- 2022
- Published
Semi-automated assembly of high-quality diploid human reference genomes
Jarvis, E. D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M. R., Porubsky, D., Cheng, H., Asri, M., Logsdon, G. A., Carnevali, P., Chaisson, M. J. P., Chin, C. S., Cody, S., Collins, J., Ebert, P., Escalona, M. & 31 others, , 2022, In: Nature. 611, 7936, 34 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
SignalP 6.0 predicts all five types of signal peptides using protein language models
Teufel, Felix Georg, Almagro Armenteros, J. J., Johansen, A. R., Gíslason, M. H., Pihl, S. I., Tsirigos, Konstantinos, Winther, Ole, Brunak, Søren, von Heijne, G. & Nielsen, H., 2022, In: Nature Biotechnology. 40, p. 1023-1025Research output: Contribution to journal › Comment/debate › Research
- Published
Single-cell transcriptomic landscape of the sheep rumen provides insights into physiological programming development and adaptation of digestive strategies
Yuan, Y., Sun, D., Qin, T., Mao, S., Zhu, W., Yin, Y., Huang, J., Heller, Rasmus, Li, Z., Liu, J. & Qiu, Q., 2022, In: Zoological research. 43, 4, p. 634-647 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Somatic structural variant formation is guided by and influences genome architecture
Sidiropoulos, N., Mardin, B. R., Rodriguez Gonzalez, Francisco G, Bochkov, I. D., Garg, S., Stuetz, A. M., Korbel, J. O., Aiden, E. L. & Weischenfeldt, Joachim Lütken, 2022, In: Genome Research. 32, 4, p. 643-655Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Spatial genetic patterns in African wild dogs reveal signs of effective dispersal across southern Africa
Tensen, L., Jansen van Vuuren, B., Groom, R., Bertola, Laura, de Iongh, H., Rasmussen, G., Du Plessis, C., Davies-Mostert, H., van der Merwe, D., Fabiano, E., Lages, F., Rocha, F., Monterroso, P. & Godinho, R., 2022, In: Frontiers in Ecology and Evolution. 10, 12 p., 992389.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Spatiotemporal influences of climate and humans on muskox range dynamics over multiple millennia
Canteri, Elisabetta, Brown, S. C., Schmidt, N. M., Heller, Rasmus, Nogues, David Bravo & Fordham, D. A., 2022, In: Global Change Biology. 28, 22, p. 6602-6617 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
Afgan, E., Nekrutenko, A., Grüning, B. A., Blankenberg, D., Goecks, J., Schatz, M. C., Ostrovsky, A. E., Mahmoud, A., Lonie, A. J., Syme, A., Fouilloux, A., Bretaudeau, A., Nekrutenko, A., Kumar, A., Eschenlauer, A. C., Desanto, A. D., Guerler, A., Serrano-Solano, B., Batut, B., Grüning, B. A. & 85 others, , 2022, In: Nucleic Acids Research. 50, W1, p. W345-W351 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The Threatened Species Imperative: Conservation assessments would benefit from population genomic insights
Andrew DeWoody, J., Jeon, J. Y., Bickham, J. W., Heenkenda, E. J., Janjua, S., Lamka, G. F., Mularo, A. J., Black, A., Brüniche-Olsen, Anna & Willoughby, J. R., 2022, In: PNAS. 119, 35, 2 p., e2210685119.Research output: Contribution to journal › Letter › Research › peer-review
- Published
The dynamic landscape of peptide activity prediction
Bárcenas, O., Pintado-Grima, C., Sidorczuk, K., Teufel, Felix Georg, Nielsen, H., Ventura, S. & Burdukiewicz, M., 2022, In: Computational and Structural Biotechnology Journal. 20, p. 6526-6533 8 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production
Geissler, Adrian Sven, Poulsen, L. D., Doncheva, Nadezhda Tsankova, Anthon, Christian, Seemann, Ernst Stefan, González-Tortuero, E., Breüner, A., Jensen, Lars Juhl, Hjort, C., Vinther, Jeppe & Gorodkin, Jan, 2022, In: Frontiers in Microbiology. 13, 17 p., 909493.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The novel inflammatory biomarker GlycA and triglyceride-rich lipoproteins are associated with the presence of subclinical myocardial dysfunction in subjects with type 1 diabetes mellitus
