Sahana, G., Mailund, T., Lund, M. S. & Guldbrandtsen, B. (2011). Local Genealogies in a Linear Mixed Model for Genome-wide Association Mapping in Complex Pedigreed Populations. PLoS One, 6(11).

Saetre, P., Grove, J., Børglum, A., Mors, O., Werge, T. M., Andreassen, O. A., Vares, M., Agartz, I., Terenius, L. & Jönsson, E. G. (2012). Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and age at onset of schizophrenia: no consistent evidence for an association in the Nordic population. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 159B(8).

Sadik, A., Dardani, C., Pagoni, P., Havdahl, A., Stergiakouli, E., Khandaker, G. M., Sullivan, S. A., Zammit, S., Jones, H. J., Davey Smith, G., Dalman, C., Karlsson, H., Gardner, R. M., Rai, D. & The iPSYCH Autism Spectrum Disorder Working Group (2022). Parental inflammatory bowel disease and autism in children. Nature Medicine, 28(7), 1406-1411. https://doi.org/10.1038/s41591-022-01845-9

Rydder, P. M., Andreasen, L., Thomsen, S. H., Jensen, U. B., Becher, N., Dunø, M. & Vogel, I. (2025). Mosaic STS gene deletions in chorionic villus samples are often confined to the placenta, and they differ in size from STS gene deletions in patients with X-linked Ichthyosis. Placenta, 165, 16-22. https://doi.org/10.1016/j.placenta.2025.03.016

Rousselle, M., Mollion, M., Nabholz, B., Bataillon, T. & Galtier, N. (2018). Overestimation of the adaptive substitution rate in fluctuating populations. Biology Letters, 14(5), Article 20180055. https://doi.org/10.1098/rsbl.2018.0055

Rousing, T., Rothmann Holm, J., Krogh, M. A., Østergaard, S. & GplusE Consortium (2020). Expert-based development of a generic HACCP-based risk management system to prevent critical negative energy balance in dairy herds. Preventive Veterinary Medicine, 175, Article 104849. https://doi.org/10.1016/j.prevetmed.2019.104849

Roug, A. S., Nederby, L., Kjeldsen, E., Villesen, P. & Nyvold, C. G. (2013). Two Hematological Pre-Malignancies In a Pair Of Homozygous Twins Revealing Differences In Their Pre-and Postnatal Development. Blood, 122(21), 5262-5262.

Ronfort, J., Bataillon, T., Santoni, S., Delalande, M., David, J. & Prosperi, J.-M. (2006). Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula. BMC Plant Biology, 6(28). https://doi.org/10.1186/1471-2229-6-28

Ronfort, J., Jenczewski, E., Bataillon, T. & Rousset, F. (1998). Analysis of population structure in autotetraploid species. Genetics, 150(2), 921-30.

Rolland, T., Cliquet, F., Anney, R. J. L., Moreau, C., Traut, N., Mathieu, A., Huguet, G., Duan, J., Warrier, V., Portalier, S., Dry, L., Leblond, C. S., Douard, E., Amsellem, F., Malesys, S., Maruani, A., Toro, R., Børglum, A. D., Grove, J. ... Bourgeron, T. (2023). Phenotypic effects of genetic variants associated with autism. Nature Medicine, 29(7), 1671-1680. https://doi.org/10.1038/s41591-023-02408-2

Røikjer, T., Hobolth, A. & Munch, K. (2022). Graph-based algorithms for phase-type distributions. Statistics and Computing, 32(6), Article 103. https://doi.org/10.1007/s11222-022-10174-3

Rogers, J., Raveendran, M., Alan Harris, R., Mailund, T., Leppälä, K., Athanasiadis, G., Schierup, M. H., Cheng, J., Munch, K., Walker, J. A., Konkel, M. K., Jordan, V., Steely, C. J., Beckstrom, T. O., Bergey, C., Burrell, A., Schrempf, D., Noll, A., Kothe, M. ... Baboon Genome Analysis Consortium (2019). The comparative genomics and complex population history of Papio baboons. Science Advances, 5(1), Article 6947. https://doi.org/10.1126/sciadv.aau6947

Rivas-González, I., Rousselle, M., Li, F., Zhou, L., Dutheil, J. Y., Munch, K., Shao, Y., Wu, D., Schierup, M. H. & Zhang, G. (2023). Pervasive incomplete lineage sorting illuminates speciation and selection in primates. Science, 380(6648), eabn4409. Article eabn4409. https://doi.org/10.1126/science.abn4409

