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
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
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
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
Rani, S., Sørensen, M. T., Noel, S. J., Nørskov, N., Krogh, U., Foldager, L. & Hojberg, O. (2022).
Minor influence of feed glyphosate on gut microbial ecology of weaned piglets. In
Book of Abstracts of the 73rd Annual Meeting of the European Federation of Animal Science (pp. 286-286). Wageningen Academic Publishers.
https://doi.org/10.3920/978-90-8686-937-4
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
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C.
, Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D. R., Li, J., Xu, J., Li, S., Li, D., Cao, J., Wang, B., Liang, H., Zheng, H. ... MetaHIT Consortium (2010).
A human gut microbial gene catalogue established by metagenomic sequencing.
Nature,
464(7285), 59-65.
https://doi.org/10.1038/nature08821
Pujolar, J. M., Jacobsen, L. M. W., Als, T. D., Frydenberg, J., Munch, K., Jonsson, B., Jian, J. B., Cheng, L., Maes, G. E., Bernatchez, L.
& Hansen, M. M. (2014).
Genome-wide single generation signatures of local selection in the panmictic European eel.
Molecular Ecology,
23, 2514-2528.
https://doi.org/10.1111/mec.12753
Prüfer, K.
, Munch, K., Hellmann, I., Akagi, K., Miller, J. R., Walenz, B., Koren, S., Sutton, G., Kodira, C., Winer, R., Knight, J. R., Mullikin, J. C., Meader, S. J., Ponting, C. P., Lunter, G., Higashino, S.
, Hobolth, A., Dutheil, J., Karakoç, E. ... Pääbo, S. (2012).
The bonobo genome compared with the chimpanzee and human genomes.
Nature,
486(7404), 527-31.
https://doi.org/10.1038/nature11128
Prüfer, K., de Filippo, C., Grote, S., Mafessoni, F., Korlević, P., Hajdinjak, M., Vernot, B.
, Skov, L., Hsieh, P., Peyrégne, S., Reher, D., Hopfe, C., Nagel, S., Maricic, T., Fu, Q., Theunert, C., Theunert, C., Rogers, R., Skoglund, P. ... Pääbo, S. (2017).
A high-coverage Neandertal genome from Vindija Cave in Croatia.
Science,
358(6363), 655-658.
https://doi.org/10.1126/science.aao1887
Privé, F., Aschard, H., Carmi, S., Folkersen, L., Hoggart, C., O'Reilly, P. F.
& Vilhjálmsson, B. J. (2022).
Portability of 245 polygenic scores when derived from the UK Biobank and applied to 9 ancestry groups from the same cohort.
American Journal of Human Genetics,
109(1), 12-23.
https://doi.org/10.1016/j.ajhg.2021.11.008
Privé, F., Albiñana, C., Arbel, J., Pasaniuc, B.
& Vilhjálmsson, B. J. (2023).
Inferring disease architecture and predictive ability with LDpred2-auto.
American Journal of Human Genetics,
110(12), 2042-2055.
https://doi.org/10.1016/j.ajhg.2023.10.010
Preker, P., Nielsen, J., Kammler, S., Lykke-Andersen, S., Christensen, M. S., Mapendano, C. K., Schierup, M. H. & Jensen, T. H. (2008).
RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters.
Science,
322(5909), 1851-1854.
https://doi.org/10.1126/science.1164096
Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., Veeramah, K. R., Woerner, A. E., O'Connor, T. D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H.
, Munch, K., Hobolth, A., Halager, A. E., Malig, M., Hernandez-Rodriguez, J. ... Marques-Bonet, T. (2013).
Great ape genetic diversity and population history.
Nature,
499, 471–475.
https://doi.org/10.1038/nature12228
Poulsgaard, G. A., Sørensen, S. G., Juul, R. I., Nielsen, M. M. & Pedersen, J. S. (2023).
Sequence dependencies and mutation rates of localized mutational processes in cancer.
Genome Medicine,
15(1), Article 63.
https://doi.org/10.1186/s13073-023-01217-z
Poulsen, N. A., Nielsen, E. E.
, Schierup, M. H., Loeschcke, V. & Grønkjær, P. (2006).
Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua). Molecular Ecology,
15, 321-331.