- Published
Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility
Kielpinski, L. J. & Vinther, Jeppe, 2014, In: Nucleic Acids Research. 42, 8, 12 p., e70.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
High-Throughput Sequencing Based Methods of RNA Structure Investigation
Kielpinski, L. J., 2014, Department of Biology, Faculty of Science, University of Copenhagen. 137 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
RNase H sequence preferences influence antisense oligonucleotide efficiency
Kiełpiński, Ł. J., Hagedorn, P. H., Lindow, M. & Vinther, Jeppe, 15 Dec 2017, In: Nucleic Acids Research. 45, 22, p. 12932-12944 13 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
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
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
Menaquinone-7 in the reaction center complex of the green sulfur bacterium Chlorobium vibrioforme functions as the electron acceptor A1
Kjaer, B., Frigaard, Niels-Ulrik, Yang, F., Zybailov, B., Miller, M., Golbeck, J. H. & Scheller, H. V., 1998, In: Biochemistry. 37, 10, p. 3237-3242 5 p.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
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)
Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., Abeliovich, H., Abildgaard, M. H., Abudu, Y. P., Acevedo-Arozena, A., Adamopoulos, I. E., Adeli, K., Adolph, T. E., Adornetto, A., Aflaki, E., Agam, G., Agarwal, A., Aggarwal, B. B., Agnello, M., Agostinis, P. & 2,908 others, , 2021, In: Autophagy. 17, p. 1-382 382 p.Research output: Contribution to journal › Review › 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
A genome-wide scan in affected sib-pairs with idiopathic recurrent miscarriage suggests genetic linkage
Kolte, A. M., Nielsen, Henriette Svarre, Moltke, Ida, Degn, B., Pedersen, B., Sunde, L., Nielsen, Finn Cilius & Christiansen, O. B., 2011, In: Molecular Human Reproduction. 17, 6, p. 379-385 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetics as a novel tool in mining impact assessment and biomonitoring of critically endangered western chimpanzees in the Nimba Mountains, Guinea
Koops, K., Humle, T., Frandsen, P., Fitzgerald, M., D'Auvergne, L., Jackson, H. A., Børsting, Claus, Siegismund, Hans Redlef, Soumah, A. G. & Hvilsom, C., 2023, In: Conservation Science and Practice. 5, 4, 17 p., e12898.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
ANGSD: analysis of next generation sequencing data
Korneliussen, Thorfinn Sand, Albrechtsen, Anders & Nielsen, Rasmus, 2014, In: B M C Bioinformatics. 15, 13 p., 356.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data
Korneliussen, Thorfinn Sand, Moltke, Ida, Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: B M C Bioinformatics. 14, 14 p., 289.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
Implications of secondary structure prediction and amino acid sequence comparison of class I and class II phosphoribosyl diphosphate synthases on catalysis, regulation, and quaternary structure.
Krath, B. N. & Hove-Jensen, B., 2001, In: Protein Science. 10, 11, p. 2317-24 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Class II recombinant phosphoribosyl diphosphate synthase from spinach. Phosphate independence and diphosphoryl donor specificity.
Krath, B. N. & Hove-Jensen, B., 2001, In: Journal of Biological Chemistry. 276, 21, p. 17851-6 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A perdeuterated cryoprotectant for neutron studies and a demonstration of its use for neutron powder diffraction on L-(--)-ephedrine hemihydrate
Krebs, F. C., Jørgensen, M., Lebech, B. & Frydenvang, Karla Andrea, 2001, In: Journal of Applied Crystallography. 34, 2, p. 203-207 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
What are artificial neural networks?
Krogh, Anders, 2008, In: Nature Biotechnology. 26, 2, p. 195-7 2 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya
Kuja, J. O., Kanoi, B. N., Balboa, Renzo Fidel Ferdinando, Shiluli, C., Maina, M., Waweru, H., Gathii, K., Mungai, M., Masika, M., Anzala, O., Mwau, M., Clark, T. G., Waitumbi, J. & Gitaka, J., 2022, In: BMC Genomics. 23, 1, 8 p., 627.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
Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track
Kuo, T., Bath, T., Ma, S., Pattengale, N., YANG, Meng, Cao, Y., Hudson, C. M., Kim, J., Post, K., Xiong, L. & Ohno-Machado, L., 2021, In: International Journal of Medical Informatics. 154, 8 p., 104559.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server.
