Publications

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Laurila, K., Øster, B., Andersen, C. L., Lamy, P., Orntoft, T., Yli-Harja, O. & Wiuf, C. (2011). A Beta-Mixture Model for Dimensionality Reduction, Sample Classification and Analysis. B M C Bioinformatics, 12(1), 215. https://doi.org/10.1186/1471-2105-12-215

Lassen, J., Nielsen, K. L., Johannsen, M. & Villesen, P. (2021). Assessment of XCMS Optimization Methods with Machine-Learning Performance. Analytical Chemistry, 93(40), 13459-13466. https://doi.org/10.1021/acs.analchem.1c02000

Lassen, J. K., Wang, T., Nielsen, K. L., Hasselstrøm, J. B., Johannsen, M. & Villesen, P. (2023). Large-Scale metabolomics: Predicting biological age using 10,133 routine untargeted LC–MS measurements. Aging Cell, 22(5), Article e13813. https://doi.org/10.1111/acel.13813

Lassalle, F., Périan, S., Bataillon, T., Nesme, X., Duret, L. & Daubin, V. (2015). GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands. P L o S Genetics, 11(2), e1004941. https://doi.org/10.1371/journal.pgen.1004941

Lasry, C., Guillemot, V., Lechat, P., Menager, H., Vilhjalmsson, B. J. & Aschard, H. (2017). Summary Statistic GWAS Joint Re-Analyses Across 30+Traits. Genetic Epidemiology, 41(7), 652-652.

Lashkari, S., Clausen, T. N., Foldager, L. & Jensen, S. K. (2021). Absorption of α-tocopheryl acetate is limited in mink kits (Mustela vison) during weaning. Scientific Reports, 11(1), Article 2686. https://doi.org/10.1038/s41598-020-80902-0

Lashkari, S., Weisbjerg, M. R., Foldager, L. & Børsting, C. F. (2022). Fat supplement for dairy cow diets during early lactation – meta analysis. In Book of Abstracts of the 73rd Annual Meeting of the European Federation of Animal Science (pp. 668-668). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-937-4

Lashkari, S., Jensen, S. K., Foldager, L., Larsen, T. & Vestergaard, M. (2024). A high fat to vitamin E ratio in the feed protects and improves uptake of the natural form of vitamin E in postweaning calves. Journal of Animal Physiology and Animal Nutrition, 108(3), 724-734. https://doi.org/10.1111/jpn.13926

Lashkari, S., Weisbjerg, M. R., Foldager, L. & Børsting, C. F. (2024). Fat supplement for dairy cows during early lactation – potentials, challenges, and risks – a meta-analysis. Journal of Applied Animal Research, 52(1), Article 2323625. https://doi.org/10.1080/09712119.2024.2323625

Larsen, A., Bøggild, H., Mortensen, J. T., Foldager, L., Hansen, J., Christensen, A., Arendt, M., Rosenberg, N. & Munk-Jørgensen, P. (2010). Psychopathology, defence mechanisms, and the psychosocial work environment. International Journal of Social Psychiatry, 56(6), 563-77. https://doi.org/10.1177/0020764008099555

Larsen, J. K., Foldager, L., Bendsen, B. B. & Munk-Jørgensen, P. (2011). Prematurity and low birth weight as risk factors for the development of affective disorder, especially depression and schizophrenia: a register study. Poster session presented at American Psychiatric Association 164th Annual Meeting, Honolulu, Hawaii, United States.

Larsen, M., Amorim Franchi, G., Herskin, M. S., Foldager, L., Larsen, M. L. V., Hernandez Castellano, L. E., Sørensen, M. T. & Jensen, M. B. (2021). Effects of feeding level, milking frequency, and single injection of cabergoline on feed intake, milk yield, milk leakage, and clinical udder characteristics during dry-off in dairy cows. Journal of Dairy Science, 104(10), 11108-11125. Article 20289. https://doi.org/10.3168/jds.2021-20289

Lan, T., Leppälä, K., Tomlin, C., Talbot, S. L., Sage, G. K., Farley, S. D., Shideler, R. T., Bachmann, L., Wiig, Ø., Albert, V. A., Salojärvi, J., Mailund, T., Drautz-Moses, D. I., Schuster, S. C., Herrera-Estrella, L. & Lindqvist, C. (2022). Insights into bear evolution from a Pleistocene polar bear genome. Proceedings of the National Academy of Sciences (PNAS), 119(24), Article e2200016119. https://doi.org/10.1073/pnas.2200016119

Lamy, P., Andersen, C. L., Wikman, F. & Wiuf, C. (2006). Genotyping and annotation of Affymetrix SNP arrays. Nucleic Acids Research, 34(14). https://doi.org/10.1093/nar/gkl475

Lamy, P., Andersen, C. L., Andersen, L. D., Tørring, N., Ørntoft, T. F. & Wiuf, C. (2006). Are microRNAs located in cancer specific regions in the genome? British Journal of Cancer, 95(10), 1415-8. https://doi.org/10.1038/sj.bjc.6603381

Lamy, P., Andersen, C. L. & Wiuf, C. (2007). Genotyping and Annotation of Affymetrix SNP Probe Sets, presented at PhD Annual Day, Graduate School of Health, University of Aarhus.. Poster session presented at Genotyping and Annotation of Affymetrix SNP Probe Sets, presented at PhD Annual Day, Graduate School of Health, University of Aarhus..

