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 2010-2011 include the development of a Web-based prenatal survey;adaptation of traditional paper-based survey techniques for Web-based deployment;calculation of the number of nucleotides in various genome partitions (e.g., intragenic, upstream, or exonic);mapping of 22-mers from the CFTR UTRs to the human genome, allowing for mismatches;analysis of ChIP-seq data to compare normal and MMS-induced DNA damaged samples;development of various Perl scripts for data re-formatting;development of an informational Web site for pigment cell genes;and annotation of putative binding sites for transcription factors that function in selected conditions. Ongoing scientific projects include the redesign of the Histone Sequence Database;annotation of the Mnemiopsis genome using NextGen sequence data;detection of gene and isoform expression changes during early development in Mnemiopsis by RNASeq;analysis of sequence traces to detect mutations in putative oncogenes in tumor samples;development of a Web site and database of hematologically important mutations;characterization of large exons in vertebrate, invertebrate, and plant genomes;ongoing updates and improvements to the Breast Cancer Information Core (BIC);development of a bioinformatic pipeline to map zebrafish retroviral integration sites using Illumina sequence tags;analysis of ChIP-seq data to assess chromatin structural changes in progeria;identification of genes that change with differing degrees of asthma using self organizing maps and linear regression modeling;analysis of alternative spliced genes in select tissue types over time;analysis of RNASeq data to detect global changes in gene expression and splicing due to RRP1B knockdown;identification of DNA binding sites of RRP1B by ChIP-seq;prediction of gene regulatory regions in select zebrafish genes by transcription factor binding site analysis and phylogenetic footprinting;discovery and identification of active enhancers in melanocytes by ChIP-seq and RNA-seq;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;use of miRNA expression levels to classify subtypes of metastatic cell lines;development of a series of Web-based surveys studying a child's eating habits from the Mothers point of view (Mother's TAKE Study);collation of multi-center survey data to study association between glucocerebrosidase mutations and Lewy body dementia;prediction of gene regulatory regions in thymocytes of Itk deficient mice;determination of the integration profile of a new HIV1-based lentiviral vector;and analysis of sequence traces to detection mutations for the zebrafish TILLING project.

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Métais, J-Y; Topp, S; Doty, R T et al. (2010) Feline leukemia virus integrase and capsid packaging functions do not change the insertion profile of standard Moloney retroviral vectors. Gene Ther 17:799-804
Winkler, Thomas; Cantilena, Amy; Métais, Jean-Yves et al. (2010) No evidence for clonal selection due to lentiviral integration sites in human induced pluripotent stem cells. Stem Cells 28:687-94
Kim, Yoo-Jin; Kim, Yoon-Sang; Larochelle, Andre et al. (2009) Sustained high-level polyclonal hematopoietic marking and transgene expression 4 years after autologous transplantation of rhesus macaques with SIV lentiviral vector-transduced CD34+ cells. Blood 113:5434-43
Sotiriou, Sotiria; Gibney, Gretchen; Baxevanis, Andreas D et al. (2009) A single nucleotide polymorphism in the 3'UTR of the SNCA gene encoding alpha-synuclein is a new potential susceptibility locus for Parkinson disease. Neurosci Lett 461:196-201
Toleno, Donna M; Renaud, Gabriel; Wolfsberg, Tyra G et al. (2009) Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees. BMC Bioinformatics 10:77
Scharschmidt, Tiffany C; List, Karin; Grice, Elizabeth A et al. (2009) Matriptase-deficient mice exhibit ichthyotic skin with a selective shift in skin microbiota. J Invest Dermatol 129:2435-42
Stanescu, Horia; Wolfsberg, Tyra G; Moreland, R Travis et al. (2009) Identifying putative promoter regions of Hermansky-Pudlak syndrome genes by means of phylogenetic footprinting. Ann Hum Genet 73:422-8
Vithayathil, J; Gibney, G; Baxevanis, A D et al. (2009) Glucocerebrosidase mutation H255Q appears to be exclusively in cis with D409H: structural implications. Clin Genet 75:503-4
Loftus, Stacie K; Antonellis, Anthony; Matera, Ivana et al. (2009) Gpnmb is a melanoblast-expressed, MITF-dependent gene. Pigment Cell Melanoma Res 22:99-110
Sidransky, E; Nalls, M A; Aasly, J O et al. (2009) Multicenter analysis of glucocerebrosidase mutations in Parkinson's disease. N Engl J Med 361:1651-61

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