Publications of KD Murray

Whiting, J.; Booker, T.; Rougeux , C.; Lind, B.; Singh, P.; Lu, M.; Huang, K.; Whitlock , M.; Aitken, S.; Andrew, R. et al.; Borevitz, J.; Bruhl, J.; Collins, T.; Fischer, M.; Hodgins, K.; Holliday, J.; Ingvarsson, P.; Janes, J.; Khandaker, M.; Koenig, D.; Kreiner, J.; Kremer, A.; Lascoux, M.; Leroy, T.; Milesi, P.; Murray, K.; Pyhäjärvi, T.; Rellstab, C.; Rieseberg, L.; Roux, F.; Stinchcombe, J.; Telford, I.; Todesco, M.; Tyrmi , J.; Wang, B.; Weigel, D.; Willi, Y.; Wright, S.; Zhou, L.; Yeaman, S.: The genetic architecture of repeated local adaptation to climate in distantly related plants. Nature Ecology & Evolution 8 (10), pp. 1933 - 1947 (2024)

Ferguson, S.; Jones, A.; Murray, K.; Andrew, R.; Schwessinger, B.; Bothwell, H.; Borevitz, J.: Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus. GigaScience 13, giae029 (2024)

Ferguson, S.; Jones, A.; Murray, K.; Andrew, S.; Schwessinger, B.; Borevitz, J.: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence. Genome Research 34 (4), pp. 606 - 619 (2024)

Murray, K.; Borevitz, J.; Weigel, D.; Warthmann, N.: Acanthophis: a comprehensive plant hologenomics pipeline. The Journal of Open Source Software (JOSS) 9 (95), 6062 (2024)

Monroe, J.; Murray, K.; Xian, W.; Srikant, T.; Carbonell-Bejerano, P.; Becker, C.; Lensink, M.; Exposito Alonso, M.; Klein, M.; Hildebrandt, J. et al.; Neumann, M.; Kliebenstein, D.; Weng, M.-E.; Imbert, L.; Ågren, J.; Rutter, M.; Fenster, C.; Weigel, D.: Reply to: Re-evaluating evidence for adaptive mutation rate variation. Nature 619 (7971), pp. E57 - E60 (2023)

Ferguson, S.; Jones, A.; Murray, K.; Schwessinger, B.; Borevitz, J.: Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus. Molecular Ecology 32 (6), pp. 1271 - 1287 (2023)

Ahrens, C.; Jordan, R.; Bragg, J.; Harrison, P.; Hopley, T.; Bothwell, H.; Murray, K.; Steane, D.; Whale, J.; Byrne, M. et al.; Andrew, R.; Rymer, P.: Regarding the F-word: The effects of data filtering on inferred genotype-environment associations. Molecular Ecology Resources 21 (5), pp. 1460 - 1474 (2021)

Bao, Z.; Rabanal, F.; Guarracino, A.; Vorbrugg, S.; Xian, W.; Movilli, A.; Teasdale, L.; Murray, K.; Shirsekar, G.; Tao, Y. et al.; Lucke, M.; Garrison, E.; Weigel, D.: Understanding mutational processes from Arabidopsis pangeome graphs. In 34th International Conference on Arabidopsis Research (ICAR 2024), C12-2, p. 156. 34th International Conference on Arabidopsis Research (ICAR 2024), San Diego, CA, USA, July 15, 2024 - July 19, 2024. (2024)

Murray, K.; Shirsekar, G.; Paul, F.; González-Hernando, A.; Schwab, R.; Tahtsidou, C.; Deusch, O.; Dürr, H.; Kontos, I.; Karawounopoulos, S. et al.; Velthoven, R.; Lanz, C.; Collenberg, M.; The Pathodopsis Team; Weigel, D.: The Coevolutionary race between Hyaloperonospora Arabidopsidis and Arabidopsis Thaliana at a Transcontinental Scale. In 12th International Congress of Plant Pathology (ICPP 2023), C2.3-2, pp. 813 - 814. 12th International Congress of Plant Pathology (ICPP 2023), Lyon, France, August 20, 2023 - August 25, 2023. (2023)

Teasdale, L.; Shirsekar, G.; Collenberg, M.; Murray, K.; Contreras-Garrido, A.; Schlegel, T.; van Ess, L.; Juettner, j.; Lanz, C.; Deusch, O. et al.; Fitz, J.; Mencia, R.; Velthoven, R.; Drost, H.-G.; Weigel, D.: Birth, Death, and Persistence in NLR Diversity in the Arabidopsis Immune System. In 12th International Congress of Plant Pathology (ICPP 2023), P5.5-010, p. 385. 12th International Congress of Plant Pathology (ICPP 2023), Lyon, France, August 20, 2023 - August 25, 2023. (2023)

Murray, K.; Shirsekar, G.; Paul, F.; González Hernando, A.; Schwab, R.; Tahtsidou, C.; Deusch, O.; Dürr, H.; Kontos, I.; Marotz, A. et al.; Karawounopoulos, S.; Velthoven, R.; Lucke, M.; Lanz, C.; Collenberg, M.; Pathodopsis Team; Weigel, D.: The coevolutionary race between Hyaloperonospora arabidopsidis and Arabidopsis thaliana at a transcontinental scale. In SMBE 2023, p. 161. Society for Molecular Biology and Evolution Conference 2023 (SMBE 2023), Ferrara, Italy, July 23, 2023 - July 27, 2023. (2023)

