- 2015
- 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
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 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
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
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
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
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
Evolutionary genomics and conservation of the endangered Przewalski's horse
Der Sarkissian, C., Ermini, L., Schubert, M., Yang, M. A., Sanz, P. L., Fumagalli, M., Jónsson, H., Bar-Gal, G. K., Albrechtsen, A., Garrett Vieira, F. J., Petersen, B., Ginolhac, A., Seguin-Orlando, A., Magnussen, K., Fages, A. A., Gamba, C., Lorente-Galdos, B., Polani, S., Steiner, C., Neuditschko, M. & 17 others, , 2015, In: Current Biology. 25, 19, p. 2577-2583 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
First estimates of genetic diversity for the highly endangered giant sable antelope using a set of 57 microsatellites
Pinto, P. V., Lopes, S., Mourao, S., Baptista, S., Siegismund, Hans Redlef, Van Vuuren, B. J., Beja, P., Ferrand, N. & Godinho, R., 2015, In: European Journal of Wildlife Research. 61, 2, p. 313-317 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
FluKB: a knowledge-based system for influenza vaccine target discovery and analysis of the immunological properties of influenza viruses
Simon, C., Kudahl, U. J., Sun, J., Olsen, L. R., Zhang, G. L., Reinherz, E. L. & Brusic, V., 2015, In: Clinical & Developmental Immunology. 2015, 11 p., 380975.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Foot-and-mouth disease virus serotype SAT 3 in long-horned ankole calf, Uganda
Dhikusooka, M. T., Tjørnehøj, K., Ayebazibwe, C., Namatovu, A., Ruhweza, S., Siegismund, Hans Redlef, Wekesa, S. N., Normann, P. & Belsham, G. J., 2015, In: Emerging Infectious Diseases (Print Edition). 21, 1, p. 111-114 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Gateways to the FANTOM5 promoter level mammalian expression atlas
Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., Mungall, C. J., Arner, E., Baillie, J. K., Bertin, N., Bono, H., de Hoon, M., Diehl, A. D., Dimont, E., Freeman, T. C., Fujieda, K. & 21 others, , 2015, In: Genome Biology (Online Edition). 16, 14 p., 22.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetic and environmental determinants of 25-hydroxyvitamin D levels in multiple sclerosis
Laursen, J. H., Søndergaard, H. B., Albrechtsen, Anders, Frikke-Schmidt, Ruth, Koch-Henriksen, N., Sørensen, Per Soelberg, Sellebjerg, Finn Thorup & Oturai, A. B., 2015, In: Multiple Sclerosis Journal. 21, 11, p. 1414-1422 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene
Stoffel, C., Dufresnes, C., Okello, J. B. A., Noirard, C., Joly, P., Nyakaana, S., Muwanika, V. B., Alcala, N., Vuilleumier, S., Siegismund, Hans Redlef & Fumagalli, L., 2015, In: Molecular Ecology. 24, 10, p. 2507–2520 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera Morales, C. E., Avila Arcos, M. D. C., Malaspinas, A. S., Eriksson, A., Moltke, I., Metspalu, M., Homburger, J. R., Wall, J., Cornejo, O. E., Moreno Mayar, J. V., Korneliussen, T. S., Pierre, T. L., Rasmussen, M. & 81 others, , 2015, In: Science (New York, N.Y.). 349, 6250, 6250.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Greenlandic Inuit show genetic signatures of diet and climate adaptation
Fumagalli, M., Moltke, Ida, Grarup, Niels, Racimo, F., Bjerregaard, P., Jørgensen, M. E., Korneliussen, Thorfinn Sand, Gerbault, P., Skotte, L., Linneberg, Allan René, Christensen, C., Brandslund, I., Jørgensen, T., Huerta-Sánchez, E., Schmidt, E. B., Pedersen, Oluf Borbye, Hansen, T., Albrechtsen, Anders & Nielsen, Rasmus, 2015, In: Science (New York, N.Y.). 349, 6254, p. 1343-1347 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Human gene promoters are intrinsically bidirectional
