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Bioinformatics Projects

As part of providing infrastructure and analysis support to the NCI/NIH community the Advanced Biomedical Computing Center has developed several projects of broad use. The projects were initiated both as part of developing its internal infrastructure and in collaboration with several institutions.

bioDBnet – the biological DataBase network

Image showing the network of databases integrated in bioDBnet

bioDBnet

bioDBnet was developed as an internal project at ABCC where the goal was to integrate all the biological information stored in our internal data warehouse. Researchers can use bioDBnet, through an easy to use web interface, with diverse types of biological identifiers and run identifier conversions, orthology conversions or get extensive annotation reports.
URL: http://biodbnet.abcc.ncifcrf.gov

Publication(s)

Mudunuri U, Che A, Yi M, and Stephens RM. bioDBnet: the biological database network. Bioinformatics 25(4):555-6 2009. (PMID: 19129209)

BotDB – a database resource for clostridial neurotoxins

Image of the front page of the BotDB website

BotDB

BotDB was developed in collaboration with the USAMRIID. BotDB is a database designed to serve as a comprehensive resource of data for botulinum research, BotDB offers several features to aid in the research efforts of understanding the toxicity and finding ways to counteract the toxic effects of clostridial neurotoxins.
URL: http://botdb.abcc.ncifcrf.gov

Publication(s)

Mudunuri U, Stephens R, Bruining D, Liu D, Lebeda FJ. botXminer: mining biomedical literature with a new web-based application. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W748-52. (PMID: 16845112)

Cer RZ, Mudunuri U, Stephens R, Lebeda FJ. IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W441-5. (PMID: 19395593)

Lebeda FJ, Cer RZ, Stephens RM, Mudunuri U. Temporal characteristics of botulinum neurotoxin therapy. Expert Rev Neurother. 2010 Jan;10(1):93-103. (PMID: 20021324)

In Silico Research Center for Excellence (ISRCE)

Image showing the non-B annotations in nonb.abcc website

ISRCE: non-B

The Advanced Biomedical Computing Center recently received funding for a new initiative that aims to identify, classify, and correlate genomic non-B DNA?forming regions with respect to their involvement in forming chromosomal breakpoints and other processes leading to cancer.
URL: http://nonb.abcc.ncifcrf.gov

Publication(s)

Cer RZ, Bruce KH, Mudunuri US, Yi M, Volfovsky N, Luke BT, Bacolla A, Collins JR, Stephens RM. Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes. Nucleic Acids Res. 2010 Nov 21. (PMID: 21097885)

medXminer

Image of an author's network in medXminer

medXminer

medXminer is an application developed by mining the complete MEDLINE. Currently more than 19million articles along with abstracts are stored in an Oracle XMLDB instance. The applications allows queries like multiple search terms, grouping artcles by authors, MeSH terms, which are not feasible through PubMed. A subset of MEDLINE containing all botulinum related articles is made available through botXminer, developed for our BotDB project
URL: http://botdb.abcc.ncifcrf.gov/botXminer

Military Systems Biology Data Cube

SysBioCube

We recently initiated working on a Systems Biology project in collaboration with the USACEHR. The project involves development of an integrated data warehouse and analysis system. This database will contain different types of experimental, high-throughput and clinical data related to the syndromes and disorders of military relevance.
URL: /dsitp/abcc/abcc-groups/bioinformatics/projects/sysbiocube/

Identification of novel MicroRNAs in a genomically unstable region of 8q24

Novel miRNA in 8q24

Novel miRNA in 8q24

The PVT1 locus is identified as a cluster of T(2;8) and T(8;22) “variant” MYC-activating chromosomal translocation breakpoints extending 400 kb downstream of MYC in a subset (approximately 20%) of Burkitt’s lymphoma (vBL). Recent reports that microRNAs (miRNA) may be associated with fragile sites and cancer-associated genomic regions prompted us to investigate whether the PVT1 region on chromosome 8q24 may contain novel miRNAs. Computational method was developed and applied to the genomic sequence covering the PVT1 locus.There were computationally identified and experimental verified seven new miRNAs. High levels of expression of the one of them, hsa-miR-1204, in several epithelial cancer cell lines with MYC/PVT1 co-amplification, suggesting a potentially broad role for these miRNAs in tumorigenesis.

Publication(s)

Huppi K., Volfovsky N., Runfola T., Jones T.L., Mackiewicz M., Martin S.E., Mushinski J.F., Stephens R.M., and Caplen N.J.(2008). The Identification of Novel MicroRNAs in a Genomically Unstable Region of Human Chromosome 8q24 . Mol Cancer Res. 6(2):212-21

WPS: WholePathwayScope

Image of Whole Pathway Scope (WPS)

WPS

WPS is a pathway-based platform for discovery integration to maximize analysis power. It was initially developed, in collaboration with University of Texas Southwestern Medical Center, to provide pathway level visualization and analysis for high throuput data. Recently two new modules were added to provide sample-level enrichment-based pathway ranking (SLEPR) and pathway pattern extraction pipeline (PPEP)
URL: http://www.abcc.ncifcrf.gov/wps/wps_index.php

Publication(s)

Yi M, Horton JD, Cohen JC, Hobbs HH, Stephens RM. WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data. BMC Bioinformatics. 2006 Jan 19;7:30. (PMID: 16423281)

Yi M, and Stephens RM. SLEPR: a sample-level enrichment-based pathway ranking method — seeking biological themes through pathway-level consistency. PLoS One. 3(9):e3288, 2008. (PMID: 18818771)

Yi M, Mudunuri U, Che A, and Stephens RM. Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis. BMC Bioinformatics 10:200, 2009. (PMID: 19563622)