Monica Muñoz‐Torres
A5106027423- Biomedical Text Mining and Ontologies
- Insect symbiosis and bacterial influences
- Bioinformatics and Genomic Networks
- Insect and Arachnid Ecology and Behavior
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Rare Diseases
- Genomics and Phylogenetic Studies
- Plant and animal studies
- Insect Resistance and Genetics
- Scientific Computing and Data Management
- Semantic Web and Ontologies
- Freshwater macroinvertebrate diversity and ecology
- Subterranean biodiversity and taxonomy
- Environmental DNA in Biodiversity Studies
- Insect-Plant Interactions and Control
- Research Data Management Practices
- Gene expression and cancer classification
- Insect and Pesticide Research
- Cancer Genomics and Diagnostics
- Phytoplasmas and Hemiptera pathogens
- Planetary Science and Exploration
- Advanced Graph Neural Networks
- Topic Modeling
- CRISPR and Genetic Engineering
- Entomopathogenic Microorganisms in Pest Control
University of Colorado Anschutz Medical Campus
2021-2025
Lawrence Berkeley National Laboratory
2013-2023
University of Colorado System
2022
University of Colorado Denver
2021
Oregon State University
2019-2020
Phoenix Bioinformatics
2019-2020
Georgetown University
2009-2015
International Center for Tropical Agriculture
2011
Clemson University
2009-2010
University of Washington
2009
Abstract The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard describe and computationally analyze phenotypic abnormalities found human disease. HPO is now worldwide for phenotype exchange. has grown steadily since its inception due considerable contributions from clinical experts researchers diverse range of disciplines. Here, we present recent major extensions the neurology, nephrology, immunology, pulmonology, newborn...
Parasitoid Wasp Genomes wasps, which prey on and reproduce in host insect species, play important roles plant herbivore interactions, may provide valuable tools the biological control of pest species. The Nasonia Genome Working Group (p. 343 ; see news story by Pennisi ) presents genome three very closely related species: vitripennis, N. giraulti , longicornis . findings document rapid evolution between a endosymbiont that can cause nuclear-cytoplasmic incompatibilities affect speciation.
JBrowse is a fast and full-featured genome browser built with JavaScript HTML5. It easily embedded into websites or apps but can also be served as standalone web page.Overall improvements to speed scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions readily added using the plugin framework; most visual aspects of tracks customized, along clicks, mouseovers, menus, popup boxes. used browse local annotation files...
The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding the biology sequenced species, phylogenetic relationships among study populations within across informed humans. As only few Metazoan genomes are approaching finished quality (human, mouse, fly worm), there is room for improvement most assemblies. honey bee (Apis mellifera) genome, published in 2006, was noted its bimodal GC content distribution that affected assembly some...
Although eusociality evolved independently within several orders of insects, research into the molecular underpinnings transition towards social complexity has been confined primarily to Hymenoptera (for example, ants and bees). Here we sequence genome stage-specific transcriptomes dampwood termite Zootermopsis nevadensis (Blattodea) compare them with similar data for eusocial Hymenoptera, better identify commonalities differences in achieving this significant transition. We show an...
The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed illuminate evolution highly insect societies. Bumblebees also invaluable natural and agricultural pollinators, there widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects bumblebee biology, including susceptibility implicated viability threats.We report high quality draft genome sequences...
Abstract Web Apollo is the first instantaneous, collaborative genomic annotation editor available on web. One of natural consequences following from current advances in sequencing technology that there are more and researchers new genomes. These require tools to describe functional features their newly sequenced With can use any common browsers (for example, Chrome or Firefox) jointly analyze precisely a genome real time, whether they same room working opposite sides world.
Insects and their arthropod relatives including mites, spiders, crustaceans play major roles in the world’s terrestrial, aquatic, marine ecosystems. Arthropods compete with humans for food transmit devastating diseases. They also comprise most diverse successful branch of metazoan evolution, millions extant species. Here, we describe an international effort to guide genomic efforts, from species prioritization methodology informatics. The 5000 genomes initiative (i5K) community met formally...
Ants are some of the most abundant and familiar animals on Earth, they play vital roles in terrestrial ecosystems. Although all ants eusocial, display a variety complex fascinating behaviors, few genomic resources exist for them. Here, we report draft genome sequence particularly widespread well-studied species, invasive Argentine ant ( Linepithema humile ), which was accomplished using combination 454 (Roche) Illumina sequencing community-based funding rather than federal grant support....
