Publications

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Sørensen, J. L., Knudsen, M., Hansen, F. T., Olesen, C., Romans Fuertes, P., Lee, T. V., Søndergaard, T. E., Pedersen, C. N. S., Brodersen, D. E. & Giese, H. (2014). Fungal NRPS-dependent siderophores: From function to prediction. In J.-F. Martin, C. Garcia-Estrada & S. Zeilinger (Eds.), Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites (pp. 317-339). Springer. https://doi.org/10.1007/978-1-4939-1191-2_15

Sørensen, M. T. & GplusE Consortium (2017). Use of metabolic clusters predicted by milk metabolites and enzymes to identify potential risk cows. In Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science (pp. 404-404). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-859-9

Sørensen, S. G., Shrikhande, A., Poulsgaard, G. A., Christensen, M. H., Bertl, J., Laursen, B. E., Hoffmann, E. R. & Pedersen, J. S. (2023). Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns. eLife, 12, Article e81224. https://doi.org/10.7554/elife.81224

Sørensen, E. F., Harris, R. A., Zhang, L., Raveendran, M., Kuderna, L. F. K., Walker, J. A., Storer, J. M., Kuhlwilm, M., Fontsere, C., Seshadri, L., Bergey, C. M., Burrell, A. S., Bergman, J., Phillips-Conroy, J. E., Shiferaw, F., Chiou, K. L., Chuma, I. S., Keyyu, J. D., Fischer, J. ... Rogers, J. (2023). Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science (New York, N.Y.), 380(6648), Article eabn8153. https://doi.org/10.1126/science.abn8153

Soraggi, S., Riera Belles, M., Rajpert-De Meyts, E., Schierup, M. H. & Almstrup, K. (2021). Evaluating genetic causes of azoospermia: What can we learn from a complex cellular structure and single-cell transcriptomics of the human testis? Human Genetics, 140(1), 183-201. https://doi.org/10.1007/s00439-020-02116-8

Soraggi, S., Rhodes, J., Altinkaya, I., Tarrant, O., Balloux, F., Fisher, M. C. & Fumagalli, M. (2022). HMMploidy: inference of ploidy levels from short-read sequencing data . Peer Community Journal, 2, Article e60. https://doi.org/10.24072/pcjournal.178

Sonntag, Y., Musgaard, M., Olesen, C., Schiøtt, B., Møller, J. V., Nissen, P. & Thøgersen, L. (2011). Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes. Nature Communications, 2, 304. https://doi.org/10.1038/ncomms1307

Søndergaard, D., Knudsen, M. & Pedersen, C. N. S. (2014). Machine learning approaches to functional prediction of P-Type ATPases.

Søndergaard, D. A., Knudsen, M. & Pedersen, C. S. (2016). Computational Classification of P-Type ATPases. Methods in Molecular Biology, 1377, 493-502. https://doi.org/10.1007/978-1-4939-3179-8

Søndergaard, D. & Pedersen, C. N. S. (2015). PATBox: A Toolbox for Classification and Analysis of P-Type ATPases. PLOS ONE, 10(9), Article e0139571. https://doi.org/10.1371/journal.pone.0139571

Søndergaard, D., Nielsen, S., Pedersen, C. N. S. & Besenbacher, S. (2017). Prediction of Primary Tumors in Cancers of Unknown Primary. Journal of integrative bioinformatics, 14(2). https://doi.org/10.1515/jib-2017-0013

Søndergaard, D. A. (2018). Classification and analysis of biological data.

Sokač, M., Kjær, A., Dyrskjøt, L., Haibe-Kains, B., Jwl Aerts, H. & Birkbak, N. J. (2023). Spatial transformation of multi-omics data unlocks novel insights into cancer biology. eLife, 12, Article RP87133. https://doi.org/10.7554/eLife.87133

Sokac, M., Ahrenfeldt, J., Litchfield, K., Watkins, T. B. K., Knudsen, M., Dyrskjøt, L., Jakobsen, M. R. & Birkbak, N. J. (2022). Classifying cGAS-STING Activity Links Chromosomal Instability with Immunotherapy Response in Metastatic Bladder Cancer. Cancer Research Communications, 2(8), 762-771. https://doi.org/10.1158/2767-9764.CRC-22-0047, https://doi.org/10.1158/2767-9764.CRC-22-0047

Slotte, T., Bataillon, T., Hansen, T. T., St Onge, K., Wright, S. I. & Schierup, M. H. (2011). Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biology and Evolution, 3, 1210-1219. https://doi.org/10.1093/gbe/evr094

Skov, L. (2017). Methods for analyzing genetic variation in modern and archaic humans.