Käll, L., Krogh, Anders & Sonnhammer, E. L. L., 2007, In: Nucleic Acids Research. 35, Web Server issue, p. W429-32Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The LEAFY floral regulator displays pioneer transcription factor properties
Lai, X., Blanc-Mathieu, R., GrandVuillemin, L., Huang, Y., Stigliani, Arnaud, Lucas, J., Thévenon, E., Loue-Manifel, J., Turchi, L., Daher, H., Brun-Hernandez, E., Vachon, G., Latrasse, D., Benhamed, M., Dumas, R., Zubieta, C. & Parcy, F., 2021, In: Molecular Plant. 14, 5, p. 829-837 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The genetic architecture of sporadic and multiple consecutive miscarriage
Laisk, T., Soares, A. L. G., Ferreira, T., Painter, J. N., Censin, J. C., Laber, S., Bacelis, J., Chen, C. Y., Lepamets, M., Lin, K., Liu, S., Millwood, I. Y., Ramu, A., Southcombe, J., Andersen, M. S., Yang, L., Becker, C. M., Børglum, A. D., Gordon, S. D., Bybjerg-Grauholm, J. & 35 others, , 2020, In: Nature Communications. 11, 5980.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The role of miRNAs in human papilloma virus (HPV)-associated cancers: bridging between HPV-related head and neck cancer and cervical cancer
Lajer, C. B., Garnæs, E., Friis-Hansen, Lennart Jan, Norrild, B., Therkildsen, M. H., Glud, M., Rossing, M., Lajer, H., Svane, D., Skotte, L., Specht, Lena, von Buchwald, Christian & Nielsen, Finn Cilius, 2012, In: B J C. 106, p. 1526-1534 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identification of gene transcription start sites and enhancers responding to pulmonary carbon nanotube exposure in Vivo
Lange, Jette Bornholdt, Saber, A. T., Lilje, B., Boyd, M., Jørgensen, M., Chen, Y., Vitezic, M., Jacobsen, N. R., Poulsen, S. S., Berthing, T., Bressendorff, Simon, Vitting-Seerup, K., Andersson, Robin, Hougaard, K. S., Yauk, C. L., Halappanavar, S., Wallin, E. H. R., Vogel, U. & Sandelin, Albin Gustav, 2017, In: A C S Nano. 11, 4, p. 3597-3613 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptional reprogramming during floral fate acquisition
Larrieu, A., Brunoud, G., Guerault, A., Laine, S., Hennet, L., Stigliani, Arnaud, Gildea, I., Just, J., Soubigou-Taconnat, L., Balzergue, S., Davies, B., Scarpella, E., Helariutta, Y., Parcy, F. & Vernoux, T., 2022, In: iScience. 25, 7, 17 p., 104683.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
MicroRNA expression analysis and Multiplex ligation-dependent probe amplification in metastatic and non-metastatic uveal melanoma
Larsen, A., Holst, L. M., Kaczkowski, B., Andersen, M. T., Manfé, V., Siersma, Volkert Dirk, Kolko, Miriam, Kiilgaard, Jens Folke, Winther, Ole, Prause, J. U., Gniadecki, R. & Heegaard, Steffen, 2014, In: Acta Ophthalmologica. 92, 6, p. 541-549Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Hepatocyte growth factor activator inhibitor-2 prevents shedding of matriptase
Larsen, B. R., Steffensen, S. D. R., Nielsen, N. V. L., Friis, S., Godiksen, S., Lange, Jette Bornholdt, Soendergaard, C., Nonboe, Annika Weile, Andersen, M. N., Poulsen, Steen Seier, Szabo, R., Bugge, T. H., Lin, C., Skovbjerg, H., Jensen, J. K. & Vogel, Lotte, 1 Apr 2013, In: Experimental Cell Research. 319, 6, p. 918-929 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
24 Messages on a Sustainable Career in Research at UCPH
Larsen, K. R. (ed.), Wegener, H. C., Stein, A., Bach, A., Williams, A. R., Gall, C., Gravert, C., Gloriam, D. E., Lorenzen, E., Yvanez, E., Cappellini, E., Poulsen, F., Mortensen, J., Bentzen, J. S., Shik, J. Z., Miskowiak, K. W., Elgaard, K. K. E., Jønsson, K. A., Won, K. J., Nørgaard, L. C. & 9 others, , 2020, University of Copenhagen. 31 p.Research output: Book/Report › Report › Communication
- Published
Genetic analysis of the estrogen-related receptor alpha and studies of association with obesity and type 2 diabetes
Larsen, L. H., Rose, C. S., Sparsø, T., Overgaard, J., Torekov, Signe Sørensen, Grarup, Niels, Jensen, Dan Funck, Albrechtsen, Anders, Andersen, G., Ek, J., Glümer, C., Borch-Johnsen, K., Jørgensen, Tina, Hansen, Teis Schjals & Pedersen, Oluf Borbye, 2007, In: International Journal of Obesity. 31, 2, p. 365-70 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genome-wide association study of genetic variants in LPS-stimulated IL-6, IL-8, IL-10, IL-1ra and TNF-α cytokine response in a Danish Cohort
