The NHGRI Bioinformatics and Scientific Programming Core actively supports the research being performed by NHGRI investigators by providing expertise and assistance in bioinformatics and computational analysis. The Core facilitates access to specialized software and hardware, develops generalized software solutions that can address a variety of questions in genomic research, develops database solutions for the efficient archiving and retrieval of experimental and clinical data, disseminates new software and database solutions to the genome community at-large, collaborates with NHGRI researchers on computationally-intensive projects, and provides educational opportunities in bioinformatics to NHGRI Investigators and trainees. Scientific projects completed in 2011-2012 include the redesign of the Histone Sequence Database;the development of a Web site and database of hematologically important mutations;the analysis of ChIP-seq data to assess chromatin structural changes in progeria;the identification of genes that change with differing degrees of asthma using self organizing maps and linear regression modeling;the prediction of gene regulatory regions in select zebrafish genes by transcription factor binding site analysis and phylogenetic footprinting;the examination of the effects of cyclodextrane on gene expression in NiemannPick Disease (NPC);the development a series of Web-based surveys studying a child's eating habits from the mother's point of view (Mother's TAKE Study);and the determination of the integration profile of a new HIV1-based lentiviral vector. Ongoing scientific projects include the annotation of the Mnemiopsis genome using NextGen sequence data;the development of a Web site, genome browser, and Wiki for Mnemiopsis genome data and annotations;the detection of gene and isoform expression changes during early development in Mnemiopsis by RNA-seq;the analysis of sequence traces to detect mutations in putative oncogenes in tumor samples;the characterization of large exons in vertebrate, invertebrate, and plant genomes;ongoing updates and improvements to the Breast Cancer Information Core (BIC);the development of a bioinformatic pipeline to map zebrafish retroviral integration sites using Illumina sequence tags and to identify integrations occurring within ENSEMBL-annotated genes;the development of a Web site and database to search for the integration sites;the analysis of alternative spliced genes in select tissue types over time;the analysis of RNA-seq data to detect global changes in gene expression and splicing due to RRP1B knockdown;the identification of DNA binding sites of RRP1B by ChIP-seq;the determination of the effects of RRP1B knockdown on gene expression;the mapping and annotation of transcription factors to experimental and predicted transcription factor binding sites;the development of a customized SQL database for storing and computing on large numbers of records for canine genotypes, phenotypes, sequences, variations, sample data and pedigree data;the analysis of ChIP-seq data to identify the genomic locations of specific histone modifications in dog bladder tumor cell lines;genome-guided, ab initio, and de novo transcript assembly for RNA-seq;the development of a Web-based survey studying how women feel about the techniques doctors use to talk with patients about their weight (Weight Management Interaction Study);identification of co-varying mutations and pathways to classify subtypes of tumors;the creation of a comprehensive list of mutations by merging lab-generated genotypes with those in COSMIC (Catalogue Of Somatic Mutations In Cancer);quality control and subsequent retrieval of genomic coordinates from HGVS-formatted cDNA and protein mutations;the prediction of gene regulatory regions in thymocytes of Itk deficient mice;the collation of multi-center survey data to study association between glucocerebrosidase mutations and Lewy Body dementia;biomarker selection of targets from RNAi screens;the analysis of RNA-seq data to identify transcriptome-wide changes in gene expression and splicing due to the knockout of the Hippo pathway;and the analysis of sequence traces to detection mutations for the zebrafish TILLING project
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