- 2020
- 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
A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome
Wu, G., Schmid, M., Rib, Leonor, Polak, P., Meola, N., Sandelin, Albin Gustav & Jensen, T. H., 2020, In: Cell Reports. 30, 7, p. 2387-2401, e1-e5Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 3 approved with reservations]
Orengo, C., Velankar, S., Wodak, S., Zoete, V., Bonvin, A. M. J. J., Elofsson, A., Feenstra, K. A., Gerloff, D. L., Hamelryck, T., Hancock, J. M., Helmer-Citterich, M., Hospital, A., Orozco, M., Perrakis, A., Rarey, M., Soares, C., Sussman, J. L., Thornton, J. M., Tuffery, P., Tusnady, G. & 3 others, , 2020, In: F1000Research. 9, 27 p., 278.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A draft genome sequence of the elusive giant squid, Architeuthis dux
da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â. M., Barrio-Hernandez, I., Hoving, H-J., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, B., Peñaloza, F., Musacchia, F., Alexander, G. C. & 24 others, , 2020, In: GigaScience. 9, 1, 12 p., giz152.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data
Moreno-Mayar, J. V., Korneliussen, Thorfinn Sand, Dalal, J., Renaud, Gabriel, Albrechtsen, Anders, Nielsen, Rasmus & Malaspinas, A., 2020, In: Bioinformatics. 36, 3, p. 828-841 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
An RNAi independent antiviral activity of the Arabidopsis thaliana DCL2
Nielsen, C. P. S., 2020, Department of Biology, Faculty of Science, University of Copenhagen. 104 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China
Cai, Y., Fu, W., Cai, D., Heller, R., Zheng, Z., Wen, J., Li, H., Wang, X., Alshawi, A., Sun, Z., Zhu, S., Wang, J., Yang, M., Hu, S., Li, Y., Yang, Z., Gong, M., Hou, Y., Lan, T., Wu, K. & 3 others, , 2020, In: Molecular Biology and Evolution. 37, 7, p. 2099-2109 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
CAncer bioMarker Prediction Pipeline (CAMPP) - A standardized framework for the analysis of quantitative biological data
Terkelsen, T., Krogh, Anders & Papaleo, E., 2020, In: PLOS Computational Biology. 16, 3, 20 p., e1007665.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cancer Cell Acid Adaptation Gene Expression Response is Correlated to Tumor-Specific Tissue Expression Profiles and Patient Survival
Yao, Jiayi, Czaplinska, D., Ialchina, Renata, Schnipper, J., Liu, B., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2020, In: Cancers. 12, 8, 27 p., 2183.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways
Thieffry, A., Vigh, Maria Louisa, Lange, Jette Bornholdt, Ivanov, M., Brodersen, Peter & Sandelin, Albin Gustav, 2020, In: The Plant Cell. 32, 6, p. 1845-1867 23 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Classifying disease-associated variants using measures of protein activity and stability
Jepsen, M. M., Fowler, D. M., Hartmann-Petersen, Rasmus, Stein, Amelie & Lindorff-Larsen, Kresten, 2020, Protein Homeostasis Diseases: Mechanisms and Novel Therapies. Pey, A. L. (ed.). Elsevier, p. 91-107Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome
Abildgaard, A. B., Andersen, Sarah Gersing, Larsen-Ledet, Sven, Nielsen, S. V., Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, In: Biomolecules. 10, 8, 24 p., 1141.Research output: Contribution to journal › Review › Research › peer-review
- Published
Community curation of bioinformatics software and data resources
Ison, J., Ménager, H., Brancotte, B., Jaaniso, E., Salumets, A., Raček, T., Lamprecht, A. L., Palmblad, M., Kalaš, M., Chmura, Piotr Jaroslaw, Hancock, J. M., Schwämmle, V. & Ienasescu, H. I., 2020, In: Briefings in Bioinformatics. 21, 5, p. 1697-1705 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Comparative transcriptomics of primary cells in vertebrates
