PEQG References

References

  1. Wray, G. A. (2007). The evolutionary significance of cis-regulatory mutations. Nature Reviews Genetics, 8, 206-216.

  2. Chan, Y. F., Marks, M. E., Jones, F. C., Villarreal Jr, G., Shapiro, M. D., Brady, S. D., … & Kingsley, D. M. (2010). Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science, 327, 302-305.

  3. Reid, K., Bell, M. A., & Veeramah, K. R. (2021). Threespine stickleback: A model system for evolutionary genomics. Annual Review Of Genomics And Human Genetics, 22, 357-383.

  4. Di-Poi, C., Lacasse, J., Rogers, S. M., & Aubin-Horth, N. (2014). Extensive behavioural divergence following colonisation of the freshwater environment in threespine sticklebacks. PLOS ONE, 9, e98980.

  5. Tarashansky, A. J., Musser, J. M., Khariton, M., Li, P., Arendt, D., Quake, S. R., & Wang, B. (2021). Mapping single-cell atlases throughout Metazoa unravels cell type evolution. eLife, 10, e66747.

  6. Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., … & Liu, X. S. (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biology, 9, R137.

  7. Stuart, T., Srivastava, A., Madad, S., Lareau, C. A., & Satija, R. (2021). Single-cell chromatin state analysis with Signac. Nature Methods, 18, 1333-1341.

  8. Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., … & Satija, R. (2019). Comprehensive integration of single-cell data. Cell, 177, 1888-1902.

  9. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25, 1754-1760.

  10. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., … & DePristo, M. A. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297.

  11. Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., … & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10, giab008.

  12. Korunes, K. L., & Samuk, K. (2021). pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Molecular Ecology Resources, 21, 1359-1368.

  13. Peichel, C. L., & Marques, D. A. (2017). The genetic and molecular architecture of phenotypic diversity in sticklebacks. Philosophical Transactions Of The Royal Society B: Biological Sciences, 372. 20150486.

  14. Becker, C. G., & Becker, T. (2015). Neuronal regeneration from ependymo-radial glial cells: cook, little pot, cook!. Developmental Cell, 32, 516-527.

  15. Kroehne, V., Freudenreich, D., Hans, S., Kaslin, J., & Brand, M. (2011). Regeneration of the adult zebrafish brain from neurogenic radial glia-type progenitors. Development, 138, 4831-4841.

  16. Chung, M. I., Kwon, T., Tu, F., Brooks, E. R., Gupta, R., Meyer, M., … & Wallingford, J. B. (2014). Coordinated genomic control of ciliogenesis and cell movement by RFX2. Elife, 3, e01439.

  17. Palla, A. R., Hilgendorf, K. I., Yang, A. V., Kerr, J. P., Hinken, A. C., Demeter, J., … & Blau, H. M. (2022). Primary cilia on muscle stem cells are critical to maintain regenerative capacity and are lost during aging. Nature Communications, 13, 1439.