Andersson, Robin, Chen, Y., Core, L., Lis, J. T., Sandelin, Albin Gustav & Jensen, T. H., 2015, In: Molecular Cell. 60, 3, p. 346-347 2 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing
Bataillon, T., Duan, J., Hvilsom, C., Jin, X., Li, Y., Skov, L., Glemin, S., Munch, K., Jiang, T., Qian, Y., Hobolth, A., Wang, J., Mailund, T., Siegismund, Hans Redlef & Schierup, M. H., 2015, In: Genome Biology and Evolution. 7, 4, p. 1122-1132 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Investigation of RNA Structure by High-Throughput SHAPE-Based Probing Methods
Poulsen, L. D., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 133 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding
Xue, Y., Prado-Martinez, J., Sudmant, P. H., Narasimhan, V., Ayub, Q., Szpak, M., Frandsen, P., Chen, Y., Yngvadottir, B., Cooper, D. N., de Manuel, M., Hernandez-Rodriguez, J., Lobon, I., Siegismund, H. R., Pagani, L., Quail, M. A., Hvilsom, C., Mudakikwa, A., Eichler, E. E., Cranfield, M. R. & 3 others, , 2015, In: Science (New York, N.Y.). 348, 6231, p. 242-245 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
New evidence for hybrid zones of forest and savanna elephants in Central and West Africa
Mondol, S., Moltke, Ida, Hart, J., Keigwin, M., Brown, L., Stephens, M. & Wasser, S. K., 2015, In: Molecular Ecology. 24, 24, p. 6134-6147 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data
Korneliussen, Thorfinn Sand & Moltke, Ida, 2015, In: Bioinformatics (Oxford, England). 31, 24, p. 4009-4011 3 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Non-Coding RNAs in Arabidopsis: Discovery of Nuclear ncRNAs from Body Methylated Genes and of miRNA Pathway Inhibition by Conserved, Bacterial Virulence Factor
van Wonterghem, M., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 109 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios
Besenbacher, S., Liu, S., Gonzalez-Izarzugaza, J. M., Grove, J., Belling, K. G., Bork-Jensen, J., Huang, S., Als, T. D., Li, S., Yadav, R., Rubio García, A., Lescai, F., Demontis, D., Rao, J., Ye, W., Mailund, T., Møllegaard Friborg, R., Pedersen, C. N. S., Xu, R., Sun, J. & 27 others, , 2015, In: Nature Communications. 6, 9 p., 5969.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Partial USH2A deletions contribute to Usher syndrome in Denmark
Dad, S., Rendtorff, N. D., Kann, E., Albrechtsen, Anders, M. Mehrjouy, M., Bak, M., Tommerup, Niels, Tranebjærg, Lisbeth, Rosenberg, T., Jensen, H. & Møller, L. B., 2015, In: European Journal of Human Genetics. 23, p. 1646-1651 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Phylogenetic ANOVA: the expression variance and evolution model for quantitative trait evolution
Rohlfs, R. V. & Nielsen, Rasmus, 2015, In: Systematic Biology. 64, 5, p. 695-708 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Post-Transcriptional Gene Regulation Mediated by Small RNAs and ARGONAUTE1 in Arabidopsis
Arribas Hernandez, Laura, 2015, Department of Biology, Faculty of Science, University of Copenhagen. 232 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Primer-dependent and primer-independent initiation of double stranded RNA synthesis by purified arabidopsis RNA-dependent RNA polymerases RDR2 and RDR6
Devert, A., Fabre, N., Floris, M. H. J., Canard, B., Robaglia, C. & Crété, P., 2015, In: PLOS ONE. 10, 3, 17 p., e0120100.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model
Andersson, Robin, 2015, In: BioEssays. 37, 3, p. 314-323 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Proteins, physics and probability kinematics: a Bayesian formulation of the protein folding problem