Alam, T., Agrawal, S., Severin, J., Young, R. S., Andersson, R., Arner, E., Hasegawa, A., Lizio, M., Ramilowski, J. A., Abugessaisa, I., Ishizu, Y., Noma, S., Tarui, H., Taylor, M. S., Lassmann, T., Itoh, M., Kasukawa, T., Kawaji, H., Marchionni, L., Sheng, G. & 5 others, , 2020, In: Genome Research. 30, 7, p. 951-961 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets
Feuerborn, Tatiana Richtman, Palkopoulou, E., van der Valk, T., von Seth, J., Munters, A. R., Chrzanová Pecnerová, Patrícia, Dehasque, M., Ureña, I., Ersmark, E., Lagerholm, V. K., Krzewinska, M., Rodríguez-Varela, R., Götherström, A., Dalén, L. & Díez-del-Molino, D., 2020, In: BMC Genomics. 21, 10 p., 844.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cytoplasmic mRNPs revisited: Singletons and condensates
Mateu-Regue, A., Nielsen, Finn Cilius & Christiansen, Jan, 2020, In: BioEssays. 42, 12, 13 p., 2000097.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Daily estimates of clinical severity of symptoms in bipolar disorder from smartphone-based self-assessments
Busk, J., Faurholt-Jepsen, M., Frost, M., Bardram, J. E., Kessing, Lars Vedel & Winther, Ole, 2020, In: Translational Psychiatry. 10, 12 p., 194.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
De Novo Pathway Enrichment with KeyPathwayMiner
Alcaraz, N., Hartebrodt, A. & List, M., 2020, Protein-Protein Interaction Networks: Methods and Protocols. Canzar, S. & Ringeling, F. R. (eds.). Humana Press, p. 181-199 19 p. (Methods in Molecular Biology, Vol. 2074).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
De Novo Pathway-Based Classification of Breast Cancer Subtypes
List, M., Alcaraz, N. & Batra, R., 2020, Protein-Protein Interaction Networks: Methods and Protocols. Canzar, S. & Ringeling, F. R. (eds.). Humana Press, p. 201-213 13 p. (Methods in Molecular Biology, Vol. 2074).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Deep Learning for Diagnostic Binary Classification of Multiple-Lesion Skin Diseases
Thomsen, K., Christensen, A. L., Iversen, L., Lomholt, H. B. & Winther, Ole, 2020, In: Frontiers in Medicine. 7, 7 p., 574329.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detection of Viable and Total Bacterial Community in the Pit Mud of Chinese Strong-Flavor Liquor Using Propidium Monoazide Combined With Quantitative PCR and 16S rRNA Gene Sequencing
Tan, G., Zhou, R., Zhang, W., Hu, Y., Ruan, Z., Li, J., Zhang, C., Shen, D., Peng, N., Liang, Y. & Zhao, S., 2020, In: Frontiers in Microbiology. 11, 9 p., 896.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Determinants of enhancer and promoter activities of regulatory elements
Andersson, Robin & Sandelin, Albin Gustav, 2020, In: Nature Reviews Genetics. 21, 2, p. 71-87 17 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Estimating narrow-sense heritability using family data from admixed populations
Athanasiadis, G., Speed, D., Lepola, Mette Andersen, Appel, E. V. R., Grarup, Niels, Brandslund, I., Jørgensen, M. E., Larsen, C. V. L., Bjerregaard, P., Hansen, Torben & Albrechtsen, Anders, 2020, In: Heredity. 124, 6, p. 751-762 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Evaluation of model fit of inferred admixture proportions
Garcia Erill, Genís & Albrechtsen, Anders, 2020, In: Molecular Ecology Resources. 20, 4, p. 936-949Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Evolutionary Study of the Crassphage Virus at Gene Level
