The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
Open accessAbstract
With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have arisen. However, novel tools and strategies are required to accommodate this large volume of genomic information and to facilitate the transfer of predictions generated by comparative sequence alignment to researchers focused on experimental annotation of genome function. Here, we present the ECR Browser, a tool that provides easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences. This web-based tool (http://ecrbrowser.dcode.org) provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignments of any user-submitted sequence to the genome of choice. The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.
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“Using the Evolutionarily Conserved Regions browser (35), we found that the miR-146a promoter contains two evolutionarily conserved regions, ECR1 and ECR2.”
From The DNA damage response induces inflammation and senescence by inhibiting autophagy of GATA4. (2015) · cites this paper as [35]
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
The UCSC Genome Browser Database
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg129 · Cited by 1,890
The Ensembl genome database project
Hubbard, T. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.38 · Cited by 1,610
Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes
Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.-M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. (2002) · Science · doi:10.1126/science.1072104 · Cited by 1,591
Human–Mouse Alignments with BLASTZPreprint
Schwartz, S., Kent, W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D. H., & Miller, W. (2002) · Genome Research · doi:10.1101/gr.809403 · Cited by 1,246
PipMaker—A Web Server for Aligning Two Genomic DNA SequencesPreprint
Schwartz, S., Zhang, Z., Frazer, K. A., Smit, A. F. A., Riemer, C., Bouck, J. B., Gibbs, R. A., Hardison, R. C., & Miller, W. (2000) · Genome Research · doi:10.1101/gr.10.4.577 · Cited by 1,165
Lettice, L. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg180 · Cited by 1,164
TRANSFAC: a database on transcription factors and their DNA binding sites
Wingender, E. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.1.238 · Cited by 1,064
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The DNA damage response induces inflammation and senescence by inhibiting autophagy of GATA4.
Kang, C., Xu, Q., Martin, T. D., Li, M. Z., Demaria, M., Aron, L., Lu, T., Yankner, B. A., Campisi, J., & Elledge, S. J. (2015) · Science · doi:10.1126/science.aaa5612 · Cited by 982
Regulation of the expression of inducible nitric oxide synthase
Pautz, A., Art, J., Hahn, S., Nowag, S., Voss, C., & Kleinert, H. (2010) · Nitric Oxide · doi:10.1016/j.niox.2010.04.007 · Cited by 549
Oshimori, N., & Fuchs, E. V. (2012) · Cell stem cell · doi:10.1016/j.stem.2011.11.005 · Cited by 394
Oct4 and LIF/Stat3 Additively Induce Krüppel Factors to Sustain Embryonic Stem Cell Self-Renewal
Hall, J., Guo, G., Wray, J. P., Eyres, I., Nichols, J., Grotewold, L., Morfopoulou, S., Humphreys, P. D., Mansfield, W. M., Walker, R. V., et al. (2009) · Cell stem cell · doi:10.1016/j.stem.2009.11.003 · Cited by 380
“species (Ovcharenko et al., 2004).”
Genome-wide scans for footprints of natural selection
Oleksyk, T. K., Smith, M. W., & O'Brien, S. J. (2010) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2009.0219 · Cited by 340
“Selection signatures can be observed by plotting the between-species divergence of homologous segments and comparing it with the genome-wide average: phylogenetic shadowing (Mayor et al. 2000; Ovcharenko et al. 2004).”
Background
Metadata
- Authors
- Ovcharenko, I., Nobrega, M. A., Loots, G. G., & Stubbs, L.
- Affiliations
- Lawrence Livermore National Laboratory (US)
- Corresponding author
- Ovcharenko, I.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-07-01
- Volume
- 32
- Issue
- Web Server
- Pages
- W280-W286
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC441493
- OpenAlex
- W1981101983
- Cited by
- 519
- References
- 32
- Citations by year
- 2026: 6 · 2025: 9 · 2024: 10 · 2023: 8 · 2022: 13 · 2021: 32 · 2020: 23 · 2019: 19 · 2018: 27 · 2017: 21 · 2016: 24 · 2015: 21 · 2014: 23 · 2013: 42 · 2012: 40
- FWCI
- 8.17
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (W-7405, -7405-ENG-48)
- Biological and Environmental Research
- Lawrence Livermore National Laboratory (W-7405-ENG 48, -7405-Eng-48)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- vertebrate genomes, gene discovery, gene regulatory elements, transcription factor binding site prediction, genome annotation
- MeSH terms
- Animals, Binding Sites, Computer Graphics, Fishes, Humans, Regulatory Sequences, Nucleic Acid, Software, Transcription Factors, Sequence Alignment, Genome, Sequence Analysis, DNA, Systems Integration, Internet, Genomics, Synteny, Mice, Rats
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