• Scholars@Duke publication: A chromosome-level reference genome and pangenome for barn swallow population genomics. (duke.edu)
  • A chromosome-level reference genome and pangenome for barn swallow population genomics. (duke.edu)
  • Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome. (duke.edu)
  • I am a researcher in population genomics. (me.uk)
  • QIAGEN CLC Genomics Workbench Premium includes all bioinformatics tools needed to power microbiology research, providing readily integrated and streamlined NGS workflows combined with state-of-the art data interpretation and visualization to shift the focus from data to discovery. (qiagen.com)
  • Yet a lack of well integrated analytics for microbial genomics leaves researchers and organisations with the burden of integrating and maintaining all the required bioinformatics, statistics and visualisation tools required to power their research. (qiagen.com)
  • QIAGEN CLC Genomics Workbench Premium expands upon CLC Genomics Workbench, the industry-standard platform for bioinformatics computing. (qiagen.com)
  • The focus is on pathogen genomes, applying advances in molecular and bioinformatics methods first developed for human genome research. (cdc.gov)
  • Topics broadly addressing the study of microbial communities, such as, meta-genomics surveys, bioinformatics, other '-omics' approaches and surveys, and community/host interaction mathematical modeling will be covered. (eurekalert.org)
  • Patrick Wincker also heads LAGE , which studies not only the structure and evolution of eukaryote genomes but also the structure and function of environmental eukaryotic communities using bioinformatics methodologies. (cea.fr)
  • Dr. Achraf El Allali is an assistant professor of bioinformatics at the African Genome Center, University Mohammed VI Polytechnic . (plos.org)
  • In his current role, he is entrusted with leading the Bioinformatics Program at the African Genome Center. (plos.org)
  • Assembly of metagenomic samples is a very complex process, with algorithms designed to address sequencing platform-specific issues, (read length, data volume, and/or community complexity), while also faced with genomes that differ greatly in nucleotide compositional biases and in abundance. (nature.com)
  • Due to the number, frequency, types and sizes of genomes present in highly diverse communities, additional sequencing of metagenome samples often captures novel genome fragments from increasingly rare members (or minor variants) of the community. (nature.com)
  • The emergence of these technologies has not only facilitated genome sequencing but also changed the landscape of life sciences. (usda.gov)
  • Here I survey their major applications ranging from whole-genome sequencing and resequencing, single nucleotide polymorphism (SNP) and structural variation discovery, to mRNA and noncoding RNA profiling and ChIP-seq. (usda.gov)
  • Using the single-celled sequencing techniques that she had perfected at the Joint Genome Institute, Woyke and her colleagues ended up with exactly 201 genomes from these candidate phyla, representing 29 branches on the tree of life that scientists knew nothing about. (doe.gov)
  • The Genomics Unit offers short read (Illumina NexSeq 2000 and Illumina MiSeq) and long read Nanopore sequencing, Library preparation, and Fragment-analyzer/TapeStation sample QC services. (gulbenkian.pt)
  • The unit provide a range of services: RNA-Seq, Whole Genome Sequencing, Spatial transcriptomics and Metagenomics (bacterial 16S rRNA, ITS). (gulbenkian.pt)
  • For Single Cell sequencing the unit operates a 10X Genomics Chromium controller and the new Chromium X capable of high-throughput experiments. (gulbenkian.pt)
  • The Microbial Genomics and Metagenomics Laboratory (MGML) provides metagenomic sequencing and analysis support to the Cincinnati Children's, University of Cincinnati and surrounding communities. (cincinnatichildrens.org)
  • The MGML is staffed and equipped to provide services ranging from 16S ribosomal RNA sequencing (16S rRNA), shotgun metagenomics and RNA sequencing. (cincinnatichildrens.org)
  • Sequencing metagenomes, metatranscriptomes, and reference single-cell genomes from Tara stations. (embl.org)
  • Annotating genomes with massive-scale RNA sequencing. (embl.org)
  • Metagenomics sequencing tuberculosis in humans. (cdc.gov)
  • Beckman Coulter Genomics specialises in next generation and Sanger sequencing services across the Illumina HiSeq 2500, Roche 454 GS FLX and ABI 3730XL sequencing platforms. (onenucleus.com)
  • Applications include exome and targeted resequencing, de novo genome sequencing, metagenomics, genotyping, expression analysis, biomarker discovery and biological safety and efficiency testing. (onenucleus.com)
  • We developed and implemented the analysis of single amplified genomes followed by restriction-site-associated DNA sequencing to bypass labor-intensive culturing and to avoid culturing bias in population genomic studies of unicellular eukaryotes. (lu.se)
  • The PhD candidate will obtain sediment samples and isolate DNA to determine the microbial community composition using 16S rRNA amplicon sequencing and genome-resolved metagenomics analyses. (fems-microbiology.org)