Rossi, A., Treu, L., Toppo, S., Zschach, Henrike, Campanaro, S. & Dutilh, B. E., 2020, In: Viruses. 12, 9, 13 p., 1035.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation
Bjørnkjær, Lene, Stein, Amelie, Grønbæk-Thygesen, Martin, Nygaard, L., Søltoft, C. L., Nielsen, S. V., Lisby, Michael, Ravid, T., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, In: PLOS Genetics. 16, 11, 28 p., e1009187.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Functional annotation of human long noncoding RNAs via molecular phenotyping
Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J-C., Ciani, Y., Kulakovskiy, I. V., Mendez, M., Ooi, J. L. C., Ouyang, J. F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I. V., Arner, E., Bonetti, A., Bono, H. & 96 others, , 2020, In: Genome Research. 30, 7, p. 1060-1072 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
GISA: using Gauss Integrals to identify rare conformations in protein structures
Grønbæk, Christian, Hamelryck, Thomas Wim & Røgen, P., 2020, In: PeerJ. 8, 16 p., e9159.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetic study of the Arctic CPT1A variant suggests that its effect on fatty acid levels is modulated by traditional Inuit diet
Senftleber, N., Jørgensen, M. E., Jørsboe, E., Imamura, F., Forouhi, N. G., Larsen, C. L., Bjerregaard, P., Hansen, Torben & Albrechtsen, Anders, 2020, In: European Journal of Human Genetics. 28, 11, p. 1592-1601 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genome wide association study of circulating interleukin 6 levels identifies novel loci
Ahluwalia, T. S., Armstrong, N. J., Aslibekyan, S., Beekman, M., Cheng, Y., deGeus, E., Delgado, G. E., Marek, D., Kanoni, S., Nolte, I. M., Porcu, E., Seppala, I., Standl, M., Teumer, A., Thalamuthu, A., Trompet, S., Benjamin, E. J., Feitosa, M. F., Homuth, G., Lahti, J. & 30 others, , 2020, In: European Journal of Human Genetics. 28, Supplement 1, p. 307-308 2 p.Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
- Published
Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena
Westbury, Michael Vincent, Hartmann, S., Barlow, A., Preick, M., Ridush, B., Nagel, D., Rathgeber, T., Ziegler, R., Baryshnikov, G., Sheng, G., Ludwig, A., Wiesel, I., Dalen, L., Bibi, F., Werdelin, L., Heller, Rasmus & Hofreiter, M., 2020, In: Science Advances. 6, 11, 11 p., eaay0456.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools
Prachar, Marek, Justesen, S., Steen-Jensen, D. B., Thorgrimsen, S., Jurgons, E., Winther, Ole & Bagger, F. O., 2020, In: Scientific Reports. 10, 8 p., 20465.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
Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo
Yang, M., Woolfenden, H. C., Zhang, Y., Fang, X., Liu, Q., Vigh, Maria Louisa, Cheema, J., Yang, X., Norris, M., Yu, S., Carbonell, A., Brodersen, Peter, Wang, J. & Ding, Y., 2020, In: Nucleic Acids Research. 48, 15, p. 8767-8781 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Investigation of transcriptional output and regulation in plants using Cap Analysis of Gene Expression (CAGE)
Thieffry, A., 2020, Department of Biology, Faculty of Science, University of Copenhagen. 128 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
JASPAR 2020: update of the open-access database of transcription factor binding profiles
Fornes, O., Castro-Mondragon, J. A., Khan, A., van der Lee, R., Zhang, X., Richmond, P. A., Modi, B. P., Correard, S., Gheorghe, M., Baranašić, D., Santana-Garcia, W., Tan, G., Chèneby, J., Ballester, B., Parcy, F., Sandelin, Albin Gustav, Lenhard, B., Wasserman, W. W. & Mathelier, A., 2020, In: Nucleic Acids Research. 48, D1, p. D87-D92 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Method Development for Next-Generation Sequencing Data in Population Genetics
