Anders Krogh
Professor
Machine Learning
Universitetsparken 1, 2100 København Ø
Center for Health Data Science
Blegdamsvej 3B
2200 København N
- Published
57miRNA regulation during oncogene-induced senescence
Christoffersen, N. R., Frankel, Lisa, Klausen, M., Jacobsen, A., Krogh, Anders & Lund, Anders H., May 2008.Research output: Contribution to conference › Conference abstract for conference › Research
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De novo assembly of a haplotype-resolved human genome
Cao, H., Wu, H., Luo, R., Huang, S., Sun, Y., Tong, X., Xie, Y., Liu, B., Yang, H., Zheng, H., Li, J., Li, B., Wang, Y., Yang, F., Sun, P., Liu, S., Gao, P., Huang, H., Sun, J., Chen, D. & 21 others, , 2015, In: Nature Biotechnology. 33, 6, p. 617-626 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation
Hansen, H. T., Rasmussen, S. H., Adolph, S. K., Plass, M., Krogh, Anders, Sanford, J., Nielsen, Finn Cilius & Christiansen, Jan, 2015, In: Genome Biology (Online Edition). 16, 16 p., 123.Research output: Contribution to journal › Journal article › Research › peer-review
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A Combined Transmembrane Topology and Signal Peptide Prediction Method
Kall, L., Krogh, Anders & Sonnhammer, E. L., 2004, In: Journal of Molecular Biology. Vol. 338 (5), p. 1027-36Research output: Contribution to journal › Journal article › Research › peer-review
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A code for transcription initiation in mammalian genomes
Frith, M. C., Valen, E. D., Krogh, Anders, Hayashizaki, Y., Carninci, P. & Sandelin, Albin Gustav, 2007, In: Genome Research. 18, 1, p. 1-12 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
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A generative, probabilistic model of local protein structure
Boomsma, Wouter, Mardia, K. V., Taylor, C. C., Ferkinghoff-Borg, J., Krogh, Anders & Hamelryck, Thomas Wim, 2008, In: Proceedings of the National Academy of Science of the United States of America. 105, 26, p. 8932-8937 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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A hidden Markov model approach for determining expression from genomic tiling micro arrays
Terkelsen, K. M., Gardner, P. P., Arctander, P. & Krogh, Anders, 2006, In: BMC Bioinformatics. 7, 239Research output: Contribution to journal › Journal article › Research › peer-review
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A manifold learning perspective on representation learning: Learning decoder and representations without an encoder
Schuster, Viktoria & Krogh, Anders, Nov 2021, In: Entropy. 23, 11, 14 p., 1403.Research output: Contribution to journal › Journal article › Research › peer-review
A sequence-profile-based HMM for predicting and discriminating β barrel membrane proteins
Martelli, P. L., Fariselli, P., Krogh, Anders & Casadio, R., 2002, In: Bioinformatics. 18, Suppl. 1, p. S46-S53Research output: Contribution to journal › Journal article › Research › peer-review
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A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies: [plus] Erratum
Cao, H., Wang, Y., Zhang, W., Chai, X., Zhang, X., Chen, S., Yang, F., Zhang, C., Guo, Y., Liu, Y., Tang, Z., Chen, C., Xue, Y., Zhen, H., Xu, Y., Rao, B., Liu, T., Zhao, M., Zhang, W., Li, Y. & 6 others, , 2013, In: Human Mutation. 34, 12, p. 1715-1720 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Accurate genotyping across variant classes and lengths using variant graphs
Sibbesen, Jonas Andreas, Maretty, L., Krogh, Anders, Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Have, C. T., Bork-Jensen, J., Guo, X., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Wang, J. & Brunak, Søren, 2018, In: Nature Genetics. 50, p. 1054-1059 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Adaptable probabilistic mapping of short reads using position specific scoring matrices
