- 2023
- Published
Global determinants of insect mitochondrial genetic diversity
French, C. M., Bertola, Laura, Carnaval, A. C., Economo, E. P., Kass, J. M., Lohman, D. J., Marske, K. A., Meier, R., Overcast, I., Rominger, A. J., Staniczenko, P. P. A. & Hickerson, M. J., 2023, In: Nature Communications. 14, 1, 15 p., 5276.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load
INSIGHT START Study Group, I. S. S. G., 2023, In: PLOS Computational Biology. 19, 1, 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating admixture pedigrees of recent hybrids without a contiguous reference genome
Garcia Erill, Genís, Hanghøj, Kristian Ebbesen, Heller, Rasmus, Wiuf, Carsten & Albrechtsen, Anders, 2023, In: Molecular Ecology Resources. 23, 7, p. 1604-1619 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics
Garg, S., 2023, In: Nature Communications. 14, 1, 11 p., 1358.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
CRISPRi screen for enhancing heterologous alpha-amylase yield in Bacillus subtilis
Geissler, Adrian Sven, Fehler, A. O., Poulsen, L. D., Gonzalez-Tortuero, E., Kallehauge, T. B., Alkan, F., Anthon, Christian, Seemann, Ernst Stefan, Rasmussen, M. D., Breuener, A., Hjort, C., Vinther, Jeppe & Gorodkin, Jan, 2023, In: Journal of Industrial Microbiology and Biotechnology. 50, 1, 16 p., kuac028.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DNA metabarcoding illuminates the contribution of small and very small prey taxa to the diet of lions
Groen, K., Beekenkamp, S., de Iongh, H. H., Lesilau, F., Chege, M., Narisha, L., Veldhuis, M., Bertola, Laura, van Bodegom, P. M. & Trimbos, K. B., 2023, In: Environmental DNA. 5, 6, p. 1321-1331 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identifying the genetic causes of phenotypically diagnosed Pakistani mucopolysaccharidoses patients by whole genome sequencing
Gul, Rutaba, Firasat, S., Schubert, Mikkel, Ullah, A., Peña, E., Thuesen, Anne Cathrine Baun, Hussain, M., Stæger, Frederik Filip Vinggaard, Gjesing, A. P., Albrechtsen, Anders & Hansen, Torben, 2023, In: Frontiers in Genetics. 14, 13 p., 1128850.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla)
Hansen, C. C. R., Láruson, Á. J., Rasmussen, Jacob Agerbo, Ballesteros, J. A. C., Sinding, Mikkel Holger Strander, Hallgrimsson, G. T., von Schmalensee, M., Stefansson, R. A., Skarphédinsson, K. H., Labansen, A. L., Leivits, M., Sonne, C., Dietz, R., Skelmose, K., Boertmann, D., Eulaers, I., Martin, M. D., Helgason, A. S., Gilbert, M Thomas P & Pálsson, S., 2023, In: Molecular Ecology. 32, 8, p. 1925-1942 18 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Between inflammation, homeostasis and adaptation: Systemic and tissue-specific responses to maternal immune activation
Hansen, Signe Schmidt Kjølner, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 177 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets
He, Yue, Døssing, Kristina Benedikte V, Sloth, Ane Beth, He, Xuening, Rossing, M. & Kjær, Andreas, 2023, In: Cancers. 15, 5, 16 p., 1557.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing
Hernández-Alonso, G., Ramos-Madrigal, J., Sun, X., Scharff-Olsen, C. H., Sinding, M. H. S., Martins, N. F., Ciucani, M. M., Mak, S. S. T., Lanigan, L. T., Clausen, C. G., Bhak, J., Jeon, S., Kim, C., Eo, K. Y., Cho, S. H., Boldgiv, B., Gantulga, G., Unudbayasgalan, Z., Kosintsev, P. A., Stenøien, H. K. & 2 others, , 2023, In: Ecology and Evolution. 13, 8, 15 p., e10404.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences
Hernández Alonso, Germán, Ramos Madrigal, Jazmin, van Grouw, H., Ciucani, Marta Maria, Cavill, Emily Louisa, Sinding, Mikkel Holger Strander, Gopalakrishnan, Shyam, Antunes Pacheco, George & Gilbert, M Thomas P, 2023, In: Molecular Biology and Evolution. 40, 11, 17 p., msad243.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning
Horlacher, M., Wagner, N., Moyon, L., Kuret, K., Goedert, N., Salvatore, Marco, Ule, J., Gagneur, J., Winther, Ole & Marsico, A., 2023, In: Genome Biology. 24, 1, 37 p., 180.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DermX: An end-to-end framework for explainable automated dermatological diagnosis
Jalaboi, R., Faye, F., Orbes-Arteaga, M., Jørgensen, D., Winther, Ole & Galimzianova, A., 2023, In: Medical Image Analysis. 83, 12 p., 102647.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Explainable Image Quality Assessments in Teledermatological Photography
Jalaboi, R., Winther, Ole & Galimzianova, A., 2023, In: Telemedicine and e-Health. 29, 9, p. 1342-1348 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Limited historical admixture between European wildcats and domestic cats