Meisner, Jonas, 2020, Department of Biology, Faculty of Science, University of Copenhagen. 154 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
No Evidence for N7-Methylation of Guanosine (m7G) in Human let-7e
Vinther, Jeppe, 2020, In: Molecular Cell. 79, 2, p. 199-200 2 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
Novel HARS2 missense variants identified in individuals with sensorineural hearing impairment and Perrault syndrome
Karstensen, H. G., Rendtorff, N. D., Hindbæk, L. S., Colombo, R., Stein, Amelie, Birkebæk, N. H., Hartmann-Petersen, Rasmus, Lindorff-Larsen, Kresten, Højland, A. T., Petersen, M. B. & Tranebjærg, Lisbeth, 2020, In: European Journal of Medical Genetics. 63, 3, 6 p., 103733.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Occurrence and Functions of m6A and Other Covalent Modifications in Plant mRNA
Arribas Hernandez, Laura & Brodersen, Peter, 2020, In: Plant Physiology. 182, 1, p. 79-96 18 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Omega-3 fatty acids and risk of cardiovascular disease in Inuit: First prospective cohort study
Senftleber, N. K., Albrechtsen, Anders, Lauritzen, Lotte, Larsen, C. L., Bjerregaard, P., Diaz, L. J., Rønn, P. F. & Jørgensen, M. E., 2020, In: Atherosclerosis. 312, p. 28-34 7 p.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
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
Population genomics of the Viking world: [incl. correction]
Margaryan, A., Lawson, D. J., Sikora, M., Racimo, F., Rasmussen, S., Moltke, I., Cassidy, L. M., Jørsboe, E., Ingason, A., Pedersen, M. W., Korneliussen, T., Wilhelmson, H., Buś, M. M., de Barros Damgaard, P., Martiniano, R., Renaud, G., Bhérer, C., Moreno-Mayar, J. V., Fotakis, A. K., Allen, M. & 30 others, , 2020, In: Nature. 585, 7825, p. 390-396 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Protein destabilization and degradation as a mechanism for hereditary disease
Nielsen, S. V., Schenstrøm, S. M., Christensen, Caspar Elo, Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, Protein Homeostasis Diseases: Mechanisms and Novel Therapies. Pey, A. L. (ed.). Elsevier, p. 111-125Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Recent insights on indirect mechanisms in developmental toxicity of nanomaterials
Dugershaw, B. B., Aengenheister, L., Hansen, Signe Schmidt Kjølner, Hougaard, Karin Sørig & Buerki-Thurnherr, T., 2020, In: Particle and Fibre Toxicology. 17, 22 p., 31.Research output: Contribution to journal › Review › Research › peer-review
- Published
Recurrent requirement for the m6A-ECT2/ECT3/ECT4 axis in the control of cell proliferation during plant organogenesis
Arribas Hernandez, Laura, Simonini, S., Hansen, M. H., Botterweg Paredes, E., Bressendorff, Simon, Dong, Y., Østergaard, L. & Brodersen, Peter, 2020, In: Development. 147, 14, 19 p., dev189134.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Replication Protein A (RPA) Mediates Radio-Resistance of Glioblastoma Cancer Stem-Like Cells
Pedersen, H., Obara, E. A. A., Elbæk, K. J., Vitting-Serup, K. & Hamerlik, P., 2020, In: International Journal of Molecular Sciences. 21, 5, 13 p., 1588.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
SPT6-driven error-free DNA repair safeguards genomic stability of glioblastoma cancer stem-like cells
Obara, E. A. A., Aguilar-Morante, D., Rasmussen, R. D., Frias, A., Vitting-Serup, K., Lim, Y. C., Elbæk, K. J., Pedersen, H., Vardouli, L., Jensen, K. E., Skjoth-Rasmussen, J., Brennum, J., Tuckova, L., Strauss, R., Dinant, C., Bartek, J. & Hamerlik, P., 2020, In: Nature Communications. 11, 14 p., 4709.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Scramble-in: A fast and efficient method to diversify and improve the yields of heterologous pathways in synthetic yeast