Kerpedjiev, P., Frellsen, J., Lindgreen, S. & Krogh, Anders, 2014, In: B M C Bioinformatics. 15, 17 p., 15:100.Research output: Contribution to journal › Journal article › Research › peer-review
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Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes
Fang, X., Seim, I., Huang, Z., Gerashchenko, M. V., Xiong, Z., Turanov, A. A., Zhu, Y., Lobanov, A. V., Fan, D., Yim, S. H., Yao, X., Ma, S., Yang, L., Lee, S-G., Kim, E. B., Bronson, R. T., Sumbera, R., Buffenstein, R., Zhou, X., Krogh, A. & 4 others, , 2014, In: Cell Reports. 8, 5, p. 1354-1364 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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Algorithms for mapping high-throughput DNA sequences
Frellsen, J., Menzel, P. & Krogh, Anders, 2014, Comprehensive Biomedical Physics: Bioinformatics. Brahme, A. (ed.). Elsevier, Vol. 6. p. 41-50 10 p. (Reference Module in Biomedical Sciences, Vol. 6).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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Alterations in polyadenylation and its implications for endocrine disease
Rehfeld, Anders Aagaard, Plass, M., Krogh, Anders & Friis-Hansen, Lennart Jan, 2013, In: Frontiers in Endocrinology. 4, 23 p., 53.Research output: Contribution to journal › Review › Research › peer-review
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Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors
Rehfeld, Anders Aagaard, Plass, M., Døssing, K., Knigge, Ulrich, Kjær, Andreas, Krogh, Anders & Friis-Hansen, Lennart Jan, 2014, In: Frontiers in Endocrinology. 5, 10 p., 46.Research output: Contribution to journal › Journal article › Research › peer-review
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An Aboriginal Australian genome reveals separate human dispersals into Asia
Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando, L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K., Avila Arcos, M. D. C. & 38 others, , 2011, In: Science. 334, 6052, p. 94-98 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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An HMM posterior decoder for sequence feature prediction that includes homology information
Käll, L., Krogh, Anders & Sonnhammer, E. L. L., 2005, In: Bioinformatics. 21, 1, p. i251 - i257Research output: Contribution to journal › Journal article › Research › peer-review
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An evolutionary method for learning HMM structure: prediction of protein secondary structure.
Won, K., Hamelryck, Thomas Wim, Prügel-Bennett, A. & Krogh, Anders, 2007, In: BMC Bioinformatics. 8, p. 357Research 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
Skov, L., Schierup, M. H., Danish Pan Genome Consortium, D. P. G. C., Sørensen, L. M., Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Belling, K. G., Have, C. T., Bork-Jensen, J., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Rasmussen, Simon, Kristiansen, Karsten & Brunak, Søren, 2017, In: PLOS Genetics. 13, 8, p. e1006834Research output: Contribution to journal › Journal article › Research › peer-review
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Ancient human genome sequence of an extinct Palaeo-Eskimo
Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, T., Wang, Y., Raghavan, M., Campos, P., Kamp, H. L. M., Wilson, A. S., Gledhill, A., Tridico, S. & 32 others, , 11 Feb 2010, In: Nature. 463, 7282, p. 757-762 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Asap: a framework for over-representation statistics for transcription factor binding sites.