Hamelryck, Thomas Wim, Boomsma, Wouter, Ferkinghoff-Borg, J., Foldager, J. I., Frellsen, J., Haslett, J. & Theobald, D., 2015, Geometry driven statistics. Dryden, I. L. & Kent, J. T. (eds.). Wiley, p. 356-376 21 p.Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Proteomic profiling of gill GSTs in Mytilus galloprovincialis from the North of Portugal and Galicia evidences variations at protein isoform level with a possible relation with water quality
Azevedo, C. C., Guzman-Guillen, R., Martins, J. C., Osório, H., Vasconcelos, V., Rodrigues da Fonseca, Rute Andreia & Campos, A., 2015, In: Marine Environmental Research. 110, p. 152-161 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Regulated Proteolysis of Arabidopsis Argonaute1
Kausika, S. P., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 201 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors
Lennartsson, A., Arner, E., Fagiolini, M., Saxena, A., Andersson, Robin, Takahashi, H., Noro, Y., Sng, J., Sandelin, Albin Gustav, Hensch, T. K. & Carninci, P., 2015, In: Epigenetics & Chromatin. 8, 15 p., 55.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Reproducible analysis of sequencing-based RNA structure probing data with user-friendly tools
Kielpinski, L. J., Sidiropoulos, N. & Vinther, Jeppe, 2015, Structures of large RNA molecules and their complexes. Woodson, S. A. & Allain, F. H. T. (eds.). Elsevier, p. 153-180 28 p. (Methods in Enzymology, Vol. 558).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Retromer contributes to immunity-associated cell death in Arabidopsis
Munch, D., Teh, O., Malinovsky, F. G., Liu, Q., Vetukuri, R. R., El Kasmi, F., Brodersen, Peter, Hara-Nishimura, I., Dangl, J. L., Petersen, Morten, Mundy, J. & Hofius, D., 2015, In: Plant Cell. 27, 2, p. 463-479 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data
Poulsen, L. D., Kielpinski, L. J., Salama, S. R., Krogh, Anders & Vinther, Jeppe, 2015, In: R N A. 21, 5, p. 1042-1052 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis
Branscheid, A., Marchais, A., Schott, G., Lange, H., Gagliardi, D., Andersen, S. U., Voinnet, O. & Brodersen, Peter, 2015, In: Nucleic Acids Research. 43, 22, p. 10975-10988 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Shotgun analysis of the marine mussel Mytilus edulis hemolymph proteome and mapping the innate immunity elements
Campos, A., Apraiz, I., Rodrigues da Fonseca, Rute Andreia & Cristobal, S., 2015, In: Proteomics. 15, 23-24, p. 4021-4029 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Software-supported USER cloning strategies for site-directed mutagenesis and DNA assembly
Genee, H. J., Bonde, M. T., Bagger, F. O., Jespersen, J. B., Sommer, M. O. A., Wernersson, R. & Olsen, L. R., 2015, In: A C S Synthetic Biology. 4, 3, p. 342-349 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Statistical Approaches Accomodating Uncertainty in Modern Genomic Data
Skotte, L., 2015, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
TGIF1 is a negative regulator of MLL-rearranged acute myeloid leukemia
Willer, A., Jakobsen, J. S., Ohlsson, E., Rapin, N., Waage, J., Billing, M., Bullinger, L., Karlsson, S. & Porse, Bo Torben, 2015, In: Leukemia. 29, p. 1018-31 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The ancestry and affiliations of Kennewick Man
Rasmussen, M., Sikora, Martin, Albrechtsen, Anders, Korneliussen, Thorfinn Sand, Moreno Mayar, J. Víctor, Poznik, G. D., Zollikofer, C. P. E., Ponce de León, M. S., Allentoft, Morten Erik, Moltke, Ida, Jónsson, H., Valdiosera Morales, C. E., Malhi, R. S., Orlando, L. A. A., Bustamante, C. D., Stafford jr., T., Meltzer, D. J., Nielsen, Rasmus & Willerslev, Eske, 2015, In: Nature. 523, 7561, p. 455-458 4 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome
