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REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species

Langer, Björn E, Roscito, Juliana G, Hiller, Michael·2018·Molecular Biology and Evolution
DOI 10.1093/molbev/msy187PMC PMC6278867
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Crossref · 10.1093/molbev/msy187

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  • PhyloG2P studies have revealed genetic replication in noncoding regions when it was not found in coding regions.

    “Similarly, PhyloG2P studies have revealed the presence of genetic replication in noncoding regions when it was not found in coding regions (Langer et al. 2018; Feigin et al. 2019; Thomas et al. 2024; Shakya et al. 2025).”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Langer et al. 2018

  • REforge performed better than rates-based methods at identifying regulatory elements associated with trait loss, but requires prior knowledge of transcription factors and their binding motifs.

    “REforge was demonstrated to perform better at identifying regulatory elements associated with trait loss than methods based on evolutionary rates. However, it also requires prior knowledge of transcription factors and their binding motifs, which makes it challenging to apply REforge to traits that have not been studied previously.”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Langer et al. 2018

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Metadata

Authors
Langer, B. E., Roscito, J. G., & Hiller, M.
Affiliations
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2018-09-26
ISSN
  • 0737-4038
  • 1537-1719
DOI
10.1093/molbev/msy187
PMC
PMC6278867
Cited by
8
References
8
Language
en
Licence
academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (am)

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