Todd Harris
A5102754107- Genetics, Aging, and Longevity in Model Organisms
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Microbial Metabolic Engineering and Bioproduction
- CRISPR and Genetic Engineering
- Microbial Community Ecology and Physiology
- Genetics, Bioinformatics, and Biomedical Research
- Evolution and Genetic Dynamics
- Chromosomal and Genetic Variations
- Nematode management and characterization studies
- Gut microbiota and health
- Scientific Computing and Data Management
- Mitochondrial Function and Pathology
- Genomics and Rare Diseases
- Cellular transport and secretion
- Research Data Management Practices
- Enzyme Production and Characterization
- Insect and Arachnid Ecology and Behavior
- Handwritten Text Recognition Techniques
- Blood Coagulation and Thrombosis Mechanisms
- Health and Conflict Studies
- Nuclear Issues and Defense
- Occupational and Professional Licensing Regulation
Ontario Institute for Cancer Research
2011-2024
École Polytechnique Fédérale de Lausanne
2019
Wellcome Sanger Institute
2007-2011
Institute of Genetics
2011
Joint Genome Institute
2011
Molecular Oncology (United States)
2011
Centre de Génétique Moléculaire
2011
Mary Lyon Centre at MRC Harwell
2011
Inserm
2011
Centre National de la Recherche Scientifique
2011
The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Genome Browser (GBrowse), a Web-based application displaying genomic annotations and other features. For end user, features of browser include ability scroll zoom through arbitrary regions genome, enter region genome by searching landmark or performing full text search all features, enable disable tracks change their...
The soil nematodes Caenorhabditis briggsae and elegans diverged from a common ancestor roughly 100 million years ago yet are almost indistinguishable by eye. They have the same chromosome number genome sizes, they occupy ecological niche. To explore basis for this striking conservation of structure function, we sequenced C. to high-quality draft stage compared it finished sequence. We predict approximately 19,500 protein-coding genes in genome, as elegans. Of these, 12,200 clear orthologs,...
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide unified interface biomedical databases that are distributed worldwide. portal provides access numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the independently administered funded their host data federation...
WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, extends beyond genomic sequence, integrating experimental results with extensively annotated views of genome. The Consortium continues to expand biological scope utility inclusion large-scale analyses, through active literature curation, new analysis visualization tools, refinement user interface. Over past year, nearly complete...
WormBase (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as service to the Caenorhabditis elegans research field, has evolved into powerful tool in its own right. In past 2 years, we expanded include complete genomic sequence, gene predictions and orthology assignments from range of related nematodes. This comparative enrich C. with improved better understanding function. turn, they bring wealth experimental knowledge other systems medical...
WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans other nematodes. The project has evolved from its original remit to collect integrate all single species, now extends numerous nematodes, ranging evolutionary comparators C. parasitic species that threaten plant, animal human health. Research activity using as model system vibrant ever, we have created new tools community curation in response ever-increasing...
FungiDB (http://FungiDB.org) is a functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic center (http://EuPathDB.org). uses same infrastructure and user interface as EuPathDB, which allows sophisticated integrated searches to be performed using an intuitive graphical system. The current release of contains genome sequence annotation from 18 species spanning several fungal classes, including Ascomycota Eurotiomycetes,...
Abstract WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as model system for studies across broad range of basic biological processes. Toward this mission, efforts are arranged in three primary facets: curation, user interface and architecture. In update, we describe progress each these areas. particular, discuss status literature curation recently added data, detail new features web options...
The genome of the common roundworm Ascaris suum, a major parasite in many parts world, has now been sequenced. Analyses reveal genes that encode peptidases linked to penetration and degradation host tissues, as well molecules likely modulate or evade immune responses. availability this sequence should contribute towards development new therapeutic interventions against ascariasis other nematode infections. Parasitic diseases have devastating, long-term impact on human health, welfare food...
