Publications

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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

Kumar, S., Warrell, J., Li, S., McGillivray, P. D., Meyerson, W., Salichos, L., Harmanci, A., Martinez-Fundichely, A., Chan, C. W. Y., Nielsen, M. M., Lochovsky, L., Zhang, Y., Li, X., Lou, S., Pedersen, J. S., Herrmann, C., Getz, G., Khurana, E. & Gerstein, M. B. (2020). Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. Cell, 180(5), 915-927.e16. https://doi.org/10.1016/j.cell.2020.01.032

Gusev, A., Lee, S. H., Trynka, G., Finucane, H., Vilhjálmsson, B. J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E., Kähler, A. K., Hultman, C. M., Purcell, S. M., McCarroll, S. A., Daly, M., Pasaniuc, B., Sullivan, P. F., Neale, B. M., Wray, N. R. ... Schizophrenia Working Group of the Psychiatric Genomics Consortium (Manuel Mattheisen and Jakob Grove, members) (2014). Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases. American Journal of Human Genetics, 95(5), 535-52. https://doi.org/10.1016/j.ajhg.2014.10.004

Sadik, A., Dardani, C., Pagoni, P., Havdahl, A., Stergiakouli, E., Khandaker, G. M., Sullivan, S. A., Zammit, S., Jones, H. J., Davey Smith, G., Dalman, C., Karlsson, H., Gardner, R. M., Rai, D. & The iPSYCH Autism Spectrum Disorder Working Group (2022). Parental inflammatory bowel disease and autism in children. Nature Medicine, 28(7), 1406-1411. https://doi.org/10.1038/s41591-022-01845-9

Mailund (1999). Parameterised coloured Petri nets. In Prorceedings of the second workshop on practical use of coloured Petri nets and Design/CPN (pp. 133-151)

Andersen, L. N. & Asmussen, S. (2008). Parallel computing, failure recovery and extreme values. Journal of Statistical Theory and Practice, 2(2), 279-292.

Hornshøj, H., Nielsen, M. M., Sinnott-Armstrong, N. A., Świtnicki, M. P., Juul, M., Madsen, T., Sallari, R., Kellis, M., Ørntoft, T., Hobolth, A. & Pedersen, J. S. (2018). Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival. npj Genomic Medicine, 3(1), 1. Article 40. https://doi.org/10.1038/s41525-017-0040-5

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

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793), 82-93. https://doi.org/10.1038/s41586-020-1969-6

Lamy, P., Nordentoft, I. K., Birkenkamp-Demtröder, K., Thomsen, M. B. H., Villesen, P., Vang, S., Hedegaard, J., Borre, M., Jensen, J. B., Ørntoft, T. F. & Andersen, L. D. (2016). Paired exome analysis reveals clonal evolution and potential therapeutic targets in urothelial carcinoma. Cancer Research, 76(19), 5894-5906. https://doi.org/10.1158/0008-5472.CAN-16-0436

Ehlers, B. & Bataillon, T. (2014). På forkant med selektionen. Evolution2. Weekendavisen.

Anderson, J. W. J., Haas, P. A., Mathieson, L.-A., Volynkin, V., Lyngsø, R., Tataru, P. & Hein, J. (2013). Oxfold: Kinetic Folding of RNA using Stochastic Context-Free Grammars and Evolutionary Information. Bioinformatics, 29(6), 704-710. https://doi.org/10.1093/bioinformatics/btt050

Rousselle, M., Mollion, M., Nabholz, B., Bataillon, T. & Galtier, N. (2018). Overestimation of the adaptive substitution rate in fluctuating populations. Biology Letters, 14(5), Article 20180055. https://doi.org/10.1098/rsbl.2018.0055

Mattila, T., Bechsgaard, J. S., Hansen, T., Schierup, M. H. & Bilde, T. (2012). Ortholog genes identified by transcriptome sequencing in the spider genus Stegodyphus. BMC Genomics, 13(70). https://doi.org/10.1186/1471-2164-13-70

Noor, B. (2023). Optimization and Application of Convolution Neural Networks to Genomics. [PhD dissertation, Aarhus University]. Aarhus Universitet.

