Center for Personal Dynamic Regulomes

个人动态调节中心

基本信息

批准号：
10705043
负责人：
Howard Y Chang
金额：
$ 264.19万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-09-01 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10705043
关键词：
Alleles Autoimmune Diseases Automobile Driving Binding Biological Biological Assay Biology Biopsy Biosensor Blood Brain CRISPR interference Cells Chromatin Chromosomes Clinic Clinical Communities Complex Coupled DNA DNA Sequence Data Data Set Dimensions Disease Distant Dreams Effectiveness Elements Encapsulated Encyclopedia of DNA Elements Engineering Enhancers Epigenetic Process Epithelium Epitopes Etiology Event Exercise Gene Expression Regulation Generations Genes Genetic Genetic Transcription Genetic Variation Genome Genomics Genotype Heterochromatin Human Human Genome Individual Intervention Investigation Knowledge Laboratories Lead Life Link Liquid substance Malignant Neoplasms Measurement Methods Modeling Modification Molecular Molecular Conformation Multiomic Data Neurodegenerative Disorders Organoids Outcome Output Pathology Patients Persons Protein Isoforms Proteins RNA Regulation Regulator Genes Regulatory Element Resolution Sampling Schizophrenia Solid Source Speed Structure System Technology The Cancer Genome Atlas Time Tissues Training Untranslated RNA Variant biological systems causal variant cell type circular RNA clinical application computational platform computerized tools connectome disease diagnosis epigenetic variation epigenomics genetic variant genome-wide genomic aberrations human data human disease human tissue improved individual patient insight multiple omics new technology novel personalized medicine precision medicine risk variant sample collection single cell technology single molecule transcription factor treatment response

项目摘要

Project Summary Tens of thousands of human genomes have been sequenced, but the central challenge is their interpretation. A comprehensive set of regulatory events across a genome—the regulome—is needed to make full use of genomic information, but is currently out of reach for most clinical applications and biological systems. The proposed Center will develop technologies that greatly increase the sensitivity, speed, and comprehensiveness of understanding genome regulation. We will develop new technologies to interrogate the transactions between the genome and regulatory factors, such as proteins and noncoding RNAs from single cells, and integrate variations in DNA sequences and chromatin states over time and across individuals. Novel molecular engineering and biosensor strategies are deployed to encapsulate the desired complex DNA transformations into the probe system, such that the probe system can be directly used on very small human clinical samples and capture genome-wide information in one or two steps. These technologies will be applied to clinical samples with genomic aberrations to exercise their robustness, and reveal for the first time epigenomic dynamics of human diseases during progression and treatment. These technologies will be broadly applicable to many biomedical investigations, and the Center will disseminate the technologies via training and diverse means.

项目概要数以万计的人类基因组已被测序，但核心挑战是他们对整个基因组的一套全面的调控事件的解释。 regulome——充分利用基因组信息所必需的，但目前还没有拟议的中心将覆盖大多数临床应用和生物系统。开发大大提高灵敏度、速度和性能的技术我们将开发新的基因组调控的全面性。询问基因组和监管因素之间的交易的技术，例如来自单细胞的蛋白质和非编码 RNA，以及整合 DNA 中的变异随着时间的推移和个体之间的序列和染色质状态。部署工程和生物传感器策略来封装所需的复合物将DNA转化为探针系统，使得探针系统可以直接用于非常小的人类临床样本，并在一个样本中捕获全基因组信息这些技术将应用于基因组临床样本。畸变以锻炼其鲁棒性，并首次揭示表观基因组这些技术将研究人类疾病在进展和治疗过程中的动态。广泛适用于许多生物医学研究，中心将传播通过培训和多种方式掌握技术。

项目成果

期刊论文数量（115）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Genetic Adaptation of Porcine Circovirus Type 1 to Cultured Porcine Kidney Cells Revealed by Single-Molecule Long-Read Sequencing Technology.

DOI：
10.1128/genomea.01539-16
发表时间：
2017-02-02
期刊：
Genome announcements
影响因子：
0
作者：
Tombácz D;Moldován N;Balázs Z;Csabai Z;Snyder M;Boldogkői Z
通讯作者：
Boldogkői Z

On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNA-seq library.

关于异构体反卷积问题的可识别性：在 RNA-seq 文库中选择合适片段长度的应用。

DOI：
10.1093/bioinformatics/btab873
发表时间：
2022
期刊：
Bioinformatics (Oxford, England)
影响因子：
0
作者：
Ferrer-Bonsoms,JuanA;Morales,Xabier;Afshar,PegahT;Wong,WingH;Rubio,Angel
通讯作者：
Rubio,Angel

Hummingbird: efficient performance prediction for executing genomic applications in the cloud.

Hummingbird：在云中执行基因组应用程序的高效性能预测。

DOI：
10.1093/bioinformatics/btab161
发表时间：
2021
期刊：
Bioinformatics (Oxford, England)
影响因子：
0
作者：
Bahmani,Amir;Xing,Ziye;Krishnan,Vandhana;Ray,Utsab;Mueller,Frank;Alavi,Amir;Tsao,PhilipS;Snyder,MichaelP;Pan,Cuiping
通讯作者：
Pan,Cuiping

Full Genome Sequence of the Western Reserve Strain of Vaccinia Virus Determined by Third-Generation Sequencing.