Marstrand, T. T., Frellsen, J., Moltke, Ida, Thiim, M., Valen, E., Retelska, D. & Krogh, Anders, 2008, In: PLoS ONE. 3, 2, p. e1623Research 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, , Sep 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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Automatic generation of gene finders for eukaryotic species
Terkelsen, K. M. & Krogh, Anders, 2006, In: BMC Bioinformatics. 7, 263Research output: Contribution to journal › Journal article › Research › peer-review
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BayesMD: Flexible Biological Modeling for Motif Discovery
Tang, M. E., Krogh, Anders & Winther, Ole, 2008, In: Journal of Computational Biology. 15, 10, p. 1347-63 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Bayesian transcriptome assembly
Sørensen, L. M., Sibbesen, Jonas Andreas & Krogh, Anders, 2014, In: Genome Biology (Online Edition). 15, 10, 11 p., 501.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, D. P. G. C., Brunak, Søren, Izarzugaza, J. M. G., Sørensen, L. M., Petersen, Bent, Sibbesen, Jonas Andreas, Liu, S., Belling, K. G., Have, C. T., Bork-Jensen, J., Sun, J., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Wang, J., Eiberg, Hans Rudolf Lytchoff & Kristiansen, Karsten, 2018, In: BMC Bioinformatics. 19, p. 1-12 239.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information
Bartoli, L., Fariselli, P., Krogh, Anders & Casadio, R., 2009, In: Bioinformatics. 25, 21, p. 2757-63 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin
Vikeså, J., Møller, A. K. H., Kaczkowski, B., Helweg-Larsen, R. B., Winther, Ole, Henao Giraldo, R., Krogh, Anders, Perell, K., Jensen, F., Daugaard, G. & Nielsen, Finn Cilius, 2015, In: B M C Cancer. 15, 14 p., 151.Research output: Contribution to journal › Journal article › Research › peer-review
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Comparative metagenomics of eight geographically remote terrestrial hot springs
Menzel, P., Islin, S. R., Rike, A. G., Lin, L., Zhang, Q., Contursi, P., Moracci, M., Kristjansson, J. K., Bolduc, B., Gavrilov, S., Ravin, N., Mardanov, A., Bonch-Osmolovskaya, E., Young, M., Krogh, Anders & Peng, Xu, 2015, In: Microbial Ecology. 70, 2, p. 411-424 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients
Rapin, N. P. J., Bagger, F. O., Jendholm, L. J., Mora-Jensen, H., Krogh, Anders, Kohlmann, A., Thiede, C., Borregaard, N., Bullinger, L., Winther, Ole, Theilgaard-Mønch, Kim & Porse, Bo Torben, 6 Feb 2014, In: Blood (online). 123, 6, p. 894-904 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Computational evidence for hundreds of non-conserved plant microRNAs
Lindow, M. & Krogh, Anders, 2005, In: BMC Genomics. 6, p. 119Research output: Contribution to journal › Journal article › Research › peer-review
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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
Context dependent prediction in DNA sequence using neural networks
Grønbæk, Christian, Liang, Yuhu, Elliott, Desmond & Krogh, Anders, 2022, In: PeerJ. 10, 22 p., e13666.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discovery of regulatory elements is improved by a discriminatory approach
Valen, E., Sandelin, Albin Gustav, Winther, Ole & Krogh, Anders, 2009, In: PLoS Computational Biology. 5, 11, p. e1000562Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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
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Evolving hidden Markov models for protein secondary structure prediction
Won, K. J., Hamelryck, Thomas Wim, Prügel-Bennett, A. & Krogh, Anders, 2005, The 2005 IEEE Congress on Evolutionary Computation, IEEE CEC 2005: Proceedings. IEEE, Vol. 3. p. 33-40 8 p.Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
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Evolving the structure of hidden Markov Models
won, K. J., Prugel-Bennett, A. & Krogh, Anders, 2006, In: IEEE Transactions on Evolutionary Computation. 10, 1, p. 39-49Research output: Contribution to journal › Journal article › Research › peer-review