Malmkvist, J., Coutant, M. P., Foldager, L., Kaiser, M. Ø. & Herskin, M. S. (2022). Optimering af procedure for lokalbedøvelse af pattegrise forud for kastration. DCA - Nationalt Center for Fødevarer og Jordbrug. Rådgivningsrapport fra DCA - Nationalt Center for Fødevarer og Jordbrug

Kristensen, T. G. & Pedersen, C. S. (2009). Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution. In J. Zhang, G.-Z. Li & J. Y. Yang (Eds.), Proceedings of the 2009 International Joint conferences on Bioinformatics, System biology and Intelligent Computing (IJCBS2009) (pp. 331-334). IEEE Computer Society Press. https://doi.org/10.1109/IJCBS.2009.36

Pedersen, C. S. & Kristensen, T. G. (2009). Optimal Overlay of Ligands with Flexible Bonds Using Differential Evolution. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Bioligy (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden. http://www.iscb.org/ismbeccb2009/poster_list.php?cat=C

Aagaard, J., Skadhede, S. C., Andersen, M. B., Kølbæk, P., Hastrup, L. H., Foldager, L. & Nielsen, J. A. (2014). Opsøgende Psykoseteams i Region Nordjylland: En monitoreringsundersøgelse med to års opfølgning af de Opsøgende Psykoseteams i Region Nordjylland og en registerbaseret undersøgelse af udviklingen i voksenpsykiatrien i Region Nordjylland. Aalborg Universitetsforlag.

Fredsted, T. & Villesen, P. (2006). Operation "Red aben". Jyllands-Posten.

Fredsted, T. & Villesen, P. (2006). Operation "Red Aben". Jyllands-Posten, 8-8.

Dinér, P., Laursen, A. K. K., Lie, M. A. & Jørgensen, K. A. (2007). On the Origin of the Stereoselectivity in Organocatalysed Reactions with Trimethylsilyl-Protected Diarylprolinol. Chemistry: A European Journal, 14(1), 122-127.

Hartfield, M. (2016). On the origin of asexual species by means of hybridization and drift. Molecular Ecology, 25(14), 3264-3265. https://doi.org/10.1111/mec.13713

Wiuf, C. & Hein, J. (1997). On the number of ancestors to a DNA sequence. Genetics, 147, 1459-1468.

Wiuf, C. (2002). On the minimum number of topologies explaining a sample of DNA sequences. Theor Pop Biol, 62, 357-363.

Wiuf, C. (2000). On the genealogy of a sample of neutral rare alleles. Theor Pop Biol, 58(1), 61-75. https://doi.org/10.1006/tpbi.2000.1469

Goldringer, I. & Bataillon, T. (2004). On the distribution of temporal variations in allele frequency: consequences for the estimation of effective population size and the detection of loci undergoing selection. Genetics, 168(1), 563-8. https://doi.org/10.1534/genetics.103.025908

Feldman, M. W., Christiansen, F. & Liberman, U. (1983). On some models of fertility selection. Genetics, 105, 1003-1010.

Davies, J., Simancik, F., Lyngsø, R., Mailund, T. & Hein, J. (2007). On Recombination-Induced Multiple and Simultaneous Coalescent Events. Genetics, 177, 2151-2160.

Østergaard, S., Krogh, M. A., Oliveira, V. H. S. D., Larsen, T., GplusE Consortium & Otten, N. D. (2020). Only few benefits from propylene glycol drench in early lactation for cows identified as physiologically imbalanced based on milk spectra analyses. Journal of Dairy Science, 103(2), 1831-1842. https://doi.org/10.3168/jds.2019-17205

Ehlers, B., Bataillon, T. & Damgaard, C. (2021). Ongoing decline in insect-pollinated plants across Danish grasslands. Biology Letters, 17(11), Article 20210493. https://doi.org/10.1098/rsbl.2021.0493

Coutant, M. P., Malmkvist, J., Kaiser, M., Foldager, L. & Herskin, M. S. (2022). On-farm administration of local anaesthetic and surgical castration of piglets: acute behavioural and physiological consequences. In M. Kjosevski, S. Waiblinger & V. Ilieski (Eds.), Proceedings of the 55th Congress of the ISAE: Animal Behaviour and Beyond (pp. 19-19). https://www.applied-ethology.org/res/ISAE_2022_PROCEEDINGS_e-version.pdf

Jimenez Mena, B., Tataru, P., Brøndum, R. F., Sahana, G., Guldbrandtsen, B. & Bataillon, T. (2016). One size fits all? Direct evidence for the heterogeneity of genetic drift throughout the genome. Biology Letters, 12(7), Article 20160426. https://doi.org/10.1098/rsbl.2016.0426

Hobolth, A., Andersen, L. N. & Mailund, T. (2011). On computing the coalescence time density in an isolation-with-migration model with few samples. Genetics, 187, 1242-1243. https://doi.org/10.1534/genetics.110.124164

Li, J., Gromov, P., Gromova, I., Moreira, J. M., Timmermans-Wielenga, V., Rank, F., Wang, K., Li, S., Li, H., Wiuf, C., Yang, H., Zhang, X., Bolund, L. & Celis, J. E. (2008). Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis. Proteomics, 8(23-24), 5038-52. https://doi.org/10.1002/pmic.200800303

Lund, H. H., Arendt, J. A., Fredslund, J. & Pagliarini, L. (1999). Ola: What Goes Up, Must Fall Down. In Proceedings of Artificial Life and Robotics 1999 (AROB'99) (pp. I-9 - I-15)

