- 2019
- Published
Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
Chen, L., Qin, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., Su, W., Liu, G., Li, Q., Fu, W., Pan, X., Liu, C., Yang, J., Zhang, C., Yin, Y., Wang, Y. & 32 others, , 2019, In: Science. 364, 6446, p. 1152-Research output: Contribution to journal › Journal article › Research › peer-review
- Published
More grist for the mill? Species delimitation in the genomic era and its implications for conservation
Stanton, D. W. G., Frandsen, P., Waples, R. K., Heller, Rasmus, Russo, I. M., Orozco-terWengel, P. A., Pedersen, C. T., Siegismund, Hans Redlef & Bruford, M. W., 2019, In: Conservation Genetics. 20, 1, p. 101-113Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML
Jakobsen, J. S., Laursen, L. G., Schuster, Mikkel Bruhn, Pundhir, Sachin, Schoof, E., Ge, Y., d'Altri, T., Vitting-Seerup, K., Rapin, N., Gentil, C., Jendholm, J., Theilgaard-Mønch, Kim, Reckzeh, K., Bullinger, L., Döhner, K., Hokland, P., Fitzgibbon, J. & Porse, Bo Torben, 2019, In: Science Advances. 5, 7, p. 1-16 16 p., eaaw4304.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
NetSurfP-2.0: improved prediction of protein structural features by integrated deep learning
Klausen, M. S., Jespersen, M. C., Nielsen, H., Jensen, K. K., Jurtz, V. I., Sønderby, C. K., Sommer, M. O. A., Winther, Ole, Nielsen, M., Petersen, Bent & Marcatili, P., 2019, In: Proteins: Structure, Function and Bioinformatics. 87, 6, p. 520-527Research output: Contribution to journal › Journal article › Research › peer-review
- Published
PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells
Agrawal-Singh, S., Lerdrup, Mads, Gomes, A. R., van de Werken, H. J. G., Johansen, Jens Vilstrup, Andersson, Robin, Sandelin, Albin Gustav, Helin, K. & Hansen, K., 2019, In: eLife. 8, p. 1-32 32 p., e40364.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array
Makarova, K. S., Karamycheva, S., Shah, S. A., Vestergaard, G. A., Garrett, Roger Antony & Koonin, E. V., 2019, In: FEMS Microbiology Letters. 366, 7, 5 p., fnz079.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Probabilistic methods for the analysis of genome-wide data for admixed populations including association studies in Greenlandic Inuit
Jørsboe, E., 2019, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
Relatedness, admixture and the genetic history of Greenland-European contact
Waples, R., 2019, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads
Prada Luengo, Inigo, Krogh, Anders, Sørensen, L. M. & Regenberg, Birgitte, 2019, In: BMC Bioinformatics. 20, 9 p., 663.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Single mRNP Analysis Reveals that Small Cytoplasmic mRNP Granules Represent mRNA Singletons
Mateu-Regué, À., Christiansen, Jan, Bagger, F. O., Winther, O., Hellriegel, C. & Nielsen, Finn Cilius, 2019, In: Cell Reports. 29, 3, p. 736-748, e1-e4Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Testing for Hardy-Weinberg equilibrium in structured populations using genotype or low-depth next generation sequencing data
Meisner, Jonas & Albrechtsen, Anders, 2019, In: Molecular Ecology Resources. 19, 5, p. 1144-1152 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The epigenetic factor BORIS (CTCFL) controls the androgen receptor regulatory network in ovarian cancer
Salgado-Albarrán, M., González-Barrios, R., Guerra-Calderas, L., Alcaraz, N., Sánchez-Correa, T. E., Castro-Hernández, C., Sánchez-Pérez, Y., Aréchaga-Ocampo, E., García-Carrancá, A., de León, D. C., Herrera, L. A., Baumbach, J. & Soto-Reyes, E., 2019, In: Oncogenesis. 8, 12 p., 41.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The splicing factor RBM25 controls MYC activity in acute myeloid leukemia