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Fast and sensitive taxonomic classification for metagenomics with Kaiju
Menzel, P., Ng, K. L. & Krogh, Anders, 2016, In: Nature Communications. 7, 9 p., 11257.Research output: Contribution to journal › Journal article › Research › peer-review
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Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii
Seim, I., Fang, X., Xiong, Z., Lobanov, A. V., Huang, Z., Ma, S., Feng, Y., Turanov, A. A., Zhu, Y., Lenz, T. L., Gerashchenko, M. V., Fan, D., Yim, S. H., Yao, X., Jordan, D., Xiong, Y., Ma, Y., Lyapunov, A. N., Chen, G., Kulakova, O. I. & 9 others, , 2013, In: Nature Communications. 4, 8 p., 2212.Research output: Contribution to journal › Journal article › Research › peer-review
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Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax
Fang, X., Nevo, E., Han, L., Levanon, E. Y., Zhao, J., Avivi, A., Larkin, D., Jiang, X., Feranchuk, S., Zhu, Y., Fishman, A., Feng, Y., Sher, N., Xiong, Z., Hankeln, T., Huang, Z., Gorbunova, V., Zhang, L., Zhao, W., Wildman, D. E. & 33 others, , 2014, In: Nature Communications. 5, 9 p., 3966.Research output: Contribution to journal › Journal article › Research › peer-review
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Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
Valen, E., Pascarella, G., Chalk, A., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H., Lazarevic, D., Motti, D., Marstrand, T. T., Tang, M-H. E., Zhao, X., Krogh, A., Winther, O., Arakawa, T., Kawai, J., Wells, C., Daub, C., Harbers, M. & 4 others, , 2009, In: Genome Research. 19, 2, p. 255-65 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., Andersson, R., Jones, P. A., Hoover, C. A., Tikhonov, A., Prokhortchouk, E., Rubin, E. M., Sandelin, A. G., Gilbert, M. T. P., Krogh, A., Willerslev, E. & 1 others, , 2014, In: Genome Research. 24, 3, p. 454-466 13 p.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, , 2018, In: Cell. 175, 2, p. 347-359, e1-e7Research output: Contribution to journal › Journal article › Research › peer-review
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Hidden Markov models for prediction of protein features.
Bystroff, C. & Krogh, Anders, 2008, In: Methods in Molecular Biology. 413, p. 173-98 25 p.Research output: Contribution to journal › Journal article › Research › peer-review
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High-throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype-specific serologically relevant biomarkers
Terkelsen, T., Pernemalm, M., Gromov, P., Borresen-Dale, A., Krogh, Anders, Haakensen, V. D., Lethio, J., Papaleo, E. & Gromova, I., 2021, In: Molecular Oncology. 15, 2, p. 429-461 33 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, Anders, 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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Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing
Nygaard, S., Jacobsen, A., Lindow, M., Eriksen, J., Balslev, E., Flyger, H., Tolstrup, N., Moller, S., Krogh, Anders & Litman, T., 2009, In: B M C Medical Genomics. 2, 1, p. 35Research output: Contribution to journal › Journal article › Research › peer-review
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Improving The Analysis Of Gene Expression Profiles By Comparing AML Blasts With Their Nearest Normal Counterparts
Rapin, N., Bagger, F. O., Jendholm, J., Mora-Jensen, H. I., Krogh, Anders, Kohlmann, A., Thiede, C., Borregaard, N., Bullinger, L., Winther, Ole, Theilgaard-Mønch, Kim & Porse, Bo Torben, 2013, In: Blood. 122, 21Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
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Improving ancient DNA read mapping against modern reference genomes
Schubert, Mikkel, Ginolhac, A., Lindgreen, S., Thompson, J. F., Al-Rasheid, K. A. S., Willerslev, Eske, Krogh, Anders & Orlando, L. A. A., 2012, In: BMC Genomics. 13, 15 p., 178.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.
