Publications

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Madsen, T. (2017). Robust statistical methods for significance evaluation and applications in cancer driver detection and biomarker discovery.

Mable, B. K., Schierup, M. H. & Charlesworth, D. (2003). Estimating the number, frequency, and dominance of S-alleles in a natural population of Arabidopsis lyrata (Brassicaceae) with sporophytic control of self-incompatibility. Iden, 90, 422-431. http://www.nature.com/hdy

Maag, E., Kulasingam, A., Grove, E. L., Pedersen, K. S., Kristensen, S. D. & Hvas, A. M. (2021). Statistical and machine learning methods for analysis of multiplex protein data from a novel proximity extension assay in patients with ST-elevation myocardial infarction. Scientific Reports, 11(1), Article 13787. https://doi.org/10.1038/s41598-021-93162-3

Ma, J. (2024). Genomic Responses to Evolution of Sociality in Stegodyphus Spiders. Aarhus University.

Luo, Y., Li, J., Liu, Y., Lin, L., Du, Y., Li, S., Yang, H., Vajta, G., Callesen, H., Bolund, L. & Sørensen, C. B. (2011). High efficiency of BRCA1 knockout using rAAV-mediated gene targeting: developing a pig model for breast cancer. Transgenic Research, 20, 975-988. https://doi.org/10.1007/s11248-010-9472-8

Luo, X.-J., Mattheisen, M., Li, M., Huang, L., Rietschel, M., Børglum, A. D., Als, T. D., van den Oord, E. J., Aberg, K. A., Mors, O., Mortensen, P. B., Luo, Z., Degenhardt, F., Cichon, S., Schulze, T. G., Nöthen, M. M., Su, B., Zhao, Z., Gan, L. ... iPSYCH-GEMS SCZ working group (Jakob Grove, member) (2015). Systematic Integration of Brain eQTL and GWAS Identifies ZNF323 as a Novel Schizophrenia Risk Gene and Suggests Recent Positive Selection Based on Compensatory Advantage on Pulmonary Function. Schizophrenia Bulletin. https://doi.org/10.1093/schbul/sbv017

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)

Ludvigsen, M., Bjerregård Pedersen, M., Lystlund Lauridsen, K., Svenstrup Poulsen, T., Hamilton-Dutoit, S. J., Besenbacher, S., Bendix, K., Møller, M. B., Nørgaard, P., d'Amore, F. & Honoré, B. (2018). Proteomic profiling identifies outcome-predictive markers in patients with peripheral T-cell lymphoma, not otherwise specified. Blood Advances, 2(19), 2533-2542. https://doi.org/10.1182/bloodadvances.2018019893

Lucotte, E. A., Laurent, R., Heyer, E., Segurel, L. & Toupance, B. (2016). Detection of Allelic Frequency Differences between the Sexes in Humans: A Signature of Sexually Antagonistic Selection. Genome Biology and Evolution, 8(5), 1489-1500. https://doi.org/10.1093/gbe/evw090

Lucotte, E. A., Skov, L., Jensen, J. M., Coll Macià, M., Munch, K. & Schierup, M. H. (2018). Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations. Genetics, 209(3), 907-920. https://doi.org/10.1534/genetics.118.300826

Lucotte, E. A., Albiñana, C., Laurent, R., Bhérer, C., Bataillon, T., Toupance, B. & Genome of the Netherland Consortium (2022). Detection of sexually antagonistic transmission distortions in trio datasets. Evolution Letters, 6(2), 203-216. https://doi.org/10.1002/evl3.271

Lucotte, E. A., Guðmundsdóttir, V. B., Jensen, J. M., Skov, L., Macià, M. C., Almstrup, K., Schierup, M. H., Helgason, A. & Stefansson, K. (2023). Characterizing the evolution and phenotypic impact of ampliconic Y chromosome regions. Nature Communications, 14(1), Article 3990. https://doi.org/10.1038/s41467-023-39644-6