We report the draft genome sequence of red harvester ant, Pogonomyrmex barbatus . The was sequenced using 454 pyrosequencing, and current assembly annotation were completed in less than 1 y. Analyses conserved gene groups (more 1,200 manually annotated genes to date) suggest a high-quality comparable recently insect genomes Sanger sequencing. ant is model for studying reproductive division labor, phenotypic plasticity, sociogenomics. Although P. similar other hymenopterans ( Apis mellifera...
Leaf-cutter ants are one of the most important herbivorous insects in Neotropics, harvesting vast quantities fresh leaf material. The use leaves to cultivate a fungus that serves as colony's primary food source. This obligate ant-fungus mutualism is few occurrences farming by non-humans and likely facilitated formation their massive colonies. Mature leaf-cutter ant colonies contain millions workers ranging size from small garden tenders large soldiers, resulting complex polymorphic caste...
Genomes of eusocial insects code for dramatic examples phenotypic plasticity and social organization. We compared the genomes seven ants, honeybee, various solitary to examine whether lineages share distinct features genomic Each ant lineage contains ∼4000 novel genes, but only 64 these genes are conserved among all ants. Many gene families have been expanded in notably those involved chemical communication (e.g., desaturases odorant receptors). Alignment revealed reduced purifying selection...
The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability adapt variety solanaceaeous plants and variable climates during its global invasion, and, notably, rapidly evolve insecticide resistance. To examine evidence rapid evolutionary change, understand genetic basis herbivory resistance, we tested for structural functional genomic changes relative other arthropod species using genome sequencing, transcriptomics, community...
Genome annotation is the process of identifying location and function a genome's encoded features. Improving biological accuracy complex iterative requiring researchers to review incorporate multiple sources information such as transcriptome alignments, predictive models based on sequence profiles, comparisons features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number scientists sequencing routine laboratory technique, there widespread demand...
Abstract In biology and biomedicine, relating phenotypic outcomes with genetic variation environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants be in genes that haven’t been characterized, research organisms recapitulate human or veterinary affecting disease are unknown undocumented, many resources must queried to find potentially significant associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on...
Abstract Background Arthropods comprise the largest and most diverse phylum on Earth play vital roles in nearly every ecosystem. Their diversity stems part from variations a conserved body plan, resulting recorded adaptive changes genome. Dissection of genomic record sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Results Using 76 whole sequences representing 21 orders spanning more than 500 million years...
The Hymenoptera Genome Database (HGD) is a comprehensive model organism database that caters to the needs of scientists working on insect species order Hymenoptera. This system implements open-source software and relational databases providing access curated data contributed by an extensive, active research community. HGD contains from 9 different across ∼200 million years in phylogeny Hymenoptera, allowing researchers leverage genetic, genome sequence gene expression data, as well...
Abstract Background The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology excellent experimental tractability molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids blood-feeding bed bugs, we present the genome sequence comparative analyses centered on milkweed bug Oncopeltus fasciatus , seed feeder family Lygaeidae. Results 926-Mb is well represented by current assembly official gene set....
Hyalella azteca is a cryptic species complex of epibenthic amphipods interest to ecotoxicology and evolutionary biology. It the primary crustacean used in North America for sediment toxicity testing an emerging model molecular ecotoxicology. To provide resources quality assessments studies, we sequenced, assembled, annotated genome H. U.S. Lab Strain. The completeness comparable with other ecotoxicological species. Through targeted investigation use gene expression data sets exposed...
Integrated, up-to-date data about SARS-CoV-2 and COVID-19 is crucial for the ongoing response to pandemic by biomedical research community. While rich biological knowledge exists related viruses (SARS-CoV, MERS-CoV), integrating this difficult time-consuming, since much of it in siloed databases or textual format. Furthermore, required community vary drastically different tasks; optimal a machine learning task, example, from used populate browsable user interface clinicians. To address these...
Abstract There are thousands of distinct disease entities and concepts, each which known by different sometimes contradictory names. The lack a unified system for managing these poses major challenge both machines humans that need to harmonize information better predict causes treatments disease. Mondo Disease Ontology is an open, community-driven ontology integrates key medical biomedical terminologies, supporting data integration improve diagnosis, treatment, translational research....
Abstract Despite progress in the development of standards for describing and exchanging scientific information, lack easy-to-use mapping between different representations same or similar objects databases poses a major impediment to data integration interoperability. Mappings often metadata needed be correctly interpreted applied. For example, are two terms equivalent merely related? Are they narrow broad matches? Or associated some other way? Such relationships mapped not documented, which...
Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing ontologies, semantic models, knowledge graphs translational research. App an integrated platform combining about genes, phenotypes, diseases across species. Monarch's APIs enable access to carefully...