Larsen, M. H., Albrechtsen, Anders, Thørner, L. W., Werge, T., Hansen, T., Gether, Ulrik, Haastrup, E. & Ullum, H., 2013, In: PLOS ONE. 8, 6, 6 p., e66262.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
CDX2 regulates interleukin-33 gene expression in intestinal epithelial cells (LS174T)
Larsen, S., Seidelin, Jakob Benedict, Davidsen, J., Dahlgaard, K., Nielsen, Claus Henrik, Bennett, Eric Paul, Pedersen, O. B., Coskun, M. & Troelsen, J. T., 2021, In: FEBS Open Bio. 11, 6, p. 1638-1644Research 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
Mind the gap
Larsen-Ledet, Sven & Stein, Amelie, 2023, In: Structure. 31, 6, p. 641-643 3 p.Research output: Contribution to journal › Comment/debate › 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
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
Opportunities and challenges of macrogenetic studies
Leigh, D. M., van Rees, C. B., Millette, K. L., Breed, M. F., Schmidt, C., Bertola, Laura, Hand, B. K., Hunter, M. E., Jensen, E. L., Kershaw, F., Liggins, L., Luikart, G., Manel, S., Mergeay, J., Miller, J. M., Segelbacher, G., Hoban, S. & Paz-Vinas, I., 2021, In: Nature Reviews Genetics. 22, 12, p. 791-807 17 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Organismal benefits of transcription speed control at gene boundaries
Leng, Xueyuan, Ivanov, M., Kindgren, P., Malik, I., Thieffry, A., Brodersen, Peter, Sandelin, Albin Gustav, Kaplan, C. D. & Marquardt, Sebastian, 2020, In: EMBO Reports. 21, 4, 16 p., e49315.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Metazoan promoters: emerging characteristics and insights into transcriptional regulation
Lenhard, B., Sandelin, Albin Gustav & Carninci, P., 2012, In: Nature Reviews. Genetics. 13, 4, p. 233-245 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
Autophagy is required for stem cell mobilization by G-CSF
Leveque-El Mouttie, L., Vu, T., Lineburg, K. E., Kuns, R. D., Bagger, F. O., Teal, B. E., Lor, M., Boyle, G. M., Bruedigam, C., Mintern, J. D., Hill, G. R., MacDonald, K. P. A. & Lane, S. W., 2015, In: Blood. 125, 19, p. 2933-2936 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Molecular contacts for chlorosome envelope proteins revealed by cross-linking studies with chlorosomes from Chlorobium tepidum
Li, H., Frigaard, Niels-Ulrik & Bryant, D. A., 2006, In: Biochemistry. 45, 30, p. 9095-9103 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Convergent molecular evolution of thermogenesis and circadian rhythm in Arctic ruminants
Li, M., Li, X., Wu, Z., Zhang, G., Wang, N., Dou, M., Liu, S., Yang, C., Meng, G., Sun, H., Hvilsom, C., Xie, G., Li, Y., Li, Z. H., Wang, W., Jiang, Y., Heller, Rasmus & Wang, Y., 2023, In: Proceedings of the Royal Society B: Biological Sciences. 290, 1999, 10 p., 20230538.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
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., Zhang, Z., Zhang, Y., Wang, W., Li, J., Wei, F., Li, H., Jian, M., Li, J., Zhang, Z., Nielsen, R. & 103 others, , 2010, In: Nature. 463, 7279, p. 311-317 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population
Li, S., Besenbacher, S., Li, Y., Kristiansen, Karsten, Grarup, Niels, Albrechtsen, Anders, Sparsø, T. H., Korneliussen, Thorfinn Sand, Hansen, Torben, Wang, J., Nielsen, Rasmus, Pedersen, Oluf Borbye, Bolund, L. & Schierup, M. H., 2014, In: European Journal of Human Genetics. 22, p. 1040-1045 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Impact of ultrasonography on identifying noninvasive prenatal screening false-negative aneuploidy
Li, W., Zeng, F., Fan, B., Yu, N., Wu, J., Yang, Y., Huang, H., Li, S. & Peng, Z., 2020, In: Molecular genetics & genomic medicine. 8, 6, 7 p., e1213.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
