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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

Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas S Almeida, William J Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, Raja Mazumder
2014 BMC Bioinformatics  
(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)

Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, Raja Mazumder
2014 Database: The Journal of Biological Databases and Curation  
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

Vahan Simonyan, Raja Mazumder
2014 Genes  
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

Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Cheng Yan, Haichen Zhang, Raja Mazumder
2015 Database: The Journal of Biological Databases and Curation  
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]

Ryan Abbott, Katherine J. Strandburg, Brett M. Frischmann, Michael J. Madison
Governing Medical Knowledge Commons  
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

Delia Braun
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