Lorenzen, E. D., Nogués-Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K. A., Ugan, A., Borregaard, M. K., Gilbert, M. T. P., Nielsen, R., Ho, S. Y. W., Goebel, T., Graf, K. E., Byers, D., Stenderup, J., Rasmussen, M., Campos, P., Leonard, J. A., Koepfli, K.-P. ... Willerslev, E. (2011). Species-specific responses of Late Quaternary megafauna to climate and humans. Nature, 479(7373), 359-64. https://doi.org/10.1038/nature10574

Lohmann, G. V., Shimoda, Y., Nielsen, M. W., Jørgensen, F. G., Grossmann, C., Sandal, N., Sørensen, K., Thirup, S., Madsen, L. H., Tabata, S., Sato, S., Stougaard, J. & Radutoiu, S. (2010). Evolution and regulation of the Lotus japonicus LysM receptor gene family. Molecular plant-microbe interactions, 23(4), 510-21. https://doi.org/10.1094/MPMI-23-4-0510

Loh, P.-R., Bhatia, G., Gusev, A., Finucane, H. K., Bulik-Sullivan, B. K., Pollack, S. J., Schizophrenia Working Group of the Psychiatric Genomics Consortium (Anders Børglum, Jakob Grove; members of -), O’Donovan, M. C., Neale, B. M., Patterson, N. & Price, A. L. (2015). Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis. Nature Genetics, 47, 1385–1392. https://doi.org/10.1038/ng.3431

Loeschcke, V. & Christiansen, F. (1990). Evolution of mutualism. In K. Wohrman & S. K. Jain (Eds.), Population Biology (pp. 393-399). Springer.

Loeschcke, V. & Christiansen, F. (1984). Evolution and intraspecific exploitative competition II. A two locus model for additive gene effects. Theoretical Population Biology, 26, 228–264.

Loeschcke, V. & Schierup, M. H. (2024). Biographical sketch: Freddy Bugge Christiansen. Theoretical Population Biology, 156, 130. https://doi.org/10.1016/j.tpb.2024.02.006

Locke, D. P., Hillier, L. W., Warren, W. C., Yang, S.-P., Wang, Z., Chinwalla, A. T., Minx, P., Mitreva, M., Cook, L., Delehaunty, K. D., Fronick, C., Schmidt, H., Fulton, L. A., Fulton, R. S., Nelson, J. O., Magrini, V., Pohl, C., Graves, T. A., Markovic, C. ... de Jong, P. J. (2011). Comparative and demographic analysis of orang-utan genomes. Nature, 469, 529-533. https://doi.org/10.1038/nature09687

Lobon, I., Tucci, S., de Manuel, M., Ghirotto, S., Benazzo, A., Prado-Martinez, J., Lorente-Galdos, B., Nam, K., Dabad, M., Hernandez-Rodriguez, J., Comas, D., Navarro, A., Schierup, M. H., Andrés, A. M., Barbujani, G., Hvilsom, C. & Marques-Bonet, T. (2016). Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions. Genome Biology and Evolution, 8(6), 2020-2030. https://doi.org/10.1093/gbe/evw124

Liu, S., Huang, S., Rao, J., Ye, W., Genome Denmark Consortium (Anders Børglum, member of -), Krogh, A. & Wang, J. (2015). Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale. GigaScience, 4, 64. https://doi.org/10.1186/s13742-015-0103-4

Liu, Y., Pedersen, H. S., Larsen, K. E., Kristensen, K., Foldager, L., Callesen, H. & Sørensen, M. T. (2019). Combined in vitro fertilization and culture (IVF/IVC) in mouse for reprotoxicity assessment of xenobiotic exposure. Reproductive Toxicology, 89(October), 115-123. https://doi.org/10.1016/j.reprotox.2019.07.006

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

Lindgreen, S., Krogh, A. & Pedersen, J. S. (2014). SNPest: a probabilistic graphical model for estimating genotypes. BMC Research Notes, 7, 698. https://doi.org/10.1186/1756-0500-7-698

