & Christiansen, Jan, 2008, In: Gene Expression Patterns. 9, 3, p. 138-143 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Emergence and radiation of distemper viruses in terrestrial and marine mammals
Stokholm, Iben, Puryear, W., Sawatzki, K., Knudsen, Steen Wilhelm, Terkelsen, Thilde Bagger, Becher, P., Siebert, U. & Olsen, Morten Tange, 2021, In: Proceedings of the Royal Society B: Biological Sciences. 288, 1961, 9 p., 20211969.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells
Bakoulis, Stylianos, Krautz, Robert, Alcaraz, N., Salvatore, Marco & Andersson, Robin, 2022, In: Nucleic acids symposium series. 50, 4, p. 2111-2127 17 p., 088.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Engineered iron oxide adhesion mutants of the lambda-receptor
Brown, Stanley, 1992, In: Proceedings of the National Academy of Science of the United States of America. 89, p. 8651-8655Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Enhancer and Transcription Factor Dynamics during Myeloid Differentiation Reveal an Early Differentiation Block in Cebpa null Progenitors
Pundhir, Sachin, Bratt Lauridsen, F. K., Schuster, Mikkel Bruhn, Jakobsen, J. S., Ge, Y., Schoof, E. M., Rapin, N. P. J., Waage, J., Hasemann, M. S. & Porse, Bo Torben, 2018, In: Cell Reports. 23, 9, p. 2744-2757 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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, , 2021, In: Nature Communications. 12, 1, 9 p., 3238.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Enterococcus faecalis infection causes inflammation, intracellular oxphos-independent ROS production, and DNA damage in human gastric cancer cells
Strickertsson, J. A. B., Desler, Claus, Martin-Bertelsen, T., Machado, A. M. D., Wadstrøm, T., Winther, Ole, Rasmussen, Lene Juel & Friis-Hansen, Lennart Jan, 2013, In: PLOS ONE. 8, 4, p. 1-13 13 p., e63147.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts
Boomsma, Wouter, Tian, P., Frellsen, J., Ferkinghoff-Borg, J., Hamelryck, Thomas Wim, Lindorff-Larsen, Kresten & Vendruscolo, M., 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 38, p. 13852-13857 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Error-prone polymerase activity causes multinucleotide mutations in humans
Harris, K. & Nielsen, Rasmus, 1 Sep 2014, In: Genome Research. 24, 9, p. 1445-1454 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways.
Hove-Jensen, B., Rosenkrantz, T. J., Haldimann, A. & Wanner, B. L., 2003, In: Journal of Bacteriology. 185, 9, p. 2793-801 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating IBD tracts from low coverage NGS data
Vieira, Filipe Garrett, Albrechtsen, Anders & Nielsen, Rasmus, 2016, In: Bioinformatics. 32, 14, p. 2096-2102 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating admixture pedigrees of recent hybrids without a contiguous reference genome
Garcia Erill, Genís, Hanghøj, Kristian Ebbesen, Heller, Rasmus, Wiuf, Carsten & Albrechtsen, Anders, 2023, In: Molecular Ecology Resources. 23, 7, p. 1604-1619 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation
Vieira, Filipe Garrett, Fumagalli, M., Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: Genome Research. 23, p. 1852-1861 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating individual admixture proportions from next generation sequencing data
Skotte, L., Korneliussen, Thorfinn Sand & Albrechtsen, Anders, Nov 2013, In: Genetics. 195, 3, p. 693-702 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating narrow-sense heritability using family data from admixed populations
Athanasiadis, G., Speed, D., Lepola, Mette Andersen, Appel, E. V. R., Grarup, Niels, Brandslund, I., Jørgensen, M. E., Larsen, C. V. L., Bjerregaard, P., Hansen, Torben & Albrechtsen, Anders, 2020, In: Heredity. 124, 6, p. 751-762 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating the timing of multiple admixture pulses during local ancestry inference
Medina, P., Thornlow, B., Nielsen, Rasmus & Corbett-Detig, R., 2018, In: Genetics. 210, 3, p. 1089-1107 19 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimation of allele frequency and association mapping using next-generation sequencing data
Kim, S. Y., Lohmueller, K. E., Albrechtsen, Anders, Li, Y., Korneliussen, Thorfinn Sand, Tian, G., Grarup, Niels, Jiang, T., Andersen, G., Witte, D., Jorgensen, T., Hansen, Torben, Pedersen, Oluf Borbye, Wang, J. & Nielsen, Rasmus, 2011, In: B M C Bioinformatics. 12, p. 231 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage
Rasmussen, Malthe Sebro, Garcia Erill, Genís, Korneliussen, Thorfinn Sand, Wiuf, Carsten & Albrechtsen, Anders, 2022, In: Genetics. 222, 4, 15 p., iyac148.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimation of the covariance structure from SNP allele frequencies
van Waaij, J., Li, Z. & Wiuf, Carsten, 2022, In: Statistical Applications in Genetics and Molecular Biology. 21, 1, 20 p., 20220005.Research output: Contribution to journal › Journal article › Research › peer-review
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Reconstructing genome evolution in historic samples of the Irish potato famine pathogen
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Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome
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True single-molecule DNA sequencing of a pleistocene horse bone
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