Publications

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Hobolth, A., Guo, Q., Kousholt, A. & Jensen, J. L. (2020). A Unifying Framework and Comparison of Algorithms for Non-negative Matrix Factorisation. International Statistical Review, 88(1), 29-53. https://doi.org/10.1111/insr.12331

Hobolth, A., Rivas-González, I., Bladt, M. & Futschik, A. (2024). Phase-type distributions in mathematical population genetics: An emerging framework. Theoretical Population Biology, 157, 14-32. https://doi.org/10.1016/j.tpb.2024.03.001

Hilker, R., Sickinger, C., Pedersen, C. N. S. & Stoye, J. (2012). UniMoG - A unifying framework for genomic distance calculation and sorting based DCJ. Bioinformatics, 28(19), 2509-2511. https://doi.org/10.1093/bioinformatics/bts440

Hess, J. L., Tylee, D. S., Mattheisen, M., Schizophrenia Working Group of the Psychiatric Genomics Consortium, Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Børglum, A. D., Als, T. D., Grove, J., Werge, T., Mortensen, P. B., Mors, O., Nordentoft, M., Hougaard, D. M., Byberg-Grauholm, J., Bækvad-Hansen, M., Greenwood, T. A., Tsuang, M. T., Curtis, D., Steinberg, S. ... Glatt, S. J. (2021). A polygenic resilience score moderates the genetic risk for schizophrenia. Molecular Psychiatry, 26(3), 800–815. https://doi.org/10.1038/s41380-019-0463-8

Herskin, M. S., Kobek-Kjeldager, C., Kaiser, M. Ø., Thodberg, K., Jensen, L. D., Chen, G., Zhang, G., Rong, L. & Foldager, L., (2022). Krav til indvendig højde ved transport af smågrise, No. 2020-0096886, 15 p., Jul 05, 2022.

Hernandez-de Sosa, N., Athanasiadis, G., Malouf, J., Laiz, A., Muñoz-Marin, A. M., Herrera, S., Farrerons, J., Soria, J. M. & Casademont, J. (2016). Genetic Contribution of Femoral Neck Bone Geometry to the Risk of Developing Osteoporosis: A Family-Based Study. PLoS One, 11(5), Article 0154833. https://doi.org/10.1371/journal.pone.0154833

Hernández-Castellano, L. E., Sørensen, M. T., Foldager, L., Herskin, M. S., Gross, J. J., Bruckmaier, R. M. & Larsen, M. (2023). Effects of feeding level, milking frequency, and single injection of cabergoline on blood metabolites, hormones, and minerals around dry-off in dairy cows. Journal of Dairy Science, 106(4), 2919-2932. https://doi.org/10.3168/jds.2022-22648

Herbsleb, M., Andersen, T. T., Wiuf, C. & Ørntoft, T. F. (2006). Identification of New Transcriptional Correlations in Cancer Using Array Databases and Functional In Vitro Studies , presented at PhD Annual Day, Graduate School of Health, University of Aarhus.. Poster session presented at Identification of New Transcriptional Correlations in Cancer Using Array Databases and Functional In Vitro Studies , presented at PhD Annual Day, Graduate School of Health, University of Aarhus..

Herbsleb, M., Birkenkamp-Demtröder, K., Andersen, T. T., Wiuf, C., Hein, A.-M. K., Ørntoft, T. F. & Andersen, L. D. (2008). Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells. BMC Medical Genomics, 1. https://doi.org/10.1186/1755-8794-1-31

Herbsleb, M., Christensen, O. F., Thykjaer, T., Wiuf, C., Borre, M., Ørntoft, T. F. & Dyrskjøt, L. (2008). Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma in situ in the urinary bladder. B M C Cancer, 8, 37. https://doi.org/10.1186/1471-2407-8-37

Herbsleb, M., Birkenkamp-Demtroder, K., Thykjaer, T., Wiuf, C., Hein, A.-M. K., Orntoft, T. F. & Andersen, L. D. (2008). Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells. BMC Medical Genomics, 1, 31. https://doi.org/10.1186/1755-8794-1-31

Henriksen, B. I. F., Rousing, T., Foldager, L. & Møller, S. H. (2024). Development of qualitative behavioural assessment of mink: Why is it hard to achieve high inter- and intra-observer agreement in QBA-scoring of mink? In Book of Abstracts of the 9th International Conference on the Welfare Assessment of Animals at Farm Level (WAFL) (pp. 44-44). Article Session 4; Poster 10 EAAP.

Henches, L., Kim, J., Yang, Z., Rubinacci, S., Pires, G., Albiñana, C., Boetto, C., Julienne, H., Frouin, A., Auvergne, A., Suzuki, Y., Djebali, S., Delaneau, O., Ganna, A., Vilhjálmsson, B., Privé, F. & Aschard, H. (2025). Polygenic risk score prediction accuracy convergence. Human Genetics and Genomics Advances, 6(3), Article 100457. https://doi.org/10.1016/j.xhgg.2025.100457

Hein, J., Pedersen, C. N. S. & Jensen, J. L. (2002). Recursions for Statistical Multiple Alignment. Proceedings of the National Academy of Sciences (PNAS), 100(25), 14960-14965.

