Ancient noncoding elements conserved in the human genome.

PubWeight™: 1.53‹?› | Rank: Top 4%

🔗 View Article (PMID 17185593)

Published in Science on December 22, 2006

Authors

Byrappa Venkatesh1, Ewen F Kirkness, Yong-Hwee Loh, Aaron L Halpern, Alison P Lee, Justin Johnson, Nidhi Dandona, Lakshmi D Viswanathan, Alice Tay, J Craig Venter, Robert L Strausberg, Sydney Brenner

Author Affiliations

1: Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673. mcbbv@imcb.a-star.edu.sg

Articles citing this

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A (2007) 4.11

Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol (2007) 2.90

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet (2013) 2.76

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res (2007) 2.27

Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence. PLoS Genet (2008) 1.59

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol (2008) 1.46

CONDOR: a database resource of developmentally associated conserved non-coding elements. BMC Dev Biol (2007) 1.35

The role of genomic data in the discovery, annotation and evolutionary interpretation of the interferon-lambda family. PLoS One (2009) 1.34

Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genet (2009) 1.26

Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells. Genome Res (2008) 1.02

Sequence evaluation of FGF and FGFR gene conserved non-coding elements in non-syndromic cleft lip and palate cases. Am J Med Genet A (2007) 1.02

Blimp-1/Prdm1 alternative promoter usage during mouse development and plasma cell differentiation. Mol Cell Biol (2009) 1.00

Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster. Proc Natl Acad Sci U S A (2008) 0.99

Sequencing of Pax6 loci from the elephant shark reveals a family of Pax6 genes in vertebrate genomes, forged by ancient duplications and divergences. PLoS Genet (2013) 0.99

Conservation of human microsatellites across 450 million years of evolution. Genome Biol Evol (2010) 0.97

Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. BMC Genomics (2013) 0.97

Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biol (2007) 0.94

Identification and characterization of new long conserved noncoding sequences in vertebrates. Mamm Genome (2008) 0.93

Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor. Genome Biol Evol (2010) 0.91

Into the blue: gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii. Genome Res (2009) 0.90

Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole-genome duplication. Mol Biol Evol (2014) 0.86

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement. Genome Res (2012) 0.86

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression. BMC Genomics (2012) 0.86

Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers. BMC Genomics (2011) 0.85

Lens development depends on a pair of highly conserved Sox21 regulatory elements. Dev Biol (2012) 0.85

Functional conservation of a forebrain enhancer from the elephant shark (Callorhinchus milii ) in zebrafish and mice. BMC Evol Biol (2010) 0.84

Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period. Genome Res (2014) 0.82

Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish. PLoS Genet (2013) 0.81

Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position. Evodevo (2010) 0.81

Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics. PLoS One (2014) 0.81

Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout. BMC Genomics (2009) 0.79

Functional and comparative genomics analyses of pmp22 in medaka fish. BMC Neurosci (2009) 0.79

Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning. Genome Biol Evol (2014) 0.79

Embryonic development of glial cells and myelin in the shark, Chiloscyllium punctatum. Gene Expr Patterns (2009) 0.78

Binding site number variation and high-affinity binding consensus of Myb-SANT-like transcription factor Adf-1 in Drosophilidae. Nucleic Acids Res (2010) 0.78

Characterization of the heart transcriptome of the white shark (Carcharodon carcharias). BMC Genomics (2013) 0.78

Insights into the evolution of mammalian telomerase: platypus TERT shares similarities with genes of birds and other reptiles and localizes on sex chromosomes. BMC Genomics (2012) 0.78

Study of microRNAs related to the liver regeneration of the whitespotted bamboo shark, Chiloscyllium plagiosum. Biomed Res Int (2013) 0.78

Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa L.) paralogous regions. Mol Genet Genomics (2008) 0.77

Evolution of parathyroid hormone receptor family and their ligands in vertebrate. Front Endocrinol (Lausanne) (2015) 0.77

Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii). PLoS One (2012) 0.77

Correlation of microsynteny conservation and disease gene distribution in mammalian genomes. BMC Genomics (2009) 0.76

Runx family genes in a cartilaginous fish, the elephant shark (Callorhinchus milii). PLoS One (2014) 0.76

Evolution of Shh endoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder. Nat Commun (2017) 0.75

Methods and compositions for amplification and detection of microRNAs (miRNAs) and noncoding RNAs (ncRNAs) using the signature sequence amplification method (SSAM). Recent Adv DNA Gene Seq (2014) 0.75

Expansion by whole genome duplication and evolution of the sox gene family in teleost fish. PLoS One (2017) 0.75

Articles by these authors

An integrated genomic analysis of human glioblastoma multiforme. Science (2008) 51.36

Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23

The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80

Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89

Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58

Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods (2009) 22.47

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (2002) 20.59

The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21

Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99

Creation of a bacterial cell controlled by a chemically synthesized genome. Science (2010) 13.45

The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48

Aggressive assembly of pyrosequencing reads with mates. Bioinformatics (2008) 11.01

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science (2008) 10.90

Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol (2009) 9.59

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59

Somatic coding mutations in human induced pluripotent stem cells. Nature (2011) 9.50

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92

A catalog of reference genomes from the human microbiome. Science (2010) 8.10

Shotgun sequence assembly and recent segmental duplications within the human genome. Nature (2004) 7.91

Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17

A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A (2006) 7.17

Mobile elements create structural variation: analysis of a complete human genome. Genome Res (2009) 7.06

Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol (2002) 6.96

Genetic variation in an individual human exome. PLoS Genet (2008) 6.68

Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A (2006) 6.31

Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08

The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84

Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A (2003) 5.10

An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A (2002) 4.45

Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet (2007) 4.25

An agenda for personalized medicine. Nature (2009) 4.14

The dynamic genome of Hydra. Nature (2010) 4.00

Genome transplantation in bacteria: changing one species to another. Science (2007) 3.95

Mutation of GATA3 in human breast tumors. Oncogene (2004) 3.92

Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res (2002) 3.91

Structural and functional diversity of the microbial kinome. PLoS Biol (2007) 3.74

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature (2012) 3.74

The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A (2009) 3.72

Cell-free cloning using phi29 DNA polymerase. Proc Natl Acad Sci U S A (2005) 3.54

Plasmodium, human and Anopheles genomics and malaria. Nature (2002) 3.42

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res (2011) 3.36

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet (2008) 3.23

The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A (2002) 3.19

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (2010) 3.18

Human chromosome 7: DNA sequence and biology. Science (2003) 3.02

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J (2011) 2.97

Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature (2010) 2.93

The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS One (2008) 2.91

Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol (2007) 2.90

Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Res (2004) 2.85

One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci U S A (2008) 2.82

Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet (2007) 2.79

Medicine. The future of psychiatric research: genomes and neural circuits. Science (2010) 2.79

Towards a comprehensive structural variation map of an individual human genome. Genome Biol (2010) 2.79

The African coelacanth genome provides insights into tetrapod evolution. Nature (2013) 2.78

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A (2010) 2.76