Rivas-González, I., Andersen, L. N. & Hobolth, A. (2023). PhaseTypeR: an R package for phase-type distributions in population genetics. The Journal of Open Source Software, 8(82). https://doi.org/10.21105/joss.05054

Rivas-González, I., Schierup, M. H., Wakeley, J. & Hobolth, A. (2024). Trails: Tree reconstruction of ancestry using incomplete lineage sorting. PLoS Genetics, 20(2), Article e1010836. https://doi.org/10.1371/journal.pgen.1010836

Rivas, S., Rougon-Cardoso, A., Smoker, M., Schauser, L., Yoshioka, H. & Jones, J. D. G. (2004). CITRX thioredoxin interacts with the tomato Cf-9 resistance protein and negatively regulates defence. The EMBO Journal, 23, 2156-2165.

Rietschel, M., Mattheisen, M., Degenhardt, F., Kahn, R. S., Linszen, D. H., Os, J. V., Wiersma, D., Bruggeman, R., Cahn, W., de Haan, L., Krabbendam, L., Myin-Germeys, I., Mühleisen, T. W., Kirsch, P., Esslinger, C., Herms, S., Demontis, D., Steffens, M., Strohmaier, J. ... Cichon, S. (2012). Association between genetic variation in a region on chromosome 11 and schizophrenia in large samples from Europe. Molecular Psychiatry, 17(9), 906–917. https://doi.org/10.1038/mp.2011.80

Riedel, C. S., Norager, N. H., Bertelsen, M., Mikkelsen, R., Juhler, M. & Hansen, T. S. (2024). Elevated systemic venous pressures as a possible pathology in prepubertal pediatric idiopathic intracranial hypertension. Child's Nervous System, 40(12), 4203-4209. https://doi.org/10.1007/s00381-024-06594-3

Richman, A. D., Herrera, L. G., Nash, D. & Schierup, M. H. (2003). Relative roles of mutation and recombination in generating allelic polymorphism at an MHC class II locus in Peromyscus maniculatus. Genetetical Research, Camb, 82, 89-99.

Riber, A. B., Herskin, M. S., Foldager, L., Berenjian, A., Sandercock, D., Murrell, J. & Tahamtani, F. (2021). Are changes in behavior of fast-growing broilers with slight gait impairment (GS0-2) related to pain? Poultry Science, 100(3), Article 100948. https://doi.org/10.1016/j.psj.2020.12.045

Riber, A. B., Herskin, M. S., Foldager, L., Sandercock, D. A., Murrell, J. & Tahamtani, F. (2021). Post-mortem examination of fast-growing broilers with different degrees of identifiable gait defects. Veterinary Record, 189(7), Article e454. https://doi.org/10.1002/vetr.454

Rheinbay, E., Nielsen, M. M., Abascal, F., Wala, J. A., Shapira, O., Tiao, G., Hornshøj, H., Hess, J. M., Juul, R. I., Lin, Z., Feuerbach, L., Sabarinathan, R., Madsen, T., Kim, J., Mularoni, L., Shuai, S., Lanzós, A., Herrmann, C., Maruvka, Y. E. ... PCAWG Consortium (2020). Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature, 578(7793), 102-111. https://doi.org/10.1038/s41586-020-1965-x

Rheinbay, E., Nielsen, M. M., Abascal, F., Wala, J. A., Shapira, O., Tiao, G., Hornshøj, H., Hess, J. M., Juul, R. I., Lin, Z., Feuerbach, L., Sabarinathan, R., Madsen, T., Kim, J., Mularoni, L., Shuai, S., Lanzós, A., Herrmann, C., Maruvka, Y. E. ... PCAWG Drivers and Functional Interpretation Working Group (2023). Erratum: Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (Nature (2020) 578 7793 (102-111)). Nature, 614(7948), E40. https://doi.org/10.1038/s41586-022-05599-9

Reyna, M. A., Haan, D., Paczkowska, M., Verbeke, L. P. C., Vazquez, M., Kahraman, A., Pulido-Tamayo, S., Barenboim, J., Wadi, L., Dhingra, P., Shrestha, R., Getz, G., Lawrence, M. S., Pedersen, J. S., Rubin, M. A., Wheeler, D. A., Brunak, S., Izarzugaza, J. M. G., Khurana, E. ... PCAWG Consortium (2020). Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications, 11(1), Article 729. https://doi.org/10.1038/s41467-020-14367-0