Mailund, T. & Westergaard, M. (2004). Obtaining Memory-Efficient Reachability Graph Representations Using the Sweep-Line Method. In Proceedings of Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2004) (pp. 177-191)

Kofod Petersen, A., Bindslev, D. A., Forgie, A., Villesen, P. & Staun Larsen, L. (2026). Objective comparison of 3D dental scans in forensic odontology identification. Forensic Imaging, 44, Article 200672. https://doi.org/10.1016/j.fri.2026.200672

Besenbacher, S., Liu, S., Izarzugaza, J. M. G., Grove, J., Belling, K., 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. ... Rasmussen, S. (2015). Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nature Communications, 6, Article 5969. https://doi.org/10.1038/ncomms6969

Hansen, M. C., Nederby, L., Roug, A., Villesen, P., Kjeldsen, E., Nyvold, C. G. & Hokland, P. (2015). Novel scripts for improved annotation and selection of variants from whole exome sequencing in cancer research. MethodsX, 2, 145-53. https://doi.org/10.1016/j.mex.2015.03.003

Børsting, C. F., Lashkari, S., Weisbjerg, M. R. & Foldager, L., (2022). Notat vedr. tildeling af fedt til malkekøer i tidlig laktation belyst ved en meta-analyse af resultater fra litteraturen samt gennemgang af andre forhold vedr. fodring af malkekøer med tilskudsfedt, No. 2021-0244527, 11 p., Mar 04, 2022. Rådgivningsnotat fra DCA - Nationalt Center for Fødevarer og Jordbrug

Waltoft, B. L. & Hobolth, A. (2018). Non-parametric estimation of population size changes from the site frequency spectrum. Statistical Applications in Genetics and Molecular Biology, 17(3), Article 20170061. https://doi.org/10.1515/sagmb-2017-0061

Jeppesen, L. D., Lildballe, D. L., Hatt, L., Hedegaard, J., Singh, R., Toft, C. L. F., Schelde, P., Pedersen, A. S., Knudsen, M. & Vogel, I. (2023). Noninvasive Prenatal Screening for Cystic Fibrosis Using Circulating Trophoblasts: Detection of the 50 Most Common Disease-Causing Variants. Obstetrical and Gynecological Survey, 78(7), 393-395. https://doi.org/10.1097/01.ogx.0000947140.57660.b6

Dutheil, J. & Boussau, B. (2008). Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evolutionary Biology, 8, 255. https://doi.org/10.1186/1471-2148-8-255

Rasmussen, M. J., Bertl, J., Guo, Q., Nielsen, M. M., Świtnicki, M., Hornshøj, H., Madsen, T., Hobolth, A. & Pedersen, J. S. (2017). Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate. eLife, 6, Article e21778. https://doi.org/10.7554/eLife.21778

Dominguez-Valentin, M., Plazzer, J. P., Sampson, J. R., Engel, C., Aretz, S., Jenkins, M. A., Sunde, L., Bernstein, I., Capella, G., Balaguer, F., Macrae, F., Winship, I. M., Thomas, H., Evans, D. G., Burn, J., Greenblatt, M., de Vos tot Nederveen Cappel, W. H., Sijmons, R. H., Nielsen, M. ... Møller, P. (2021). No difference in penetrance between truncating and missense/aberrant splicing pathogenic variants in mlh1 and msh2: A prospective lynch syndrome database study. Journal of Clinical Medicine, 10(13), Article 2856. https://doi.org/10.3390/jcm10132856

Poulsen, I., Balle, M. & Givard, K. L. (2019). Nociception Coma Scale–Revised: Nurses’ Experience in Clinical Practice. Pain Management Nursing, 20(6), 592-598. https://doi.org/10.1016/j.pmn.2019.02.003

Hedegaard, J., Thorsen, K., Lund, M. K., Hein, A.-M. K., Hamilton-Dutoit, S. J., Vang, S., Nordentoft, I., Birkenkamp-Demtröder, K., Kruhøffer, M., Hager, H., Knudsen, B., Andersen, C. L., Sørensen, K. D., Pedersen, J. S., Orntoft, T. F. & Dyrskjøt, L. (2014). Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue. PLoS One, 9(5), e98187. https://doi.org/10.1371/journal.pone.0098187

Lindgren, L. H., Thomsen, T., de Thurah, A., Aadahl, M., Hetland, M. L., Kristensen, S. D. & Esbensen, B. A. (2023). Newly diagnosed with inflammatory arthritis (NISMA)–development of a complex self-management intervention. BMC Health Services Research, 23(1), Article 123. https://doi.org/10.1186/s12913-022-09007-w

Bataillon, T., David, J. L. & Schoen, D. J. (1996). Neutral genetic markers and conservation genetics: simulated germplasm collections. Genetics, 144(1), 409-17.

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