Bryne, J. C., Valen, E., Tang, M. E., Marstrand, T., Winther, Ole, da Piedade, I., Krogh, Anders, Lenhard, B. & Sandelin, Albin Gustav, 2008, In: Nucleic Acids Research. 36, Database issue, p. D102-6Research output: Contribution to journal › Journal article › Research › peer-review
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Large-scale prokaryotic gene prediction and comparison to genome annotation
Nielsen, P. & Krogh, Anders, 2005, In: Bioinformatics. 21, 24, p. 4322-9Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Long- and short-term selective forces on malaria parasite genomes
Nygaard, S., Braunstein, A., Malsen, G., Van Dongen, S., Gardner, P. P., Krogh, Anders, Otto, T. D., Pain, A., Berriman, M., McAuliffe, J., Dermitzakis, E. T. & Jeffares, D. C., 1 Sep 2010, In: P L o S Genetics. 6, 9Research output: Contribution to journal › Journal article › Research › peer-review
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Loss of miR-10a activates Lpo and collaborates with activated Wnt signaling in inducing intestinal Neoplasia in female mice
Stadthagen Gomez, G., Tehler, D. E., Høyland-Kroghsbo, Nina Molin, Wen, J., Krogh, Anders, Jensen, K. T., Santoni Rugiu, Eric, Engelholm, Lars Henning & Lund, Anders H., 2013, In: P L o S Genetics. 9, 10, 12 p., e1003913.Research output: Contribution to journal › Journal article › Research › peer-review
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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
Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns
Weischenfeldt, Joachim Lütken, Waage, J. E., Tian, G., Zhao, J., Damgaard, I., Jakobsen, J. S., Kristiansen, Karsten, Krogh, Anders, Wang, J. & Porse, Bo Torben, 2012, In: Genome Biology (Online Edition). 13, 5, 19 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Measuring covariation in RNA alignments: Physical realism improves information measures
Lindgreen, S., Gardner, P. P. & Krogh, Anders, 2006, In: Bioinformatics. 22, 24, p. 2988-2995 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action
Wen, J., Parker, B. J., Jacobsen, A. & Krogh, Anders, 2011, In: R N A. 17, 5, p. 820-34 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
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MicroRNA-145 targets YES and STAT1 in colon cancer cells
Gregersen, Lea Haarup, Jacobsen, A. B., Frankel, Lisa, Wen, J., Krogh, Anders & Lund, Anders H., 2010, In: PLoS ONE. 5, 1, p. e8836Research output: Contribution to journal › Journal article › Research › peer-review
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Modeling promoter grammars with evolving hidden Markov models
Won, K., Sandelin, Albin Gustav, Marstrand, T. T. & Krogh, Anders, 2008, In: Bioinformatics. 24, 15, p. 1669-75 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Molecular composition of IMP1 ribonucleoprotein granules.
Jønson, L., Vikesaa, J., Krogh, Anders, Nielsen, Lars Kamp, Hansen, T. V., Borup, R., Johnsen, A. H., Christiansen, Jan & Nielsen, Finn Cilius, 2007, In: Molecular and Cellular Proteomics. 6, 5, p. 798-811 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Multiple alignment and structure prediction of non-coding RNA sequences
Lindgreen, S., Gardner, P. P. & Krogh, Anders, 2007, In: BMC Bioinformatics. 8, Suppl. 8, 1 p., P8.Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
- Published
N-of-one differential gene expression without control samples using a deep generative model
Prada Luengo, Inigo, Schuster, Viktoria, Liang, Yuhu, Terkelsen, Thilde Bagger, Sora, Valentina & Krogh, Anders, 2023, In: Genome Biology. 24, 1, 17 p., 263.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Novel overlapping coding sequences in Chlamydia trachomatis
Jensen, K. T., Petersen, L., Falk, S., Iversen, P., Andersen, P., Theisen, Michael & Krogh, Anders, 2006, In: FEMS Microbiology Reviews. 265, 1, p. 106-17Research output: Contribution to journal › Journal article › Research › peer-review
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Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios
Besenbacher, S., Liu, S., Gonzalez-Izarzugaza, J. M., Grove, J., Belling, K. G., Bork-Jensen, J., Huang, S., Als, T. D., Li, S., Yadav, R., Rubio García, A., Lescai, F., Demontis, D., Rao, J., Ye, W., Mailund, T., Møllegaard Friborg, R., Pedersen, C. N. S., Xu, R., Sun, J. & 27 others, , 2015, In: Nature Communications. 6, 9 p., 5969.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs
Islin, S. R., Menzel, P., Krogh, Anders, Young, M. & Peng, Xu, 2016, In: Environmental Microbiology. 18, 3, p. 863-874 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
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On the accuracy of short read mapping
Menzel, K. P., Frellsen, J., Plass, M., Rasmussen, S. H. & Krogh, Anders, 2013, Deep Sequencing Data Analysis. Shomron, N. (ed.). Springer Science+Business Media, p. 39-59 21 p. (Methods in Molecular Biology, Vol. 1038).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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On the total number of genes and their length distribution in complete microbial genomes
Skovgaard, M., Jensen, Lars Juhl, Brunak, Søren, Ussery, D. & Krogh, Anders, 2001, In: Trends in Genetics. 17, 8, p. 425-8 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins
Amico, M., Finelli, M., Rossi, I., Zauli, A., Elofsson, A., Viklund, H., Heijne, G. V., Joes, D., Krogh, Anders, Fariselli, P., Luigi, M. P. & Casadio, R., 2006, In: Nucleic Acids Research. 34, p. W169-72Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models
Fariselli, P., Molinini, D., Casadio, R. & Krogh, Anders, 2007, Bioinformatics Research and Development: First International Conference, BIRD 2007 Proceedings. Hochreiter, S. & Wagner, R. (eds.). Springer, p. 292-302 11 p. (Lecture Notes in Bioinformatics, Vol. 4414).Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
Prediction of lipoprotein signal peptides in Gram-negative bacteria.
