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Convergent evolution of noncoding elements associated with short tarsus length in birds
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Lineages may achieve a similar phenotypic change through substitutions in, or duplications of, distinct genetic elements that are part of the same genetic pathway or network where changes have similar impacts on network function.
“These distinct genetic elements may be part of the same genetic pathway or network where changes have similar impacts on network function (Láruson et al. 2020; Shakya et al. 2025) (Fig. 2d).”
From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Shakya et al. 2025
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
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“Conserved elements as estimated by phastCons [32] represent regions of the genome with average substitution rates much lower than the neutral rate.”
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Progressive Cactus is a multiple-genome aligner for the thousand-genome era
Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2871-y · Cited by 586
Forces shaping the fastest evolving regions in the human genome
Pollard, K. S., Salama, S. R., King, B., Kern, A. D., Dreszer, T., Katzman, S., Siepel, A., Pedersen, J. S., Bejerano, G., Baertsch, R., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020168 · Cited by 511
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers
de Almeida, B. P., Reiter, F., Pagani, M., & Stark, A. (2021) · doi:10.1101/2021.10.05.463203 · Cited by 284
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Integrating gene annotation with orthology inference at scale
Kirilenko, B. M., Munegowda, C., Osipova, E., Jebb, D., Sharma, V., Blumer, M., Morales, A. E., Ahmed, A.-W., Kontopoulos, D.-G., Hilgers, L., et al. (2023) · Science · doi:10.1126/science.abn3107 · Cited by 209
Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees
Hu, Z., Sackton, T. B., Edwards, S. V., & Liu, J. S. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz049 · Cited by 69
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From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions
Macdonald, A. R., James, M. E., Mitchell, J. D., & Holland, B. R. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf150 · Cited by 5
Metadata
- Authors
- Shakya, S. B., Edwards, S. V., & Sackton, T. B.
- Venue
- BMC Biology
- Published
- 2025-02-21
- Volume
- 23
- Issue
- 1
- ISSN
- 1741-7007
- PMC
- PMC11846207
- Cited by
- 10
- References
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