Publications

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Fredslund, J. & Hein, J. (2003). Determining the Optimal Set of Indels Explaining the Gaps in a Multiple Alignment Using Affine Gap Cost Function. Poster session presented at International Conference on Research in Computational Molecular Biology (RECOMB 2003), Berlin, Germany.

Fredslund, J. (2000). Teaching a new dog old tricks – the Assumption Architecture. Poster session presented at Learning'00 Workshop, Madrid, Spain.

Fredslund, J. & Matarić, M. J. (2001). Robot Formations.

Fredslund, J. & Lange, M. (2007). primique: automatic design of specific PCR primers for each sequence in a family. B M C Bioinformatics, 8(369). https://doi.org/10.1186/1471-2105-8-369

Fredslund, J. (2008). DATFAP: A Database of Primers and Homology Alignments for Transcription Factors from 13 Plant Species. B M C Genomics.

Frankell, A. M., Dietzen, M., Al Bakir, M., Lim, E. L., Karasaki, T., Ward, S., Veeriah, S., Colliver, E., Huebner, A., Bunkum, A., Hill, M. S., Grigoriadis, K., Moore, D. A., Black, J. R. M., Liu, W. K., Thol, K., Pich, O., Watkins, T. B. K., Naceur-Lombardelli, C. ... TRACERx Consortium (2023). The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature, 616(7957), 525-533. https://doi.org/10.1038/s41586-023-05783-5

TRACERx Consortium (2024). Author Correction: The evolution of lung cancer and impact of subclonal selection in TRACERx (Nature, (2023), 616, 7957, (525-533), 10.1038/s41586-023-05783-5). Nature, 631(8022), E15. https://doi.org/10.1038/s41586-024-07738-w

Frank, M., Fechete, L. I., Tedeschi, F., Nadzieja, M., Nørgaard, M. M. M., Montiel, J., Andersen, K. R., Schierup, M. H., Reid, D. & Andersen, S. U. (2023). Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus. Nature Communications, 14(1), Article 7171. https://doi.org/10.1038/s41467-023-42911-1

Frandsen, J., Hobolth, A., Østergaard, L., Vestergaard-Poulsen, P. & Jensen, E. B. V. (2007). Bayesian regularization of diffusion tensor images. Biostatistics, 8(4), 784-799. https://doi.org/10.1093/biostatistics/kxm005

Frandsen, P., Fontsere, C., Nielsen, S. V., Hanghøj, K., Castejon-Fernandez, N., Lizano, E., Hughes, D., Hernandez-Rodriguez, J., Korneliussen, T. S., Carlsen, F., Siegismund, H. R., Mailund, T., Marques-Bonet, T. & Hvilsom, C. (2020). Targeted conservation genetics of the endangered chimpanzee. Heredity, 125(1-2), 15-27. https://doi.org/10.1038/s41437-020-0313-0

Franceschini, S., Grelet, C., Leblois, J., Gengler, N., Soyeurt, H. & GplusE Consortium (2022). Can unsupervised learning methods applied to milk recording big data provide new insights into dairy cow health? Journal of Dairy Science, 105(8), 6760-6772. https://doi.org/10.3168/jds.2022-21975

Fragata, I., Matuszewski, S., Schmitz, M. A., Bataillon, T., Jensen, J. D. & Bank, C. (2018). The fitness landscape of the codon space across environments. Heredity, 121(5), 422-437. https://doi.org/10.1038/s41437-018-0125-7

Forsberg, R. & Christiansen, F. B. (2003). A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol. Biol. Evol., 20(8), 1252-1259.