Lin, Y., Rasmussen, M. H., Christensen, M. H., Frydendahl, A., Maretty, L., Andersen, C. L. & Besenbacher, S. (2024). Evaluating Bioinformatics Processing of Somatic Variant Detection in cfDNA Using Targeted Sequencing with UMIs. International Journal of Molecular Sciences , 25(21), Article 11439. https://doi.org/10.3390/ijms252111439

Liljas, A., Liljas, L., Piskur, J., Lindblom, G., Nissen, P. & Kjeldgaard, M. (2009). Textbook on Structural Biology. (1 ed.) World Scientific.

Lie, M. A., Thomsen, R., Pedersen, C. N. S., Schiøtt, B. & Christensen, M. H. (2011). Molecular Docking with Ligand Attached Water Molecules. Journal of Chemical Information and Modeling, 51(4), 909-917. https://doi.org/10.1021/ci100510m

Liboriussen, P., Pedersen, B. P., Ifrim, G., Nissen, P. & Pedersen, C. S. (2009). Automatic classification of P-Type ATPases using SLR. Poster session presented at 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden.

Li, S., Ma, L., Li, H., Vang, S., Hu, Y., Bolund, L. & Wang, J. (2007). Snap: An Integrated SNP Annotation Platform. Nucleic Acids Research, 35, D707-D710. https://doi.org/10.1093/nar/gkl969

Li, J., Wang, K., Wiuf, C. & Bolund, L. (2007). Array CGH Reveals High Similar Genetic Profiles between the Primary Tumor and Axillary Lymph Node Metastasis in Breast Cancer, presented at PhD Annual Day, Graduate School of Health, University of Aarhus.. Poster session presented at Array CGH Reveals High Similar Genetic Profiles between the Primary Tumor and Axillary Lymph Node Metastasis in Breast Cancer, presented at PhD Annual Day, Graduate School of Health, University of Aarhus., Denmark.

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

Li, J., Wang, K., Li, S., Timmermans-Wielenga, V., Rank, F., Wiuf, C., Zhang, X., Yang, H. & Bolund, L. (2009). DNA copy number aberrations in breast cancer by array comparative genomic hybridization. Genomics Proteomics & Bioinformatics, 7(1-2), 13-24. https://doi.org/10.1016/S1672-0229(08)60029-7

Li, J., Gao, F., Li, N., Li, S., Yin, G., Tian, G., Jia, S., Wang, K., Zhang, X., Yang, H., Nielsen, A. L. & Bolund, L. (2009). An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. B M C Genomics, 10, 223. https://doi.org/10.1186/1471-2164-10-223

Li, J., Wang, K., Jensen, T. D., Li, S., Bolund, L. & Wiuf, C. (2010). Tumor heterogeneity in neoplasms of breast, colon, and skin. BMC Research Notes, 3, 321. https://doi.org/10.1186/1756-0500-3-321

Li, Q., Li, N., Hu, X., Li, J., Du, Z., Chen, L., Yin, G., Duan, J., Zhang, H., Zhao, Y., Wang, J. & Li, N. (2011). Genome-wide mapping of DNA methylation in chicken. P L o S One, 6(5), e19428. https://doi.org/10.1371/journal.pone.0019428

Li, J., Wang, K., Gao, F., Jensen, T. D., Li, S. T., Deangelis, P. M., Kølvraa, S., Proby, C., Forslund, O., Bolund, L. & Clausen, O. P. F. (2012). Array comparative genomic hybridization of keratoacanthomas and squamous cell carcinomas: different patterns of genetic aberrations suggest two distinct entities. Journal of Investigative Dermatology, 132(8), 2060-6. https://doi.org/10.1038/jid.2012.104

Li, S., Li, R., Li, H., Lu, J., Li, Y., Bolund, L., Schierup, M. H. & Wang, J. (2013). SOAPindel: efficient identiﬁcation of indels from short paired reads. Genome Research, 23(1), 195-200. https://doi.org/10.1101/gr.132480.111

Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., Li, S., Yang, H., Wang, J. & Wang, J. (2010). De novo assembly of human genomes with massively parallel short read sequencing. Genome Research, 20(2), 265-72. https://doi.org/10.1101/gr.097261.109

Li, S., Besenbacher, S., Li, Y., Kristiansen, K., Grarup, N., Albrechtsen, A., Sparsø, T. H., Korneliussen, T. S., Hansen, T., Wang, J., Nielsen, R., Pedersen, O., Bolund, L. & Schierup, M. H. (2014). Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population. European Journal of Human Genetics. https://doi.org/10.1038/ejhg.2013.282

Li, C. H., Prokopec, S. D., Sun, R. X., Yousif, F., Schmitz, N., PCAWG Tumour Subtypes and Clinical Translation, Boutros, P. C. & PCAWG Consortium (2020). Sex differences in oncogenic mutational processes. Nature Communications, 11, Article 4330. https://doi.org/10.1038/s41467-020-17359-2

Lescai, F., Als, T. D., Li, Q., Nyegaard, M., Andorsdottir, G., Biskopstø, M., Hedemand, A., Fiorentino, A., O'Brien, N. L., Jarram, A., Liang, T. J., Grove, J., Pallesen, J., Eickhardt, E., Mattheisen, M., Bolund, L., Demontis, D., Wang, A. G., McQuillin, A. ... Børglum, A. D. (2017). Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder. Translational Psychiatry, 7(2), e1034. Article 3. https://doi.org/10.1038/tp.2017.3

Leroy, T., Rousselle, M., Tilak, M. K., Caizergues, A. E., Scornavacca, C., Recuerda, M., Fuchs, J., Illera, J. C., De Swardt, D. H., Blanco, G., Thébaud, C., Milá, B. & Nabholz, B. (2021). Island songbirds as windows into evolution in small populations. Current Biology, 31(6), 1303-1310.e4. https://doi.org/10.1016/j.cub.2020.12.040

Leppälä, J., Bechsgaard, J. S., Schierup, M. H. & Savolainen, O. (2007). Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus. Heredity, 100(1), 71-8. https://doi.org/10.1038/sj.hdy.6801066

Leppälä, J., Bechsgaard, J. S., Schierup, M. H. & Savolainen, O. (2008). Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus. Heredity, 100, 71-78.

Leppälä, K. (2016). EXPLICIT LOWER BOUNDS FOR LINEAR FORMS. Mathematics of Computation, 85(302), 2995-3008. https://doi.org/10.1090/mcom/3078

Leppälä, K., Matala-aho, T. & Törmä, T. (2017). Rational approximations of the exponential function at rational points. Journal of Number Theory, 179, 220-239. https://doi.org/10.1016/j.jnt.2017.03.014

Leppälä, K., Nielsen, S. & Mailund, T. (2017). admixturegraph: an R package for admixture graph manipulation and fitting. Bioinformatics (Online), 33(11), 1738-1740. https://doi.org/10.1093/bioinformatics/btx048

Lee, Y. L., Takada, H., Moreira, G. C. M., Karim, L., GplusE Consortium, Bosse, M., Bouwman, A., Mullaart, E., Coppieters, W., Georges, M., Druet, T. & Charlier, C. (2020). Fine resolution CNV catalogue from deeply sequenced cattle genomes. In Book of Abstracts of the 71st Annual Meeting of the European Federation of Animal Science (Vol. 26, pp. 188). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-900-8

Lavigne, F., Martin, G., Anciaux, Y., Papaix, J. & Roques, L. (2020). When sinks become sources: Adaptive colonization in asexuals. Evolution, 74(1), 29-42. https://doi.org/10.1111/evo.13848

Lauterbur, M. E., Munch, K. & Enard, D. (2023). Versatile Detection of Diverse Selective Sweeps with Flex-Sweep. Molecular Biology and Evolution, 40(6), Article msad139. https://doi.org/10.1093/molbev/msad139

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