  • We concluded that depending on the focus of a research project, amplicon-based MinION Nanopore sequencing can be an ideal cost- and time-effective alternative to Illumina in producing optimal genome coverage. (frontiersin.org)
  • The missions of Jean-Marc Aury's team include sequencing data formatting, data quality control, genome and transcriptome assembly and eukaryote genome annotation. (cea.fr)
  • A research team from Bigelow Laboratory for Ocean Sciences, the University of Hawai'i at Mānoa, and the Department of Energy Joint Genome Institute bypassed the problem of cultivation with genetic sequencing methods called genomics, a suite of novel techniques used to sequence large groups of genetic information. (bigelow.org)
  • Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. (biomedcentral.com)
  • Whole-genome sequencing allows searching and comparing one's own genome to millions and soon billions of other human genomes. (biomedcentral.com)
  • Whole-genome sequencing studies often identify only a few genomic regions that contain elements with large effects on the penetrance or expressivity of gene products but hundreds of genomic regions that have small effects and are highly dependent on genetic background, environmental factors, or social and lifestyle determinants [ 3 ]. (biomedcentral.com)
  • Whole-genome sequencing enables the detection of resistance genes, mutations, and mobile genetic elements, aiding in surveillance efforts and guiding antibiotic prescribing practices. (alliedacademies.org)
  • Clinical Value of Metagenomics Next-Generation Sequencing in Antibiotic Resistance of a Patient with Severe Refractory Mycoplasma pneumoniae Pneumonia: A Case Report. (cdc.gov)
  • Use whole genome sequencing to study how and why certain fungi spread and make people sick. (cdc.gov)
  • The use of whole-genome sequencing has enabled more precise evaluation of engraftment, they add. (medscape.com)
  • IMG provides users a set of tools for comparative analysis of microbial genomes along three dimensions: genes, genomes and functions. (wikipedia.org)
  • We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. (duke.edu)
  • In particular, because aphids possess many genes that are absent from Drosophila and other holometabolous insect taxa, aphid genome annotation efforts cannot rely entirely on homology to the best-studied insect systems. (biomedcentral.com)
  • Further, our results indicate that microarrays are a useful tool for inferring functional roles of genes in A. pisum and other insects and suggest that the pea aphid genome may contain many gene paralogs that are differentially regulated. (biomedcentral.com)
  • The study and comparison of entire genomes, including the complete set of genes and their nucleotide sequence and organization, is called genomics. (americascupmagazine.com)
  • Metagenomics and metatranscriptomics allow researchers to study genes and gene expression from a collection of multiple species, many of which may not be easily cultured or cultured at all in the laboratory. (americascupmagazine.com)
  • Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
  • For example, genomics has been instrumental in tracking the spread of antimicrobial resistance genes, allowing for tailored antibiotic stewardship programs and the development of novel therapeutics [ 3 ]. (alliedacademies.org)
  • The Integrated Microbial Genomes with Microbiome Samples (IMG/M) system is an extension of the IMG system providing a comparative analysis context of assembled metagenomic data with the publicly available isolate genomes. (wikipedia.org)
  • The IMG-HMP is focused on analysis of genomes related to the Human Microbiome Project (HMP) in the context of all publicly available genomes in IMG. (wikipedia.org)
  • Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
  • QIAGEN CLC Genomics Workbench Premium delivers novel insights in metagenomics, microbiome profiling, pathogen typing or genome-based outbreak investigations. (qiagen.com)
  • Eric Wommack, from the University of Delaware's College of Earth, Ocean and Environment and Jacques Ravel, from the University of Maryland School of Medicine's Institute for Genome Sciences are the Editors-in-Chief of Microbiome , a BioMed Central (BMC) publication, which launched its first issue this week. (eurekalert.org)
  • Active research programs within the unit provide a foundation for advanced training in microbiome science including human and animal pathogenic microbiology, virology, aquatic microbiology, microbial cell biology, computational biology, genomics and microbial cell evolution. (oregonstate.edu)
  • Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases. (cdc.gov)
  • Shotgun metagenomics reveals an enrichment of potentially cross-reactive bacterial epitopes in ankylosing spondylitis patients, as well as the effects of TNFi therapy upon microbiome composition. (cdc.gov)
  • RESULTS: We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. (bvsalud.org)
  • The unit offers 10X Genomics Visium Spatial Transcriptomics service with the Histopathology Facility. (gulbenkian.pt)
