NHGRI/DIR Bioinformatics and Scientific Programming Core

NHGRI/DIR 生物信息学和科学编程核心

基本信息

批准号：
8350237
负责人：
Andreas Baxevanis
金额：
$ 281.59万
依托单位：
NATIONAL HUMAN GENOME RESEARCH INSTITUTE
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/8350237
关键词：
Address Alternative Splicing Archives Asthma Behavioral Binding Sites Bioinformatics Canis familiaris Cell Line Cells Child Chromatin Clinical Clinical Data Communities Computer Analysis Computer software Cystic Fibrosis Transmembrane Conductance Regulator DNA Binding DNA Damage Data Databases Detection Development Diagnosis Diet Habits Enhancers Exons Gene Expression Genes Genome Genomics Genotype Global Change Goals HIV-1 Hereditary Disease Histocompatibility Testing Histones Human Genome Lentivirus Vector Lewy Body Disease Linear Regressions Maps MicroRNAs Mnemiopsis Modeling Mothers Mus Mutation Mutation Detection National Human Genome Research Institute Nucleic Acid Regulatory Sequences Nucleotides Oncogenes Online Systems Paper Phenotype Phylogenetic Analysis Pigments Plant Genome Progeria Protein Isoforms RNA Records Research Research Personnel Research Support Retrieval Sampling Sequence Analysis Series Site Solutions Spliced Genes Surveys Techniques Time Transcription factor genes Untranslated Regions Update Variant Zebrafish base computerized tools genetic pedigree glucosylceramidase innovation invertebrate genome malignant breast neoplasm melanocyte prenatal programs thymocyte transcription factor tumor vertebrate genome web site

项目摘要

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.

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。该核心促进对专用软件和硬件的访问，开发可以解决基因组研究中的各种问题的通用软件解决方案，开发用于实验和临床数据高效归档和检索的数据库解决方案，向基因组社区传播新的软件和数据库解决方案与 NHGRI 研究人员合作开展计算密集型项目，并为 NHGRI 研究人员和学员提供生物信息学教育机会。 2010-2011 年完成的科学项目包括开发基于网络的产前调查；将传统的纸质调查技术改造为基于网络的部署；计算不同基因组分区（例如基因内、上游或外显子）中的核苷酸数量；将 22-mers 从 CFTR UTR 映射到人类基因组，允许错配；分析 ChIP-seq 数据以比较正常样品和 MMS 诱导的 DNA 损伤样品；开发用于数据重新格式化的各种 Perl 脚本；开发色素细胞基因信息网站；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 序列数据对 Mnemiopsis 基因组进行注释；通过 RNASeq 检测 Mnemiopsis 早期发育过程中基因和亚型表达的变化；分析序列轨迹以检测肿瘤样本中假定癌基因的突变；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；开发生物信息学管道，使用 Illumina 序列标签绘制斑马鱼逆转录病毒整合位点图；分析 ChIP-seq 数据以评估早衰症的染色质结构变化；使用自组织图和线性回归模型识别随不同程度的哮喘而变化的基因；随着时间的推移分析选定组织类型中的选择性剪接基因；分析 RNASeq 数据以检测 RRP1B 敲低导致的基因表达和剪接的全局变化；通过 ChIP-seq 鉴定 RRP1B 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预测选定斑马鱼基因中的基因调控区域；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，用于存储和计算大量犬基因型、表型、序列、变异、样本数据和谱系数据记录；使用 miRNA 表达水平对转移细胞系的亚型进行分类；开展一系列基于网络的调查，从母亲的角度研究孩子的饮食习惯（Mother's TAKE Study）；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缺陷小鼠胸腺细胞基因调控区的预测；确定新的基于 HIV1 的慢病毒载体的整合特征；斑马鱼 TILLING 项目的序列追踪分析以检测突变。