Jamieson, A., Carmagnini, A., Howard-McCombe, J., Doherty, S., Hirons, A., Dimopoulos, E., Lin, A. T., Allen, R., Anderson-Whymark, H., Barnett, R., Batey, C., Beglane, F., Bowden, W., Bratten, J., De Cupere, B., Drew, E., Foley, N. M., Fowler, T., Fox, A., Geigl, E-M. & 35 others, , 2023, In: Current Biology. 33, 21, p. 4751-4760.e14Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Association of SLC12A1 and GLUR4 Ion Transporters with Neoadjuvant Chemoresistance in Luminal Locally Advanced Breast Cancer
Justo-Garrido, M., López-Saavedra, A., Alcaraz, N., Cortés-González, C. C., Oñate-Ocaña, L. F., Caro-Sánchez, C. H. S., Castro-Hernández, C., Arriaga-Canon, C., Díaz-Chávez, J. & Herrera, L. A., 2023, In: International Journal of Molecular Sciences. 24, 22, 16 p., 16104.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
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
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
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
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
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
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
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
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
Plant YTHDF proteins are direct effectors of antiviral immunity against an N6-methyladenosine-containing RNA virus
Martínez-Pérez, M., Aparicio, F., Arribas Hernandez, Laura, Tankmar, Mathias Due, Rennie, Sarah, von Bülow, Sören, Lindorff-Larsen, Kresten, Brodersen, Peter & Pallas, V., 2023, In: EMBO Journal. 42, 18, 17 p., e113378.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Pooled analysis of frontal lobe transcriptomic data identifies key mitophagy gene changes in Alzheimer's disease brain
Mei, T., Li, Yuan, Orduña Dolado, A., Li, Zhiquan, Andersson, Robin, Berliocchi, Laura & Rasmussen, Lene Juel, 2023, In: Frontiers in Aging Neuroscience. 15, 14 p., 1101216.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Benchmarking RNA Editing Detection Tools
Morales, D. R., Rennie, Sarah & Uchida, S., 2023, In: BioTech. 12, 3, 18 p., 56.Research output: Contribution to journal › Review › Research › peer-review
- Published
Application of whole genome sequencing data in population genetics: identifying sex-linked scaffolds and inferring admixture in a unique cattle population
Nursyifa, Casia, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 225 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Exploring antidepressant treatment response using biological and clinical measurements
Nøhr, A. K., 2023, Department of Biology, Faculty of Science, University of Copenhagen. 125 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network
Pan, X., Ma, Z., Sun, X., Li, H., Zhang, T., Zhao, C., Wang, N., Heller, Rasmus, Hung Wong, W., Wang, W., Jiang, Y. & Wang, Y., 2023, In: Genomics, Proteomics and Bioinformatics. 21, 3, p. 632-648 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation
Pikkupeura, Laura Maarit, Bardini Bressan, Raul, Guiu, J., Chen, Y., Maimets, Martti, Mayer, Daniela, Schweiger, P. J., Hansen, Stine Lind, Maciag, Grzegorz Jerzy, Larsen, Hjalte List, Lõhmussaar, Kadi, Pedersen, M. T., Teves, Joji Marie Yap, Lange, Jette Bornholdt, Benes, V., Sandelin, Albin Gustav & Jensen, Kim Bak, 2023, In: Science Advances. 9, 28, 16 p., eadf9460.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Functions of m6A-YTH modules in plants: Lessons from high-throughput sequencing analyses
Porcelli, C., 2023, Department of Biology, Faculty of Science, University of Copenhagen. 178 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Systematic Analysis of Long Non-Coding RNAs in Inflammasome Activation in Monocytes/Macrophages
Qian, N., Distefano, R., Ilieva, M., Madsen, J. H., Rennie, Sarah & Uchida, S., 2023, In: Non-coding RNA. 9, 5, 16 p., 50.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A population of stem cells with strong regenerative potential discovered in deer antlers
Qin, T., Zhang, G., Zheng, Y., Li, S., Yuan, Y., Li, Q., Hu, M., Si, H., Wei, G., Gao, X., Cui, X., Xia, B., Ren, J., Wang, K., Ba, H., Liu, Z., Heller, R., Li, Z., Wang, W., Huang, J. & 2 others, , 2023, In: Science (New York, N.Y.). 379, 6634, p. 840-847 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo
