Research output per year
Research output per year
Personal profile
Short presentation
I am professor of Bioinformatics and the head of the Section for Computational and RNA Biology in the Department of Biology. I have a Ph.D. in theoretical physics, but moved into bioinformatics in 1991 as a postdoc at UCSC. Since then I have worked at the Sanger Centre in Cambridge and at the Technical University of Denmark before joining the University of Copenhagen in 2002. I have worked in many areas of bioinformatics, both with theory and applications. I am probably most well known for early work on hidden Markov models for biological sequences. In recent years I have focussed on analysis of data from high-throughput DNA sequencing with applications in post-transcriptional regulation, ancient genomics, metagenomics, and transcriptome analysis.
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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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Accurate genotyping across variant classes and lengths using variant graphs
Sibbesen, J. A., Maretty, L., Krogh, A., Petersen, B., Sibbesen, J. A., Liu, S., Have, C. T., Bork-Jensen, J., Guo, X., Hansen, T., Krogh, A., Sørensen, T. I. A., Pedersen, O. B., Wang, J. & Brunak, S., 1 Jul 2018, In: Nature Genetics. 50, p. 1054-1059 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios
Matey-Hernandez, M. L., Danish Pan Genome Consortium, Brunak, S., Izarzugaza, J. M. G., Sørensen, L. M., Petersen, B., Sibbesen, J. A., Liu, S., Belling, K. G., Have, C. T., Bork-Jensen, J., Sun, J., Hansen, T., Krogh, A., Sørensen, T. I. A., Pedersen, O. B., Wang, J., Eiberg, H. R. L. & Kristiansen, K., 2018, In: BMC Bioinformatics. 19, p. 1-12 239.Research output: Contribution to journal › Journal article › Research › peer-review
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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, 4 Oct 2018, In: Cell. 175, 2, p. 347-359, e1-e7Research output: Contribution to journal › Journal article › Research › peer-review
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Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion
Danish Pan Genome Consortium, Sørensen, L. M., Petersen, B., Sibbesen, J. A., Liu, S., Belling, K. G., Have, C. T., Bork-Jensen, J., Hansen, T., Krogh, A., Sørensen, T. I. A., Pedersen, O. B., Rasmussen, S., Kristiansen, K. & Brunak, S., Aug 2017, In: PLOS Genetics. 13, 8, p. e1006834Research output: Contribution to journal › Journal article › Research › peer-review
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Assembly and analysis of 100 full MHC haplotypes from the Danish population
Jensen, J. M., Villesen, P., Friborg, R. M., Mailund, T., Besenbacher, S., Sørensen, L. M., Petersen, B., Sibbesen, J. A., Liu, S., Skov, L., Belling, K. G., Have, C. T., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., Xu, R., & 39 others, Sept 2017, In: Genome Research. 27, 9, p. 1597-1607 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors
Plass, M., Rasmussen, S. H. & Krogh, A., 14 Apr 2017, In: PLoS Computational Biology. 13, 4, 26 p., e1005460.Research output: Contribution to journal › Journal article › Research › peer-review
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Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
Sørensen, L. M., Jensen, J. M., Petersen, B., Sibbesen, J. A., Liu, S., Villesen, P., Skov, L., Belling, K. G., Have, C. T., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., Xu, R., Ye, W., Rao, J., Guo, X., & 39 others, 3 Aug 2017, In: Nature. 548, 7665, p. 87-91 5 p.Research output: Contribution to journal › Letter › peer-review
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Sugar metabolism of the first thermophilic Planctomycete Thermogutta terrifontis: comparative genomic and transcriptomic approaches
Elcheninov, A. G., Menzel, P., Gudbergsdottir, S. R., Slesarev, A. I., Kadnikov, V. V., Krogh, A., Bonch-Osmolovskaya, E. A., Peng, X. & Kublanov, I. V., 2 Nov 2017, In: Frontiers in Microbiology. 8, 11 p., 2140.Research output: Contribution to journal › Journal article › Research › peer-review
Datasets
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Additional file 1 of Context dependency of nucleotide probabilities and variants in human DNA
Liang, Y. (Creator), Grønbæk, C. (Creator), Fariselli, P. (Creator) & Krogh, A. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.19101791, https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Context_dependency_of_nucleotide_probabilities_and_variants_in_human_DNA/19101791
Dataset
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Additional file 1 of Context dependency of nucleotide probabilities and variants in human DNA
Liang, Y. (Creator), Grønbæk, C. (Creator), Fariselli, P. (Creator) & Krogh, A. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.19101791.v1, https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Context_dependency_of_nucleotide_probabilities_and_variants_in_human_DNA/19101791/1
Dataset
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Context dependency of nucleotide probabilities and variants in human DNA
Liang, Y. (Creator), Grønbæk, C. (Creator), Fariselli, P. (Creator) & Krogh, A. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.c.5819663, https://springernature.figshare.com/collections/Context_dependency_of_nucleotide_probabilities_and_variants_in_human_DNA/5819663
Dataset
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Additional file 3 of N-of-one differential gene expression without control samples using a deep generative model
Prada-Luengo, I. (Creator), Schuster, V. (Creator), Liang, Y. (Creator), Terkelsen, T. (Creator), Sora, V. (Creator) & Krogh, A. (Creator), figshare, 2024
DOI: 10.6084/m9.figshare.26641237.v1, https://springernature.figshare.com/articles/dataset/Additional_file_3_of_N-of-one_differential_gene_expression_without_control_samples_using_a_deep_generative_model/26641237/1
Dataset
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scDGD pretrained models
Schuster, V. (Creator) & Krogh, A. (Creator), Zenodo, 2023
DOI: 10.1093/bioinformatics/btad497, https://zenodo.org/records/10696952
Dataset
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Context dependency of nucleotide probabilities and variants in human DNA
Liang, Y. (Creator), Grønbæk, C. (Creator), Fariselli, P. (Creator) & Krogh, A. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.c.5819663.v1, https://springernature.figshare.com/collections/Context_dependency_of_nucleotide_probabilities_and_variants_in_human_DNA/5819663/1
Dataset
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Additional file 5 of N-of-one differential gene expression without control samples using a deep generative model
Prada-Luengo, I. (Creator), Schuster, V. (Creator), Liang, Y. (Creator), Terkelsen, T. (Creator), Sora, V. (Creator) & Krogh, A. (Creator), figshare, 2024
DOI: 10.6084/m9.figshare.26641243.v1, https://springernature.figshare.com/articles/dataset/Additional_file_5_of_N-of-one_differential_gene_expression_without_control_samples_using_a_deep_generative_model/26641243/1
Dataset
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N-of-one differential gene expression without control samples using a deep generative model
Prada-Luengo, I. (Creator), Schuster, V. (Creator), Liang, Y. (Creator), Terkelsen, T. (Creator), Sora, V. (Creator) & Krogh, A. (Creator), figshare, 2024
DOI: 10.6084/m9.figshare.c.6935315.v1, https://springernature.figshare.com/collections/N-of-one_differential_gene_expression_without_control_samples_using_a_deep_generative_model/6935315/1
Dataset