ArticleGenome biology2005
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.
Article in Genome biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 1 of them a synthesis that pooled it.
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Who cites it
78 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.BMC bioinformatics · 2006Pooled it
- Species-aware DNA language models capture regulatory elements and their evolution.Genome biology · 2024Article
- Reb1, Cbf1, and Pho4 Bias Histone Sliding and Deposition Away from Their Binding Sites.Molecular and cellular biology · 2022Article
- Deep Conservation ofThe Plant cell · 2019Article
- Genome-wide discovery of active regulatory elements and transcription factor footprints inGenome research · 2017Article
- Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization.BMC systems biology · 2017Article
- BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.Bioinformatics (Oxford, England) · 2015Article
- Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation.Genome research · 2015Article
- Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.Bioinformatics (Oxford, England) · 2015Article
- Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets.PLoS biology · 2015Article
- Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions.Genes & development · 2014Article
- Robust k-mer frequency estimation using gapped k-mers.Journal of mathematical biology · 2014Article
- iRegulon: from a gene list to a gene regulatory network using large motif and track collections.PLoS computational biology · 2014Article
- Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.Genome research · 2014Article
- Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes.PLoS genetics · 2014Article
- TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets.Genetics · 2014Article
- Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts.Cell reports · 2014Article
- Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization.Genome biology · 2013Article
- Spatial promoter recognition signatures may enhance transcription factor specificity in yeast.PloS one · 2013Article
- Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics.Plant physiology · 2012Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We describe a powerful new approach for discovering globally conserved regulatory elements between two genomes. The method is fast, simple and comprehensive, without requiring alignments. Its application to pairs of yeasts, worms, flies and mammals yields a large number of known and novel putative regulatory elements. Many of these are validated by independent biological observations, have spatial and/or orientation biases, are co-conserved with other elements and show surprising conservation across large phylogenetic distances.
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