Steven J Marygold
A5005252212- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Neurobiology and Insect Physiology Research
- Microbial Natural Products and Biosynthesis
- Insect symbiosis and bacterial influences
- Genetics, Bioinformatics, and Biomedical Research
- RNA modifications and cancer
- RNA Research and Splicing
- Insect Resistance and Genetics
- Genomics and Rare Diseases
- Machine Learning in Bioinformatics
- Invertebrate Immune Response Mechanisms
- CRISPR and Genetic Engineering
- Viral Infectious Diseases and Gene Expression in Insects
- Ubiquitin and proteasome pathways
- Hippo pathway signaling and YAP/TAZ
- Cancer-related molecular mechanisms research
- Protein Structure and Dynamics
- Insect behavior and control techniques
- Microbial Metabolic Engineering and Bioproduction
- Gene expression and cancer classification
- Insect-Plant Interactions and Control
- Phytoplasmas and Hemiptera pathogens
University of Cambridge
2015-2025
Stanford University
2023
Phoenix Bioinformatics
2023
University at Buffalo, State University of New York
2023
SIB Swiss Institute of Bioinformatics
2023
University of Padua
2023
University College London
2023
University of Southern California
2023
Technical University of Munich
2014
Indiana University Bloomington
2012
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,...
FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes wild-type gene products: their molecular function, the biological processes in which they play role, subcellular location. This article describes recent changes GO annotation strategy that improving quality data. Many these stem from our participation Reference Genome Annotation Project--a multi-database collaboration producing comprehensive...
Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on most extensively studied species, melanogaster, includes information genes (molecular and genetic), transgenic constructs, phenotypes, genetic physical interactions, reagents such as stocks cDNAs. Access to data is provided through a number of tools, reports, bulk-data downloads. Looking future, expanding its focus serve broader scientific In this update, we...
FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As enters our fourth decade service to research community, we reflect on unique aspects look forward continued collaboration with larger model organism communities. In this study, emphasize dedicated reports tools have constructed meet specialized needs fly researchers but also facilitate use by other We highlight ways that support including an external resources page, help resources,...
FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports overview displays ('ribbons') expression data. We also variety recent...
Abstract Background Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects a variety organisms. In Drosophila melanogaster , disruption RP can result the 'Minute' syndrome dominant, haploinsufficient phenotypes, which include prolonged development, short thin bristles, poor fertility viability. While more than 50 Minute loci defined genetically, only 15 so far characterized molecularly correspond genes. Results We combined...
Many publications describe sets of genes or gene products that share a common biology. For example, genome-wide studies and phylogenetic analyses identify related in sequence; high-throughput genetic molecular screens reveal functionally products; advanced proteomic methods can determine the subunit composition multi-protein complexes. It is useful for such collections to be presented as discrete lists within appropriate Model Organism Database (MOD) so researchers readily access these data...
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides single access point to 44 resources and >18 million ncRNA from wide range organisms types. now also includes secondary (2D) structure information for >13 sequences, making the world's largest 2D database. The diagrams are displayed using R2DT, new visualization method uses consistent, reproducible recognizable layouts related RNAs. sequence similarity search has been updated with faster interface...
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...
An accurate, comprehensive, non-redundant and up-to-date bibliography is a crucial component of any Model Organism Database (MOD). Principally, the provides set references that are specific to field served by MOD. Moreover, it serves as backbone which all curated biological data can be attributed. Here, we describe organization main features in FlyBase (flybase.org), MOD for Drosophila melanogaster. We present an overview current content bibliography, pipeline identifying adding new...
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 FlyBase (flybase.org) is a model organism database and knowledge base about Drosophila melanogaster, commonly known as the fruit fly. Researchers from around world rely on genetic, genomic, functional information available in FlyBase, well its tools to view interrogate these data. In this article, we describe latest developments updates FlyBase. These include introduction of single-cell RNA sequencing data, improved content display information, updated orthology pipelines, new...
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...
Abstract During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding rRNA secondary structures and therefore function. Along with pseudouridine, methylation the 2′-hydroxyl ribose moiety (Nm) is most abundant modification rRNAs. The majority Nm eukaryotes placed Fibrillarin, a conserved methyltransferase belonging to ribonucleoprotein complex guided C/D box small nucleolar (C/D snoRNAs). These impact interactions...
The breadth and depth of biomedical literature are increasing year upon year. To keep abreast these increases, FlyBase, a database for Drosophila genomic genetic information, is constantly exploring new ways to mine the published increase efficiency accuracy manual curation automate some aspects, such as triaging entity extraction. Toward this end, we present 'tagtog' system, web-based annotation framework that can be used mark up biological entities (such genes) concepts Gene Ontology...
UDP-glycosyltransferases (UGTs) are important conjugation enzymes found in all kingdoms of life, catalyzing a sugar with small lipophilic compounds and playing crucial role detoxification homeostasis. The UGT gene family is defined by signature motif the C-terminal domain where uridine diphosphate (UDP)-sugar donor binds. UGTs have been identified number insect genomes over last decade much progress has achieved characterizing their expression patterns molecular functions. Here, we present...
The identification and characterization of gene paralogs is crucial to understand the functional contribution individual genes/proteins biological pathways. Here, we have identified 51 genes belonging fifteen paralogous groups encoding enzymes involved in carbohydrate metabolism Drosophila melanogaster . Strikingly, most comprise a single 'canonical' enzyme that expressed ubiquitously one or more variants predominantly testis. Most these testis-specific forms are predicted be catalytically...
Abstract A comprehensive, computable representation of the functional repertoire all macromolecules encoded within human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating structured body information about gene functions, which now includes experimental findings reported in more than 175,000 publications genes experimentally tractable model organisms 1,2 . Here, we describe results large,...
The Minute mutations of Drosophila melanogaster are thought to disrupt genes that encode ribosomal proteins (RPs) and thus impair ribosome function protein synthesis. However, relatively few Minutes have been tied distinct RP more loci likely be discovered. We identified point in RpL38 RpL5 a screen for factors limiting growth the D. wing. Here, we present first genetic characterization these loci. is located centric heterochromatin chromosome arm 2R identical previously Minute, M(2)41A,...