A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Filters
The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments
[article]
2011
arXiv
pre-print
Preserved Fulltext
need for a database to enable sharing, visualization, and meta-analyses of these data. ...
We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely ...
Acknowledgements and Funding We thank the authors of RNAstructure, ViennaRNA, VARNA, and the Stanford Visualization Team for making their source code freely available. We also thank R. ...
arXiv:1110.0235v1
fatcat:bir5gpfpfrcnjoz7gblzrd4ndy
An RNA Mapping DataBase for curating RNA structure mapping experiments
2012
Computer applications in the biosciences : CABIOS
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2013; you can also visit the original URL.
The file type is application/pdf.
for sharing, visualization, search and meta-analysis. ...
We have established an RNA mapping database (RMDB) to enable structural, thermodynamic and kinetic comparisons across single-nucleotide-resolution RNA structure mapping experiments. ...
ACKNOWLEDGEMENTS We thank the authors of RNAstructure, VARNA and the Stanford Visualization Team for making their source code freely available, the Laederach laboratory for aid with SNRNASM integration ...
doi:10.1093/bioinformatics/bts554
pmid:22976082
pmcid:PMC3496344
fatcat:fu26yxe7h5ef3namgo3fldkc2q
Sharing and archiving nucleic acid structure mapping data
2011
RNA: A publication of the RNA Society
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Supplemental http://rnajournal.cshlp.org/content/suppl/2011/05/13/rna.2753211.DC1.html References http://rnajournal.cshlp.org/content/17/7/1204.full.html#related-urls Article cited in: http://rnajournal.cshlp.org ...
At present, there is currently no standard database for archiving and sharing nucleic acid structure mapping data, despite the compelling opportunities to incorporate such data in studies with direct relevance ...
We used a tool to project structure mapping data on an RNA secondary structure diagram provided with the SAFA software (Das et al. 2005) to visualize the DMS data from these experiments on two-dimensional ...
doi:10.1261/rna.2753211
pmid:21610212
pmcid:PMC3138558
fatcat:fbs2tdppyvgornwjwwqx7rd2jy
RNA structure inference through chemical mapping after accidental or intentional mutations
2017
Proceedings of the National Academy of Sciences of the United States of America
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The data were displayed in a 2D heatmap visualization analogous to that used for prior mutate-and-map experiments: a 1D chemical-mapping profile was estimated for each single-nucleotide variant in the ...
To understand whether M2-seq signals could be enhanced for the GIR1 ribozyme and other RNAs, we carried out extensive experiments to understand the mechanism for the signal in the P4-P6 RNA, varying transcription ...
The data were displayed in a 2D heatmap visualization analogous to that used for prior mutate-and-map experiments: a 1D chemical-mapping profile was estimated for each single-nucleotide variant in the ...
doi:10.1073/pnas.1619897114
pmid:28851837
pmcid:PMC5603990
fatcat:jgtlwjcvsjab7mi4tqzf6jz3ey
Web-Based Arabidopsis Functional and Structural Genomics Resources
2008
The Arabidopsis Book
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
ACKNOWLEDGMENTS The Chloroplast 2010 Project was supported by the National Science Foundation (grant no. MCB-0519740). ...
One useful feature is that users can visualize protein gel images for the proteome experiments. ...
After clicking the 'submit' button, a new window opens up, showing a list of miRNA candidates with miRNA precursor candidates and RNA fold structures, which is unique for this database. ...
doi:10.1199/tab.0118
pmid:22303243
pmcid:PMC3243351
fatcat:swsrfjpxszaobflnda7udjizwa
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review
2021
Biomolecules
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between ...
To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability ...
RNA network structures are presented as interactive graphs, where nodes depict the basic secondary structure of motifs and edges represent either shared bases or tertiary interactions. ...
doi:10.3390/biom11081245
pmid:34439912
pmcid:PMC8391349
fatcat:32aums2jtbc5vdcdknzfczajsy
Correcting a SHAPE-directed RNA structure by a mutate-map-rescue approach
[article]
2014
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
These results correct an erroneous SHAPE inference of a ribosomal conformational change and suggest a general mutate-map-rescue approach for dissecting RNA dynamic structure landscapes. ...
Computational support estimates, data from alternative chemical probes, and mutate-and-map (M2) experiments expose limitations of prior methodology and instead give a near-crystallographic secondary structure ...