Juncker, A. S., Willenbrock, H., Heijne, G. V., Nielsen, H. & Krogh, Anders, 2003, In: Protein Science. 12(8), p. 1652-1662Research output: Contribution to journal › Journal article › Research › peer-review
- Published
RNA sequencing of trigeminal ganglia in Rattus Norvegicus after glyceryl trinitrate infusion with relevance to migraine
Pedersen, S. H., Sørensen, L. M., Ramachandran, R., Sibbesen, Jonas Andreas, Yakimov, V., Christensen, R. E., Hansen, Thomas Folkmann, Krogh, Anders, Olesen, Jes & Olesen, I. J., 2016, In: P L o S One. 11, 5, 13 p., e0155039.Research output: Contribution to journal › Journal article › Research › peer-review
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Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology
Cao, H., Hastie, A. R., Cao, D., Lam, E. T., Sun, Y., Huang, H., Liu, X., Lin, L., Andrews, W., Chan, S., Huang, S., Tong, X., Requa, M., Anantharaman, T., Krogh, Anders, Yang, H., Cao, H. & Xu, X., 2014, In: GigaScience. 3, 11 p., 34.Research output: Contribution to journal › Journal article › Research › peer-review
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Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
Orlando, L. A. A., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P. L. F., Fumagalli, M., Mouatt, J. T. V., Raghavan, M., Korneliussen, T. S., Malaspinas, A. S., Vogt, J., Szklarczyk, D. M., Kelstrup, C., Vinther, J. & 36 others, , 4 Jul 2013, In: Nature. 499, 7456, p. 74-78 5 p.Research output: Contribution to journal › Letter › Research › peer-review
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Reconstructing genome evolution in historic samples of the Irish potato famine pathogen
Martin, M. D., Cappellini, Enrico, Samaniego Castruita, J. A., Zepeda Mendoza, M. L., Campos, P., Seguin-Orlando, A., Wales, N., Orlando, L. A. A., Ho, S. Y. W., Dietrich, F. S., Mieczkowski, P. A., Heitman, J., Willerslev, Eske, Krogh, Anders, Ristaino, J. B. & Gilbert, M Thomas P, 18 Jul 2013, In: Nature Communications. 4, 7 p., 2172.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Reliability measures for membrane protein topology prediction algorithms
Melén, K., Krogh, Anders & Heijne, G. V., 2003, In: Journal of Molecular Biology. 327(3), p. 735-744Research output: Contribution to journal › Journal article › Research › peer-review
- Published
RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box
Petersen, L., Larsen, T. S., Ussery, D. W., On, S. L. W. & Krogh, Anders, 2003, In: Journal of Molecular Biology. 326(5), p. 1361-1372Research output: Contribution to journal › Journal article › Research › peer-review
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SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data
Poulsen, L. D., Kielpinski, L. J., Salama, S. R., Krogh, Anders & Vinther, Jeppe, 2015, In: R N A. 21, 5, p. 1042-1052 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
Sampling Realistic Protein Conformations Using Local Structural Bias
Hamelryck, Thomas Wim, Kent, J. T. & Krogh, Anders, 2006, In: PLoS ONE. 2, 9, p. e131Research output: Contribution to journal › Journal article › Research › peer-review
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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
Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads
Prada Luengo, Inigo, Krogh, Anders, Sørensen, L. M. & Regenberg, Birgitte, 2019, In: BMC Bioinformatics. 20, 9 p., 663.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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, , 2017, In: Nature. 548, 7665, p. 87-91 5 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
Signatures of RNA binding proteins globally coupled to effective microRNA target sites