Ge, Y., Schuster, Mikkel Bruhn, Pundhir, Sachin, Rapin, N., Bagger, F. O., Sidiropoulos, N., Hashem, N. & Porse, Bo Torben, 2019, In: Nature Communications. 10, 1, p. 1-14 14 p., 172.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The transmembrane autophagy cargo receptors ATI1 and ATI2 interact with ATG8 through intrinsically disordered regions with distinct biophysical properties
Sjøgaard, Ida Marie Zobbe, Bressendorff, Simon, Prestel, Andreas, Kausika, S., Oksbjerg, Emilie Duus, Kragelund, Birthe Brandt & Brodersen, Peter, 2019, In: Biochemical Journal. 476, 3, p. 449-465 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2018
- Published
Circular DNA elements of chromosomal origin are common in healthy human somatic tissue
Møller, H. D., Mohiyuddin, M., Prada Luengo, Inigo, Sailani, M. R., Halling, Jens Frey, Plomgaard, Peter Stendahl, Maretty, L., Hansen, Anders Johannes, Snyder, M. P., Pilegaard, Henriette, Lam, H. Y. K. & Regenberg, Birgitte, 1 Dec 2018, In: Nature Communications. 9, 12 p., 1069.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits
Gilly, A., Suyeges, D., Kuchenbaecker, K., Pollard, M., Southam, L., Hatzikotoulas, K., Farmaki, A-E., Bjornland, T., Waples, R., Appel, E. V. R., Casalone, E., Melloni, G., Kilian, B., Rayner, N. W., Ntalla, I., Kundu, K., Walter, K., Danesh, J., Butterworth, A., Barroso, I. & 5 others, , 1 Dec 2018, In: Nature Communications. 9, p. 1-9 4674.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
FoxA1 in synergy with IFNβ controls PDL1 expression in anti-inflammatory T cells via binding to a 60-nucleotide region in the Pdl1 promoter
Hadi, M., Rasmussen, L. M., Kosicki, M., Carlsson, R. & Issazadeh-Navikas, Shohreh, Oct 2018, p. 596-597.Research output: Contribution to conference › Conference abstract for conference › Research
- Published
Identification of novel high-impact recessively inherited type 2 diabetes risk variants in the Greenlandic population
Grarup, Niels, Moltke, Ida, Lepola, Mette Andersen, Bjerregaard, P., Larsen, C. V. L., Dahl-Petersen, I. K., Jørsboe, E., Tiwari, H. K., Hopkins, S. E., Wiener, H. W., Boyer, B. B., Linneberg, Allan René, Pedersen, Oluf Borbye, Jørgensen, M. E., Albrechtsen, Anders & Hansen, Torben, 1 Sep 2018, In: Diabetologia. 61, 9, p. 2005–2015Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations
Barbosa, C. S., Rodrigues da Fonseca, Rute Andreia, Batista, T. M., Barreto, M. A., Argolo, C. S., de Carvalho, M. R., Jordao do Amaral, D. O., de Andrade Silva, E. M., Arevalo-Gardini, E., Hidalgo, K. S., Franco, G. R., Pirovani, C. P., Micheli, F. & Gramacho, K. P., 3 Jul 2018, In: BMC Genomics. 19, 12 p., 509.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
- Published
YeastFab: High-Throughput Genetic Parts Construction, Measurement, and Pathway Engineering in Yeast
Garcia-Ruiz, E., Auxillos, Jamie Yam, Li, T., Dai, J. & Cai, Y., 1 Jan 2018, Methods in Enzymology. Scrutton, N. (ed.). Academic Press, p. 277-306 30 p. (Methods in Enzymology, Vol. 608).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
"Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus
Machado, A. M., Tørresen, O. K., Kabeya, N., Couto, A., Petersen, Bent, Felicio, M., Campos, P. F., Fonseca, E., Bandarra, N., Lopes-Marques, M., Ferraz, R., Ruivo, R., Fonseca, M. M., Jentoft, S., Monroig, Ó., Rodrigues da Fonseca, Rute Andreia & Castro, L. F. C., 2018, In: Genes. 9, 10, p. 1-13 485.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A new class of genic nuclear RNA species in Arabidopsis
van Wonterghem, M., Thieffry, A., Boyd, M., Lange, Jette Bornholdt & Brodersen, Peter, 2018, In: FEBS Letters. 592, 4, p. 631-643 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias
Machado, A. M., Felício, M., Fonseca, E., Rodrigues da Fonseca, Rute Andreia & Castro, L. F. C., 2018, In: Data in Brief. 18, p. 276-284 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A southern African origin and cryptic structure in the highly mobile plains zebra