Renaud, G., Nørgaard, M., Lindberg, J., Grönberg, H., De Laere, B., Jensen, J. B., Borre, M., Andersen, C. L., Sørensen, K. D., Maretty, L. & Besenbacher, S. (2022). Unsupervised detection of fragment length signatures of circulating tumor DNA using non-negative matrix factorization. eLife, 11, Article e71569. https://doi.org/10.7554/ELIFE.71569

Reinert, T., Modin, C., Mansilla Castano, F., Lamy, P., Wojdacz, T. K., Hansen, L. L., Wiuf, C., Borre, M., Andersen, L. D. & Ørntoft, T. F. (2011). Comprehensive genome methylation analysis in bladder cancer;identification and validation of novel methylated genes and application of these as urinary tumor markers. Clinical Cancer Research. https://doi.org/10.1158/1078-0432.CCR-10-2659

Refoyo-Martínez, A., da Fonseca, R. R., Halldórsdóttir, K., Árnason, E., Mailund, T. & Racimo, F. (2019). Identifying loci under positive selection in complex population histories. Genome Research, 29(9), 1506-1520. https://doi.org/10.1101/gr.246777.118

Ravn, P., Forsberg, R. & Christiansen, F. (2007). Influenza: - menneskets uforudsigelige følgesvend. Aktuel Naturvidenskab, 2007(2), 16-20.

Raveane, A., Aneli, S., Montinaro, F., Athanasiadis, G., Barlera, S., Birolo, G., Boncoraglio, G., Di Blasio, A. M., Di Gaetano, C., Pagani, L., Parolo, S., Paschou, P., Piazza, A., Stamatoyannopoulos, G., Angius, A., Brucato, N., Cucca, F., Hellenthal, G., Mulas, A. ... Capelli, C. (2019). Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe. Science Advances, 5(9), Article eaaw3492. https://doi.org/10.1126/sciadv.aaw3492

Ratmann, O., Jørgensen, O., Hinkley, T., Stumpf, M., Richardson, S. & Wiuf, C. (2007). Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PLoS Comp Biol, 3(e320). https://doi.org/10.1371/journal.pcbi.0030230.eor

Ratmann, O., Wiuf, C. H. & Pinney, J. W. (2009). From evidence to inference: probing the evolution of protein interaction networks. HFSP Journal, 3(5), 290-306. https://doi.org/10.2976/1.3167215

Ratmann, O., Andrieu, C., Wiuf, C. H. & Richardson, S. (2009). Model criticism based on likelihood-free inference: with an application to protein network evolution. Proceedings of the National Academy of Sciences (PNAS), 106, 10576-10581. https://doi.org/10.1073/pnas.0807882106

Rasmussen, M. J., Bertl, J., Guo, Q., Nielsen, M. M., Świtnicki, M., Hornshøj, H., Madsen, T., Hobolth, A. & Pedersen, J. S. (2017). Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate. eLife, 6, Article e21778. https://doi.org/10.7554/eLife.21778

Rasmussen, M. Q., Tindbæk, G., Nielsen, M. M., Merrild, C., Steiniche, T., Pedersen, J. S., Moestrup, S. K., Degn, S. E. & Madsen, M. (2023). Epigenetic Silencing of LRP2 Is Associated with Dedifferentiation and Poor Survival in Multiple Solid Tumor Types. Cancers, 15(6), Article 1830. https://doi.org/10.3390/cancers15061830

Rasmussen, A. M., Okholm, T. L. H., Knudsen, M., Vang, S., Dyrskjøt, L., Hansen, T. B. & Pedersen, J. S. (2023). Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer. NAR cancer, 5(3), Article zcad041. https://doi.org/10.1093/narcan/zcad041

Rasmussen, M. Q., Bønnelykke-Behrndtz, M. L., Merrild, C., Tvilling, I. K. S., Christensen, J. N., Nielsen, M. M., Georgsen, J. B., Naumann, N., Gudbergsson, J. M., Etzerodt, A., Pedersen, J. S., Jenkins, R. W., Degn, S. E., Moestrup, S. K., Schmidt, H., Steiniche, T. & Madsen, M. (2025). LRP2 Expression in Melanoma Is Associated With a Transitory Cell State, Increased T Cell Infiltration, and Is Upregulated by IFNy Signaling. Pigment Cell & Melanoma Research, 38(5), Article e70053. https://doi.org/10.1111/pcmr.70053