Quinn, Liam James Elgaard, Garcia Erill, Genís, Santander, Cindy, Brüniche-Olsen, Anna, Liu, Xiaodong, Sinding, Mikkel Holger Strander, Heaton, M. P., Smith, T. P. L., Chrzanová Pecnerová, Patrícia, Bertola, Laura, Hanghøj, Kristian Ebbesen, Rasmussen, Malthe Sebro, De Jager, Deon, Siegismund, Hans Redlef, Albrechtsen, Anders, Heller, Rasmus & Moltke, Ida, 2023, In: Molecular Ecology. 32, 8, 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Probabilistic modelling in genomics
Rasmussen, Malthe Sebro, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 158 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Uncertainty-aware and explainable machine learning for early prediction of battery degradation trajectory
Rieger, L. H., Flores, E., Nielsen, K. F., Norby, P., Ayerbe, E., Winther, Ole, Vegge, T. & Bhowmik, A., 2023, In: Digital Discovery. 2, 1, p. 112-122 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Potential usages of A-to-I RNA editing patterns as diagnostic biomarkers
Rodriguez Morales, D., Ilieva, M., Rennie, Sarah & Uchida, S., 2023, In: American journal of physiology. Cell physiology. 324, 4, p. C837-C842 6 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Chronic acidosis rewires cancer cell metabolism through PPARα signaling
Rolver, M. G., Holland, L. K. K., Ponniah, M., Prasad, N. S., Yao, Jiayi, Schnipper, J., Kramer, S., Elingaard-Larsen, L., Pedraz-Cuesta, E., Liu, B., Pardo, L. A., Maeda, K., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2023, In: International Journal of Cancer. 152, 8, 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transfer learning identifies sequence determinants of cell-type specific regulatory element accessibility
Salvatore, Marco, Horlacher, M., Marsico, A., Winther, Ole & Andersson, Robin, 2023, In: NAR Genomics and Bioinformatics. 5, 2, 10 p., 026.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetic Loss of Sucrase-Isomaltase Function: Mechanisms, Implications, and Future Perspectives
Senftleber, N. K., Ramne, Stina, Moltke, Ida, Jørgensen, M. E., Albrechtsen, Anders, Hansen, Torben & Lepola, Mette Andersen, 2023, In: Application of Clinical Genetics. 16, p. 31-39 9 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Bridging the gap in African biodiversity genomics and bioinformatics
Sharaf, A., Ndiribe, C. C., Omotoriogun, T. C., Abueg, L., Badaoui, B., Badiane Markey, F. J., Beedessee, G., Diouf, D., Duru, V. C., Ebuzome, C., Eziuzor, S. C., Jaufeerally Fakim, Y., Formenti, G., Ghanmi, N., Guerfali, F. Z., Houaga, I., Ideozu, J. E., Katee, S. M., Khayi, S., Kuja, J. O. & 16 others, , 2023, In: Nature Biotechnology. 41, 9, p. 1348-1354 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Hepatitis C virus RNA is 5'-capped with flavin adenine dinucleotide
Sherwood, A. V., Rivera-Rangel, L. R., Ryberg, L. A., Larsen, H. S., Anker, K. M., Costa, R., Vågbø, C. B., Jakljevič, E., Pham, L. V., Fernandez-Antunez, C., Indrisiunaite, G., Podolska-Charlery, A., Grothen, J. E. R., Langvad, N. W., Fossat, N., Offersgaard, A., Al-Chaer, A., Nielsen, L., Kuśnierczyk, A., Sølund, C. & 8 others, , 2023, In: Nature. 619, p. 811-818Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Deep integrative models for large-scale human genomics
Sigurdsson, Arnór Ingi, Louloudis, Ioannis, Banasik, Karina, Westergaard, David, Winther, Ole, Lund, O., Ostrowski, Sisse Rye, Erikstrup, C., Pedersen, Ole Birger Vesterager, Nyegaard, Mette, Brunak, Søren, Vilhjálmsson, B. & Rasmussen, Simon, 2023, In: Nucleic Acids Symposium Series. 51, 12, 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Characterization of industrially-produced Lacticaseibacillus rhamnosus GG and Lactobacillus acidophilus LA-5: Analysis of genomic integrity, transcriptome and phenotypes
Strickertsson, Marianne Stage, 2023, Department of Biology, Faculty of Science, University of Copenhagen. 206 p.Research output: Book/Report › Ph.D. thesis › Research
- Published
Possible signs of recovery of the nearly extirpated Spitsbergen bowhead whales: calves observed in east Greenland
Tervo, O. M., Louis, Marie Georgette Yolande J, Sinding, Mikkel Holger Strander, Heide-Jørgensen, M. P. & Hansen, R. G., 2023, In: Polar Research. 42, 4 p., 8809.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
DeepPeptide predicts cleaved peptides in proteins using conditional random fields
Teufel, Felix Georg, Refsgaard, J. C., Madsen, C. T., Stahlhut, C., Grønborg, M., Winther, Ole & Madsen, D., 2023, In: Bioinformatics (Oxford, England). 39, 10, 6 p., btad616.Research output: Contribution to journal › Journal article › Research › peer-review
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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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