The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
GWIPS-viz: development of a ribo-seq genome browser
Open accessAbstract
We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing.
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Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
<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
Mammalian microRNAs predominantly act to decrease target mRNA levels
Guo, H., Ingolia, N. T., Weissman, J. S., & Bartel, D. P. (2010) · Nature · doi:10.1038/nature09267 · Cited by 3,886
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853
Detection of nonneutral substitution rates on mammalian phylogenies
Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., & Siepel, A. (2010) · Genome Research · doi:10.1101/gr.097857.109 · Cited by 2,353
Ingolia, N. T., Lareau, L. F., & Weissman, J. S. (2011) · Cell · doi:10.1016/j.cell.2011.10.002 · Cited by 2,187
Saccharomyces Genome Database: the genomics resource of budding yeast
Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1029 · Cited by 1,796
A unifying model for mTORC1-mediated regulation of mRNA translation
Thoreen, C. C., Chantranupong, L., Keys, H. R., Wang, T., Gray, N. S., & Sabatini, D. M. (2012) · Nature · doi:10.1038/nature11083 · Cited by 1,477
Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists
Blankenberg, D., Kuster, G. V., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., & Taylor, J. (2010) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb1910s89 · Cited by 1,427
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Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma
Smith, C. C., Beckermann, K. E., Bortone, D. S., De Cubas, A. A., Bixby, L. M., Lee, S. J., Panda, A., Ganesan, S., Bhanot, G., Wallen, E. M., et al. (2018) · Journal of Clinical Investigation · doi:10.1172/jci121476 · Cited by 303
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The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals
Henriques, W. S., Young, J. M., Nemudryi, A., Nemudraia, A., Wiedenheft, B., & Malik, H. S. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae061 · Cited by 31
Metadata
- Authors
- Michel, A. M., Fox, G., M. Kiran, A., De Bo, C., O’Connor, P. B. F., Heaphy, S. M., Mullan, J. P. A., Donohue, C. A., Higgins, D. G., & Baranov, P. V.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-10-31
- Volume
- 42
- Issue
- D1
- Pages
- D859-D864
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2168138973
- Cited by
- 256
- References
- 41
- FWCI
- 4.84
- Type
- journal article
- Language
- en
- Open access
- gold
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- Michel, A. M., Fox, G., M. Kiran, A., De Bo, C., O’Connor, P. B. F., Heaphy, S. M., Mullan, J. P. A., Donohue, C. A., Higgins, D. G., & Baranov, P. V. (2014). GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Research. https://doi.org/10.1093/nar/gkt1035
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