  • We are looking for a highly motivated and curiosity-driven PhD candidate with an interest in microbiology, specifically on the integration of various 'omics' approaches (metagenomics, transcriptomics, proteomics) to study the microbial physiology of prokaryotes in anoxic marine and hot spring sediments. (fems-microbiology.org)
  • In this section, we'll provide a brief overview of the whole-genome fields of genomics, transcriptomics, and proteomics. (americascupmagazine.com)
  • When genomics and transcriptomics are applied to entire microbial communities, we use the terms metagenomics and metatranscriptomics, respectively. (americascupmagazine.com)
  • Another up-and-coming clinical application of genomics and transcriptomics is pharmacogenomics, also called toxicogenomics, which involves evaluating the effectiveness and safety of drugs on the basis of information from an individual's genomic sequence. (americascupmagazine.com)
  • Genomes are found at all three corners of the epidemiologic triangle: human or animal hosts are engaged in genomic contests with pathogens of all kinds, played out in an environment teeming with the genomes of other people, animals, plants, and microbes. (cdc.gov)
  • Alan's work focuses on the evolutionary genomics of pathogenesis and antimicrobial resistance in bacterial pathogens, but in April Alan was seconded to the Milton Keynes Lighthouse Lab as the Lead for Infectious Disease at the government's first flagship Covid-19 testing facility and he's currently heading up the new Covid testing lab at the University of Birmingham. (birmingham.ac.uk)
  • We routinely use metagenomics to characterize and obtain multi-gene data for such pathogens, and to reconstruct whole genomes of novel pathogens. (cefas.co.uk)
  • Genomics has emerged as a powerful tool in the fight against infectious diseases, enabling researchers to delve deeper into the molecular characteristics of pathogens and their interactions with hosts. (alliedacademies.org)
  • Genomics has shed light on the complex interactions between pathogens and their hosts, unravelling the mechanisms underlying virulence, immune evasion, and disease progression. (alliedacademies.org)
  • Advance the use of genomics and metagenomics for detecting fungal pathogens and antifungal drug resistance. (cdc.gov)
  • Scan several protein sequences or a whole genome (all ORFs) against HAMAP family profiles. (expasy.org)
  • This approach has been called " genomic epidemiology "-using pathogen genome sequences to detect emerging diseases, assess their potential virulence and resistance to antibiotics, and monitor their spread in populations. (cdc.gov)
  • However, compared to other flaviviruses, USUV has received less research attention and there is therefore limited access to whole-genome sequences and also to in-depth phylogenetic and phylodynamic analyses. (frontiersin.org)
  • In contrast to reference-based approaches which relate sequences to a single genome, these data structures encode the mutual relationships between all the genomes represented. (biorxiv.org)
  • Genome sequences of Tropheus moorii and Petrochromis trewavasae , two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. (tugraz.at)
  • The systematic study of the complete DNA sequences (GENOME) of organisms. (bvsalud.org)
  • bacterial genome editing using of 'suicide' vectors for allelic exchange. (uibk.ac.at)
  • The Integrated Microbial Genomes (IMG) system is a genome browsing and annotation platform developed by the U.S. Department of Energy (DOE)-Joint Genome Institute. (wikipedia.org)
  • IMG also includes a genome annotation pipeline that integrates information from several tools, including KEGG, Pfam, InterPro, and the Gene Ontology, among others. (wikipedia.org)
  • The Integrated Microbial Genomes- Expert Review (IMG/ER) system provides support to individual scientists or group of scientists for functional annotation and curation of their microbial genomes of interest. (wikipedia.org)
  • Users can submit their annotated genomes (or request the IMG automated annotation pipeline to be applied first) into IMG-ER and proceed with manual curation and comparative analysis in the system, through secure (password protected) access. (wikipedia.org)
  • These case studies in comparative and functional genomics, epigenomics, and metagenomics are providing a more complete picture of the genome structures and functions. (usda.gov)
  • Leverage whole genome analysis for epidemiological outbreak investigation, accurately type and characterize microbial isolates and monitor outbreaks and track pathogen transmission back to the source using modern phylogenetic tools. (qiagen.com)
  • My research group investigates the genomics of natural pathogen populations, focusing on issues of disease risk, transmission, evolution and detecting selection. (me.uk)
  • Genomics has revolutionized pathogen detection and surveillance, enabling rapid and accurate identification of infectious agents. (alliedacademies.org)
  • The IMG-VR system (with the recent updated version IMG/VR v.2.0) is the largest publicly available database for viral genomes and metagenomes. (wikipedia.org)