Hurst, L. D., Ghanbarian, A. T., Forrest, A. R. R., Huminiecki, L., Rehli, M., Kenneth Baillie, J., de Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E. & 243 others, , 2015, In: PLoS Biology. 13, 12, 48 p., e1002315.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The frequent evolutionary birth and death of functional promoters in mouse and human
Young, R. S., Hayashizaki, Y., Andersson, Robin, Sandelin, Albin Gustav, Kawaji, H., Itoh, M., Lassmann, T., Carninci, P., Bickmore, W. A., Forrest, A. R. & Taylor, M. S., 2015, In: Genome Research. 25, p. 1546-1557 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The genomic and phenotypic diversity of Schizosaccharomyces pombe
Jeffares, D. C., Rallis, C., Rieux, A., Speed, D., Převorovský, M., Mourier, T., Marsellach, F. X., Iqbal, Z., Lau, W., Cheng, T. M. K., Pracana, R., Mülleder, M., Lawson, J. L. D., Chessel, A., Bala, S., Hellenthal, G., O'Fallon, B., Keane, T., Simpson, J. T., Bischof, L. & 22 others, , 2015, In: Nature Genetics. 47, 3, p. 235-241 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The origin and evolution of maize in the Southwestern United States: [+ erratum]
Rodrigues da Fonseca, Rute Andreia, Smith, B. D., Wales, N., Cappellini, Enrico, Skoglund, P., Fumagalli, M., Samaniego Castruita, J. A., Carøe, C., Avila Arcos, M. D. C., Hufnagel, D. E., Korneliussen, Thorfinn Sand, Vieira, Filipe Garrett, Jakobsson, M., Arriaza, B., Willerslev, Eske, Nielsen, Rasmus, Hufford, M. B., Albrechtsen, Anders, Ross-Ibarra, J. & Gilbert, M Thomas P, 2015, In: Nature Plants. 1, 5 p., 14003.Research output: Contribution to journal › Letter › Research › peer-review
- Published
Time clustered sampling can inflate the inferred substitution rate in foot-and-mouth disease virus analyses
Pedersen, C. T., Frandsen, P., Wekesa, S. N., Heller, Rasmus, Sangula, A. K., Wadsworth, J., Knowles, N. J., Muwanika, V. B. & Siegismund, Hans Redlef, 2015, In: PLOS ONE. 10, 12, 13 p., e0143605.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments
Sanz, P. L., Der Sarkissian, C., Ermini, L., Schubert, M., Jónsson, H., Albrechtsen, A., Fumagalli, M., Yang, M. A., Gamba, C., Seguin-Orlando, A., Mortensen, C. D., Petersen, B., Hoover, C. A., Lorente-Galdos, B., Nedoluzhko, A., Boulygina, E., Tsygankova, S., Neuditschko, M., Jagannathan, V., Theves, C. & 20 others, , 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 50, p. E6889-E6897 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
Arner, E., Daub, C. O., Vitting-Seerup, K., Andersson, R., Lilje, B., Drabløs, F., Lennartsson, A., Rönnerblad, M., Hrydziuszko, O., Vitezic, M., Freeman, T. C., Alhendi, A. M. N., Arner, P., Axton, R., Baillie, J. K., Beckhouse, A., Bodega, B., Briggs, J., Brombacher, F., Davis, M. & 89 others, , 2015, In: Science (New York, N.Y.). 347, 6225, p. 1010-1014 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptome dynamics of the microRNA inhibition response
Wen, J., Leucci, E., Vendramin, R., Kauppinen, S., Lund, Anders H., Krogh, Anders & Parker, B. J., 2015, In: Nucleic Acids Research. 43, 13, p. 6207-6221 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals
Wu, X., Bekker-Jensen, I. H., Christensen, J., Rasmussen, K. D., Sidoli, S., Qi, Y., Kong, Y., Wang, X., Cui, Y., Xiao, Z., Xu, G., Williams, K., Rappsilber, J., Sønderby, C. K., Winther, Ole, Jensen, O. N. & Helin, K., 2015, In: Cell Research. 25, p. 1205-1218 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Uncovering the genetic history of the present-day greenlandic population
Moltke, Ida, Fumagalli, M., Korneliussen, Thorfinn Sand, Crawford, J. E., Bjerregaard, P., Jørgensen, M. E., Grarup, Niels, Gulløv, H. C., Linneberg, Allan René, Pedersen, Oluf Borbye, Hansen, Torben, Nielsen, Rasmus & Albrechtsen, Anders, 2015, In: American Journal of Human Genetics. 96, 1, p. 54-69 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
- 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
- Published