Li, Y., Zhao, S., Ma, J., Li, D., Yan, L., Li, J., Qi, X., Guo, X., Zhang, L., He, W., Chang, R., Liang, Q., Guo, Y., Ye, C., Wang, X., Tao, Y., Guan, R., Wang, J., Liu, Y., Jin, L. & 15 others, , 2013, In: BMC Genomics. 14, 12 p., 579.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants
Li, Y., Vinckenbosch, N., Tian, G., Huerta-Sanchez, E., Jiang, T., Jiang, H., Albrechtsen, A., Andersen, G., Cao, H., Korneliussen, T. S., Grarup, N., Guo, Y., Hellman, I., Jin, X., Li, Q., Liu, J., Liu, X., Sparsø, T., Tang, M., Wu, H. & 18 others, , 2010, In: Nature Genetics. 42, 11, p. 969-72 4 p.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
vcfpp: a C++ API for rapid processing of the variant call format
Li, Z., 2024, In: Bioinformatics. 40, 2, 4 p., btae049.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Fast and accurate out-of-core PCA framework for large scale biobank data
Li, Z., Meisner, Jonas & Albrechtsen, Anders, 2023, In: Genome Research. 33, 9, p. 1599-1608 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Context dependency of nucleotide probabilities and variants in human DNA
Liang, Yuhu, Grønbæk, Christian, Fariselli, P. & Krogh, Anders, 2022, In: BMC Genomics. 23, 1, 15 p., 87.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Alternative Promoter Usage in Healthy and Inflamed Tissue
Lilje, B., 2015, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties
Lillestøl, R. K., Shah, S. A., Brügger, K., Redder, P., Phan, Safir Hien, Christiansen, Jan & Garrett, Roger Antony, 2009, In: Molecular Microbiology. 72, 1, p. 259-272Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A Targeted Multiomics Approach to Identify Biomarkers Associated with Rapid eGFR Decline in Type 1 Diabetes
Limonte, C. P., Valo, E., Montemayor, D., Afshinnia, F., Ahluwalia, T. S., Costacou, T., Darshi, M., Forsblom, C., Hoofnagle, A. N., Groop, P-H., Miller, R. G., Orchard, T. J., Pennathur, S., Rossing, P., Sandholm, N., Snell-Bergeon, J. K., Ye, H., Zhang, J., Natarajan, L., De Boer, I. H. & 1 others, , 2020, In: American Journal of Nephrology. 51, 10, p. 839-848 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Urinary Proteomics Identifies Cathepsin D as a Biomarker of Rapid eGFR Decline in Type 1 Diabetes
Limonte, C. P., Valo, E., Drel, V., Natarajan, L., Darshi, M., Forsblom, C., Henderson, C. M., Hoofnagle, A. N., Ju, W., Kretzler, M., Montemayor, D., Nair, V., Nelson, R. G., O’toole, J. F., Toto, R. D., Rosas, S. E., Ruzinski, J., Sandholm, N., Schmidt, I. M., Vaisar, T. & 12 others, , 2022, In: Diabetes Care. 45, 6, p. 1416-1427 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The history of Coast Salish “woolly dogs” revealed by ancient genomics and Indigenous Knowledge
Lin, A. T., Hammond-Kaarremaa, L., Liu, H-L., Stantis, C., McKechnie, I., Pavel, M., Pavel, S. S. M., Wyss, S. S., Sparrow, D. Q., Carr, K., Aninta, S. G., Perri, A., Hartt, J., Bergström, A., Carmagnini, A., Charlton, S., Dalén, L., Feuerborn, T. R., France, C. A. M., Gopalakrishnan, S. & 13 others, , 2023, In: Science. 382, 6676, p. 1303-1309 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
Lin, M. F., Kheradpour, P., Washietl, S., Parker, B. J., Pedersen, Jakob Skou & Kellis, M., 2011, In: Genome Research. 21, 11, p. 1916-28 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus)
Lin, Z., Chen, L., Chen, X., Zhong, Y., Yang, Y., Xia, W., Liu, C., Zhu, W., Wang, H., Yan, B., Yang, Y., Liu, X., Kvie, K. S., Røed, K. H., Wang, K., Xiao, W., Wei, H., Li, G., Heller, R., Gilbert, M. T. P. & 3 others, , 2019, In: Science. 364, 6446, p. 1154-+ 7 p., eaav6312.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A high-resolution map of human evolutionary constraint using 29 mammals
Lindblad-Toh, K., Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Jordan, G., Mauceli, E., Ward, L. D., Lowe, C. B., Holloway, A. K., Clamp, M., Gnerre, S., Moltke, Ida, Wen, J. & Pedersen, Jakob Skou, 27 Oct 2011, In: Nature. 478, 7370, p. 476-82 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Bioinformatical approaches to RNA structure prediction & Sequencing of an ancient human genome
Lindgreen, S., 2010, Biologisk Institut: Museum Tusculanum. 111 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.