Foo, J. C., Streit, F., Frank, J., Treutlein, J., Baune, B. T., Moebus, S., Joeckel, K.-H., Forstner, A. J., Noethen, M. M., Rietschel, M., Sartorius, A., Kranaster, L. & Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (Jakob Grove, member of -) (2019). Evidence for increased genetic risk load for major depression in patients assigned to electroconvulsive therapy. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 180(1), 35-45. https://doi.org/10.1002/ajmg.b.32700

Fonseca, B., Zakaria, C., Jia, J. J., Graber, T. E., Svitkin, Y., Tahmasebi, S., Healy, D., Hoang, HD., Jensen, J. M., Diao, I. T., Lussier, A., Dajadian, C., Padmanabhan , N., Wang, W., Matta-Camacho, E., Hearnden, J., Smith, EM., Tsukumo , Y., Yanagiya, A. ... Damgaard, C. K. (2015). La-related protein 1 (LARP1) represses terminal oligopyrimidine (TOP) mRNA translation downstream of mTOR complex 1 (mTORC1). Journal of Biological Chemistry, 290, 15996-16020. https://doi.org/10.1074/jbc.M114.621730

Foldager, L., Steffensen, R. N., Thiel, S., Als, T. D., Kristensen, A. S., Straarup, S., Nielsen, H. J., Nordentoft, M., Mortensen, P. B., Rosenberg, R., Mors, O. & Jensenius, J. C. (2008). Schizophrenia and innate immune defense: association study of mannan-bindinglectin (MBL) and MBL-associated serine proteases-2 (MASP-2) deficiency. In WCPG 2008 Abstract Book (pp. 225)

Foldager, L., Steffensen, R. N., Thiel, S., Als, T. D., Kristensen, A. S., Straarup, S., Nielsen, H. J., Nordentoft, M., Mortensen, P. B., Rosenberg, R., Mors, O. & Jensenius, J. C. (2009). Are defects in the innate immune defense contributing factors for mental disorders? In PhD Day 2009 Abstract Book (pp. 107)

Foldager, L. (2010). Using logic regression to identify SNP interactions based on individually time-matched case-control data. Abstract from PhD Day 2010, Århus, Denmark.

Foldager, L., Steffensen, R. N., Thiel, S., Als, T. D., Nielsen, H. J., Nordentoft, M., Mortensen, P. B., Mors, O. & Jensenius, J. C. (2012). MBL and MASP-2 concentrations in serum and MBL2 promoter polymorphisms are associated to schizophrenia. Acta Neuropsychiatrica, 24(4), 199-207. https://doi.org/10.1111/j.1601-5215.2011.00618.x

Foldager, L., Als, T. D. & Grove, J. (2013). Comparison of methods for genome-wide gene-environment interaction analysis. Poster session presented at XXIst World Congress of Psychiatric Genetics, Boston, United States.

Foldager, L., Köhler, K. O., Steffensen, R. N., Thiel, S., Kristensen, A. S., Jensenius, J. C. & Mors, O. (2014). Bipolar and panic disorders may be associated with hereditary defects in the innate immune system. Journal of Affective Disorders, 164, 148-154. https://doi.org/10.1016/j.jad.2014.04.017

Foldager, L. (2014). A statistical perspective on association studies of psychiatric disorders: Genetic effects of single-markers, haplotypes, gene-environment interactions and gene-gene interactions.

Foldager, L., Als, T. D. & Grove, J. (2014). Comparing methods for genome-wide gene-environment interaction analysis.

Foldager, L., Munksgaard, L., Trénel, P. & Thomsen, P. T. (2015). Predicting daily eating activity of dairy cows from 3D accelerometer data and RFID signals by use of a random forests model. In C. H. Knight (Ed.), Proceedings of the Third DairyCare Conference 2015 (pp. 31-31)

Foldager, L., Gildbjerg, L. B., Voss, H., Trénel, P., Munksgaard, L. & Thomsen, P. T. (2017). Daily eating activity of dairy cows from 3D accelerometer data and RFID signals: prediction by random forests and detection of sick cows. In P. Linde (Ed.), Symposium i Anvendt Statistik (pp. 109-122)

Foldager, L. & GplusE Consortium (2017). Random forests prediction of blood metabolic clusters by milk metabolites and enzymes in dairy cows. In Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science (pp. 402-402). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-859-9