YeastFab: The design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae
Guo, Y., Dong, J., Zhou, T., Auxillos, Jamie Yam, Li, T., Zhang, W., Wang, L., Shen, Y., Luo, Y., Zheng, Y., Lin, J., Chen, G. Q., Wu, Q., Cai, Y. & Dai, J., 27 Apr 2015, In: Nucleic Acids Research. 43, 13, p. e88Research output: Contribution to journal › Journal article › Research › peer-review
- Published
CENTRAL LIMIT THEOREMS FOR DIRECTIONAL AND LINEAR RANDOM VARIABLES WITH APPLICATIONS
Garcia-Portugues, E., Crujeiras, R. M. & Gonzalez-Manteiga, W., Jul 2015, In: Statistica Sinica. 25, 3, p. 1207-1229Research 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
A unified architecture of transcriptional regulatory elements
Andersson, Robin, Sandelin, Albin Gustav & Danko, C. G., Aug 2015, In: Trends in Genetics. 31, 8, p. 426-433 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2016
- Published
A genomic history of aboriginal Australia
Malaspinas, A. S., Westaway, M. C., Muller, C. E., Sousa, V. C., Lao, O., Alves, I., Bergström, A., Athanasiadis, G., Cheng, J. Y., Crawford, J. E., Heupink, T. H., Macholdt, E., Peischl, S., Rasmussen, S., Schiffels, S., Subramanian, S., Wright, J. L., Albrechtsen, A., Barbieri, C., Dupanloup, I. & 55 others, , 2016, In: Nature. 538, 7624, p. 207-214 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
Schubert, Mikkel, Lindgreen, S. & Orlando, L. A. A., 2016, In: BMC Research Notes. 9, 7 p., 88.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
An easy method for plant polysome profiling
Lecampion, C., Floris, M. H. J., Fantino, J. R., Robaglia, C. & Laloi, C., 2016, In: Journal of Visualized Experiments. 2016, 114, e54231.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Analysis of telomerase target gene expression effects from murine models in patient cohorts by homology translation and random survival forest modeling
Bagger, F. O., Bruedigam, C. & Lane, S. W., 2016, In: Genomics Data. 7, p. 275-280 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Autoencoding beyond pixels using a learned similarity metric
Larsen, A. B. L., Sønderby, S. K., Larochelle, H. & Winther, Ole, 2016, Proceedings of The 33rd International Conference on Machine Learning. Balcan, M. F. & Weinberger, K. Q. (eds.). p. 1558–1566 9 p. (JMLR: Workshop and Conference Proceedings, Vol. 48).Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation
Feng, Y., Vlassis, A., Roques, C., Lalonde, M. E., Gonzalez Aguilera, C., Lambert, J. P., Lee, S., Zhao, X., Alabert, C., Johansen, Jens Vilstrup, Paquet, E., Yang, X. J., Gingras, A. C., Côté, J. & Groth, Anja, 2016, In: EMBO Journal. 35, 2, p. 176-192 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Bayesian inference of protein ensembles from SAXS data
Antonov, L. D., Olsson, S., Boomsma, Wouter & Hamelryck, Thomas Wim, 2016, In: Physical Chemistry Chemical Physics. 18, 8, p. 5832-5838 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
- 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, , 2016, In: Science. 354, 6311, p. 477-481 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
- Published
Coalescent inference using serially sampled, high-throughput sequencing data from intrahost HIV infection
Dialdestoro, K., Sibbesen, Jonas Andreas, Sørensen, L. M., Raghwani, J., Gall, A., Kellam, P., Pybus, O. G., Hein, J. & Jenkins, P. A., 2016, In: Genetics (Print). 202, 4, p. 1449-1472 24 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Combined transcriptomic and proteomic analysis of the posterior salivary gland from the southern blue-ringed octopus and the southern sand octopus
Whitelaw, B. L., Strugnell, J. M., Faou, P., Rodrigues da Fonseca, Rute Andreia, Hall, N. E., Norman, M., Finn, J. & Cooke, I. R., 2016, In: Journal of Proteome Research. 15, 9, p. 3284-3297 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.)