  • Analysis of genomes and metagenomes. (genopole.com)
  • 2023). First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale . (uibk.ac.at)
  • Final Round of 2022 CSP Functional Genomics Awardees Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call. (doe.gov)
  • Research at the intersection of biological and microbial oceanography and functional genomics. (ucsd.edu)
  • Functional genomics, metabolism. (genopole.com)
  • We've also got with us Professor Alan McNally who is Professor in Microbial Genomics and the Director of the Institute of Microbiology and Infection at the University of Birmingham. (birmingham.ac.uk)
  • Jacques Ravel, is a professor of microbiology and immunology and associate director for genomics at the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine. (eurekalert.org)
  • With over 40 peer-reviewed papers published, his research focuses on the integration of experimental and computational research, specifically in the field of computational genomics and metagenomics. (plos.org)
  • You can assemble and annotate high-quality reference genomes for critical type strains and manage your database of reference genomes. (qiagen.com)
  • Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. (duke.edu)
  • The tailed phage possesses a 53,187 bp linear dsDNA genome, with 84 ORFs encoding structural proteins, genome replication, host lysis, etc. in a modular pattern. (bvsalud.org)
  • This field has great potential for future medical advances through the study of the human genome as well as the genomes of infectious organisms. (americascupmagazine.com)
  • This article aims to explore the applications of genomics in infectious diseases and highlight its potential in transforming prevention, diagnosis, and treatment [ 1 ]. (alliedacademies.org)
  • Additionally, genomics has facilitated the discovery of novel biomarkers and therapeutic targets for infectious diseases, aiding in the development of vaccines and immunotherapies The rise of antimicrobial resistance poses a significant threat to public health. (alliedacademies.org)
  • There is also a need to study disease pathogenesis on genome, epigenome, transcriptome, proteome, and metabolome levels and combine these dimensions through multi-omics research. (biomedcentral.com)
  • The lab is structured around a transversal research theme (orphan gene dynamics) and three study domains: plant genomics, fungal genomics and marine plankton metagenomics. (cea.fr)
  • Development of this dual-genome array represents a first attempt to characterize gene expression in this emerging model system. (biomedcentral.com)
  • We examined gene expression under heat shock of an insect and its bacterial symbiont in a single assay using a dual-genome microarray. (biomedcentral.com)
  • The phage genome is integrated into the host chromosome near the 3'-end of deoD, a gene encoding purine nucleoside phosphorylase (PNP). (bvsalud.org)
  • The QIAGEN CLC Genomics Workbench Premium is intended for molecular biology applications. (qiagen.com)
  • Julie Poulain is a molecular biologist working in the field of marine environmental genomics at t he Laboratory for the Genomic Analysis of Eukaryotes (LAGE) within Genoscope's UMR 8030 Genomics Metabolics Unit. (cea.fr)
  • This makes this educational crowdsourced genomic project the single largest contributor to the global growth of phage genome data. (bytesizebio.net)
  • Another interesting thing that was found was the large number of recombinations that go on the phage genome. (bytesizebio.net)
  • Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). (duke.edu)
  • Working in partnership with the Department of Energy's Joint Genome Institute, the researchers sorted and analyzed the microbes in the Single Cell Genomics Center at Bigelow Laboratory. (bigelow.org)
  • This work was supported by the National Science Foundation, the NASA Astrobiology Institute, the DOE Joint Genome Institute, and the Center for Dark Energy Biosphere Investigations (C-DEBI). (bigelow.org)
  • Genome Insider: Methane Makers in Yosemite's Lakes Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work. (doe.gov)
  • 1 year subscription for static licenses for CLC Genomics Workbench, CLC Microbial Genomics Module, CLC Single Cell Analysis Module and CLC Genome Finishing Module to use the software on a single computer. (qiagen.com)
  • Plugins and modules add a layer of specialized tools and workflows to CLC Genomics Workbench, creating a comprehensive solution for microbial genomics and metagenomics data analysis. (qiagen.com)
  • Analysis of microbial genomes has contributed to the development of new antibiotics, diagnostic tools, vaccines, medical treatments, and environmental cleanup techniques. (americascupmagazine.com)
  • Comparative Genome Analysis of Two Bacillus pumilus Strains Producing High Level of Extracellular Hydrolases. (uibk.ac.at)
  • AlCoB aims at promoting and displaying excellent research using string and graph algorithms and combinatorial optimization to deal with problems in biological sequence analysis, genome rearrangement, evolutionary trees, and structure prediction. (rwth-aachen.de)