Hein, J., Schierup, M. H. & Wiuf, C. (2004). Gene genealogies, variation and evolution: A primer in coalescent theory.

Hein, J., Schierup, M. H. & Wiuf, C. (2005). Gene Genealogies, Variation and Evolution.

Hein, J., Wiuf, C., Møller, M., Knudsen, B. & Wibling, G. (2000). Statistical alignment: computational properties, homology testing and goodness-of-fit. J. Mol. Biol., 302(1), 265-279. https://doi.org/10.1006/jmbi.2000.4061

Hein, J. & Wiuf, C. (2002). Review of GR Grant and WJ Ewens, `Statistical Methods in Bioinformatics: An Introduction' In Briefings in Bioinformatics (Vol. 3, pp. 318-319). Springer.

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

Hebsgaard, MB., Wiuf, C., Gilbert, MTP., Glenner, H. & Willerslev, E. (2007). Evaluating Neandertal genetics and phylogeny. J. Mol. Evol., 64, 50-60. https://doi.org/10.1007/s00239-006-0017-y

Hayeck, T. J., Busby, G. B., Chun, S., Lewis, A. C. F., Roberts, M. C. & Vilhjálmsson, B. J. (2023). Polygenic Risk Scores: Genomes to Risk Prediction. Clinical Chemistry, 69(6), 551–557. https://doi.org/10.1093/clinchem/hvad049

Haudry, A., Cenci, A., Ravel, C., Bataillon, T., Brunel, D., Poncet, C., Hochu, I., Poirier, S., Santoni, S., Glemin, S. & David, J. (2007). Grinding up Wheat: a Massive Loss of Nucleotide Diversity Since Domestication. Molecular Biology and Evolution, 24(7), 1506-1517. https://doi.org/10.1093/molbev/msm077

Hauberg, M. E., Holm-Nielsen, M. H., Mattheisen, M., Askou, A. L., Grove, J., Børglum, A. D. & Corydon, T. J. (2016). Schizophrenia risk variants affecting microRNA function and site-specific regulation of NT5C2 by miR-206. European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology, 26(9), 1522-6. https://doi.org/10.1016/j.euroneuro.2016.06.014

Hartfield, M. & Glemin, S. (2016). Limits to Adaptation in Partially Selfing Species. Genetics, 203(2), 959-+. https://doi.org/10.1534/genetics.116.188821

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

Hartfield, M. (2016). Evolutionary genetic consequences of facultative sex and outcrossing. Journal of Evolutionary Biology, 29(1), 5-22. https://doi.org/10.1111/jeb.12770

Hartfield, M., Wright, S. I. & Agrawal, A. F. (2016). Coalescent times and patterns of genetic diversity in species with facultative sex: Effects of gene conversion, population structure, and heterogeneity. Genetics, 202(1), 297-312. https://doi.org/10.1534/genetics.115.178004

Hartfield, M., Bataillon, T. & Glemin, S. (2017). The Evolutionary Interplay between Adaptation and Self-Fertilization. Trends in Genetics, 33(6), 420-431. https://doi.org/10.1016/j.tig.2017.04.002

Hartfield, M. (2018). Digest: Effects of spatially-spreading adaptive mutations on genome-wide diversity. Evolution, 72(4), 1015-1016. https://doi.org/10.1111/evo.13462

Hartfield, M., Wright, S. I. & Agrawal, A. F. (2018). Coalescence and linkage disequilibrium in facultatively sexual diploids. Genetics, 210(2), 683-701. https://doi.org/10.1534/genetics.118.301244

Hartfield, M. & Bataillon, T. (2020). Selective Sweeps Under Dominance and Inbreeding. G3 (Bethesda, Md.), 10(3), 1063-1075. https://doi.org/10.1534/g3.119.400919

Hartfield, M., Poulsen, N. A., Guldbrandtsen, B. & Bataillon, T. (2021). Using singleton densities to detect recent selection in Bos taurus. Evolution Letters, 5(6), 595-606. https://doi.org/10.1002/evl3.263

Hargreaves, A., Bailey, S. & Laird, R. (2015). Fitness declines towards range limits and local adaptation to climate affect dispersal evolution during climate‐induced range shifts. Journal of Evolutionary Biology, 28(8), 1489-1501. https://doi.org/10.1111/jeb.12669

Hansen, AJ., Mitchell, D., Wiuf, C., Paniker, L., Brand, TB., Binladen, J., Gilichinsky, DA., Rønn, R. & Willerslev, E. (2006). Crosslinks rather than Strand Breaks Determine Access to Ancient DNA Sequences from Frozen Sediments. Genetics, 173, 1175-1179. https://doi.org/10.1534/genetics.106.057349

Hansen, AJ., Willerslev, E., Wiuf, C., Mourier, T. & Arctander, P. (2001). Statistical evidence for miscoding lesions in ancient DNA templates. Mol. Biol. Evol., 18, 262-265.

