Terence D. Murphy
A5016199185- Genomics and Phylogenetic Studies
- Insect behavior and control techniques
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- Forensic Entomology and Diptera Studies
- Diptera species taxonomy and behavior
- Chromosomal and Genetic Variations
- Genetics, Bioinformatics, and Biomedical Research
- Insect symbiosis and bacterial influences
- Hemiptera Insect Studies
- Gene expression and cancer classification
- Insect Resistance and Genetics
- Phytoplasmas and Hemiptera pathogens
- Research on scale insects
- Genomics and Chromatin Dynamics
- Animal Genetics and Reproduction
- Biomedical Text Mining and Ontologies
- CRISPR and Genetic Engineering
- Insect-Plant Interactions and Control
- Viral Infectious Diseases and Gene Expression in Insects
- Insect and Arachnid Ecology and Behavior
- Microtubule and mitosis dynamics
- Genomic variations and chromosomal abnormalities
- RNA modifications and cancer
- Nutrition, Genetics, and Disease
National Center for Biotechnology Information
2015-2024
National Institutes of Health
2015-2024
United States Department of Health and Human Services
2014
Howard Hughes Medical Institute
2006
Department of Embryology
2003-2006
Carnegie Institution for Science
2003-2006
Carnegie Observatories
2003-2006
Wellcome Trust
2001
Addenbrooke's Hospital
2001
Virtua Memorial Hospital
2000
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). leverages data submitted to International Nucleotide Sequence Database Collaboration (INSDC) against combination computation, manual curation, collaboration produce standard set stable, non-redundant reference sequences. augments these sequences with current...
Abstract The National Center for Biotechnology Information (NCBI) produces a variety of online information resources biology, including the GenBank® nucleic acid sequence database and PubMed® citations abstracts published in life science journals. NCBI provides search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface Resources receiving significant updates past year include PubMed, PMC, Bookshelf, RefSeq, SRA, Virus, dbSNP, dbVar,...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published life science journals. Entrez system search retrieval operations most these data from 39 distinct databases. E-utilities serve as programming interface system. Augmenting many Web applications are custom implementations BLAST program optimized to specialized sets. New...
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public archives computation, curation collaboration (http://www.ncbi.nlm.nih.gov/refseq/). We report here on growth the mammalian human subsets, changes to NCBI's eukaryotic annotation pipeline modifications affecting records. Recent genome provide higher throughput, addition RNAseq results significant...
The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing update since 2009; it reflects resolution roughly 1000 issues encompasses modifications ranging from thousands single base changes to megabase-scale path reorganizations, gap closures, localization previously orphaned sequences. We developed new approach sequence generation for targeted updates used data mapping technologies haplotype...
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.
The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes viruses, prokaryotes and eukaryotes are the primary foundation records in that they form critical association between sequence a tracked gene upon which additional functional descriptive content is anchored. Additional integrated based on genomic location RefSeq transcript protein data....
Abstract Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library 7404 protein trap and enhancer lines, the Carnegie collection, to facilitate mapping at single-cell resolution. By sequencing genomic insertion sites, determining splicing downstream enhanced green fluorescent (EGFP) exon, analyzing ovary salivary gland, found 600–900 different genes are trapped our collection. A core set...
Effective use of the human and mouse genomes requires reliable identification genes their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation genes, transcripts, proteins. The collaborative consensus coding sequence (CCDS) project tracks protein annotations on reference with a stable identifier (CCDS ID), ensures they consistently represented NCBI, Ensembl, UCSC Genome Browsers. Importantly,...
Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of developing tools to fight them has been slowed by lack a high-quality genome assembly. Here we combine diverse technologies produce markedly improved, fully re-annotated AaegL5 assembly, demonstrate how it accelerates mosquito science. We anchored physical cytogenetic maps, doubled number...
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...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published in life science journals. Entrez system search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface system. Custom implementations BLAST program provide sequence-based searching many specialized datasets. New released...
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...
The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. model underlying the can accommodate a range of structures, including sets unordered contig or scaffold sequences, bacterial genomes consisting single complete chromosome, complex structures such as human with modeled allelic variation. an accession version to unambiguously identify set sequences that make up particular assembly, tracks changes updated...
The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence database and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface New include Comparative Genome Resource (CGR) BLAST ClusteredNR database. Resources receiving significant updates past year PubMed, PMC, Bookshelf,...
Abstract Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, absence a standard for clinical reporting and browser display complicates process consistent interpretation reporting. To address these challenges, Ensembl/GENCODE 1 RefSeq 2 launched joint initiative, Matched Annotation from NCBI EMBL-EBI (MANE) collaboration, converge on human gene transcript jointly define high-value set transcripts corresponding proteins. Here, we...
Adult house flies, Musca domestica L., are mechanical vectors of more than 100 devastating diseases that have severe consequences for human and animal health. House fly larvae play a vital role as decomposers wastes, thus live in intimate association with many pathogens. We sequenced analyzed the genome using DNA from female flies. The is 691 Mb. Compared Drosophila melanogaster, contains rich resource shared novel protein coding genes, significantly higher amount repetitive elements,...
Abstract The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence database and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface Resources receiving significant updates past year include PubMed, PMC, Bookshelf, SciENcv, NIH Comparative Genomics Resource (CGR), Virus,...
Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant in new genomes. FCS-GX screens most genomes 0.1-10 min. Testing on artificially fragmented demonstrates high sensitivity specificity for diverse species. We used screen 1.6 million GenBank assemblies identified 36.8 Gbp contamination, comprising 0.16% total bases, with half from 161...
The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence repository and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 31 distinct repositories knowledgebases. E-utilities serve as programming interface these. Resources receiving significant updates past year include PubMed, PubMed Central, Bookshelf, NIH Comparative Genomics...