Lindgreen, S., Gardner, P. P. & Krogh, Anders, 2007, In: Bioinformatics. 23, 24, p. 3304-11 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
SNPest: a probabilistic graphical model for estimating genotypes
Lindgreen, S., Krogh, Anders & Pedersen, Jakob Skou, 2014, In: BMC Research Notes. 7, 12 p., 298.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling
Lindgreen, S., Umu, S. U., Lai, A. S., Eldai, H., Liu, W., McGimpsey, S., Wheeler, N. E., Biggs, P. J., Thomson, N. R., Barquist, L., Poole, A. M. & Gardner, P. P., 2014, In: P L o S One. 10, 10, 10 p., e1003907.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
AdapterRemoval: easy cleaning of next generation sequencing reads
Lindgreen, S., 2012, In: BMC Research Notes. 5, 337, 7 p., 337.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.
Lindow, M., Jacobsen, A., Nygaard, S., Mang, Y. & Krogh, Anders, 2007, In: PLoS Computational Biology. 3, 11, p. e238Research output: Contribution to journal › Journal article › 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
Giraffa camelopardalis
Liu, C., Gao, J., Huang, J., Wang, W., Heller, Rasmus & Qiu, Q., 2021, In: Trends in Genetics. 37, 9, p. 860-861 2 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
A towering genome: Experimentally validated adaptations to high blood pressure and extreme stature in the giraffe
Liu, C., Gao, J., Cui, X., Li, Z., Chen, L., Yuan, Y., Zhang, Y., Mei, L., Zhao, L., Cai, D., Hu, M., Zhou, B., Li, Z., Qin, T., Si, H., Li, G., Lin, Z., Xu, Y., Zhu, C., Yin, Y. & 9 others, , 2021, In: Science Advances. 7, 12, 13 p., eabe9459.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears
Liu, S., Lorenzen, E., Fumagalli, M., Li, B., Harris, K., Xiong, Z., Zhou, L., Korneliussen, T. S., Somel, M., Babbitt, C., Wray, G., Li, J., He, W., Wang, Z., Fu, W., Xiang, X., Morgan, C. C., Doherty, A., O'Connell, M. J., McInerney, J. O. & 9 others, , 2014, In: Cell. 157, 4, p. 785-794 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Analysing human genomes at different scales
Liu, S., 2017, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- 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
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
Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations
Liu, X., Lin, L., Sinding, M. H. S., Bertola, L. D., Hanghøj, K., Quinn, L., Garcia-Erill, G., Rasmussen, M. S., Schubert, M., Pečnerová, P., Balboa, R. F., Li, Z., Heaton, M. P., Smith, T. P. L., Pinto, R. R., Wang, X., Kuja, J., Brüniche-Olsen, A., Meisner, J., Santander, C. G. & 8 others, , 2024, In: Nature Communications. 15, 1, 16 p., 2921.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Origin and expansion of the world’s most widespread pinniped: Range-wide population genomics of the harbour seal (Phoca vitulina)
Liu, X., Schjøtt, S. R., Granquist, S. M., Rosing-Asvid, A., Dietz, R., Teilmann, J., Galatius, A., Cammen, K., O’Corry-Crowe, G., Harding, K., Härkönen, T., Hall, A., Carroll, E. L., Kobayashi, Y., Hammill, M., Stenson, G., Kirstine Frie, A., Lydersen, C., Kovacs, K. M., Andersen, L. W. & 6 others, , 2022, In: Molecular Ecology. 31, 6, p. 1682-1699Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Clinical diagnosis of genetic disorders at both single-nucleotide and chromosomal levels based on BGISEQ-500 platform