Hansen, L. L., Madsen, B. E., Pedersen, K. & Wiuf, C. (2007). Conflicting results in SNP genotype assessment. BioTechniques, (43), 756-762.

Hansen, S. K., Vestergaard, M., Thøgersen, L., Schiøtt, B., Nielsen, N. C. & Vosegaard, T. (2014). Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations. Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 118(19), 5119-5129. https://doi.org/10.1021/jp5000304

Hansen, M. C., Nyvold, C. G., Roug, A. S., Kjeldsen, E., Villesen, P., Nederby, L. & Hokland, P. (2015). Nature and nurture: a case of transcending haematological pre-malignancies in a pair of monozygotic twins adding possible clues on the pathogenesis of B-cell proliferations. British Journal of Haematology, 169(3), 391–400. https://doi.org/10.1111/bjh.13305

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

Hansen, E. K. B., Fredsøe, J. H., Okholm, T. L. H., Ulhøi, B. P., Klingenberg, S., Jensen, J. B., Kjems, J., Bouchelouche, K., Borre, M., Damgaard, C. K., Pedersen, J. S., Kristensen, L. S. & Sørensen, K. D. (2022). The transcriptional landscape and biomarker potential of circular RNAs in prostate cancer. Genome Medicine, 14(1), Article 8. https://doi.org/10.1186/s13073-021-01009-3

Hansen, N. P., Kristensen, T., Johansen, M., Wiking, L., Poulsen, N. A., Hellwing, A. L. F., Foldager, L., Jensen, S. K., Larsen, L. B. & Weisbjerg, M. R. (2022). Effects on feed intake, milk production, and methane emission in dairy cows fed silage or fresh grass with concentrate or fresh grass harvested at early or late maturity stage without concentrate. Journal of Dairy Science, 105(10), 8036-8053. https://doi.org/10.3168/jds.2022-21885

Hannon, E., Schendel, D., Ladd-Acosta, C., Grove, J., Hansen, C. S., Andrews, S. V., Hougaard, D. M., Bresnahan, M., Mors, O., Hollegaard, M. V., Bækvad-Hansen, M., Hornig, M., Mortensen, P. B., Børglum, A. D., Werge, T., Pedersen, M. G., Nordentoft, M., Buxbaum, J., Daniele Fallin, M. ... iPSYCH-Broad ASD Group (Mette Nyegaard, Per Qvist, Jane Hvarregaard Christensen - members of -) (2018). Elevated polygenic burden for autism is associated with differential DNA methylation at birth. Genome Medicine, 10(1), Article 19. https://doi.org/10.1186/s13073-018-0527-4

Hannon, E., Schendel, D., Ladd-Acosta, C., Grove, J., Hansen, C. S., Hougaard, D. M., Bresnahan, M., Mors, O., Hollegaard, M. V., Bækvad-Hansen, M., Hornig, M., Mortensen, P. B., Børglum, A. D., Werge, T., Pedersen, M. G., Nordentoft, M., Buxbaum, J. D., Fallin, M. D., Bybjerg-Grauholm, J. ... Mill, J. (2019). Variable DNA methylation in neonates mediates the association between prenatal smoking and birth weight. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1770), Article 20180120. https://doi.org/10.1098/rstb.2018.0120

Hanghøj, K., Seguin, A., Schubert, M., Madsen, T., Pedersen, J. S., Willerslev, E. & Orlando, L. (2016). Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX. Molecular Biology and Evolution, 33(12), 3284-3298. https://doi.org/10.1093/molbev/msw184

Hancl, J. & Leppälä, K. (2016). IRRATIONALITY MEASURES FOR CONTINUED FRACTIONS WITH ASYMPTOTIC CONDITIONS. Kyushu journal of mathematics, 70(2), 205-216. https://doi.org/10.2206/kyushujm.70.205

Hammami, H., Colinet, F. G., Bastin, C., Grelet, C., Vanlierde, A., Dehareng, F., Gengler, N. & GplusE Consortium (2017). Genetic analysis of milk MIR predicted blood and milk biomarkers linked to the physiological status. In Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science (pp. 403-403). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-859-9

Hammami, H., Mota, R. R., Vanderick, S., Naderi, S., Bastin, C., Gengler, N. & GplusE Consortium (2019). Using milk MIR spectra to identify candidate genes associated with climate--smart traits in cattle. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science (Vol. 25, pp. 607). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-890-2

Hagberg, O. & Wiuf, C. (2006). Convergence properties of the degree distribution of some network models. Bull Math Biol, 68, 1275-1291. https://doi.org/10.1007/s11538-006-9085-9

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

Gupta, V., Markmann, K., Pedersen, C. N. S., Stougaard, J. & Andersen, S. U. (2012). shortran: A pipeline for small RNA-seq data analysis. Bioinformatics, 28(20), 2698-2700. https://doi.org/10.1093/bioinformatics/bts496

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Revised 21.08.2024

Palle Villesen