Stacia R. Engel
A5036217383- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Fermentation and Sensory Analysis
- Microbial Natural Products and Biosynthesis
- Advanced Proteomics Techniques and Applications
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Rare Diseases
- Neurotransmitter Receptor Influence on Behavior
- Neuroscience and Neuropharmacology Research
- Biofuel production and bioconversion
- Yeasts and Rust Fungi Studies
- Cancer-related molecular mechanisms research
- Cancer Genomics and Diagnostics
- Sustainable Agricultural Systems Analysis
- Evolution and Paleontology Studies
- RNA Research and Splicing
- Plant Parasitism and Resistance
- Neuropeptides and Animal Physiology
- Legal and Policy Issues
- Neurogenesis and neuroplasticity mechanisms
Stanford University
2015-2025
Palo Alto University
2019-2025
Phoenix Bioinformatics
2023
SIB Swiss Institute of Bioinformatics
2023
University at Buffalo, State University of New York
2023
University of Southern California
2023
University of Padua
2023
University College London
2023
Palo Alto Institute
2020
Princeton University
2007-2009
The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular cellular biology are freely available for community use in the annotation genes, gene products sequences. Many model organism databases genome groups GO contribute their sets to resource. database integrates contributed annotations full access this information formats. Members Consortium continually work collectively,...
Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding functions of genes and gene products. Here, we report advances consortium over past two years. new GO-CAM annotation framework was notably improved, formalized model with a computational schema to check validate rapidly increasing repository 2838 GO-CAMs. In addition, describe impacts several collaborations refine GO 10% increase in number annotations,...
The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for budding yeast cerevisiae. SGD project provides highest-quality manually curated information from peer-reviewed literature. experimental results reported in literature are extracted and integrated within a well-developed database. These data combined with quality high-throughput provided through Locus Summary pages, powerful query engine rich genome browser. acquisition, integration retrieval of...
The genome of the budding yeast Saccharomyces cerevisiae was first completely sequenced from a eukaryote. It released in 1996 as work worldwide effort hundreds researchers. In time since, has been intensively studied by geneticists, molecular biologists, and computational scientists all over world. Maintenance annotation sequence have long provided Genome Database, one original model organism databases. To deepen our understanding eukaryotic genome, S. strain S288C reference updated recently...
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences all types from broad range organisms. We have recently added new genome mapping pipeline that identifies genomic locations for in 296 species. also several functional annotations, such as tRNA secondary structures, Gene Ontology and miRNA-target interactions. A quality control mechanism based Rfam family assignments potential contamination, incomplete more. The has become...
RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides single entry point for accessing all types organisms. Since its launch in 2014, has integrated twelve new resources, taking the total number collaborating to 22, began importing data, such as modified nucleotides MODOMICS PDB. We created species-specific identifiers refer unique within context species. The website been subject continuous improvements focusing on...
Abstract The Alliance of Genome Resources (Alliance) is a consortium the major model organism databases and Gene Ontology that guided by vision facilitating exploration related genes in human well-studied organisms providing highly integrated comprehensive platform enables researchers to leverage extensive body genetic genomic studies these organisms. Initiated 2016, building central portal (www.alliancegenome.org) for access data primary along with gene ontology data. All types represented...
Abstract As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting scientific research community since 1993. technologies and evolve, so does SGD: from updates in software architecture, to curation novel data types, incorporation from, collaboration with, other knowledgebases. We are continuing make steps toward providing with an S. cerevisiae pan-genome. Here, we describe upgrades, a new nomenclature system for genes not found reference...
The Alliance of Genome Resources (the Alliance) is a combined effort 7 knowledgebase projects: Saccharomyces Database, WormBase, FlyBase, Mouse the Zebrafish Information Network, Rat and Gene Ontology Resource. seeks to provide several benefits: better service various communities served by these projects; harmonized view data for all biomedical researchers, bioinformaticians, clinicians, students; more sustainable infrastructure. has cross-organism useful comparative views gene function,...
Abstract The Alliance of Genome Resources (Alliance) is an extensible coalition knowledgebases focused on the genetics and genomics intensively studied model organisms. organized as individual knowledge centers with strong connections to their research communities a centralized software infrastructure, discussed here. Model organisms currently represented in are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, rat, Gene Ontology Consortium. project rapid...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features gene products of budding yeast cerevisiae. Although published data from traditional experimental methods are primary sources evidence supporting Gene Ontology (GO) annotations for a product, high-throughput experiments computational predictions can also provide valuable insights in absence an extensive body literature. Therefore, GO available at...
The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in highly systematic way species-neutral manner with aim unifying representation function across different organisms. Each contributing member GO Consortium independently associates terms to from organism(s) they are annotating. Here we introduce Reference Genome project, which brings together those independent...
Abstract Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over years, SGD maintained genetic nomenclature, chromosome maps, functional annotation, developed various tools methods for analysis curation a variety emerging data types. More recently, six other model organism focused...
The murid rodent subfamily Sigmodontinae contains 79 genera which are distributed throughout the New World. time of arrival first sigmodontines in South America and estimated divergence time(s) different lineages American have been controversial due to lack a good fossil record immense number extant species. "early-arrival hypothesis" states that must arrived no later than early Miocene, at least 20 MYA, order account for their vast present-day diversity, whereas "late-arrival includes as...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of yeast cerevisiae, which commonly known as baker's or budding yeast. information in SGD includes functional annotations, mapping sequence information, protein domains structure, expression data, mutant phenotypes, physical genetic interactions primary literature from these data are derived. Here we describe how published phenotypes interaction annotated displayed SGD.
The characterization and public release of genome sequences from thousands organisms is expanding the scope for genetic variation studies. However, understanding phenotypic consequences remains a challenge in eukaryotes due to complexity genotype-phenotype map. One approach this intensive study model systems which diverse sources information can be accumulated integrated. Saccharomyces cerevisiae an extensively studied organism, with well-known protein functions thoroughly curated phenotype...
Abstract The S. cerevisiae genome is the most well‐characterized eukaryotic and one of simplest in terms identifying open reading frames (ORFs), yet its primary annotation has been updated continually decade since initial release 1996 (Goffeau et al. , ). Saccharomyces Genome Database (SGD; www.yeastgenome.org ) (Hirschman 2006 ), community‐designated repository for this reference genome, strives to ensure that as accurate useful possible. At SGD, sequence are treated a working hypothesis,...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the community resource for genomic, gene and protein information about budding yeast cerevisiae, containing a variety of functional each product. We have recently added regulatory to SGD present it on new tabbed section Locus Summary entitled 'Regulation'. are compiling transcriptional regulator–target relationships, which curated from literature at or imported, with permission, YEASTRACT database. For nearly every S....
Abstract Short paragraphs that describe gene function, referred to as summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects function. Manual curation while desirable, is difficult sustain. We developed an algorithm uses curated, structured data at Alliance Genome Resources (Alliance; www.alliancegenome.org) automatically generate summaries simulate natural language. The used this purpose include curated associations (annotations) ontology...
The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available information prompted Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) to enhance depth accessibility annotations. In particular, we have ongoing improve integration experimental sequence-based predictions redesigned web pages. A key feature this redesign is development a GBrowse-derived interactive Proteome...
The first completed eukaryotic genome sequence was that of the yeast Saccharomyces cerevisiae, and Genome Database (SGD; http://www.yeastgenome.org/) is original model organism database. SGD remains authoritative community resource for S. cerevisiae reference its annotation, continues to provide comprehensive biological information correlated with genes their products. A diverse set strains have been sequenced explore commercial laboratory applications, a brief history those provided....