NHGRI/DIR Bioinformatics and Scientific Programming Core

NHGRI生物信息学和科学编程核心通过提供生物信息学和计算分析方面的专业知识和帮助，积极支持NHGRI研究人员正在进行的研究。核心促进获得专业的软件和硬件，开发通用的软件解决方案，可以解决基因组研究中的各种问题，开发数据库解决方案，用于有效存档和检索实验和临床数据，向基因组社区传播新的软件和数据库解决方案。并为NHGRI研究人员和受训人员提供生物信息学方面的教育机会。 2010-2011年完成的科学项目包括开发基于网络的产前调查;将传统的基于纸张的调查技术改造为基于网络的部署;计算各种基因组分区中的核苷酸数量（例如，基因内、上游或外显子）;从CFTR UTR到人类基因组的22聚体的映射，允许错配; ChIP-seq数据的分析以比较正常和MMS诱导的DNA损伤样品;用于数据重新格式化的各种Perl脚本的开发;色素细胞基因的信息网站的开发;以及在选定条件下起作用的转录因子的推定结合位点的注释。 正在进行的科学项目包括重新设计组蛋白序列数据库;使用NextGen序列数据注释拟记忆体基因组;通过RNASeq检测拟记忆体早期发育过程中的基因和同种型表达变化;分析序列痕迹以检测肿瘤样本中推定致癌基因的突变;开发血液学重要突变的网站和数据库;脊椎动物、无脊椎动物和植物基因组中大外显子的表征;乳腺癌信息核心（BIC）的持续更新和改进;使用Illumina序列标签绘制斑马鱼逆转录病毒整合位点的生物信息学管道的开发;分析ChIP-seq数据以评估早老症中的染色质结构变化;使用自组织图谱和线性回归建模识别随着不同程度的哮喘而变化的基因;分析随时间推移在选择的组织类型中的可变剪接基因;分析RNASeq数据以检测由于RRP 1B敲低引起的基因表达和剪接的全局变化;通过ChIP-seq鉴定RRP 1B的DNA结合位点;通过转录因子结合位点分析和系统发育足迹法预测选定斑马鱼基因中的基因调控区;通过ChIP-seq和RNA-seq发现和鉴定黑素细胞中的活性增强子;开发定制的SQL数据库，用于存储和计算犬基因型、表型、序列、变异、样本数据和谱系数据的大量记录;使用miRNA表达水平对转移性细胞系的亚型进行分类;开发一系列基于网络的调查，从母亲的角度研究儿童的饮食习惯（母亲的TAKE研究）;整理多中心调查数据，研究葡萄糖脑苷脂酶突变与路易体痴呆之间的关联; Itk缺陷小鼠胸腺细胞中基因调控区的预测;一种新的基于HIV 1的慢病毒载体的整合谱的测定;以及斑马鱼TILLING项目检测突变的序列痕迹分析。

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.