Publications

Čapek, D.; Safroshkin, M.; Morales-Navarrete, H.; Toulany, N.; Arutyunov, G.; Kurzbach, A.; Bihler, J.; Hagauer, J.; Kick, S.; Jones, F. et al.; Jordan, B.; Müller, P.: EmbryoNet: using deep learning to link embryonic phenotypes to signaling pathways. Nature Methods 20 (6), pp. 815 - 823 (2023)

Marques, D.; Jones, F.; Di Palma, F.; Kingsley, D.; Reimchen, T.: Genomic changes underlying repeated niche shifts in an adaptive radiation. Evolution: international journal of organic evolution 76 (6), pp. 1301 - 1319 (2022)

Roberts Kingman, G.; Vyas, D.; Jones, F.; Brady, S.; Chen, H.; Reid, K.; Milhaven, M.; Bertino , T.; Aguirre, W.; Heins, D. et al.; von Hippel, F.; Kirch, M.; Absher, D.; Myers, R.; Di Palma, F.; Bell, M.; Kingsley, D.; Veeramah, K.: Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. Science Advances 7 (25), eabg5285 (2021)

Kirch, M.; Romundset, A.; Gilbert, M.; Jones, F.; Foote, A.: Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Current Biology 31 (9), pp. 2027 - 2036 (2021)

Verta, J.-P.; Jones, F.: mRNA Extraction from Gill Tissue for RNA-sequencing. Bio-protocol 10 (5), e3539 (2020)

Dréau, A.; Venu, V.; Avdievich, E.; Gaspar, L.; Jones, F.: Genome-wide recombination map construction from single individuals using linked-read sequencing. Nature Communications 10 (1), 4309 (2019)

Verta, J.-P.; Jones, F.: Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks. eLife 8, e43785 (2019)

Marques, D.; Jones, F.; Di Palma, F.; Kingsley, D.; Reimchen, T.: Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. Nature Ecology & Evolution 2 (7), pp. 1128 - 1138 (2018)

Lv, S.; Wu, W.; Wang, M.; Meyer, R.; Ndjiondjop, M.-N.; Tan, L.; Zhou, H.; Zhang, J.; Fu, Y.; Cai, H. et al.; Sun, C.; Wing, R.; Zhu, Z.: Genetic control of seed shattering during African rice domestication. Nature Plants 4 (6), pp. 331 - 337 (2018)

Stein, J.; Yu, Y.; Copetti, D.; Zwickl, D.; Zhang, L.; Zhang, C.; Chougule, K.; Gao, D.; Iwata, A.; Goicoechea, J. et al.; Wei, S.; Wang, J.; Liao, Y.; Wang, M.; Jacquemin, J.; Becker, C.; Kudrna, D.; Zhang, J.; Londono, C.; Song, X.; Lee, S.; Sanchez, P.; Zuccolo, A.; Ammiraju, J.; Talag, J.; Danowitz, A.; Rivera, L.; Gschwend, A.; Noutsos, C.; Wu, C.; Kao, S.; Zeng, J.; Wei, F.; Zhao, Q.; Feng, Q.; El Baidouri, M.; Carpentier, M.; Lasserre, E.; Cooke, R.; Rosa Farias, D.; da Maia, L.; Dos Santos, R.; Nyberg, K.; McNally, K.; Mauleon, R.; Alexandrov, N.; Schmutz, J.; Flowers, D.; Fan, C.; Weigel, D.; Jena, K.; Wicker, T.; Chen, M.; Han, B.; Henry, R.; Hsing, Y.; Kurata, N.; de Oliveira, A.; Panaud, O.; Jackson, S.; Machado, C.; Sanderson, M.; Long, M.; Ware, D.; Wing, R.: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics 50 (2), pp. 285 - 296 (2018)