Swidah, R., Auxillos, Jamie Yam, Liu, W., Jones, S., Chan, T. F., Dai, J. & Cai, Y., 2020, Methods in Molecular Biology. Humana Press, p. 305-327 23 p. (Methods in Molecular Biology, Vol. 2205).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration
Terkelsen, T., Russo, F., Gromov, P., Haakensen, V. D., Brunak, Søren, Gromova, I., Krogh, Anders & Papaleo, E., 2020, In: Breast Cancer Research. 22, 1, 36 p., 73.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Sinonasal cancer
Husgafvel-Pursiainen, K., Carton, M., Luce, D., Wolff, H., Holmila, R., Schlünssen, V., Lange, Jette Bornholdt & Hansen, J., 2020, Occupational Cancers. Anttila, S. & Boffetta, P. (eds.). 2. ed. ed. Springer, p. 147-178 32 p.Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Systematic review of machine learning for diagnosis and prognosis in dermatology
Thomsen, K., Iversen, L., Titlestad, T. L. & Winther, Ole, 2020, In: Journal of Dermatological Treatment. 31, 5, p. 496-510Research output: Contribution to journal › Review › Research › peer-review
- Published
Targeted conservation genetics of the endangered chimpanzee
Frandsen, P., Fontsere, C., Nielsen, S. V., Hanghøj, Kristian Ebbesen, Castejon-Fernandez, N., Lizano, E., Hughes, D., Hernandez-Rodriguez, J., Korneliussen, Thorfinn Sand, Carlsen, F., Siegismund, Hans Redlef, Mailund, T., Marques-Bonet, T. & Hvilsom, C., 2020, In: Heredity. 125, 1-2, p. 15-27 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The Draft Genome of Red Lechwe, Kobus leche leche
Wang, B., Wang, Z., Zhou, J., Liu, W., Lin, Z., Zhang, C., Liu, G., Zhou, B., Wan, W., Zhao, R., Wang, W., Heller, Rasmus & Chen, L., 2020, In: Frontiers in Genetics. 11, 7 p., 582638.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The RNA exosome shapes the expression of key protein-coding genes
Wu, M., Karadoulama, Evdoxia, Lloret-llinares, M., Rouviere, J. O., Vaagensø, C. S., Moravec, M., Li, B., Wang, J., Wu, G., Gockert, M. A. M., Pelechano, V., Jensen, T. H. & Sandelin, Albin Gustav, 2020, In: Nucleic Acids Research. 48, 15, p. 8509-8528Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1
Gazova, I., Lefevre, L., Bush, S. J., Clohisey, S., Arner, E., de Hoon, M., Severin, J., van Duin, Lucas, Andersson, Robin, Lengeling, A., Hume, D. A. & Summers, K. M., 2020, In: Frontiers in Cell and Developmental Biology. 8, 21 p., 498.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The derived allele of a novel intergenic variant at chromosome 11 associates with lower body mass index and a favorable metabolic phenotype in Greenlanders
Andersen, M. K., Jørsboe, E., Skotte, L., Hanghøj, K., Sandholt, C. H., Moltke, I., Grarup, N., Kern, T., Mahendran, Y., Søborg, B., Bjerregaard, P., Larsen, C. V. L., Dahl-Petersen, I. K., Tiwari, H. K., Feenstra, B., Koch, A., Wiener, H. W., Hopkins, S. E., Pedersen, O., Melbye, M. & 4 others, , 2020, In: PLOS Genetics. 16, 1, 17 p., e1008544.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The effect of diabetes and the common diabetogenic TBC1D4 p.Arg684Ter variant on cardiovascular risk in Inuit in Greenland
Overvad, M., Diaz, L. J., Bjerregaard, P., Pedersen, M. L., Larsen, C. V. L., Senftleber, N., Grarup, Niels, Hansen, Torben & Jørgensen, M. E., 2020, In: Scientific Reports. 10, 9 p., 22081.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 origin of domestication genes in goats
