ArticleMolecular biology and evolution2016
"Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 64 citations in OpenAlex.
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc.Integrative and comparative biology · 2024Article
- A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution.PLoS computational biology · 2024Article
- Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages.Molecular biology and evolution · 2023Article
- PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance.Molecular biology and evolution · 2023Article
- Review
- Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages.bioRxiv : the preprint server for biology · 2023Article
- Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles.Animals : an open access journal from MDPI · 2023Review
- Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin.BMC genomics · 2022Article
- Alternative splicing level related to intron size and organism complexity.BMC genomics · 2021Article
- Bottleneck-associated changes in the genomic landscape of genetic diversity in wild lynx populations.Evolutionary applications · 2021Article
- Convergent evolution of a genomic rearrangement may explain cancer resistance in hystrico- and sciuromorpha rodents.NPJ aging and mechanisms of disease · 2021Article
- Genome-enabled discovery of evolutionary divergence in brains and behavior.Scientific reports · 2021Article
- A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals.Nucleic acids research · 2020Article
- Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD.PLoS genetics · 2020Article
- A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers.GigaScience · 2020Article
- A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Robust Method for Detecting Convergent Shifts in Evolutionary Rates.Molecular biology and evolution · 2019Article
- Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees.Molecular biology and evolution · 2019Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Evolutionary changes in cis-regulatory elements are thought to play a key role in morphological and physiological diversity across animals. Many conserved noncoding elements (CNEs) function as cis-regulatory elements, controlling gene expression levels in different biological contexts. However, determining specific associations between CNEs and related phenotypes is a challenging task. Here, we present a computational "reverse genomics" approach that predicts the phenotypic functions of human CNEs. We identify thousands of human CNEs that were lost in at least two independent mammalian lineages (IL-CNEs), and match their evolutionary profiles against a diverse set of phenotypes recently annotated across multiple mammalian species. We identify 2,759 compelling associations between human CNEs and a diverse set of mammalian phenotypes. We discuss multiple CNEs, including a predicted ear element near BMP7, a pelvic CNE in FBN1, a brain morphology element in UBE4B, and an aquatic adaptation forelimb CNE near EGR2, and provide a full list of our predictions. As more genomes are sequenced and more traits are annotated across species, we expect our method to facilitate the interpretation of noncoding mutations in human disease and expedite the discovery of individual CNEs that play key roles in human evolution and development.
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