Foldager, L., Liu, Y., Pedersen, H. S., Larsen, K. E., Kristensen, K., Callesen, H. & Sørensen, M. T. (2018). In-vitro fertilization and in-vitro embryo culture in mouse as a reprotoxicity model for xenobiotics: some considerations on how to analyse data and present results. In P. Linde (Ed.), Symposium i anvendt statistik 2018 (pp. 188-199)

Foldager, L. & Jensen, M. B. (2019). Behaviour changes associated with diarrhoea and respiratory diseases in Danish pre-weaned dairy calves. In P. Linde (Ed.), Symposium i anvendt statistik 2019 (pp. 15-16).

Foldager, L. & Ingvartsen, K. L. (2019). A follow-up on blood metabolic clusters in dairy cows. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science (Vol. 25, pp. 151). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-890-2

Foldager, L., Gaillard, C., Sørensen, M. T., Larsen, T., Matthews, E., O'Flaherty, R., Carter, F., Crowe, M., Grelet, C., Salavati, M., Hostens, M., GplusE Consortium, Ingvartsen, K. L. & Krogh, M. A. (2020). Predicting physiological imbalance in Holstein dairy cows by three different sets of milk biomarkers. Preventive Veterinary Medicine, 179, Article 105006. https://doi.org/10.1016/j.prevetmed.2020.105006

Foldager, L., Trenel, P., Munksgaard, L. & Thomsen, P. T. (2020). Technical note: Random forests prediction of daily eating time of dairy cows from 3-dimensional accelerometer and radiofrequency identification. Journal of Dairy Science, 103(7), 6271–6275. https://doi.org/10.3168/jds.2019-17613

Foldager, L., Winters, J., Nørskov, N. & Sørensen, M. T. (2021). Impact of feed glyphosate residues on broiler breeder egg production and egg hatchability. Scientific Reports, 11, Article 19290. https://doi.org/10.1038/s41598-021-98962-1

Foldager, L., Kaiser, M. Ø., Chen, G., Jensen, L. D., Kristensen, J. K., Kobek-Kjeldager, C., Thodberg, K., Rong, L. & Herskin, M. S. (2022). Deck height during transport of weaners – piglet height and microclimatic conditions inside trucks. 129-142. Abstract from Symposium i Anvendt Statistik 2022, København, Denmark.

Foldager, L., Kaiser, M., Chen, G., Jensen, L. D., Kristensen, J. K., Kobek-Kjeldager, C., Thodberg, K., Rong, L. & Herskin, M. S. (2022). Deck height during transport of weaners – piglet height and microclimatic conditions inside trucks. In Book of Abstracts of the 73rd Annual Meeting of the European Federation of Animal Science (pp. 181-181). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-937-4

Foldager, L., Kaiser, M. Ø., Chen, G., Jensen, L. D., Kristensen, J. K., Kobek-Kjeldager, C., Thodberg, K., Rong, L. & Herskin, M. S. (2022). Deck height during transport of weaners – piglet height and microclimatic conditions inside trucks. In P. Linde (Ed.), Symposium i anvendt statistik (pp. 129-142). SEGES Innovation. http://www.statistiksymposium.dk/Symposium%202022_Web.pdf

Foldager, L., Thorup, V. M., Pastell, M., Jensen, B. B. & Krogh, M. A. (2024). Prediction of mortality in land-based recirculating aquaculture system (RAS) trout farms. In P. Linde (Ed.), Symposium i Anvendt Statistik 2024 (pp. 17-24). Økonomisk Institut, Københavns Universitet & Symposium i Anvendt Statistik. http://www.statistiksymposium.dk/Symposium 2024 WEB.pdf

Foldager, L., Thodberg, K., Chen, G., Kristensen, J. K., Jensen, L. D., Kaiser, M., Kobek-Kjeldager, C., Rong, L. & Herskin, M. S. (2024). Effects of deck height during transport of weaners: in-vehicle conditions and clinical indicators. In Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (pp. 487-487). Article Session 38, Poster 12 Wageningen Academic Publishers.

