Forrest Y. Tanaka
A5079783845- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Genetic Associations and Epidemiology
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Data Quality and Management
- Forensic and Genetic Research
- Genomics and Rare Diseases
- Biomedical Text Mining and Ontologies
- RNA Research and Splicing
- Scientific Computing and Data Management
- Monoclonal and Polyclonal Antibodies Research
- Research Data Management Practices
- Genetics, Bioinformatics, and Biomedical Research
Stanford University
2015-2023
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as source for data metadata generated by Consortium. Two principles have motivated design. First, experimental protocols, analytical procedures themselves should be made publicly accessible through a coherent, web-based search download interface. Second, same interface serve carefully curated that record provenance justify its interpretation in biological terms. Since...
The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in human and mouse genomes. Data generated by ENCODE consortium are freely accessible portal (https://www.encodeproject.org/), which developed maintained Coordinating Center (DCC). Since initial release 2013, DCC has updated to make data more findable, accessible, interoperable reusable. Here, we report on recent updates, including new assays, uniform...
The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase creating a comprehensive catalog functional elements the human genome. This project includes an expansion assays that measure diverse RNA populations, identify proteins interact with and DNA, probe regions hypersensitivity, levels methylation wide range cell tissue types to putative regulatory elements. To date, results for almost 5000 experiments have been released use by scientific community. These data are available...
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on single haploid reference genome. Here, we present the EN-TEx resource 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating catalog >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes less conserved...
Abstract The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create comprehensive catalog functional in the human genome. current database comprises more than 19000 genomics experiments across 1000 cell lines and tissues using wide array experimental techniques study chromatin structure, regulatory transcriptional landscape Homo sapiens Mus musculus genomes. All data, metadata, associated computational analyses created by ENCODE consortium are submitted Data...
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create comprehensive catalog functional in the human genome. current database comprises more than 19000 genomics experiments across 1000 cell lines and tissues using wide array experimental techniques study chromatin structure, regulatory transcriptional landscape
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by ENCODE project. description these data, known as metadata, includes biological sample used input, protocols assays performed on samples, files from results computational methods analyze data. Here, we outline principles philosophy define metadata in order create a standard that can be applied multiple genomic projects. In...
Abstract The Encyclopedia of DNA Elements (ENCODE) web portal hosts genomic data generated by the ENCODE Consortium, Genomics Gene Regulation, NIH Roadmap Epigenomics and modENCODE modERN projects. goal project is to build a comprehensive map functional elements human mouse genomes. Currently, database stores over 500 TB raw processed from 15,000 experiments spanning assays that measure gene expression, accessibility, RNA binding, methylation, 3D chromatin structure across numerous cell...
Abstract Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all functional elements in human and mouse genomes. To best serve scientific community, data generated by consortium shared through web-portal (https://www.encodeproject.org/) with no access restrictions. The fourth final phase added diverse set new samples (including those associated disease), wide range assays aimed at detection, characterization validation...
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog functional initiated shortly after the completion Human Genome Project. current database exceeds 6500 experiments across more than 450 cell lines and tissues using wide array experimental techniques study chromatin structure, regulatory transcriptional landscape H. sapiens M. musculus genomes. All ENCODE data, metadata, associated computational analyses are submitted Data...
Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all functional elements in human and mouse genomes. To best serve scientific community, data generated by consortium shared through web-portal (https://www.encodeproject.org/) with no access restrictions. The fourth final phase added diverse set new samples (including those associated disease), wide range assays aimed at detection, characterization validation genomic...
https://www.encodeproject.org/.
ABSTRACT Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on single haploid reference genome. Here, we present the EN-TEx resource personal epigenomes, for ∼25 tissues and >10 assays in four donors (>1500 open-access genomic proteomic datasets, total). Each dataset mapped to matched, diploid genome, which has long-read phasing structural variants. The mappings enable us identify >1 million loci with...
Abstract The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort[1–6] to create a comprehensive catalog functional initiated shortly after the completion Human Genome Project[7][1]. current database exceeds 6500 experiments across more than 450 cell lines and tissues using wide array experimental techniques study chromatin structure, regulatory transcriptional landscape H. sapiens M. musculus genomes. All ENCODE data, metadata, associated computational analyses...