Rebecca F. Lowdon
A5057170701- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Cancer-related gene regulation
- Chromosomal and Genetic Variations
- Advances in Cucurbitaceae Research
- Plant Virus Research Studies
- CRISPR and Genetic Engineering
- Plant Disease Resistance and Genetics
- RNA Research and Splicing
- Neurobiology and Insect Physiology Research
- Genomics and Phylogenetic Studies
- Genetics, Aging, and Longevity in Model Organisms
- Banana Cultivation and Research
- Cocoa and Sweet Potato Agronomy
- Genomics and Rare Diseases
- Cancer-related molecular mechanisms research
- Animal Genetics and Reproduction
- Genetic Syndromes and Imprinting
- Zebrafish Biomedical Research Applications
- Nutrition, Genetics, and Disease
- Bioinformatics and Genomic Networks
- Biomedical and Engineering Education
- Plant Pathogenic Bacteria Studies
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2022
Mathématiques et Informatique Appliquées
2022
Bayer (United States)
2022
AgroParisTech
2022
Université Paris-Saclay
2022
Washington University in St. Louis
2013-2021
UCSF Helen Diller Family Comprehensive Cancer Center
2014
University of California, San Francisco
2014
National Human Genome Research Institute
2010-2014
National Institutes of Health
2010-2014
The reference human genome sequence set the stage for studies of genetic variation and its association with disease, but epigenomic lack a similar reference. To address this need, NIH Roadmap Epigenomics Consortium generated largest collection so far epigenomes primary cells tissues. Here we describe integrative analysis 111 as part programme, profiled histone modification patterns, DNA accessibility, methylation RNA expression. We establish global maps regulatory elements, define modules...
From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation still needed characterize how used help produce functional organism (see Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for Caenorhabditis elegans genome, and The modENCODE Consortium 1787 Drosophila melanogaster full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites,...
From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation still needed characterize how used help produce functional organism (see Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for Caenorhabditis elegans genome, and The modENCODE Consortium 1787 Drosophila melanogaster full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites,...
DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and tissue-specific gene expression. Sequencing-based profiling provides an unprecedented opportunity to map compare complete methylomes. This includes one of the most widely applied technologies for measuring methylation: methylated immunoprecipitation followed by sequencing (MeDIP-seq), coupled with a complementary method,...
Uncovering mechanisms of epigenome evolution is an essential step towards understanding the different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic mechanism in mammalian development, little known about conservation tissue-specific genome-wide patterns.Using comparative epigenomics approach, we identified and compared patterns rat against those mouse human across three shared tissue types. We that differentially methylated regions are strongly...
DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap distal cis-regulatory elements. However, developmental dynamics of the majority genomic CpGs outside gene promoters CpG islands has not been extensively characterized. Here, we generate compare comprehensive methylome maps zebrafish developing embryos. From these maps, identify thousands...
Aberrant DNA methylation is a hallmark of many cancers. Classically there are two types endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I, and uterine papillary serous carcinoma (UPSC), II. However, the whole genome changes in these classical cancer still unknown. Here we described complete genome-wide methylome maps EAC, UPSC, normal endometrium by applying combined strategy methylated immunoprecipitation sequencing (MeDIP-seq) methylation-sensitive restriction enzyme...
Abstract Summary: We present methylC track, an efficient mechanism for visualizing single-base resolution DNA methylation data on a genome browser. The track dynamically integrates the level of methylation, position and context methylated cytosine (i.e. CG, CHG CHH), strand confidence (e.g. read coverage depth in case whole-genome bisulfite sequencing data). Investigators can access integrate these information visually at specific locus or genome-wide WashU EpiGenome Browser other rich...
Abstract Background Zebrafish pigment cell differentiation provides an attractive model for studying fate progression as a neural crest progenitor engenders diverse types, including two morphologically distinct cells: black melanophores and reflective iridophores. Nontrivial classical genetic transcriptomic approaches have revealed essential molecular mechanisms gene regulatory circuits that drive crest-derived decisions. However, how the epigenetic landscape contributes to differentiation,...
Evidence that noncoding mutation can result in cancer driver events is mounting. However, it more difficult to assign molecular biological consequences mutations than coding mutations, and a typical genome contains many protein-coding mutations. Accordingly, parsing functional signal from noise remains an important challenge. Here we use empirical approach identify putatively somatic single nucleotide variants (SNVs) liver genomes. Annotation of candidate by publicly available epigenome...
<ns3:p>In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal hackathon was to advance research on structural variants (SVs) by prototyping iterating open-source software. This led nine projects focused diverse genomics interests, including various SV discovery genotyping methods, sequence reconstruction, clinically relevant variation, SARS-CoV-2...
Abstract The mapping and introduction of sustainable resistance to viruses in crops is a major challenge modern breeding, especially regarding vegetables. We hence assembled panel cucumber elite lines landraces from different horticultural groups for testing with six virus species. mapped 18 quantitative trait loci (QTL) multiloci genome wide association studies (GWAS), some which have already been described the literature. detected two hotspots, one on chromosome 5 mosaic (CMV), vein...
Abstract Banana is an important fruit and staple crop, which vital for food income security in developing countries. A genomics initiative was undertaken as part of the Global Alliance against TR4 (Tropical Race 4 Fusarium Wilt Banana) Alliance, with Bayer Crop Science, International Institute Tropical Agriculture, University Queensland to collectively accelerate breeding efforts Eastern Africa. The goal this project develop resources improve banana breeding, productivity, quality traits...
The assembly of the human genome sequence revealed that there are 3.2 billion bases in our genome, but what was less clear at time how this vast amount information organised and expressed to ensure a single-celled zygote able develop into fully functioning body. ENCODE project began quest identify assign function different elements within Roadmap Epigenome Project has continued journey by mapping chemical modifications such as DNA methylation, which known affect gene expression....