Liu, Y., Mao, L., Huang, H., Li, W., Man, J., Zhang, W., Wang, L., Li, L., Sun, Y., Zhai, T., Guo, X., Du, L., Huang, J., Li, H., Wan, Y. & Wei, X., 2023, In: Human Genome Variation. 10, 1, 43 p., 15.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
FoxA1 directs the lineage and immunosuppressive properties of a novel regulatory T cell population in EAE and MS
Liu, Yawei, Carlsson, R., Comabella, M., Wang, J., Kosicki, M. K., Carrion, B., Hasan, M., Wu, X., Montalban, X., Dziegiel, Morten Hanefeld, Sellebjerg, Finn Thorup, Sørensen, Per Soelberg, Helin, K. & Issazadeh-Navikas, Shohreh, 16 Feb 2014, In: Nature Medicine.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals
Lizio, M., Harshbarger, J., Abugessaisa, I., Noguchi, S., Kondo, A., Severin, J., Mungall, C., Arenillas, D., Mathelier, A., Medvedeva, Y. A., Lennartsson, A., Drabløs, F., Ramilowski, J. A., Rackham, O., Gough, J., Andersson, R., Sandelin, A. G., Ienasescu, H-I., Ono, H., Bono, H. & 5 others, , 2017, In: Nucleic Acids Research. 45, D1, p. D737-D743 7 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
Can large language models reason about medical questions?
Liévin, V., Hother, C. E., Motzfeldt, A. G. & Winther, Ole, 2024, In: Patterns. 5, 3, 12 p., 100943.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Optimal Variance Control of the Score-Function Gradient Estimator for Importance Weighted Bounds
Liévin, V., Dittadi, A., Christensen, Anders & Winther, Ole, 2020, In: Advances in Neural Information Processing Systems. 2020-December, 12 p.Research output: Contribution to journal › Conference article › Research › peer-review
- Published
Variational Open-Domain Question Answering
Liévin, V., Motzfeldt, A. G., Jensen, I. R. & Winther, Ole, 2023, In: Proceedings of Machine Learning Research. 202, p. 20950-20977 28 p.Research output: Contribution to journal › Conference article › Research › peer-review
- Published
The RNA exosome contributes to gene expression regulation during stem cell differentiation
Llinares, M. L., Karadoulama, Evdoxia, Chen, Y., Wojenski, L. A., Villafano, G. J., Lange, Jette Bornholdt, Andersson, Robin, Core, L., Sandelin, Albin Gustav & Jensen, T. H., 2018, In: Nucleic Acids Research. 46, 21, p. 11502-11513Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome
Lohmueller, K. E., Albrechtsen, Anders, Li, Y., Kim, S. Y., Korneliussen, Thorfinn Sand, Vinckenbosch, N., Tian, G., Huerta-Sanchez, E., Feder, A. F., Grarup, Niels, Jørgensen, T., Jiang, T., Witte, D. R., Sandbæk, A., Hellmann, I., Lauritzen, T., Hansen, Torben, Pedersen, Oluf Borbye, Wang, J. & Nielsen, Rasmus, 2011, In: P L o S Genetics. 7, 10, 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes
Lohmueller, K. E., Sparsø, T. H., Li, Q., Galijatovic, E. A. A., Korneliussen, T. S., Albrechtsen, A., Banasik, K., Grarup, N., Hallgrimsdottir, I., Kiil, K., Oskari Kilpeläinen, T., Krarup, N. T., Pers, T. H., Sanchez, G., Hu, Y., DeGiorgio, M., Jørgensen, T., Sandbæk, A., Lauritzen, T., Brunak, S. & 6 others, , 5 Dec 2013, In: American Journal of Human Genetics. 93, 6, p. 1072-1086 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea
Lopes-Marques, M., Machado, A. M., Alves, L. Q., Fonseca, M. M., Barbosa, S., Sinding, M. S., Rasmussen, M. H., Iversen, M. R., Bertelsen, Mads Frost, Campos, P. F., Rodrigues da Fonseca, Rute Andreia, Ruivo, R. & Castro, L. F. C., 2019, In: MOLECULAR BIOLOGY AND EVOLUTION . 36, 6, p. 1270-1280Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Comparative phylogeography of African savannah ungulates