Puig-Jové, C., Julve, J., Castelblanco, E., Julián, M. T., Amigó, N., Andersen, H. U., Ahluwalia, Tarun Veer Singh, Rossing, Peter, Mauricio, D., Jensen, M. T. & Alonso, N., 2022, In: Cardiovascular Diabetology. 21, 257.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The population genomic legacy of the second plague pandemic
Gopalakrishnan, S., Ebenesersdóttir, S. S., Lundstrøm, I. K. C., Turner-Walker, G., Moore, K. H. S., Luisi, P., Margaryan, A., Martin, M. D., Ellegaard, M. R., Magnússon, Ó., Sigurðsson, Á., Snorradóttir, S., Magnúsdóttir, D. N., Laffoon, J. E., van Dorp, L., Liu, X., Moltke, I., Ávila-Arcos, M. C., Schraiber, J. G., Rasmussen, S. & 40 others, , 2022, In: Current Biology. 32, 21, p. 4743-4751.e6Research output: Contribution to journal › Journal article › Research › peer-review
- Published
- 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
Transfer learning reveals sequence determinants of regulatory element accessibility
Salvatore, Marco, Horlacher, M., Winther, Ole & Andersson, Robin, 2022, bioRxiv, 24 p.Research output: Working paper › Preprint › Research
- Published
Transition1x: a dataset for building generalizable reactive machine learning potentials
Schreiner, M., Bhowmik, A., Vegge, T., Busk, J. & Winther, Ole, 2022, In: Scientific Data. 9, 1, 9 p., 779.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation
YANG, Meng, Zhang, C., Wang, X., Liu, X., Li, S., Huang, J., Feng, Z., Sun, X., Chen, F., Yang, S., Ni, M., Li, L., Cao, Y. & Mu, F., 2022, In: Cell Systems. 13, 9, p. 752-767.e6 23 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Two novel truncating variants of the ASPM gene identified in a nonconsanguineous Chinese family associated with primary microcephaly
Xu, S., Zhang, W., Zhou, R., Huang, H., Chen, W., Xiang, W., Liu, L. & Song, J., 2022, In: Clinical Dysmorphology. 31, 1, p. 1-5 5 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
Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes
Garcia Erill, Genís, Jørgensen, C. H. F., Muwanika, V. B., Wang, X., Rasmussen, Malthe Sebro, de Jong, Y. A., Gaubert, P., Olayemi, A., Salmona, J., Butynski, T. M., Bertola, Laura, Siegismund, Hans Redlef, Albrechtsen, Anders & Heller, Rasmus, 2022, In: Molecular Biology and Evolution. 39, 7, 17 p., msac134.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site
Parker, M. T., Soanes, B. K., Kusakina, J., Larrieu, A., Knop, K., Joy, N., Breidenbach, F., Sherwood, Anna, Barton, G. J., Fica, S. M., Davies, B. H. & Simpson, G. G., 2022, In: eLife. 11, 34 p., 78808.Research output: Contribution to journal › Journal article › Research › peer-review
- 2021
- Published
Quantitative single-cell proteomics as a tool to characterize cellular hierarchies
Schoof, E. M., Furtwängler, Benjamin, Üresin, Nil, Rapin, N., Savickas, S., Gentil, C., Lechman, E., Keller, U. A. D., Dick, J. E. & Porse, Bo Torben, 7 Jun 2021, In: Nature Communications. 12, 1, p. 3341Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Plasma IL-8 and ICOSLG as prognostic biomarkers in glioblastoma
Holst, Camilla Bjørnbak, Christensen, I. J., Vitting-Seerup, K., Skjøth-Rasmussen, J., Hamerlik, P., Poulsen, H. S. & Johansen, Julia Sidenius, 1 Jan 2021, In: Neuro-Oncology Advances. 3, 1Research output: Contribution to journal › Journal article › Research › peer-review
- Published
De novo whole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope
Gonçalves, M., Siegismund, Hans Redlef, Van Vuuren, B. J., Koepfli, K., Ferrand, N. & Godinho, R., 2021, In: G3: Genes, Genomes, Genetics. 11, 2, 9 p., jkab002.Research output: Contribution to journal › Journal article › 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