Stein, J.; Yu, Y.; Copetti, D.; Zwickl, D.; Zhang, L.; Zhang, C.; Chougule, K.; Gao, D.; Iwata, A.; Goicoechea, J. et al.; Wei, S.; Wang, J.; Liao, Y.; Wang, M.; Jacquemin, J.; Becker, C.; Kudrna, D.; Zhang, J.; Londono, C.; Song, X.; Lee, S.; Sanchez, P.; Zuccolo, A.; Ammiraju, J.; Talag, J.; Danowitz, A.; Rivera, L.; Gschwend, A.; Noutsos, C.; Wu, C.; Kao, S.; Zeng, J.; Wei, F.; Zhao, Q.; Feng, Q.; El Baidouri, M.; Carpentier, M.; Lasserre, E.; Cooke, R.; Rosa Farias, D.; da Maia, L.; Dos Santos, R.; Nyberg, K.; McNally, K.; Mauleon, R.; Alexandrov, N.; Schmutz, J.; Flowers, D.; Fan, C.; Weigel, D.; Jena, K.; Wicker, T.; Chen, M.; Han, B.; Henry, R.; Hsing, Y.; Kurata, N.; de Oliveira, A.; Panaud, O.; Jackson, S.; Machado, C.; Sanderson, M.; Long, M.; Ware, D.; Wing, R.: Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics 50 (11), p. 1618 (2018)

Marques, D.; Taylor, J.; Jones, F.; Di Palma, F.; Kingsley, D.; Reimchen, T.: Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments. PLoS Biology 15 (4), e2001627 (2017)

Prunier, J.; Verta, J.-P.; MacKay, J.: Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. New Phytologist 209 (1), pp. 44 - 62 (2016)

Arif, S.; Kittelmann, S.; McGregor, A.: From shavenbaby to the naked valley: trichome formation as a model for evolutionary developmental biology. Evolution and Development 17 (1), pp. 120 - 126 (2015)

Seehausen, O.; Butlin, R.; Keller, I.; Wagner, C.; Boughman, J.; Hohenlohe, P.; Peichel, C.; Saetre, G.-P.; Bank, C.; Brännström, A. et al.; Brelsford, A.; Clarkson, C.; Eroukhmanoff, F.; Feder, J.; Fischer, M.; Foote, A.; Franchini, P.; Jiggins, C.; Jones, F.; Lindholm, A.; Lucek, K.; Maan, M.; Marques, D.; Martin, S.; Matthews, B.; Meier, J.; Möst, M.; Nachman, M.; Nonaka, E.; Rennison, D.; Schwarzer, J.; Watson, E.; Westram, A.; Widmer, A.: Genomics and the origin of species. Nature Reviews Genetics 15 (3), pp. 176 - 192 (2014)

Faria, R.; Renaut, S.; Galindo, J.; Pinho, C.; Melo-Ferreira, J.; Melo, M.; Jones, F.; Salzburger, W.; Schluter, D.; Butlin, R.: Advances in Ecological Speciation: an integrative approach. Molecular Ecology 23 (3), pp. 513 - 521 (2014)

Laine, J.; Mak, S.; Martins, N.; Chen, X.; Gilbert, M.; Jones, F.; Winther Pedersen, M.; Romundset, A.; Foote, A.: Ancient stickleback environmental genomes track adaptation across ecological transitions. In SMBE 2023, pp. 57 - 58. Society for Molecular Biology and Evolution Conference 2023 (SMBE 2023), Ferrara, Italy, July 23, 2023 - July 27, 2023. (2023)

Neufeld, S.; Verta, J.-P.; Wang, M.; Schwickert, J.; John, M.; Ritter, M.; Scionti, D.; Kick, S.; Kirch, M.; Avdievich, E. et al.; Venu, V.; Jones, F.: The importance of cis-regulatory variation in regulatory and gene-expression divergence of stickleback ecotypes. In SMBE 2021, SYMP4-5, p. 486. Society for Molecular Biology and Evolution Conference 2021 (SMBE 2021), July 03, 2019 - July 08, 2019. (2021)

Foote, A.; Kirch, M.; Romundset, A.; Gilbert, T.; Jones, F.: Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. In 54th Population Genetics Group Meeting (PopGroup 54), 74, p. 36. 54th Population Genetics Group Meeting (PopGroup 54), Liverpool, UK, January 04, 2021 - January 06, 2021. (2021)

Jones, F.: Chromatin and epigenomic variation reveals the gene regulatory landscape of adaptive divergence in sticklebacks. In 6th International Conference of Quantitative Genetics (ICQG 2020), 80, p. 67. 6th International Conference of Quantitative Genetics (ICQG 2020), November 02, 2020 - November 13, 2020. (2020)