Zheng, Z., Wang, X., Li, M., Li, Y., Yang, Z., Wang, X., Pan, X., Gong, M., Zhang, Y., Guo, Y., Wang, Y., Liu, J., Cai, Y., Chen, Q., Okpeku, M., Colli, L., Cai, D., Wang, K., Huang, S., Sonstegard, T. S. & 16 others, , 2020, In: Science Advances. 6, 21, eaaz5216.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The traditional diet and genetic architecture of the Greenlandic Inuit and their cardiovascular effects
Senftleber, N. K., 2020, Department of Biology, Faculty of Science, University of Copenhagen. 163 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
scVAE: variational auto-encoders for single-cell gene expression data
Grønbech, Christopher Heje, Vording, M. F., Timshel, P., Sønderby, C. K., Pers, Tune H & Winther, Ole, 2020, In: Bioinformatics. 36, 16, p. 4415-4422 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2019
- Published
ERG Controls B Cell Development by Promoting Igh V-to-DJ Recombination
Søndergaard, E., Rauch, A., Michaut, Magali, Rapin, N., Rehn, M., Wilhelmson, Anna, Camponeschi, A., Hasemann, M. S., Bagger, F. O., Jendholm, J., Knudsen, K. J., Mandrup, S., Mårtensson, I. L. & Porse, Bo Torben, 26 Nov 2019, In: Cell Reports. 29, 9, p. 2756-2769.e6 21 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A step-by-step guide to analyzing CAGE data using R/Bioconductor
Thodberg, Malte & Sandelin, Albin Gustav, 18 Jun 2019, In: F1000Research. 8, 49 p., 886.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding
Hanghøj, Kristian Ebbesen, Moltke, Ida, Andersen, P. A., Manica, A. & Korneliussen, Thorfinn Sand, May 2019, In: GigaScience. 8, 5, 9 p., giz034.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Multiplex Genome Engineering for Optimizing Bioproduction in Saccharomyces cerevisiae
Auxillos, Jamie Yam, Garcia-Ruiz, E., Jones, S., Li, T., Jiang, S., Dai, J. & Cai, Y., 19 Mar 2019, In: Biochemistry. 58, 11, p. 1492-1500 9 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Comprehensive profiling of the fission yeast transcription start site activity during stress and media response
Thodberg, Malte, Thieffry, A., Lange, Jette Bornholdt, Boyd, M., Holmberg, Christian, Azad, A., Workman, C. T., Chen, Y., Ekwall, K., Nielsen, Olaf & Sandelin, Albin Gustav, 28 Feb 2019, In: Nucleic Acids Research. 47, 4, p. 1671-1691 21 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
SignalP 5.0 improves signal peptide predictions using deep neural networks
Armenteros, J. J. A., Tsirigos, Konstantinos, Sønderby, C. K., Petersen, T. N., Winther, Ole, Brunak, Søren, von Heijne, G. & Nielsen, H., 18 Feb 2019, In: Nature Biotechnology. 37, 4, p. 420-423Research output: Contribution to journal › Journal article › Communication
- Published
Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers [version 1; peer review: not peer reviewed]
Shome, S., Parra, R. G., Fatima, N., Monzon, A. M., Cuypers, B., Moosa, Y., Coimbra, N. D. R., Assis, J., Giner-Delgado, C., Dönertaş, H. M., Cuesta-Astroz, Y., Saarunya, G., Allali, I., Gupta, S., Srivastava, A., Kalsan, M., Valdivia, C., Olguin-Orellana, G. J., Papadimitriou, S., Parisi, D. & 22 others, , 1 Jan 2019, In: F1000Research. 8, 9 p., 1574.Research output: Contribution to journal › Editorial › Research
- Published
A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2
Garland, W., Comet, I., Wu, M., Radzisheuskaya, A., Rib, Leonor, Vitting-Seerup, K., Lloret-Llinares, M., Sandelin, Albin Gustav, Helin, K. & Jensen, T. H., 2019, In: Cell Reports. 29, 7, p. 1800-1811 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A Probabilistic Programming Approach to Protein Structure Superposition