Abstract WormBase (www.wormbase.org) is the central repository for genetics and genomics of nematode Caenorhabditis elegans. We provide research community with data tools to facilitate use C. elegans related nematodes as model organisms studying human health, development, many aspects fundamental biology. Throughout our 22-year history, we have continued evolve reflect progress innovation in science technologies involved study strive incorporate new types richer sets, integrated displays...
WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, continues to advance its practices on data acquisition, curation retrieval most effectively deliver comprehensive about Caenorhabditis elegans, genomic information other nematodes parasitic flatworms. Recent notable enhancements include user-directed submission such as micropublication; presentation, including...
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...
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 WormBase has been the major repository and knowledgebase of information about genome genetics Caenorhabditis elegans other nematodes experimental interest for over 2 decades. We have 3 goals: to keep current with fast-paced C. research, provide better integration resources, be sustainable. Here, we discuss state as well progress plans moving core infrastructure Alliance Genome Resources (the Alliance). As an member, will continue interact community, develop new features needed,...
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...
Synaptojanin is a polyphosphoinositide phosphatase that found at synapses and binds to proteins implicated in endocytosis. For these reasons, it has been proposed synaptojanin involved the recycling of synaptic vesicles. Here, we demonstrate unc-26 gene encodes Caenorhabditis elegans ortholog synaptojanin. mutants exhibit defects vesicle trafficking several tissues, but most are termini. Specifically, observed budding vesicles from plasma membrane, uncoating after fission, recovery...
WormBook (Author Webpage) is an open-access, online collection of original, peer-reviewed chapters on the biology Caenorhabditis elegans and related nematodes. Since was launched in June 2005 with 12 chapters, it has grown to over 100 covering nearly every aspect C.elegans research, from Cell Biology Neurobiology Evolution Ecology. also serves as text companion WormBase, model organism database. Objects such genes, proteins cells are linked relevant pages providing easily accessible...
Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on single species and serving dedicated research community, to one now spanning 15 essential the broader biomedical agricultural fields. To enhance rate of curation, we have automated identification key data scientific literature use similar methodology for extraction. ease access data, are collaborating with journals link entities publications their report pages at WormBase. facilitate...
WormBase (http://www.wormbase.org/) is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans. With an electronic history predating World Wide Web, contains information ranging from sequence and phenotype of individual alleles genome-wide studies generated next-generation sequencing technologies. In recent years, we have expanded contents include data on additional nematodes agricultural medical significance, bringing knowledge C. elegans...
BioMart Central Portal is a first of its kind, community-driven effort to provide unified access dozens biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource the Portal, allowing it be exposed shared with research community, linking other resources in portal. Users take advantage common interface quickly utilize different sources without learning new system for each. The...
WormBase ( http://www.wormbase.org/ ) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen significant expansion in the biological scope of WormBase, including integration large-scale, genome-wide sets, inclusion genome sequence gene predictions from species active literature curation. This has also driven development refinement user interfaces operability, new Genome Browser, searches facilities access...
WormBase (Author Webpage), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve expand. Over the past year has added new data on C.elegans, including classical genetics, cell biology functional genomics; expanded annotation of closely nematodes with genome browser remanei; deployed hardware stronger performance. Several existing datasets phenotype descriptions RNAi experiments have seen large increase in content. New such as C.remanei draft...
WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from initial ACeDB C. elegans genetic sequence information, now includes genomic, anatomical functional other species nematodes. As such, it a crucial resource not only biologists but larger bioinformatics communities. Coverage core areas biology will allow community to make full use results intensive...
Abstract Background While the C. elegans genome is extensively annotated, relatively little information available for other Caenorhabditis species. The nematode annotation assessment project (nGASP) was launched to objectively assess accuracy of protein-coding gene prediction software in , and apply this knowledge genomes four additional species nematodes. Seventeen groups worldwide participated nGASP, submitted 47 sets across 10 Mb genome. Predictions were compared reference consisting...