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Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data
2014
BMC Bioinformatics
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(nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. ...
a proteome-wide variation effect analysis tool (SNVDis). ...
Acknowledgements We want to thank P Satti and JH Yu for help with database and interface development. We thank the TCGA tumor-specific groups for providing the data. ...
doi:10.1186/1471-2105-15-28
pmid:24467687
pmcid:PMC3916084
fatcat:b2o3s5grcrf6hi6xkm2j64un6m
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)
2014
Database: The Journal of Biological Databases and Curation
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Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. ...
This information along with variationrelated annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations ...
Shanker for performing preliminary analysis that shows the feasibility of using literature mining methods to identify variations. We thank the TCGA tumor-specific groups for providing the data. ...
doi:10.1093/database/bau022
pmid:24667251
pmcid:PMC3965850
fatcat:cob43ptnp5hgnfmouec26ozvp4
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
2014
Genes
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In addition to tools, HIVE also provides knowledgebases that can be used in conjunction with the tools for NGS sequence and metadata analysis. ...
The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. ...
Acknowledgements We would like to acknowledge the following people for providing feedback and HIVE support: ...
doi:10.3390/genes5040957
pmid:25271953
pmcid:PMC4276921
fatcat:fpkwi7qj6bhkxp6y3k2nxv2lre
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis
2015
Database: The Journal of Biological Databases and Curation
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In addition to data directly retrieved from RNA-seq data repositories, manual biocuration of publications supplements the available cancer association annotations in the database. ...
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. ...
Torcivia and K. Smith for useful comments.
Funding This project was partially funded by NCI/EDRN Associate Member contract #156620. Funding open access charge: RM research funds. ...
doi:10.1093/database/bav019
pmid:25819073
pmcid:PMC4377087
fatcat:icbyogkhkrecjozhrwd5iy2qy4
The Sentinel Initiative as a Knowledge Commons
[chapter]
Governing Medical Knowledge Commons
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prioritizing traditional intellectual property rights; and third, knowledge commons can succeed in the critical fields of medicine and health. ...
The editors' knowledge commons framework adapts Elinor Ostrom's groundbreaking research on natural resource commons to the distinctive attributes of knowledge and information, providing a systematic means ...
Interestingly, in a system built on openness and designed to avoid intellectual property claims, this centralized structure establishes something of a proprietary interest in the data on the part of the ...
doi:10.1017/9781316544587.007
fatcat:lefya2gjp5hwnfdvl4fnjqdrvq
Inducing and suppressing the alternative lengthening of telomeres mechanism in cancer cells
2018
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nducing )nd suppressing .he )0.ern).ive 0eng.hening of .e0omeres mech)nism in c)ncer ce00s Referees: ...
In another example, a correlation was performed with data from the TCGA data set. In the TCGA pan- for either telomere lengths as well as log2 of gene expression data. ...
S2 TelNet genes from TCGA data analysis.Suppl. table S2. TelNet genes from TCGA data analysis. ...
doi:10.11588/heidok.00025661
fatcat:3lkv7qiddffnbmqfa5sjbypduq