Journal: BioData Mining

Article Title: Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms

doi: 10.1186/1756-0381-2-2

Figure Lengend Snippet: Schematic of flanking regions in 3' and 5' direction . Each position in the NCBI dataset was evaluated with regard to nucleotide identity, and by nucleotide and also purine/pyrimidine identity in the Broad Institute dataset.

Article Snippet: The NCBI dataset allowed us to confirm, expand, and refine the results from the Broad Institute based pilot study.

Techniques:

Journal: BioData Mining

Article Title: Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms

doi: 10.1186/1756-0381-2-2

Figure Lengend Snippet: NCBI Dataset Distributions

Article Snippet: The NCBI dataset allowed us to confirm, expand, and refine the results from the Broad Institute based pilot study.

Techniques:

Journal: BioData Mining

Article Title: Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms

doi: 10.1186/1756-0381-2-2

Figure Lengend Snippet: NCBI Dataset Motifs

Article Snippet: The NCBI dataset allowed us to confirm, expand, and refine the results from the Broad Institute based pilot study.

Techniques:

Journal: Nucleic Acids Research

Article Title: NCBI Epigenomics: a new public resource for exploring epigenomic data sets

doi: 10.1093/nar/gkq1146

Figure Lengend Snippet: Visualization of epigenetic features in the vicinity of the NANOG gene locus using the NCBI sequence viewer. Epigenomic data tracks can be displayed allowing peaks at specific features to be visualized and compared across different samples. Epigenomic track data are displayed in the middle (blue) tracks. In this example, the track labels indicate we are comparing the epigenetic marks H3K4me3 and H3K27me3 at the NANOG gene locus in both H1 embryonic stem cells (top two tracks) and IMR90 fibroblasts (bottom two tracks). Peaks in the tracks indicate areas of the genome that are enriched for a particular epigenetic feature. The NANOG gene product participates in maintaining stem cell pluripotency. In H1 embryonic stem cells, where the NANOG gene is expressed, the genome tracks show an enrichment of H3K4me3 (a mark associated with actively transcribed genes), and a lack of H3K27me3 (a mark of repressed chromatin). Conversely, in IMR90 fibroblasts the NANOG gene is no longer expressed. In this instance, levels of H3K4me3 are reduced, and there is an enrichment of H3K27me3 at the NANOG locus.

Article Snippet: The Epigenomics website provides an easy way for users to visualize a chosen set of tracks using either the NCBI Sequence Viewer or the UCSC Genome Browser.

Techniques: Sequencing

Journal: Nucleic Acids Research

Article Title: The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

doi: 10.1093/nar/gkq1243

Figure Lengend Snippet: New molecular biology databases featured in the 2011 NAR Database Issue

Article Snippet: NCBI Epigenomics , http://www.ncbi.nlm.nih.gov/epigenomics/ , Genomic maps of nuclear changes that control gene expression.

Techniques: Functional Assay, Sequencing, Activity Assay, Alternative Splicing, Binding Assay, Selection, Cryo-Electron Microscopy, Protein-Protein interactions, Knock-Out, Expressing, Gene Expression, Control, Next-Generation Sequencing, DNA Methylation Assay, Membrane, Bacteria, Circular Dichroism, Modification, Mass Spectrometry, Phospho-proteomics