Idan Gabdank
A5021119888- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Genetics, Aging, and Longevity in Model Organisms
- Single-cell and spatial transcriptomics
- Forensic and Genetic Research
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
Stanford University
2016-2024
Stanford Medicine
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...
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...
Abstract The ENCODE Consortium’s efforts to annotate noncoding cis -regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, CRISPR screens offer a systematic approach investigate mechanisms. ENCODE4 Functional Characterization Centers conducted 108 in human cell lines, comprising >540,000 perturbations across 24.85 megabases the genome. Using 332 functionally confirmed CRE–gene links K562 cells, we established guidelines for screening endogenous...
Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, N2 has many differences any available today. To provide more accurate genome, we performed long-read of VC2010, modern derived N2. Our VC2010 99.98% identity but an additional 1.8 Mb including tandem repeat expansions duplications. For...
The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3' end choice. Detecting quantifying across tissues, cell types, species has been extremely challenging because transcripts are much longer than the short reads normally used for RNA-seq. By contrast, long-read RNA-seq (LR-RNA-seq) gives complete structure most transcripts. We sequenced 264 LR-RNA-seq PacBio libraries totaling over 1...
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
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...
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...