Lamy, P., Andersen, C. L., Andersen, L. D., Tørring, N. & Wiuf, C. (2007). A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays. B M C Bioinformatics, 8(434).

Lamy, P., Wiuf, C., Ørntoft, T. F. & Andersen, C. L. (2010). Rseg - an R package to optimize segmentation of SNP array data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btq668

Lamy, P., Grove, J. & Wiuf, C. (2011). A review of software for microarray genotyping. Human Genomics (Online), 5(4), 304-9.

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

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

Kuderna, L. F. K., Lizano, E., Julia, E., Gomez-Garrido, J., Serres-Armero, A., Kuhlwilm, M., Alandes, R. A., Alvarez-Estape, M., Juan, D., Simon, H., Alioto, T., Gut, M., Gut, I., Schierup, M. H., Fornas, O. & Marques-Bonet, T. (2019). Selective single molecule sequencing and assembly of a human Y chromosome of African origin. Nature Communications, 10(1), Article 4. https://doi.org/10.1038/s41467-018-07885-5

Kuderna, L. F. K., Gao, H., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., Manu, S., Valenzuela, A., Bergman, J., Rousselle, M., Silva, F. E., Agueda, L., Blanc, J., Gut, M., de Vries, D., Goodhead, I., Harris, R. A., Raveendran, M., Jensen, A. ... Bonet, T. M. (2023). A global catalog of whole-genome diversity from 233 primate species. Science, 380(6648), 906-913. https://doi.org/10.1126/science.abn7829

Kuderna, L. F. K., Ulirsch, J. C., Rashid, S., Ameen, M., Sundaram, L., Hickey, G., Cox, A. J., Gao, H., Kumar, A., Aguet, F., Christmas, M. J., Clawson, H., Haeussler, M., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., Manu, S., Valenzuela, A. ... Farh, K. K. H. (2024). Identification of constrained sequence elements across 239 primate genomes. Nature, 625(7996), 735-742. https://doi.org/10.1038/s41586-023-06798-8

Krogh, M. A., Ettema, J., Østergaard, S. & GplusE Consortium (2018). Cost/benefit analyses on indicator-based intervention on physiological imbalance in dairy cows. 471-471. Poster session presented at The 15th International Symposium of Veterinary Epidemiology and Economic. , Chiang Mai, Thailand.

Krogh, M. A., Hostens, M., Salavati, M., Grelet, C., Sørensen, M. T., Wathers, D. C., Ferris, C. P., Marchitelli, C., Signorelli, F., Napolitano, F., Becker, F., Larsen, T., Matthews, E., Carter, F., Vanlierde, A., Opsomer, G., Gengler, N., Dehareng, F., Crowe, M. A. ... Foldager, L. (2020). Between- and within-herd variation in blood and milk biomarkers in Holstein cows in early lactation. Animal, 14(5), 1067-1075. Article 1751731119002659. https://doi.org/10.1017/S1751731119002659

Krogh, M. A., Enemark, P. S. & Foldager, L. (2019). Unsupervised outlier detection in questionnaire data. Poster session presented at Annunal Conference of the Society for Veterinary Epidemiology and Preventive Medicine (SVEPM), Utrecht, Netherlands.

Krogh, U., Højberg, O., Foldager, L., Rani, S., Nørskov, N. P. & Sørensen, M. T. (2021). Performance and mineral status of weaning pigs fed diets with different levels of glyphosate and tryptophan. Livestock Science, 252, Article 104681. https://doi.org/10.1016/j.livsci.2021.104681

Kristensen, L. M. & Mailund (2003). Efficient Path Finding with the Sweep-Line Method using External Storage. In Proceedings of International Conference on Formal Engineering Methods (ICFEM 2003) (pp. 319-337)

Kristensen, T. G. & Pedersen, C. S. (2008). All-to-all RF Distance Methods. Poster session presented at Bioinformatics 2008, Warszawa, Poland.

Kristensen, T. G. (2009). Recombining Angles in Differential Evolution. In IEEE Congress on Evolutionary Computation, CEC 2009 (pp. 3353 - 3356). IEEE Press. https://doi.org/10.1109/CEC.2009.4983370

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

Kristensen, T. G., Pedersen, C. S., Thomsen, R. & Christensen, M. H. (2009). Largest Common Chemical Feature Subtree as a Virtual Screening Method. 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

Kristensen, T. G., Nielsen, J. & Pedersen, C. N. S. (2009). A tree based method for the rapid screening of chemical fingerprints. Lecture Notes in Computer Science, 5724, 194-205. https://doi.org/10.1007/978-3-642-04241-6_17

Kristensen, L. S., Wojdacz, T. K., Thestrup, B. B., Wiuf, C. H., Hager, H. & Hansen, L. L. (2009). Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM. B M C Cancer, 9(453), 453.