Jacobsen, M. W., Rodrigues da Fonseca, Rute Andreia, Bernatchez, L. & Hansen, M. M., 2016, In: Molecular Phylogenetics and Evolution. 95, p. 161-170 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Computational Investigations of Post-Transcriptional Regulation: The Intricate Dependency of MicroRNA Regulation on RNA-Binding Proteins
Rasmussen, S. H., 2016, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
Computational redesign of thioredoxin is hypersensitive towards minor conformational changes in the backbone template
Johansson, Kristoffer Enøe, Johansen, Nicolai Tidemand, Christensen, S., Horowitz, S., Bardwell, J. C. A., Olsen, Johan Gotthardt, Willemoës, Martin, Lindorff-Larsen, Kresten, Ferkinghoff-Borg, J., Hamelryck, Thomas Wim & Winther, Jakob R., 2016, In: Journal of Molecular Biology. 428, 21, p. 4361-4377 17 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
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
Fast and sensitive taxonomic classification for metagenomics with Kaiju
Menzel, P., Ng, K. L. & Krogh, Anders, 2016, In: Nature Communications. 7, 9 p., 11257.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetic consequences of human forest exploitation in two colobus monkeys in Guinea Bissau
Minhos, T., Chikhi, L., Sousa, C., Vicente, L. M., da Silva, M. F., Heller, Rasmus, Casanova, C. & Bruford, M. W., 2016, In: Biological Conservation. 194, p. 194-208 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetics of Type 2 diabetes: the power of isolated populations
Lepola, Mette Andersen, Pedersen, C. T., Moltke, Ida, Hansen, Torben, Albrechtsen, Anders & Grarup, Niels, 2016, In: Current Diabetes Reports. 16, 7, 9 p., 65.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
Smitz, N., Van Hooft, P., Heller, Rasmus, Cornélis, D., Chardonnet, P., Kraus, R., Greyling, B., Crooijmans, R., Groenen, M. & Michaux, J., 2016, In: Mammalian Biology. 81, 6, p. 595-603 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identification of novel genetic determinants of erythrocyte membrane fatty acid composition among Greenlanders
Lepola, Mette Andersen, Jørsboe, E., Sandholt, C. H., Grarup, Niels, Jørgensen, M. E., Færgeman, N. J., Bjerregaard, P., Pedersen, Oluf Borbye, Moltke, Ida, Hansen, Torben & Albrechtsen, Anders, 2016, In: P L o S Genetics. 12, 6, 19 p., e1006119.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Iron replacement therapy: do we need new guidelines?
Nielsen, Ole Haagen, Coskun, M. & Weiss, G., 2016, In: Current Opinion in Gastroenterology. 32, 2, p. 128-135 8 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Isolation and characterization of the first Xylanolytic hyperthermophilic euryarchaeon Thermococcus sp strain 2319x1 and its unusual multidomain glycosidase
Gavrilov, S. N., Stracke, C., Jensen, K., Menzel, P., Kallnik, V., Slesarev, A., Sokolova, T., Zayulina, K., Bräsen, C., Bonch-Osmolovskaya, E. A., Peng, Xu, Kublanov, I. V. & Siebers, B., 2016, In: Frontiers in Microbiology. 7, 17 p., 552.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
Mathelier, A., Fornes, O., Arenillas, D. J., Chen, C., Denay, G., Lee, J., Shi, W., Shyr, C., Tan, G., Worsley-Hunt, R., Zhang, A. W., Parcy, F., Lenhard, B., Sandelin, Albin Gustav & Wasserman, W. W., 2016, In: Nucleic Acids Research. 44, D1, p. D110-D115 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Ladder variational autoencoders
Sønderby, C. K., Raiko, T., Maaløe, L., Sønderby, S. K. & Winther, Ole, 2016, Advances in Neural Information Processing Systems 29 (NIPS 2016). Lee, D. D., Sugiyama, M., Luxburg, U. V., Guyon, I. & Garnett, R. (eds.). Curran Associates, Inc., p. 3745-3753 9 p. (Advances in Neural Information Processing Systems, Vol. 29).Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
Next-generation biology: sequencing and data analysis approaches for non-model organisms
Rodrigues da Fonseca, Rute Andreia, Albrechtsen, Anders, Themudo, G. E. C., Ramos Madrigal, Jazmin, Sibbesen, Jonas Andreas, Sørensen, L. M., Zepeda Mendoza, M. L., Campos, P., Heller, Rasmus & Pereira, R., 2016, In: Marine Genomics. 30, p. 3-13Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs
Islin, S. R., Menzel, P., Krogh, Anders, Young, M. & Peng, Xu, 2016, In: Environmental Microbiology. 18, 3, p. 863-874 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Nye artsbestemmelser af skind fra jernalderen– forhistoriske proteiner fra skindkapper fundet i danske moser
