ArticleMolecular systems biology2011
Inferring regulatory mechanisms from patterns of evolutionary divergence.
Article in Molecular systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP).BMC bioinformatics · 2022Pooled it
- Interspecific hybridization as a driver of fungal evolution and adaptation.Nature reviews. Microbiology · 2021Review
- Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid.Molecular biology and evolution · 2021Article
- Protein Complexes Form a Basis for Complex Hybrid Incompatibility.Frontiers in genetics · 2021Review
- Dissecting the Heterogeneous Population Genetic Structure ofFrontiers in microbiology · 2019Article
- Evolution of gene regulation during transcription and translation.Genome biology and evolution · 2015Article
- Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.PLoS computational biology · 2014Article
- Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes.PLoS genetics · 2014Article
- Evolution at two levels of gene expression in yeast.Genome research · 2014Article
- Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes.BMC genomics · 2013Article
- Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress.Frontiers in plant science · 2013Article
- Article
- Functional primate genomics--leveraging the medical potential.Journal of molecular medicine (Berlin, Germany) · 2012Review
- An allele of an ancestral transcription factor dependent on a horizontally acquired gene product.PLoS genetics · 2012Article
- Comparative interaction networks: bridging genotype to phenotype.Advances in experimental medicine and biology · 2012Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The number of sequenced species is increasing at a staggering rate, calling for new approaches for incorporating evolutionary information in the study of biological mechanisms. Evolutionary conservation is widely used for assigning a function to new proteins and for predicting functional coding or non-coding sequences. Here, we argue for a complementary approach that focuses on the divergence of regulatory programs. Regulatory mechanisms can be learned from patterns of evolutionary divergence in regulatory properties such as gene expression, transcription factor binding or nucleosome positioning. We review examples of this concept using yeast as a model system, and highlight a hybrid-based approach that is highly instrumental in this analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.