  • To illuminate the phylogenetic and environmental distribution of these metabolic and adaptive traits across the Verrucomicrobia phylum, we performed a comparative genomic analysis of 31 publicly available, nearly complete Verrucomicrobia genomes. (unh.edu)
  • A Comprehensive Analysis of Genomics and Metagenomics in a Heterozygote Familial Hypercholesterolemia Family. (cdc.gov)
  • Included is construction of complete genetic, physical, and transcript maps, and the analysis of this structural genomic information on a global scale such as in GENOME WIDE ASSOCIATION STUDIES. (bvsalud.org)
  • Comparative metagenomics of eukaryotes. (embl.org)
  • Genoscope is currently focusing its own research activity on the metagenomics of microorganisms from the environment, and more specifically marine eukaryotes (the TARA Oceans project), soilborne organisms, the bacterial flora of the human digestive tract, or those involved in effluent treatment. (genopole.com)
  • Most of the 61 articles on human genomics were related to epidemiology. (cdc.gov)
  • Using shotgun metagenomics, we identified an imported socioeconomic survey. (cdc.gov)
  • Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet ( 13 C and 15 N content), mobility ( 87 Sr/ 86 Sr ratio) and vegetation cover (pollen). (lu.se)
  • Tracing the Evolution of Shiitake Mushrooms Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. (doe.gov)
  • Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. (embl.org)
  • The Ectocarpus genome and the independent evolution of multicellularity in brown algae. (embl.org)
  • Recent advances in metagenomics have generated numerous insights related to the cell biology, ecology, evolution, and biogeochemistry of microbial life in the ocean. (jcvi.org)
  • These flexible models let us encode any kind of variation, allowing the generation of comprehensive data systems that builds the basis for the analyses of genome evolution. (biorxiv.org)
  • But with two projects, communities are forming to generate high quality genomes to benefit researchers. (doe.gov)
  • Beckman Coulter Genomics is a leading provider of genomic services for life science researchers and the biotech and pharmaceutical industries worldwide. (onenucleus.com)
  • Patrick Wincker directs the UMR 8030 Genomics Metabolics Unit , Genoscope's basic research unit. (cea.fr)
  • This research is performed in close collaboration with the UMR 8030 Metabolic Genomics research unit. (genopole.com)
  • Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. (embl.org)
  • Genomics provides critical insights into the genetic determinants of drug resistance, allowing for the rapid identification of resistance mechanisms and the development of targeted therapies. (alliedacademies.org)
  • By providing technical expertise, combined with personalised service, Beckman Coulter Genomics delivers the highest quality data, robust analyses and innovative thinking. (onenucleus.com)
  • A key point of the reference genome is that it is not a single sequence. (scienceblogs.com)
  • When a single genome is being sequenced, measuring the quality of the assembly is relatively straightforward, with a minimal number of large contigs being ideal. (nature.com)
  • Notably, advances in single cell genomics (SCG), fluorescence activated cell sorting (FACS) capture of specific populations and metagenomic assembly are providing valuable information related to within and between lineage genomic content. (jcvi.org)
  • homologous regions between genomes are compressed into a single representative of all alleles present in the pangenome. (biorxiv.org)
  • These findings emphasize why single cell genomics are such important tools for discovering how a huge proportion of life functions. (bigelow.org)
  • Analyzing Hydrothermarchaeota genomes revealed that these microbes belong to the group of single-celled life known as archaea and evolved early in the history of life on Earth - as did their unusual metabolic processes. (bigelow.org)
  • While Verrucomicrobia remain poorly represented in culture collections, numerous genomes have been reconstructed from metagenomic data sets in recent years. (unh.edu)
  • A metagenome is the collection of all genetic material present in an environmental sample and includes the genomes of a diverse community of microbes. (cincinnatichildrens.org)
  • The project team also analyzed the microbes using metagenomics, a technique that extracts genomic information directly from environmental samples. (bigelow.org)
  • Eventually, the entire world population could be used as a reference population in order to link genome information with many other types of physiological, clinical, environmental, and lifestyle data. (biomedcentral.com)
  • Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface. (unh.edu)
  • Despite the widespread availability of microbial genome data-close to 2,000 microbes have been and are being decoded to date-a vast unknown realm awaits scientists intent on exploring microorganisms that inhabit this "undiscovered country. (doe.gov)