Skov, L., Schierup, M. H. & Danish Pan Genome Consortium (2017). Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion. P L o S Genetics (Online), 13(8), Article 1006834. https://doi.org/10.1371/journal.pgen.1006834

Skov, L., Hui, R., Shchur, V., Hobolth, A., Scally, A., Schierup, M. H. & Durbin, R. (2018). Detecting archaic introgression using an unadmixed outgroup. PLOS Genetics, 14(9), Article e1007641. https://doi.org/10.1371/journal.pgen.1007641

Skov, L., Coll Macià, M., Sveinbjörnsson, G., Mafessoni, F., Lucotte, E. A., Einarsdóttir, M. S., Jonsson, H., Halldorsson, B., Gudbjartsson, D. F., Helgason, A., Schierup, M. H. & Stefansson, K. (2020). The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes. Nature, 582(7810), 78-83. https://doi.org/10.1038/s41586-020-2225-9

Skov, L., Coll Macià, M., Lucotte, E. A., Cavassim, M. I. A., Castellano, D., Schierup, M. H. & Munch, K. (2023). Extraordinary selection on the human X chromosome associated with archaic admixture. Cell Genomics, 3(3), Article 100274. https://doi.org/10.1016/j.xgen.2023.100274

Skotte, L., Fadista, J., Bybjerg-Grauholm, J., Appadurai, V., Hildebrand, M. S., Hansen, T. F., Banasik, K., Grove, J., Albiñana, C., Geller, F., Bjurström, C. F., Vilhjálmsson, B. J., Coleman, M., Damiano, J. A., Burgess, R., Scheffer, I. E., Pedersen, O. B. V., Erikstrup, C., Westergaard, D. ... Feenstra, B. (2022). Genome-wide association study of febrile seizures implicates fever response and neuronal excitability genes. Brain : a journal of neurology, 145(2), 555–568. https://doi.org/10.1093/brain/awab260

Skakkebæk, A., Nielsen, M. M., Trolle, C., Vang, S., Hornshøj, H., Hedegaard, J., Wallentin, M., Bojesen, A., Hertz, J. M., Fedder, J., Østergaard, J. R., Pedersen, J. S. & Gravholt, C. H. (2018). DNA hypermethylation and differential gene expression associated with Klinefelter syndrome. Scientific Reports, 8(1), Article 13740. https://doi.org/10.1038/s41598-018-31780-0

Sjödin, P., Bataillon, T. & Schierup, M. H. (2010). Insertion and deletion processes in recent human history. P L o S One, 5(1), e8650. https://doi.org/10.1371/journal.pone.0008650

Siuda, I. A. (2012). Modelling Protein Dynamics on the Microsecond Time Scale: Problems and Solutions. Aarhus University, Faculty of Science and Technology.

Siuda, I. & Thøgersen, L. (2013). Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics. Journal of Molecular Modeling, 19(11), 4931-4945. https://doi.org/10.1007/s00894-013-1991-9

Singh, T., Poterba, T., Curtis, D., Akil, H., Al Eissa, M., Barchas, J. D., Bass, N., Bigdeli, T. B., Breen, G., Bromet, E. J., Buckley, P. F., Bunney, W. E., Bybjerg-Grauholm, J., Byerley, W. F., Chapman, S. B., Chen, W. J., Churchhouse, C., Craddock, N., Cusick, C. M. ... Daly, M. J. (2022). Rare coding variants in ten genes confer substantial risk for schizophrenia. Nature, 604(7906), 509-516. https://doi.org/10.1038/s41586-022-04556-w

Simonsen, M., Mailund, T. & Pedersen, C. S. (2008). Rapid Neighbour-Joining. In Proceedings of the 8th International Workshop on Algorithms in Bioinformatics (WABI) (pp. 113-122)

Simonsen, M., Mailund, T. & Pedersen, C. S. (2009). Building very large neighbour-joining trees. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden.

Simonsen, M., Mailund, T. & Pedersen, C. N. S. (2010). Building Very Large Neighbour-Joining Trees. In A. Fred, J. Filipe & H. Gamboa (Eds.), BIOINFORMATICS 2010: Proceedings of the First International Conference on Bioinformatics (part of the 3rd International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2010) (pp. 26). Institute for Systems and Technologies of Information, Control and Communication.

Simonsen, V. & Christiansen, F. (1985). Genetics of Zoarces populations XIV. Variation of the lactate dehydrogenase isoenzymes. Hereditas, 103, 177–185.

Simonsen, V. & Christiansen, F. (1984). Genetics of Zoarces populations XIII. Three loci determining isoenzymes of glutamic-oxaloacetic transaminase. Hereditas, 101, 129–136.

Simonsen, V. & Christiansen, F. (1981). Genetics of Zoarces populations XI. Inheritance of electrophoretic variants of the enzyme adenosine deaminase. Hereditas, 95, 289-294.

Simonsen, M., Sand, A., Mailund, T. & Pedersen, C. N. S. (2010). Using the Power of Modern Processors in Bioformatics. Poster session presented at Conference on IT research at AU, Århus, Denmark.