Brandt, Luise Ørsted, Cappellini, Enrico, Mannering, U. & Schmidt, A., 2016, In: Nationalmuseets Arbejdsmark. p. 234-247Research output: Contribution to journal › Journal article › Research › peer-review
- Published
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
Ienasescu, H., Li, K., Andersson, Robin, Vitezic, M., Rennie, Sarah, Chen, Y., Vitting-Seerup, K., Lagoni, E., Boyd, M., Lange, Jette Bornholdt, de Hoon, M. J. L., Kawaji, H., Lassmann, T., FANTOM Consortium, F. C., Hayashizaki, Y., Forrest, A. R. R., Carninci, P. & Sandelin, Albin Gustav, 2016, In: Database: The Journal of Biological Databases and Curation. 2016, 0, 10 p., baw144.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Oncogenic p95HER2 regulates Na+-HCO3- cotransporter NBCn1 mRNA stability in breast cancer cells via 3'UTR-dependent processes
Gorbatenko, A., Olesen, C. W., Loebl, N., Sigurdsson, H. H., Bianchi, C., Pedraz Cuesta, E., Christiansen, Jan & Pedersen, Stine Helene Falsig, 2016, In: Biochemical Journal. 473, 21, p. 4027-4044 18 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality
Pundhir, Sachin, Bagger, F. O., Lauridsen, F. K. B., Rapin, N. P. J. & Porse, Bo Torben, 2016, In: Nucleic Acids Research. 44, 9, p. 4037-4051 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Pharmacology and optimization of thiopurines and methotrexate in inflammatory bowel disease
Coskun, M., Steenholdt, Casper, de Boer, N. K. & Nielsen, Ole Haagen, 2016, In: Clinical Pharmacokinetics. 55, 3, p. 257-274 18 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Postglacial viability and colonization in North America’s ice-free corridor
Pedersen, Mikkel Winther, Ruter, Anthony Henry, Schweger, C., Friebe, H., Staff, R. A., Kjeldsen, Kristian Kjellerup, Zepeda Mendoza, M. L., Beaudoin, A. B., Zutter, C., Larsen, Nicolaj Krog, Potter, B. A., Nielsen, Rasmus, Rainville, R. A., Orlando, L. A. A., Meltzer, D. J., Kjær, Kurt H. & Willerslev, Eske, 2016, In: Nature. 537, 7618, p. 45–49 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters
Chen, Y., Pai, A. A., Herudek, J., Lubas, M., Meola, N., Järvelin, A. I., Andersson, Robin, Pelechano, V., Steinmetz, L. M., Jensen, T. H. & Sandelin, Albin Gustav, 2016, In: Nature Genetics. 48, 9, p. 984-994 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Probabilistic Methods for Processing High-Throughput Sequencing Signals
Sørensen, L. M., 2016, Department of Biology, Faculty of Science, University of Copenhagen. 173 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Probabilistic Transcriptome Assembly and Variant Graph Genotyping
Sibbesen, Jonas Andreas, 2016, Department of Biology, Faculty of Science, University of Copenhagen. 119 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
RNA assemblages orchestrate complex cellular processes
Nielsen, Finn Cilius, Hansen, H. T. & Christiansen, Jan, 2016, In: BioEssays. 38, 7, p. 674-681 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
RNA sequencing of trigeminal ganglia in Rattus Norvegicus after glyceryl trinitrate infusion with relevance to migraine
Pedersen, S. H., Sørensen, L. M., Ramachandran, R., Sibbesen, Jonas Andreas, Yakimov, V., Christensen, R. E., Hansen, Thomas Folkmann, Krogh, Anders, Olesen, Jes & Olesen, I. J., 2016, In: P L o S One. 11, 5, 13 p., e0155039.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Regulating retrotransposon activity through the use of alternative transcription start sites
Persson, J., Steglich, B., Smialowska, A., Boyd, M., Lange, Jette Bornholdt, Andersson, Robin, Schurra, C., Arcangioli, B., Sandelin, Albin Gustav, Nielsen, Olaf & Ekwall, K., 2016, In: E M B O Reports. 17, 5, p. 753-768 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Sequential neural models with stochastic layers
Fraccaro, M., Sønderby, S. K., Paquet, U. & Winther, Ole, 2016, Neural Information Processing Systems 2016. Lee, D. D., Sugiyama, M., Luxburg, U. V., Guyon, I. & Garnett, R. (eds.). Neural Information Processing Systems Foundation, p. 2207-2215 9 p. (Advances in Neural Information Processing Systems, Vol. 29).Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
Testing parametric models in linear-directional regression
Garcia Portugues, E., van Keilegom, I., Crujeiras, R. M. & González-Manteiga, W., 2016, In: Scandinavian Journal of Statistics. 43, 4, p. 1178-1191 14 p.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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