Jacobsen, A., Wen, J., Marks, D. S. & Krogh, Anders, 1 Aug 2010, In: Genome Research. 20, 8, p. 1010-9 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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, Anders, Bonch-Osmolovskaya, E. A., Peng, Xu & Kublanov, I. V., 2 Nov 2017, In: Frontiers in Microbiology. 8, 11 p., 2140.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Synthetic Data Generation by Artificial Intelligence to Accelerate Research and Precision Medicine in Hematology
D'Amico, S., Dall'Olio, D., Sala, C., Dall'Olio, L., Sauta, E., Zampini, M., Asti, G., Lanino, L., Maggioni, G., Campagna, A., Ubezio, M., Russo, A., Bicchieri, M. E., Riva, E., Tentori, C. A., Travaglino, E., Morandini, P., Savevski, V., Santoro, A., Prada-Luengo, I. & 9 others, , 2023, In: JCO clinical cancer informatics. 7, p. 1-22 e2300021.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju
Tovo, A., Menzel, P., Krogh, Anders, Cosentino Lagomarsino, M. & Suweis, S., 2020, In: Nucleic Acids Research. 48, 16, 13 p., e93.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Teaching computers to fold proteins
Winther, O. & Krogh, Anders, 2004, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). Vol. 70 (3) pt. 1, p. 030903Research output: Contribution to journal › Journal article › Research
- Published
The Block Hidden Markov Model for Biological Sequence Analysis
Won, K. J., Prügel-Bennett, A. & Krogh, Anders, 2004, Knowledge-BasedIntelligent Informationand Engineering Systems: 8th International Conference, KES 2004, Proceedings. Negoita, M. G., Howlett, R. J. & Jain, L. (eds.). Springer, Vol. 1. p. 64-70 7 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 3213).Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
The Deep Generative Decoder: MAP estimation of representations improves modelling of single-cell RNA data
Schuster, Viktoria & Krogh, Anders, 2023, In: Bioinformatics. 39, 9, 14 p., btad497.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming
Nygaard, S., Zhang, G., Schiøtt, M., Li, C., Wurm, Y., Hu, H., Zhou, J., Ji, L., Qiu, F., Rasmussen, M., Pan, H., Hauser, Frank, Krogh, Anders, Grimmelikhuijzen, Cornelis (Cok), Wang, J. & Boomsma, Jacobus J., 2011, In: Genome Research. 21, 8, p. 1339-1348 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Suzuki, H., Forrest, A. R. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J. L., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M. & 31 others, , 2009, In: Nature Genetics. 41, 5, p. 553-62 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Training HMM structure with genetic algorithm for biological sequence analysis
Won, K. J. & Krogh, Anders, 2004, In: Bioinformatics. Vol. 20 (18), p. 3613-9Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptome dynamics of the microRNA inhibition response
Wen, J., Leucci, E., Vendramin, R., Kauppinen, S., Lund, Anders H., Krogh, Anders & Parker, B. J., 2015, In: Nucleic Acids Research. 43, 13, p. 6207-6221 15 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
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization
Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., Cheng, J., Zhao, S., Xu, M., Luo, Y., Yang, Y., Wu, Z., Mao, L., Wu, H., Ling-Hu, C., Zhou, H., Lin, H., Gonzalez-Morales, S., Trejo-Saavedra, D. L., Tian, H. & 53 others, , 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 14, p. 5135-5140 6 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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microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-κB by targeting CARD10 and COPS8 in gastric cancer
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Improving ancient DNA read mapping against modern reference genomes
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