Pedersen, C. T., Albrechtsen, Anders, Etter, P. D., Johnson, E. A., Orlando, L., Chikhi, L., Siegismund, Hans Redlef & Heller, Rasmus, 2018, In: Nature Ecology & Evolution. 2, 3, p. 491-498 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Accurate genotyping across variant classes and lengths using variant graphs
Sibbesen, Jonas Andreas, Maretty, L., Krogh, Anders, Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Have, C. T., Bork-Jensen, J., Guo, X., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Wang, J. & Brunak, Søren, 2018, In: Nature Genetics. 50, p. 1054-1059 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis
Arribas Hernandez, Laura, Bressendorff, Simon, Hansen, M. H., Poulsen, C., Erdmann, S. & Brodersen, Peter, 2018, In: Plant Cell. 30, 5, p. 952-967 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Ancient genomes revisit the ancestry of domestic and Przewalski's horses
Gaunitz, C., Fages, A. A., Hanghøj, K. E., Albrechtsen, A., Khan, N., Schubert, M., Seguin-Orlando, A., Owens, I. J., Felkel, S., Bignon-Lau, O., Damgaard, P. D. B., Mittnik, A., Mohaseb, A. F., Davoudi, H., Alquraishi, S., Alfarhan, A. H., Al-Rasheid, K. A. S., Crubézy, E., Benecke, N., Olsen, S. & 27 others, , 2018, In: Science. 360, 6384, p. 111-114 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios
Matey-Hernandez, M. L., Danish Pan Genome Consortium, D. P. G. C., Brunak, Søren, Izarzugaza, J. M. G., Sørensen, L. M., Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Belling, K. G., Have, C. T., Bork-Jensen, J., Sun, J., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Wang, J., Eiberg, Hans Rudolf Lytchoff & Kristiansen, Karsten, 2018, In: BMC Bioinformatics. 19, p. 1-12 239.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Binning microbial genomes using deep learning
Nissen, J. N., Sønderby, C. K., Armenteros, J. J. A., Grønbech, Christopher Heje, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2018, (bioRxiv).Research output: Working paper › Preprint › Research
- Published
CTCF-KDM4A complex correlates with histone modifications that negatively regulate CHD5 gene expression in cancer cell lines
Guerra-Calderas, L., González-Barrios, R., Patiño, C. C., Alcaraz, N., Salgado-Albarrán, M., de León, D. C., Hernández, C. C., Sánchez-Pérez, Y., Maldonado-Martínez, H. A., De la Rosa-Velazquez, I. A., Vargas-Romero, F., Herrera, L. A., García-Carrancá, A. & Soto-Reyes, E., 2018, In: OncoTarget. 9, 24, p. 17028-17042 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies
Boyd, M., Thodberg, M., Vitezic, M., Lange, J. B., Vitting-Seerup, K., Chen, Y., Coskun, M., Li, Y., Lo, B. Z. S., Klausen, P., Schweiger, P., Pedersen, A. G., Rapin, N. P. J-P., Skovgaard, K., Dahlgaard, K., Andersson, R., Terkelsen, T. B., Lilje, B., Troelsen, J. T., Petersen, A. M. & 7 others, , 2018, In: Nature Communications. 9, 19 p., 1661.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Characterization of the human RFX transcription factor family by regulatory and target gene analysis
Sugiaman-Trapman, D., Vitezic, M., Jouhilahti, E., Mathelier, A., Lauter, G., Misra, S., Daub, C. O., Kere, J. & Swoboda, P., 2018, In: BMC Genomics. 19, 15 p., 181.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
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
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
Exploring the central dogma from both ends. Omics integration of Hi-C sequencing and Raman spectroscopic data
Kumar, V., 2018, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
Farnesylated heat shock protein 40 is a component of membrane-bound RISC in Arabidopsis