Bothwell, H.; Murray, K.; Tan, C.; James , F.; Borevitz, J.: Divergence in drought adaptation strategies in native Australian eucalyptus. In Evolution 2023, 85. Evolution 2023: Joint Annual Meeting of the American Society of Naturalists, the Society for the Study of Evolution, and the Society of Systematic Biologists, Albuquerque, NM, USA, June 21, 2023 - June 25, 2023. (2023)

Teasdale, L.; Shirsekar, G.; Collenberg, M.; Murray, K.; Contreras Garrido, A.; van Ess, L.; Juettner, j.; Lanz, C.; Fitz, J.; Drost, H.-G. et al.; Weigel, D.: Challenges of annotating complex genes in the Arabidopsis long read genome collection. In 33rd International Conference on Arabidopsis Research (ICAR 2023), WS02-06. 33rd International Conference on Arabidopsis Research (ICAR 2023), Chiba, Japan, June 05, 2023 - June 06, 2023. (2023)

Shirsekar, G.; Murray, K.; Paul, F.; Schwab, R.; Tahtsidou, C.; Velthoven, R.; Deusch, O.; Teasdale, L.; Collenberg, M.; Pathodopsis Team et al.; Weigel, D.: Entangled co-evolutionary history of Hyaloperonospora arabidopsidis and its host Arabidopsis thaliana. In 21st Annual Meeting of the Oomycete Molecular Genetics Network (OMGN 2022), 7.1, p. 35. 21st Annual Meeting of the Oomycete Molecular Genetics Network (OMGN 2022), Brno, Czech Republic, August 22, 2022 - August 25, 2022. (2022)

Warthmann, N.; Murray, K.; Morales Zambrana, A.; Conde, M.; Morales, L.; Ali, A.; Ali Ghanim, A.; Borevitz, J.; Ingelbrecht, I.: Mainstreaming Genomics: Protocols for Genome Re-Sequencing at the Population Scale. Plant & Animal Genome Conference (PAG 30), San Diego, CA, USA (2023)

The 1001 Genomes Plus Consortium; Alonso-Blanco, C.; Ashkenazy, H.; Baduel, P.; Bao, Z.; Becker, C.; Caillieux, E.; Colot, V.; Crosbie, D.; De Oliveira, L. et al.; Fitz, J.; Fritschi, K.; Grigoreva, E.; Guo, Y.; Habring, A.; Henderson, I.; Hou, X.-H.; Hu, Y.; Igolkina, A.; Kang, M.; Kemen, E.; Kersey, P.; Kornienko, A.; Lian, Q.; Liu, H.; Liu, J.; Lucke, M.; Mayjonade, B.; Mercier, R.; Mollá Morales, A.; Movilli, A.; Murray, K.; Naish, M.; Nordborg, M.; Rabanal, F.; Roux, F.; Schandry, N.; Schneeberger, K.; Schwab, R.; Shirsekar, G.; Sushko, S.; Tao, Y.; Teasdale, L.; Vorbrugg, S.; Weigel, D.; Xian, W.: The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research. (submitted)

Teasdale, L.; Murray, K.; Collenberg, M.; Contreras-Garrido, A.; Schlegel, T.; van Ess, L.; Jüttner, J.; Lanz, C.; Deusch, O.; Fitz, J. et al.; Mencia, R.; van Velthoven, R.; Drost, H.-G.; Weigel, D.; Shirsekar, G.: Pangenomic context reveals the extent of intraspecic plant NLR evolution. (submitted)

Yeaman, S.; Whiting, J.; Booker, T.; Rougeux, C.; Lind, B.; Singh, P.; Lu, M.; Huang, K.; Whitlock, M.; Aitken, S. et al.; Andrew, R.; Borevitz, J.; Bruhl, J.; Collins, T.; Fischer, M.; Hodgins, K.; Holliday, J.; Ingvarsson, P.; Janes, J.; Khandaker, M.; Koenig, D.; Kreiner, J.; Kremer, A.; Lascoux, M.; Leroy, T.; Milesi, P.; Murray, K.; Rellstab, C.; Rieseberg, L.; Roux, F.; Stinchcombe, J.; Telford, I.; Tedesco, M.; Wang, B.; Weigel, D.; Willi, Y.; Wright, S.; Zhou, L.: Core genes driving climate adaptation in plants. (submitted)

Ferguson, S.; Jones, A.; Murray, K.; Andrew, R.; Bothwell, H.; Schwessinger, B.; Borevitz, J.: Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence. (submitted)

Monroe, J.; Murray, K.; Xian, W.; Carbonell-Bejerano, P.; Fenster, C.; Weigel, D.: Report of mutation biases mirroring selection in Arabidopsis thaliana unlikely to be entirely due to variant calling errors. (submitted)