Rani, S., Sørensen, M. T., Estellé, J., Noel, S. J., Nørskov, N., Krogh, U., Foldager, L. & Højberg, O. (2023). Gastrointestinal Microbial Ecology of Weaned Piglets Fed Diets with Different Levels of Glyphosate. Microbiology Spectrum, 11(4), Article e0061523. https://doi.org/10.1128/spectrum.00615-23

Rajkumar, A. P., Christensen, J. H., Mattheisen, M., Jacobsen, I., Bache, I., Pallesen, J., Grove, J., Qvist, P., Mcquillin, A., Gurling, H. M., Tümer, Z., Mors, O. & Børglum, A. D. (2015). Analysis of t(9;17)(q33.2;q25.3) chromosomal breakpoint regions and genetic association reveals novel candidate genes for bipolar disorder. Bipolar Disorders (English Edition, Online), 17(2), 205-211. https://doi.org/10.1111/bdi.12239

Rajagopal, V. M., Duan, J., Vilar-Ribó, L., Grove, J., Zayats, T., Ramos-Quiroga, J. A., Satterstrom, F. K., Artigas, M. S., Bybjerg-Grauholm, J., Bækvad-Hansen, M., Als, T. D., Rosengren, A., Daly, M. J., Neale, B. M., Nordentoft, M., Werge, T., Mors, O., Hougaard, D. M., Mortensen, P. B. ... Demontis, D. (2022). Differences in the genetic architecture of common and rare variants in childhood, persistent and late-diagnosed attention-deficit hyperactivity disorder. Nature Genetics, 54(8), 1117-1124. https://doi.org/10.1038/s41588-022-01143-7

Rajagopal, V. M., Ganna, A., Coleman, J. R. I., Allegrini, A., Voloudakis, G., Grove, J., Als, T. D., Horsdal, H. T., Petersen, L., Appadurai, V., Schork, A., Buil, A., Bulik, C. M., Bybjerg-Grauholm, J., Bækvad-Hansen, M., Hougaard, D. M., Mors, O., Nordentoft, M., Werge, T. ... Demontis, D. (2023). Genome-wide association study of school grades identifies genetic overlap between language ability, psychopathology and creativity. Scientific Reports, 13, Article 429. https://doi.org/10.1038/s41598-022-26845-0

Rafnar, T., Thorlacius, S., Steingrimsson, E., Schierup, M. H., Madsen, J. N., Calian, V., Eldon, B. J., Jonsson, T., Hein, J. & Thorgeirsson, S. S. (2004). The Icelandic Cancer Project--a population-wide approach to studying cancer. Nat Rev Cancer Jun, 4(6), 488-492.

Rafnar, T., Vermeulen, S. H., Sulem, P., Thorleifsson, G., Aben, K. K., Witjes, J. A., Grotenhuis, A. J., Verhaegh, G. W., Hulsbergen-van de Kaa, C. A., Besenbacher, S., Gudbjartsson, D., Stacey, S. N., Gudmundsson, J., Johannsdottir, H., Bjarnason, H., Zanon, C., Helgadottir, H., Jonasson, J. G., Tryggvadottir, L. ... Kiemeney, L. A. (2011). European genome-wide association study identifies SLC14A1 as a new urinary bladder cancer susceptibility gene. Human Molecular Genetics, 20(21), 4268-4281. https://doi.org/10.1093/hmg/ddr303

Rafnar, T., Gudbjartsson, D. F., Sulem, P., Jonasdottir, A., Sigurdsson, A., Jonasdottir, A., Besenbacher, S., Lundin, P., Stacey, S. N., Gudmundsson, J., Magnusson, O. T., le Roux, L., Orlygsdottir, G., Helgadottir, H. T., Johannsdottir, H., Gylfason, A., Tryggvadottir, L., Jonasson, J. G., de Juan, A. ... Stefansson, K. (2011). Mutations in BRIP1 confer high risk of ovarian cancer. Nature Genetics, 43(11), 1104-7. https://doi.org/10.1038/ng.955

Radel, D., Sand, A. & Steel, M. (2013). Hide and seek: placing and finding an optimal tree for thousands of homoplasy-rich sequences. Molecular Phylogenetics and Evolution, 69(3), 1186–1189. https://doi.org/10.1016/j.ympev.2013.08.001