Sjögren, L., Floris, M., Barghetti, A., Völlmy, F., Linding, R. & Brodersen, Peter, 2018, In: Journal of Biological Chemistry. 293, 43, p. 16608-16622Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetic architecture of obesity and related metabolic traits - recent insights from isolated populations
Lepola, Mette Andersen, Grarup, Niels, Moltke, Ida, Albrechtsen, Anders & Hansen, Torben, 2018, In: Current Opinion in Genetics and Development. 50, p. 74-78 5 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Genetic determinants of glycated hemoglobin levels in the Greenlandic Inuit population
Appel, V. R., Moltke, Ida, Jørgensen, M. E., Bjerregaard, P., Linneberg, Allan René, Pedersen, Oluf Borbye, Albrechtsen, Anders, Hansen, Torben & Grarup, Niels, 2018, In: European Journal of Human Genetics. 26, 6, p. 868-875 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History
Liu, S., Huang, S., Chen, F., Zhao, L., Yuan, Y., Francis, S. S., Fang, L., Li, Z., Lin, L., Liu, R., Zhang, Y., Xu, H., Li, S., Zhou, Y., Davies, R. W., Liu, Q., Walters, R. G., Lin, K., Ju, J., Komeliussen, T. & 18 others, , 2018, In: Cell. 175, 2, p. 347-359, e1-e7Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic insights into early maritime adaptations in Western Patagonia
jxb425, jxb425, Moreno Mayar, J. Víctor, Alfonso-Durruty, M., Morello, F., Vilar, M., Wells, S., Campos, P. & Willerslev, Eske, 2018, p. 64. 1 p.Research output: Contribution to conference › Conference abstract for conference › Research
- Published
Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia
De la Fuente, C., Avila-Arcos, M. C., Galimany, J., Carpenter, M. L., Homburger, J. R., Blanco, A., Contreras, P., Davalos, D. C., Reyes, O., Roman, M. S., Moreno-Estrada, A., Campos, P., Eng, C., Huntsman, S., Burchard, E. G., Malaspinas, A-S., Bustamante, C. D., Willerslev, E., Llop, E., Verdugo, R. A. & 1 others, , 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 17, p. E4006-E4012 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic investigations of horse domestication using ancient DNA and a novel statistical method for epigenomic inference from ancient DNA sequencing data
Hanghøj, Kristian Ebbesen, 2018, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
High definition urban fashion: Proteins reveal preferred resources for medieval leather shoes
Brandt, Luise Ørsted, 2018, Urban Network Evolutions: Towards a high-definition archaeology. Aarhus: Aarhus University Press, p. 241-247 7 p.Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Human adult HSCs can be discriminated from lineage-committed HPCs by the expression of endomucin
Reckzeh, K., Kizilkaya, Hüsün Sheyma, Helbo, A. S., Estruch Alrich, Montserrat, Deslauriers, A. G., Grover, A., Rapin, N., Asmar, F., Grønbæk, Kirsten, Porse, Bo Torben, Borregaard, N., Vestweber, D., Nerlov, C. & Theilgaard-Mønch, Kim, 2018, In: Blood advances. 2, 13, p. 1628-1632 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Inference and Learning in Deep Generative Models
Sønderby, C. K., 2018, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data
Meisner, Jonas & Albrechtsen, Anders, 2018, In: Genetics. 210, 2, p. 719-731Research output: Contribution to journal › Journal article › Research › peer-review
- Published
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
Khan, A., Fornes, O., Stigliani, A., Gheorghe, M., Castro-Mondragon, J. A., van der Lee, R., Bessy, A., Chèneby, J., Kulkarni, S. R., Tan, G., Baranasic, D., Arenillas, D. J., Sandelin, Albin Gustav, Vandepoele, K., Lenhard, B., Ballester, B., Wasserman, W. W., Parcy, F. & Mathelier, A., 2018, In: Nucleic Acids Research. 46, D1, p. D260-D266 7 p., gkx1126.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Jagten på antikkens bindemidler
Brandt, Luise Ørsted, 2018, In: Sfinx. 41, 1, p. 26-29 4 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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