Lorenzen, Eline, Heller, Rasmus & Siegismund, Hans Redlef, 2012, In: Molecular Ecology. 21, 15, p. 3656-3670 15 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Species-specific responses of Late Quaternary megafauna to climate and humans
Lorenzen, E., Nogues, D. B., Orlando, L. A. A., Weinstock Arenovitz, J., Binladen, J. K. M. A., Marske, K. A., Ugan, A., Borregaard, M. K., Gilbert, M. T. P., Nielsen, R., Ho, S. Y. W., Goebel, T., Graf, K. E., Byers, D., Stenderup, J., Rasmussen, M., Campos, P., Leonard, J. A., Koepfli, K-P., Froese, D. & 35 others, , 2011, In: Nature. 479, 7373, p. 359-364 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A long-standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope
Lorenzen, Eline, Masembe, C., Arctander, P. & Siegismund, Hans Redlef, 2010, In: Journal of Biogeography. 37, 3, p. 571-581 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
Louis, Marie Georgette Yolande J, Korlević, P., Nykänen, M., Archer, F., Berrow, S., Brownlow, A., Lorenzen, Eline, O'Brien, J., Post, K., Racimo, Fernando, Rogan, E., Rosel, P. E., Sinding, Mikkel Holger Strander, van der Es, H., Wales, N., Fontaine, M. C., Gaggiotti, O. E. & Foote, A. D., 2023, In: Nature Communications. 14, 13 p., 4020.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Lactate receptor GPR81 drives breast cancer growth and invasiveness through regulation of ECM properties and Notch ligand DLL4
Jørgensen, Kathrine Lundø, Dmytriyeva, O., Spøhr, L., Alves, Eliana Carolina Goncalves, Yao, Jiayi, Puig Blasco, Laia, Trauelsen, Mette, Ponniah, M., Severin, M., Sandelin, Albin Gustav, Kveiborg, Marie, Schwartz, Thue W. & Pedersen, Stine Helene Falsig, 2023, In: BMC Cancer. 23, 1, 20 p., 1136.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Three de novo variants in KMT2A (MLL) identified by whole exome sequencing in patients with Wiedemann–Steiner syndrome
Luo, S., Bi, B., Zhang, W., Zhou, R., Chen, W., Zhao, P., Huang, Y., Yuan, L. & He, X., 2021, In: Molecular Genetics & Genomic Medicine. 9, 10, 11 p., e1798.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs
Lv, W., Pan, X., Han, P., Wang, Z., Feng, W., Xing, X., Wang, Q., Qu, K., Zeng, Y., Zhang, C., Xu, Z., Li, Y., Zheng, T., Lin, L., Liu, C., Liu, X., Li, H., Henriksen, R. A., Bolund, L., Lin, L. & 7 others, , 2022, In: Clinical and Translational Medicine. 12, 4, 16 p., e817.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes
Lykke-Andersen, S., Chen, Y., Ardal, B., Lilje, B., Waage, J. E., Sandelin, Albin Gustav & Jensen, T. H., 2014, In: Genes & Development. 28, p. 2498-2517 20 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Regulation of plant immunity via small RNA-mediated control of NLR expression
López Márquez, Diego, Del-Espino, Á., Ruiz-Albert, J., Bejarano, E. R., Brodersen, Peter & Beuzón, C. R., 2023, In: Journal of Experimental Botany. 74, 19, p. 6052-6068 17 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Modification of T cell responses by stem cell mobilization requires direct signaling of the T cell by G-CSF and IL-10
MacDonald, K. P. A., Le Texier, L., Zhang, P., Morris, H., Kuns, R. D., Lineburg, K. E., Leveque, L., Don, A. L., Markey, K. A., Vuckovic, S., Bagger, F. O., Boyle, G. M., Blazar, B. R. & Hill, G. R., 2014, In: Journal of Immunology. 192, 7, p. 3180-3189 10 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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