Foldager, L., Thorup, V. M., Pastell, M., Frandsen, M., Jensen, B. B. & Krogh, M. A. (2024). IntelliRAS - some results from a project on precision fish farming in recirculation aquaculture systems. In Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (pp. 284-284). Article Session 14; Theatre 11 Wageningen Academic Publishers.

Finucane, H. K., Reshef, Y. A., Anttila, V., Slowikowski, K., Gusev, A., Byrnes, A., Gazal, S., Loh, P.-R., Lareau, C., Shoresh, N., Genovese, G., Saunders, A., Macosko, E., Pollack, S., Brainstorm Consortium, Perry, J. R. B., Buenrostro, J. D., Bernstein, B. E., Raychaudhuri, S. ... Price, A. L. (2018). Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nature Genetics, 50(4), 621-629. https://doi.org/10.1038/s41588-018-0081-4

Finster, K., Wang, T., Borchsenius, F. & Christiansen, F. B. (Eds.) (2016). Evolutionsbiologiske milepæle. (1 ed.) Aarhus Universitetsforlag.

Feyera, T., Pedersen, T. F., Larsen, U. K., Foldager, L. & Theil, P. K. (2018). Impact of sow energy status during farrowing on farrowing kinetics, frequency of stillborn piglets, and farrowing assistance: Sow energy status and farrowing kinetics. Journal of Animal Science, 96(6), 2320–2331. Article 96. https://doi.org/10.1093/jas/sky141

Feng, S., Bai, M., Rivas-González, I., Li, C., Liu, S., Tong, Y., Yang, H., Chen, G., Xie, D., Sears, K. E., Franco, L. M., Gaitan-Espitia, J. D., Nespolo, R. F., Johnson, W. E., Yang, H., Brandies, P. A., Hogg, C. J., Belov, K., Renfree, M. B. ... Zhang, G. (2022). Incomplete lineage sorting and phenotypic evolution in marsupials. Cell, 185(10), 1646-1660.e18. https://doi.org/10.1016/j.cell.2022.03.034

Feliu, E., Knudsen, M., Wiuf, C. H. & Andersen, L. N. (2010). An Algebraic Approach to Signaling Cascades with n Layers. Poster session presented at The 11th International Conference on Systems Biology, Edinburgh, United Kingdom.

Feliu, E., Knudsen, M., Andersen, L. N. & Wiuf, C. H. (2011). An Algebraic Approach to Signaling Cascades with n Layers. Bulletin of Mathematical Biology, 74(1), 45-72. https://doi.org/10.1007/s11538-011-9658-0

Feliu, E., Knudsen, M. & Wiuf, C. H. (2012). Signaling Cascades: Consequences of Varying Substrate and Phosphatase Levels. Advances in Experimental Medicine and Biology, 736, 81-94. https://doi.org/10.1007/978-1-4419-7210-1_4

Feliu, E. & Wiuf, C. H. (2012). Enzyme-sharing as a cause of multi-stationarity in signalling systems. Journal of the Royal Society. Interface, 9(71), 1224-1232. https://doi.org/10.1098/rsif.2011.0664

Feldman, M. W., Otto, S. P. & Christiansen, F. B. (2000). Genes, Culture and Inequality. In K. Arrow, S. Bowles & S. Durlauf (Eds.), Meritocracy and Economic Inequality (pp. 61–85). Princeton University Press.

Feldman, M. W., Otto, S. P. & Christiansen, F. (1996). Population genetic perspectives on the evolution of recombination. Annual Review of Genetics, 49, 261-295.

Feldman, M., Christiansen, F. & Holsinger, K. (1984). The evolution of self-pollination in plants. American Naturalist, 124, 446–453.

Feldman, M. & Christiansen, F. (1984). Population genetic theory of the cost of inbreeding. American Naturalist, 123, 642–653.

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Palle Villesen