Data Reposition All chemical mapping datasets, including one-dimensional mapping, mutate-and-map, and mutation/rescue, have been deposited at the RNA Mapping Database (http://rmdb.stanford.edu) (Cordero ...
doi:10.1101/001966
fatcat:yojo5r7iw5ckbfka7l324peiwq
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
2011
PLoS Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Data and derived results are made available through a freely accessible database. ...
The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and ...
Wexler and Julia Zhang at the National Human Genome Research Institute for their support in administering the ENCODE Consortium, additional members of our laboratories and institutions who have contributed ...
doi:10.1371/journal.pbio.1001046
pmid:21526222
pmcid:PMC3079585
fatcat:cfshtutffzhfvdqgwnda2sxlym
The changing mouse embryo transcriptome at whole tissue and single-cell resolution
2020
Nature
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular ...
The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif ...
Sample size Two bioreplicates are the ENCODE standard sampling, supporting IDR for companion chromatin data. The bulk RNA-Seq libraries match the chromatin samples. ...
doi:10.1038/s41586-020-2536-x
pmid:32728245
pmcid:PMC7410830
fatcat:luwwbtcvwjhmxkltuoraiq2fte
eXframe: reusable framework for storage, analysis and visualization of genomics experiments
2011
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration ...
Results: We have developed eXframe -a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple ...
Acknowledgements We would like to acknowledge the Harvard Stem Cell Institute (HSCI) for funding and support. We thank Dr. Daniel Tenen, Dr. David Scadden, Dr. Len Zon, Dr. Stuart Orkin and Dr. ...
doi:10.1186/1471-2105-12-452
pmid:22103807
pmcid:PMC3235155
fatcat:w4xj72om4rcttnhrnxzbxkwyze
High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states
2014
RNA: A publication of the RNA Society
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Other Versions
Computational support estimates, data from alternative chemical probes, and mutate-and-map (M(2)) experiments highlight issues of prior methodology and instead give a near-crystallographic secondary structure ...
These results correct an erroneous SHAPE inference of a ribosomal conformational change, expose critical limitations of conventional structure mapping methods, and illustrate practical steps for more incisively ...
ACKNOWLEDGMENTS We acknowledge financial support from a Stanford Graduate Fellowship (S.T.), a Conacyt fellowship (P.C.), the Burroughs Wellcome Foundation (CASI to R.D.), and NIH R01 R01GM102519. ...
doi:10.1261/rna.044321.114
pmid:25183835
pmcid:PMC4201832
fatcat:xxbufh5ywjftbgdosb3l4lujky
The UCSC Genome Browser Database: 2008 update
2007
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line ...
This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for ...
and sharing (40) . ...
doi:10.1093/nar/gkm966
pmid:18086701
pmcid:PMC2238835
fatcat:zdlffcr2vvhpdhn5epwzsneyky
OUP accepted manuscript
2016
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line ...
This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for ...
and sharing (40) . ...
doi:10.1093/nar/gkw1134
pmid:27899642
pmcid:PMC5210591
fatcat:h6hqicfojzaifoxt3ndyhoy5pi
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
2008
PLoS Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2011; you can also visit the original URL.
The file type is application/pdf.
To test this hypothesis and to extend and deepen our understanding of RBP-RNA interactions, we systematically searched for the RNA targets of a select sample of 40 out of the more than 500 known and predicted ...
Steps in RNA processing in the nucleus are functionally and physically coupled, providing an opportunity for coordinated control [23] . ...
We thank Maitreya Dunham, Donna Storton, Joseph DeRisi, and Adam Carroll and members of the Brown and Herschlag labs for advice and discussions. ...
doi:10.1371/journal.pbio.0060255
pmid:18959479
pmcid:PMC2573929
fatcat:zwfe46biinbc5eoig5fxrlauli
The Immunological Genome Project: networks of gene expression in immune cells
2008
Nature Immunology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
ACKNOWLEDGMENTS We thank eBiosciences, Affymetrix and Expression Analysis for participation and support. ...
Supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (R24 AI072073 to C.B.). ...
)
RNA
Cells
'Metadata'
Graphic
structures
Computational
biologists
BU
Stanford
Scientific
visualization
Immunologists
Raw data
'Clean' data
Data analysis
Biological curation ...
doi:10.1038/ni1008-1091
pmid:18800157
fatcat:hbupcrf43fb2pkckqovq5eugxi
« Previous
Showing results 1 — 15 out of 3,195 results