Sanz Moreta, Lys, Al-Sibahi, A. S., Theobald, D., Bullock, W., Rommes, B. N., Manoukian, Andreas & Hamelryck, Thomas Wim, 2019, 2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2019. Baruzzo, G., Daberdaku, S., Di Camillo, B., Furini, S., Giordano, E. D. & Nicosia, G. (eds.). IEEE, 5 p. 8791469Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
A perspective on inverse design of battery interphases using multi-scale modelling, experiments and generative deep learning
Bhowmik, A., Castelli, I. E., Garcia-Lastra, J. M., Bjørn-Jørgensen, P., Winther, Ole & Vegge, T., 2019, In: Energy Storage Materials. 21, p. 446-456Research output: Contribution to journal › Review › Research › peer-review
- Published
Allele frequency-free inference of close familial relationships from genotypes or low-depth sequencing data
Waples, R. K., Albrechtsen, Anders & Moltke, Ida, 2019, In: Molecular Ecology. 28, 1, p. 35-48 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Ancestry-specific association mapping in admixed populations
Skotte, L., Jørsboe, E., Korneliussen, Thorfinn Sand, Moltke, Ida & Albrechtsen, Anders, 2019, In: Genetic Epidemiology. 43, 5, p. 506-521Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Bioinformatic Analysis of Breast Tumor Interstitial Fluids: Insights into a Pan-molecular Secretome
Terkelsen, Thilde Bagger, 2019, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- 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
CAGEfightR: analysis of 5'-end data using R/Bioconductor
Thodberg, Malte, Thieffry, A., Vitting-Seerup, K., Andersson, Robin & Sandelin, Albin Gustav, 2019, In: BMC Bioinformatics. 20, 13 p., 487.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Catchment properties and the photosynthetic trait composition of freshwater plant communities
Iversen, L. L., Winkel, A., Baastrup-Spohr, L., Hinke, A. B., Alahuhta, J., Baattrup-Pedersen, A., Birk, S., Brodersen, P., Chambers, P. A., Ecke, F., Feldmann, T., Gebler, D., Heino, J., Jespersen, T. S., Moe, S. J., Riis, T., Sass, L., Vestergaard, O., Maberly, S. C., Sand-jensen, K. & 1 others, , 2019, In: Science. 366, 6467, p. 878-881 4 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
Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families
Shah, S. A., Alkhnbashi, O. S., Behler, J., Han, W., She, Q., Hess, W. R., Garrett, Roger Antony & Backofen, R., 2019, In: RNA Biology. 16, 4, p. 530-542 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome
Abildgaard, A. B., Stein, Amelie, Nielsen, S. V., Schultz-Knudsen, Katrine, Papaleo, E., Shrikhande, A., Hoffmann, Eva, Bernstein, I., Gerdes, Anne-Marie Axø, Takahashi, M., Ishioka, C., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2019, In: eLife. 8, 28 p., e49138 .Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle
Rodrigues da Fonseca, Rute Andreia, Urena, I., Afonso, S., Pires, A. E., Jørsboe, E., Chikhi, L. & Ginja, C., 2019, In: BMC Genomics. 20, p. 1-13 334.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage
Hanghøj, Kristian Ebbesen, Renaud, Gabriel, Albrechtsen, Anders & Orlando, L., 2019, In: GigaScience. 8, 4, 6 p., giz025.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
Detecting sequence signals in targeting peptides using deep learning
Almagro Armenteros, J. J., Salvatore, Marco, Emanuelsson, O., Winther, Ole, von Heijne, G., Elofsson, A. & Nielsen, H., 2019, In: Life Science Alliance. 2, 5, 14 p., 201900429.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing
Enroth, Christel Hougård, Poulsen, L. D., Iversen, S., Kirpekar, F., Albrechtsen, Anders & Vinther, Jeppe, 2019, In: Nucleic Acids Research. 47, 20, 13 p., e126.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detection of slicer activity by immunopurified plant ARGONAUTE1
