NHGRI/DIR Bioinformatics and Scientific Programming Core

NHGRI/DIR 生物信息学和科学编程核心

• 批准号: 8565616
• 负责人: Andreas Baxevanis
• 金额: $ 356.59万
• 依托单位: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
• 依托单位国家: 美国
• 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/8565616
• 关键词: Address; Alternative Splicing; Archives; Asthma; Behavioral; Binding Sites; Bioinformatics; Biological Markers; Bladder Neoplasm; Canis familiaris; Cataloging; Catalogs; ChIP-seq; Child; Chromatin; Clinical; Clinical Data; Communities; Complementary DNA; Computer Analysis; Computer software; DNA Binding; Data; Databases; Detection; Development; Diagnosis; Diet Habits; Disease; Exons; Gene Expression; Gene Expression Profile; Genes; Genome; Genomics; Genotype; Global Change; Goals; HIV-1; Hereditary Disease; Histocompatibility Testing; Histones; Knock-out; Lentivirus Vector; Lewy Body Disease; Linear Regressions; Location; Malignant Neoplasms; Maps; Mnemiopsis; Modeling; Mothers; Mus; Mutation; Mutation Detection; National Human Genome Research Institute; Nucleic Acid Regulatory Sequences; Oncogenes; Online Systems; Pathway interactions; Patients; Phenotype; Phylogenetic Analysis; Plant Genome; Progeria; Protein Isoforms; Proteins; Quality Control; RNA; RNA Interference; RNA analysis; Records; Research; Research Personnel; Research Support; Retrieval; Sampling; Sequence Analysis; Series; Site; Solutions; Somatic Mutation; Spliced Genes; Surveys; Techniques; Time; Transcript; Transcription factor genes; Tumor Cell Line; Tumor Subtype; Update; Variant; Weight; Weight maintenance regimen; Woman; Zebrafish; base; computerized tools; genetic pedigree; glucosylceramidase; histone modification; innovation; invertebrate genome; malignant breast neoplasm; programs; thymocyte; transcription factor; tumor; vertebrate genome; web site; wiki

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

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。 2011-2012年完成的科学项目包括：重新设计组蛋白序列数据库;开发一个网站和血液学重要突变数据库;分析ChIP-seq数据，以评估早老症的染色质结构变化;利用自组织图谱和线性回归建模，确定随着哮喘程度不同而变化的基因;应用转录因子结合位点分析和系统发育足迹法预测斑马鱼基因调控区，研究环糊精对尼曼匹克病（NPC）基因表达的影响;开发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）;以及确定新的基于HIV 1的慢病毒载体的整合概况。 正在进行的科学项目包括使用NextGen序列数据注释Mnemiopsis基因组;为Mnemiopsis基因组数据和注释开发网站，基因组浏览器和Wiki;通过RNA-seq检测Mnemiopsis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假定癌基因的突变;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，并识别ENSEMBL注释基因内发生的整合;开发网站和数据库以搜索整合位点;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RNA-seq数据以检测由于RRP 1B敲低引起的基因表达和剪接的总体变化;通过ChIP-seq鉴定RRP 1B的DNA结合位点;确定RRP 1B敲低对基因表达的影响;将转录因子映射和注释到实验和预测的转录因子结合位点;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;分析ChIP-seq数据以鉴定狗膀胱肿瘤细胞系中特定组蛋白修饰的基因组位置;用于RNA-seq的基因组引导、从头开始和从头转录组装;开展一项基于网络的调查，研究女性对医生与患者谈论体重的技巧的看法（体重管理相互作用研究）;鉴定共变突变和途径以分类肿瘤亚型;通过将实验室产生的基因型与COSMIC中的基因型合并，癌症体细胞突变目录质量控制和随后从HGVS格式的cDNA和蛋白质突变中检索基因组坐标; Itk缺陷小鼠胸腺细胞中基因调控区的预测;多中心调查数据的整理，以研究葡萄糖脑苷脂酶突变和路易体痴呆之间的关联;从RNAi筛选中选择靶点的生物标志物; RNA-seq数据的分析，以鉴定由于敲除Hippo通路而引起的基因表达和剪接的全转录组变化;以及分析序列痕迹以检测斑马鱼TILLING项目的突变