Mammuthus sp. (Early and Middle Pleistocene Mammoths)
Chrzanová Pecnerová, Patrícia, Díez-del-Molino, D., van der Valk, T., Dehasque, M., Götherström, A. & Dalén, L., 2021, In: Trends in Genetics. 37, 7, p. 682-683 2 p.Research output: Contribution to journal › Editorial › Research › peer-review
- Published
A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data
Gabrielaite, M., Torp, M., Rasmussen, M., Andreu-Sánchez, S., Vieira, Filipe Garrett, Pedersen, C., Kinalis, S., Madsen, M., Yde, C., Rønn, O. L., Marvig, R., Østrup, O., Rossing, Caroline Maria, Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2021, bioRxiv, 29 p.Research output: Working paper › Preprint › Research
- Published
A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data
Gabrielaite, M., Torp, M. H., Rasmussen, Malthe Sebro, Andreu-Sánchez, S., Vieira, Filipe Garrett, Pedersen, C. B., Kinalis, S., Madsen, M. B., Kodama, M., Demircan, G. S., Simonyan, A., Yde, C. W., Olsen, L. R., Marvig, R. L., Østrup, O., Rossing, Caroline Maria, Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2021, In: Cancers. 13, 24, 6283.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A large-scale genome-wide gene expression analysis in peripheral blood identifies very few differentially expressed genes related to antidepressant treatment and response in patients with major depressive disorder
Nøhr, A. K., Lindow, M., Forsingdal, A., Demharter, S., Nielsen, T., Buller, R., Moltke, Ida, Vitezic, M. & Albrechtsen, Anders, 2021, In: Neuropsychopharmacology. 46, 7, p. 1324-1332 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A reference-free approach to analyse RADseq data using standard next generation sequencing toolkits
Heller, Rasmus, Nursyifa, Casia, Garcia Erill, Genís, Salmona, J., Chikhi, L., Meisner, Jonas, Korneliussen, Thorfinn Sand & Albrechtsen, Anders, 2021, In: Molecular Ecology Resources. 21, 4, p. 1085-1097 13 p.Research output: Contribution to journal › Journal article › 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
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
Xie, F., Jin, W., Si, H., Yuan, Y., Tao, Y., Liu, J., Wang, X., Yang, C., Li, Q., Yan, X., Lin, L., Jiang, Q., Zhang, L., Guo, C., Greening, C., Heller, R., Guan, L. L., Pope, P. B., Tan, Z., Zhu, W. & 4 others, , 2021, In: Microbiome. 9, 20 p., 137.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
AutoCNV: a semiautomatic CNV interpretation system based on the 2019 ACMG/ClinGen Technical Standards for CNVs
Fan, C., Wang, Z., Sun, Y., Sun, J., Liu, X., Kang, L., Xu, Y., Yang, M., Dai, W., Song, L., Wei, X., Xiang, J., Huang, H., Zhou, M., Zeng, F., Huang, L., Xu, Z. & Peng, Z., 2021, In: BMC Genomics. 22, 12 p., 721.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
Bending during seedling emergence: Mechanochemical insight
Bai, B., 2021, In: Trends in Plant Science. 26, 9, p. 879-881 3 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
Bsgatlas: A unified bacillus subtilis genome and transcriptome annotation atlas with enhanced information access
Geissler, Adrian Sven, Anthon, Christian, Alkan, F., González-Tortuero, E., Poulsen, L. D., Kallehauge, T. B., Breüner, A., Seemann, Ernst Stefan, Vinther, Jeppe & Gorodkin, Jan, 2021, In: Microbial Genomics. 7, 2, 17 p., 000524.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
Cardiovascular autonomic neuropathy and the impact on progression of diabetic kidney disease in type 1 diabetes