Kristensen, T. G. (2010). Transforming Tanimoto queries on real valued vectors to range queries in Euclidian space. Journal of Mathematical Chemistry, 48(2), 287-289. https://doi.org/10.1007/s10910-010-9668-4

Kristensen, T. G. & Pedersen, C. N. S. (2010). Data Structures for Accelerating Tanimoto Queries on Real Valued Vectors. In V. Moulton & M. Singh (Eds.), Algorithms in Bioinformatics: 10th International Workshop (WABI 2010) (Vol. 6293, pp. 28-39). Springer.

Kristensen, T. G., Nielsen, J. & Pedersen, C. N. S. (2010). A tree-based method for the rapid screening of chemical fingerprints. Algorithms for Molecular Biology, 5(9). https://doi.org/10.1186/1748-7188-5-9

Kristensen, T. G., Nielsen, J. & Pedersen, C. N. S. (2011). Using Inverted Indices for Accelerating LINGO Calculations. Journal of Chemical Information and Modeling, 51(3), 597-600. https://doi.org/10.1021/ci100437e

Kristensen, T. G. (2011). Virtual screening algorithms. Department of Computer Science, Aarhus University.

Kristensen, T. G., Nielsen, J. & Pedersen, C. N. S. (2013). Methods for Similarity-Based Virtual Screening. Computational and Structural Biotechnology Journal, 5(6). https://doi.org/10.5936/csbj.201302009

Kringelbach, T., Højgaard, M., Rohrberg, K., Spanggaard, I., Laursen, B. E., Ladekarl, M., Haslund, C. A., Harsløf, L., Belcaid, L., Gehl, J., Søndergaard, L., Eefsen, R. L., Hansen, K. H., Kodahl, A. R., Jensen, L. H., Holt, M. I., Oellegaard, T. H., Yde, C. W., Ahlborn, L. B. & Lassen, U. (2023). ProTarget: a Danish Nationwide Clinical Trial on Targeted Cancer Treatment based on genomic profiling – a national, phase 2, prospective, multi-drug, non-randomized, open-label basket trial. BMC Cancer, 23(1), Article 182. https://doi.org/10.1186/s12885-023-10632-9

Kresge, H. A., Blostein, F., Goleva, S., Albiñana, C., Revez, J. A., Wray, N. R., Vilhjálmsson, B. J., Zhu, Z., McGrath, J. J. & Davis, L. K. (2024). Phenomewide Association Study of Health Outcomes Associated With the Genetic Correlates of 25 Hydroxyvitamin D Concentration and Vitamin D Binding Protein Concentration. Twin Research and Human Genetics, 27(2), 69-79. https://doi.org/10.1017/thg.2024.19

Kraft, J. F., Lie, M. A. & Schiøtt, H. B. (2009). Molecular Docking Simulations: Improvement of methodologies for membrane proteins. Poster session presented at iNANO autumn school 2007.

Kraft, J. F., Vestergaard, M., Schiøtt, B. & Thøgersen, L. (2012). Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations. Journal of Chemical Theory and Computation, 8(5), 1556–1569. https://doi.org/10.1021/ct200921u

Kousholt, A., Ziegel, J., Kiderlen, M. & Jensen, E. B. V. (2017). Stereological estimation of mean particle volume tensors in R3 from vertical sections. In E. B. V. Jensen & M. Kiderlen (Eds.), Tensor Valuations and Their Applications in Stochastic Geometry and Imaging (Vol. 2177, pp. 423-434). Springer.

Kongsted, H., Foldager, L. & Sørensen, J. T., (2018). Identifikation af mulighederne for at minimere forekomsten af læsioner hos økologiske svin og frilandssvin (del 2), No. 2018-760-000666, 28 p., Jun 04, 2018.

Kongsted, H., Foldager, L. & Sørensen, J. T. (2018). Sygdomsproblemer hos økologiske grise og frilandsgrise. DCA - Nationalt Center for Fødevarer og Jordbrug. DCA rapport No. 128 http://web.agrsci.dk/djfpublikation/index.asp?action=show&id=1271

Kongsted, H., Foldager, L. & Sørensen, J. T. (2019). Tail bites in free-range based finisher pig systems: prevalence and risk factors. Abstract from 11th symposium of porcine health management, Utrecht, Netherlands.

Kongsted, H., Foldager, L. & Sørensen, J. T. (2020). Data from routine meat inspection is a poor indicator of the prevalence of tail lesions in undocked pigs. Porcine Health Management, 6(1), Article 10. https://doi.org/10.1186/s40813-020-00149-z

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Palle Villesen