A5081346976- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- SARS-CoV-2 and COVID-19 Research
- Genomic variations and chromosomal abnormalities
- vaccines and immunoinformatics approaches
- Cardiac Health and Mental Health
- Birth, Development, and Health
- Cardiac, Anesthesia and Surgical Outcomes
- Diet and metabolism studies
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- RNA modifications and cancer
- Advanced Breast Cancer Therapies
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Adipose Tissue and Metabolism
- Animal Virus Infections Studies
- BRCA gene mutations in cancer
University of California, Santa Cruz
2019-2025
Abstract For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to research community. As field of grows become available, new modes display are required accommodate technologies. New features released this past year include a Hi-C heatmap display, phased family trio for VCF files, various track improvements. Striving keep up-to-date, updates gene GENCODE Genes, NCBI RefSeq Ensembl...
Abstract The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen emphasis in clinical data, with new tracks expanded Recommended Track Sets feature on hg38 well addition of a single cell track group. SARS-CoV-2 remain focus, regular annotation updates browser continued curation our phylogenetic sequence placing tool, hgPhyloPlace,...
The UCSC Genome Browser, https://genome.ucsc.edu, is a graphical viewer for exploring genome annotations. website provides integrated tools visualizing, comparing, analyzing, and sharing both publicly available user-generated genomic datasets. Data highlights this year include collection of easily accessible public hub assemblies on new organisms, now featuring BLAT alignment PCR capabilities, updated clinical tracks (gnomAD, DECIPHER, CADD, REVEL). We introduced Track Sets feature enhanced...
The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation on thousands of genome assemblies, ranging from human SARS-CoV2. This year, we have introduced new the Human Pangenome Reference Consortium viral genomes including We added 1,200 our GenArk system, increasing overall diversity representation. support for nine user-contributed track hubs public hub...
The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year providing high-quality genomics data visualization and genome annotations to the research community. In past year, we have added a new option our web BLAT tool that allows search against all genomes, single-cell expression viewer (https://cells.ucsc.edu), 'lollipop' plot display mode for high-density variation data, RESTful API extraction custom-track backup feature. New datasets...
The UCSC Genome Browser (https://genome.ucsc.edu) is a widely utilized web-based tool for visualization and analysis of genomic data, encompassing over 4000 assemblies from diverse organisms. Since its release in 2001, it has become an essential resource genomics bioinformatics research. Annotation data available on includes both internally created maintained tracks as well custom track hubs provided by the research community. This last year's updates include 25 new annotation such gnomAD...
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such only available a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling most accurate genomes date. Here we summarize these developments, introduce set quality standards, present lessons...
Variants of uncertain significance (VUS) are considered one the most significant impediments to translation genetic test results into precise clinical recommendations. The 2015 American College Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) classification guidelines established a general framework assessment variants; yet, gene-specific specifications needed enable better variant reduce number VUS. process adaptations ACMG/AMP codes is led accompanied by ClinGen...
Abstract Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent assemblies. We create Genome Archive (GenArk) collection of UCSC Browsers from NCBI Built on our established track hub system, this enables fast visualization annotations. Assemblies come with gene models, repeat masks, BLAT, and silico PCR. Users can add annotations via hubs custom tracks. bulk-import third-party resources, demonstrated TOGA Ensembl models for hundreds...
ABSTRACT Background Researchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during COVID-19 pandemic. As a result, there is critical need for rapid continuously updated access latest in format which all can be quickly cross-referenced compared. We adapted our browser visualization tool viral this purpose. Molecular data, curated from published studies or database submissions, mapped grouped together into “annotation tracks”...
The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of human genome was first released in 2000. As it grown scope to display more types data also complicated. data, which are dispersed at many locations worldwide, collected into one view on Browser, where graphical interface presents location. This supports expertise researcher interpret variants genome. Because analysis single nucleotide copy number require interpretation very different...
Early-life exposure to maternal obesity or a calorically dense Western-style diet (WSD) is strongly associated with greater risk of metabolic diseases in offspring, most notably insulin resistance and dysfunction-associated steatotic liver disease (MASLD). Prior studies our well-characterized Japanese macaque model demonstrated that offspring dams fed WSD, even when weaned onto control (CTR) diet, had reductions skeletal muscle mitochondrial metabolism increased compared on CTR diet. In the...
The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of human genome was first released in 2000. As it grown scope to display more types data also complicated. data, which are dispersed at many locations worldwide, collected into one view on Browser, where graphical interface presents location. This supports expertise researcher interpret variants genome. Because analysis Single Nucleotide Variants (SNVs) Copy Number (CNVs) require...
Interactive graphical genome browsers are essential tools for biologists working with DNA sequences. Although tens of thousands new assemblies have become available over the last decade, accessibility is limited by work involved in manually creating and curating annotations. The results can push limits data storage infrastructure. To facilitate managing this increasing number assemblies, we created Genome Archive (GenArk) collection UCSC Browsers from hosted at NCBI(1). Built on our...