Bjerre-Christensen, T., Winther, S. A., Tofte, N., Theilade, S., Ahluwalia, Tarun Veer Singh, Lajer, M., Hansen, T. W., Rossing, Peter & Hansen, C. S., 2021, In: B M J Open Diabetes Research & Care. 9, 1, 9 p., e002289.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Circulating Free Fatty Acid and Phospholipid Signature Predicts Early Rapid Kidney Function Decline in Patients With Type 1 Diabetes
Afshinnia, F., Rajendiran, T. M., He, C., Byun, J., Montemayor, D., Darshi, M., Tumova, J., Kim, J., Limonte, C. P., Miller, R. G., Costacou, T., Orchard, T. J., Ahluwalia, Tarun Veer Singh, Rossing, Peter, Snell-Bergeon, J. K., de Boer, I. H., Natarajan, L., Michailidis, G., Sharma, K. & Pennathur, S., 2021, In: Diabetes Care. 44, 9, p. 2098-2106 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia
Dehasque, M., Chrzanová Pecnerová, Patrícia, Muller, H., Tikhonov, A., Nikolskiy, P., Tsigankova, V. I., Danilov, G. K., Díez-del-Molino, D., Vartanyan, S., Dalén, L. & Lister, A. M., 2021, In: Quaternary Science Reviews. 259, 10 p., 106913.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection
Salgado-Albarrán, M., Navarro-Delgado, E. I., Del Moral-Morales, A., Alcaraz, N., Baumbach, J., González-Barrios, R. & Soto-Reyes, E., 2021, In: n p j Systems Biology and Applications. 7, 14 p., 21.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Computational methods for chromosome-scale haplotype reconstruction
Garg, S., 2021, In: Genome Biology. 22, 24 p., 101.Research output: Contribution to journal › Review › Research › peer-review
- Published
Detecting selection in low-coverage high-throughput sequencing data using principal component analysis
Meisner, Jonas, Albrechtsen, Anders & Hanghøj, Kristian Ebbesen, 2021, In: BMC Bioinformatics. 22, 13 p., 470.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I., Aitken, S. & 31 others, , 2021, In: Nature Communications. 12, 18 p., 3297.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Disorder in a two-domain neuronal Ca2+-binding protein regulates domain stability and dynamics using ligand mimicry
Staby, L., Kemplen, K. R., Stein, Amelie, Ploug, Michael, Clarke, J., Skriver, Karen, Heidarsson, P. O. & Kragelund, Birthe Brandt, 2021, In: Cellular and molecular life sciences : CMLS. 78, p. 2263-2278 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model
Thygesen, Christian Bahne, Al-Sibahi, A. S., Steenmanns, C. S., Sanz Moreta, Lys, Sørensen, A. B. & Hamelryck, Thomas Wim, 2021, International Conference on Machine Learning, 18-24 July 2021, Virtual. PMLR, p. 10258-10267 (Proceedings of Machine Learning Research, Vol. 139).Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
Emergence and radiation of distemper viruses in terrestrial and marine mammals
Stokholm, Iben, Puryear, W., Sawatzki, K., Knudsen, Steen Wilhelm, Terkelsen, Thilde Bagger, Becher, P., Siebert, U. & Olsen, Morten Tange, 2021, In: Proceedings of the Royal Society B: Biological Sciences. 288, 1961, 9 p., 20211969.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning
Xiang, X., Corsi, G. I., Anthon, C., Qu, K., Pan, X., Liang, X., Han, P., Dong, Z., Liu, L., Zhong, J., Ma, T., Wang, J., Zhang, X., Jiang, H., Xu, F., Liu, X., Xu, X., Wang, J., Yang, H., Bolund, L. & 4 others, , 2021, In: Nature Communications. 12, 1, 9 p., 3238.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Evolutionary history of the roan antelope across its African range
Gonçalves, M., Siegismund, Hans Redlef, van Vuuren, B. J., Ferrand, N. & Godinho, R., 2021, In: Journal of Biogeography. 48, 11, p. 2812-2827 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq
Petryk, N., Reveron-Gomez, Nazaret, González-Aguilera, C., Dalby, M., Andersson, Robin & Groth, Anja, 2021, In: Nature Protocols. 16, p. 4446-4493Research 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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