Arribas Hernandez, Laura, Vigh, Maria Louisa & Brodersen, Peter, 2019, Plant MicroRNAs: Methods and Protocols. Folter, S. D. (ed.). Humana Press, p. 295-316 22 p. (Methods in Molecular Biology, Vol. 1932).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- Published
Excess primer degradation by Exo I improves the preparation of 3' cDNA ligation-based sequencing libraries
Enroth, Christel Hougård, Fehler, A. O., Poulsen, L. D. & Vinther, Jeppe, 2019, In: BioTechniques. 67, 3, p. 110-116Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli
Pedersen, Steen, Terkelsen, Thilde Bagger, Eriksen, M., Hauge, M. K., Lund, C. C., Sneppen, Kim & Mitarai, Namiko, 2019, In: Journal of Molecular Biology. 431, 6, p. 1088-1097 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetic basis of ruminant headgear and rapid antler regeneration
Wang, Y., Zhang, C., Wang, N., Li, Z., Heller, R., Liu, R., Zhao, Y., Han, J., Pan, X., Zheng, Z., Dai, X., Chen, C., Dou, M., Peng, S., Chen, X., Liu, J., Li, M., Wang, K., Liu, C., Lin, Z. & 18 others, , 2019, In: Science. 364, 6446, p. 1153-+ eaav6335.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites
Colonna, V., D’Agostino, N., Garrison, E., Albrechtsen, Anders, Meisner, Jonas, Facchiano, A., Cardi, T. & Tripodi, P., 2019, In: Scientific Reports. 9, 14 p., 10067.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K., Barr, J. J., Bibby, K., Brouns, S. J. J., Cazares, A., de Jonge, P. A., Desnues, C., Díaz Muñoz, S. L., Fineran, P. C., Kurilshikov, A., Lavigne, R., Mazankova, K. & 97 others, , 2019, In: Nature Microbiology. 4, p. 1727-1736Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Investigating the possible function of DCL2 as a viral RNA sensor in Arabidopsis
Han, L., 2019, Department of Biology, Faculty of Science, University of Copenhagen.Research output: Book/Report › Ph.D. thesis › Research
- Published
IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences
Vitting-Seerup, K. & Sandelin, Albin Gustav, 2019, In: Bioinformatics. 35, 21, p. 4469-4471Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples
Renaud, Gabriel, Hanghøj, Kristian Ebbesen, Korneliussen, Thorfinn Sand, Willerslev, Eske & Orlando, L., 2019, In: Genetics (Print). 212, 3, p. 587-614 28 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Lack of the Major Multifunctional Catalase KatA in Pseudomonas aeruginosa Accelerates Evolution of Antibiotic Resistance in Ciprofloxacin-Treated Biofilms
Ahmed, M. N., Porse, A., Abdelsamad, A., Sommer, M., Høiby, Niels & Ciofu, Oana, 2019, In: Antimicrobial Agents and Chemotherapy. 63, 10, 12 p., e00766-19.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Langevin diffusions on the torus: estimation and applications
García-Portugués, E., Sørensen, Michael, Mardia, K. V. & Hamelryck, Thomas Wim, 2019, In: Statistics and Computing. 29, 1, p. 1-22 22 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
Brown, P., Tan, A-C., El-Esawi, M. A., Liehr, T., Blanck, O., Gladue, D. P., Almeida, G. M. F., Cernava, T., Sorzano, C. O., Yeung, A. W. K., Engel, M. S., Chandrasekaran, A. R., Muth, T., Staege, M. S., Daulatabad, S. V., Widera, D., Zhang, J., Meule, A., Honjo, K., Pourret, O. & 1,560 others, , 2019, In: Database: The Journal of Biological Databases and Curation. 2019, 66 p., baz085.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
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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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