Simonsen, M., Mailund, T. & Pedersen, C. N. S. (2011). Inference of Large Phylogenies Using Neighbour-Joining. Biomedical Engineering Systems and Technologies, 127(5), 334-344. https://doi.org/10.1007/978-3-642-18472-7_26

Simonsen, M., Maetschke, S. R. & Ragan, M. A. (2012). Automatic selection of reference taxa for protein–protein interaction prediction with phylogenetic profiling. Bioinformatics, 28(6), 851-857. https://doi.org/10.1093/bioinformatics/btr720

Simonsen, M. & Pedersen, C. N. S. (2011). Rapid Computation of Distance Estimators from Nucleotide and Amino Acid Alignments. In Proceedings of the 26th Annual ACM Symposium on Applied Computing Association for Computing Machinery.

Simonsen, M., Thomsen, R., Christensen, M. H. & Pedersen, C. N. S. (2011). GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution. In GECCO'11 Proceedings of the 13th annual conference on Genetic and evolutionary computation (pp. 1803-1810). Association for Computing Machinery. https://doi.org/10.1145/2001576.2001818

Simonsen, M. (2011). Efficient algorithms for tree reconstruction and prediction of molecular interactions. Department of Computer Science, Aarhus University.

Simonsen, M., Maetschke, S. R. & Ragan, M. A. (2012). Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. Bioinformatics, 28(6), 851-857. https://doi.org/10.1093/bioinformatics/btr720

Simonsen, M., Christensen, M. H., Thomsen, R. & Pedersen, C. N. S. (2013). GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution. In S. tsutsui & P. Collet (Eds.), Massively Parallel Evolutionary Computation on GPGPUs Springer Publishing Company.

Sigurdsson, A. I., Louloudis, I., Banasik, K., Westergaard, D., Winther, O., Lund, O., Ostrowski, S. R., Erikstrup, C., Pedersen, O. B. V., Nyegaard, M., Brunak, S., Vilhjálmsson, B. J., Rasmussen, S. & DBDS Genomic Consortium (2023). Deep integrative models for large-scale human genomics. Nucleic Acids Research, 51(12), E67. Article e67. https://doi.org/10.1093/nar/gkad373

Siegismund, H. & Christiansen, F. (1985). Selection component analysis of natural polymorphisms using population samples including mother-offspring combinations, III. Theoretical Population Biology, 27, 268–297.

Shuai, S., PCAWG Drivers and Functional Interpretation Working Group, Gallinger, S., Stein, L. & PCAWG Consortium (2020). Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications, 11(1), Article 734. https://doi.org/10.1038/s41467-019-13929-1

Shao, Y., Zhou, L., Li, F., Zhao, L., Zhang, B. L., Shao, F., Chen, J. W., Chen, C. Y., Bi, X., Zhuang, X. L., Zhu, H. L., Hu, J., Sun, Z., Li, X., Wang, D., Rivas-González, I., Wang, S., Wang, Y. M., Chen, W. ... Wu, D. D. (2023). Phylogenomic analyses provide insights into primate evolution. Science (New York, N.Y.), 380(6648), 913-924. https://doi.org/10.1126/science.abn6919

Shah, N., Hirakawa, H., Kusakabe, S., Sandal, N., Stougaard, J., Schierup, M. H., Sato, S. & Andersen, S. U. (2016). High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines. D N A Research, 23(5), 487-495. https://doi.org/10.1093/dnares/dsw033

Shah, N., Wakabayashi, T., Kawamura, Y., Skovbjerg, C. K., Wang, M.-Z., Mustamin, Y., Isomura, Y., Gupta, V., Jin, H., Mun, T., Sandal, N., Azuma, F., Fukai, E., Seren, Ü., Kusakabe, S., Kikuchi, Y., Nitanda, S., Kumaki, T., Hashiguchi, M. ... Andersen, S. U. (2020). Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan. Nature Communications, 11(1), Article 253. https://doi.org/10.1038/s41467-019-14213-y

Sengpiel, V., Elind, E., Bacelis, J., Nilsson, S., Grove, J., Myhre, R., Haugen, M., Margrete Meltzer, H., Alexander, J., Jacobsson, B. & Brantsæter, A.-L. (2013). Maternal caffeine intake during pregnancy is associated with birth weight but not with gestational length: results from a large prospective observational cohort study. B M C Medicine, 11(42). https://doi.org/10.1186/1741-7015-11-42

Sendrowski, J. & Bataillon, T. (2024). FastDFE: Fast and Flexible Inference of the Distribution of Fitness Effects. Molecular Biology and Evolution, 41(5), Article msae070. https://doi.org/10.1093/molbev/msae070

Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Blazier, J. C., Sankararaman, S., Andolfatto, P., Rosenthal, G. G. & Przeworski, M. (2018). Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science, 360(6389), 656-660. https://doi.org/10.1126/science.aar3684

Schultz, T. R., Solomon, S. A., Mueller, U. G., Villesen, P., Boomsma, JJ., Adams, R. M. M. & Norden, B. (2002). Cryptic speciation in the fungus-growing ant Cyphomyrmex longiscapus Weber and Cyphomyrmex muelleri Schultz and Solomon, new species (Formicidae, Attini). Insectes Sociaux, 49, 331-343.

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