Publications

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Höglund, J., Sørensen, M. T., Larsen, T., Foldager, L., Ferris, C., Bell, M., Carter, F., Santoro, A., Crowe, M. & Ingvartsen, K. L. (2016). Potential for novel metabolite measurements in milk as biomarker phenotypes for dairy traits. In Book of abstracts of the 67th Annual Meeting of the European Federation of Animal Science (pp. 299). Wageningen Academic Publishers, The Netherlands. https://doi.org/10.3920/978-90-8686-830-8

Hobor, S., Al Bakir, M., Hiley, C. T., Skrzypski, M., Frankell, A. M., Bakker, B., Watkins, T. B. K., Markovets, A., Dry, J. R., Brown, A. P., van der Aart, J., van den Bos, H., Spierings, D., Oukrif, D., Novelli, M., Chakrabarti, T., Rabinowitz, A. H., Ait Hassou, L., Litière, S. ... TRACERx Consortium (2024). Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling. Nature Communications, 15(1), Article 4871. https://doi.org/10.1038/s41467-024-47606-9

Hobolth, A., Christensen, O. F., Mailund, T. & Schierup, M. H. (2007). Genomic Relationships and Speciation Times of Human, Chimpanzee and Gorilla inferred from a Coalescent Hidden Markov Model. Poster session presented at Beyond the HapMap, Boston, United States.

Hobolth, A., Christensen, O. F., Mailund, T. & Schierup, M. H. (2007). Genomic relationships and speciation times of human, chimpanzee and gorilla inferred from a coalescent hidden Markov model. PLoS Genetics, 3(2). https://doi.org/10.1371/journal.pgen.0030007

Hobolth, A., Uyenoyama, M. K. & Wiuf, C. (2008). Importance sampling for the infinite sites model. Statistical Applications in Genetics and Molecular Biology, 7(1). https://doi.org/10.2202/1544-6115.1400

Hobolth, A. (2008). A Markov chain Monte Carlo Expectation Maximization Algorithm for Statistical Analysis of DNA Sequence Evolution with Neighbor-Dependent Substitution Rates. Journal of Computational and Graphical Statistics, 17(1), 138-162.

Hobolth, A. & Wiuf, C. H. (2009). The genealogy, site frequency spectrum and ages of two nested mutant alleles. Theoretical Population Biology, 75(4), 260-265. https://doi.org/10.1016/j.tpb.2009.02.001

Hobolth, A. & Stone, E. (2009). Simulation from endpoint-conditioned, continuous-time Markov chains on a finite state space, with applications to molecular evolution. Annals of Applied Statistics, 3(3), 1204-1231. https://doi.org/10.1214/09-AOAS247

Hobolth, A., Dutheil, J., Hawks, J., Schierup, M. H. & Mailund, T. (2011). Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection. Genome Research, 21(3), 349-356. https://doi.org/10.1101/gr.114751.110

Hobolth, A. & Jensen, J. L. (2010). Summary statistics for end-point conditioned continuous-time Markov chains. Thiele Centre, Institut for Matematiske Fag, Aarhus Universitet.

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

Hobolth, A. & Jensen, J. L. (2011). Summary statistics for endpoint-conditioned continuous-time Markov chains. Journal of Applied Probability, 48(4), 911-924. https://doi.org/10.1239/jap/1324046009

Hobolth, A. (2012). Ancestral population genomics. In M. Anisimova (Ed.), Evolutionary Genomics: Statistical and Computational Methods (Vol. 856, pp. 293-313). Springer.

Hobolth, A. & Jensen, J. L. (2014). Markovian approximation to the finite loci coalescent with recombination along multiple sequences. Theoretical Population Biology, 98, 48-58. https://doi.org/10.1016/j.tpb.2014.01.002

Hobolth, A. & Jeff, T. (2014). Sampling and summary statistics of endpoint-conditioned paths in DNA sequence evolution. In M.-H. Chen, L. Kuo & P. O. Lewis (Eds.), Bayesian Phylogenetics: Methods, Algorithms, and Applications (1 ed., Vol. 1). CRC Press.

Hobolth, A. & Siren, J. (2016). The multivariate Wright–Fisher process with mutation: Moment-based analysis and inference using a hierarchical Beta model. Theoretical Population Biology, 108, 36-50. https://doi.org/10.1016/j.tpb.2015.11.001

Hobolth, A. (2016). Hvem er bedst? metoder til rangering i sport og videnskab. Aktuel Naturvidenskab, 5, 26-29.

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

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Palle Villesen