Nathan Johnson
A5004865707- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Machine Learning in Bioinformatics
- Cancer-related gene regulation
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Textile materials and evaluations
- Genomic variations and chromosomal abnormalities
- Parallel Computing and Optimization Techniques
- Biomedical Text Mining and Ontologies
- Genetic Neurodegenerative Diseases
- Statistical Methods and Applications
- Congenital heart defects research
- Health Sciences Research and Education
- Lung Cancer Treatments and Mutations
- Quality and Safety in Healthcare
- Cancer-related Molecular Pathways
- Genetic Mapping and Diversity in Plants and Animals
- Bioinformatics and Genomic Networks
- Color perception and design
- Genetic Associations and Epidemiology
- Data-Driven Disease Surveillance
Vanderbilt University
2021
Florida State University
2020
Illumina (United States)
2017
Wellcome Trust
2006-2016
European Bioinformatics Institute
2007-2016
Wellcome Sanger Institute
2007-2013
Defense Threat Reduction Agency
2009
The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates key model organisms. It provides data 87 species across our main early Pre! websites. This year we introduced three newly annotated released numerous updates supported with concentration on latest assemblies human, mouse, zebrafish rat. We also provided two previous human assembly, GRCh37, through dedicated...
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms farm animals. Over the past year we have increased number of that support 77 expanded our genome browser a new scrollable overview improved variation phenotype views. We also report updates core datasets improvements gene homology relationships from addition species. Our REST service has been extended additional for...
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions variation) on new human assembly, GRCh38, although continue to support researchers using GRCh37.p13 assembly through dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped identify of interest...
The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets all supported species; large-scale whole multiple species alignments across vertebrates clade-specific eutherian mammals, primates, birds fish; variation data 17 regulation annotations based ENCODE other sets. are accessible through the browser at http://www.ensembl.org tools...
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human data as well key model organisms such mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) Tasmanian devil (Sarcophilus harrisii) bringing total number of supported to 61 release 64 (September 2011). Of these, 55 appear main website six are provided preview site (Pre!Ensembl; http://pre.ensembl.org)...
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of annotation, databases, and other for chordate, selected model organism disease vector genomes. As release 51 (November 2008), fully supports 45 species, three additional species have preliminary support. New in the past year include orangutan six low coverage mammalian Major additions improvements to since our previous report major redesign website; generation multiple...
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation chordate genome sequences. Over the past year number genomes available from has increased 15 to 33, with addition sites for mammalian elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat european hedgehog; fish stickleback medaka second example sea squirt (Ciona savignyi) mosquito (Aedes aegypti). Some major features added during include first...
The Ensembl project ( http://www.ensembl.org ) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations set of includes additional data focused variation, comparative, evolutionary, functional regulatory annotation. most advanced resources are provided for key including human, mouse, rat zebrafish...
Abstract Most genomic variants associated with phenotypic traits or disease do not fall within gene coding regions, but in regulatory rendering their interpretation difficult. We collected public data on epigenetic marks and transcription factor binding human cell types used it to construct an intuitive summary of regions the genome. verified against independent assays for sensitivity. The Ensembl Regulatory Build will be progressively enriched when more is made available. It freely...
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of annotation, databases and other for chordate selected model organism disease vector genomes. As release 47 (October 2007), fully supports 35 species, with preliminary support six additional species. New species in the past year include platypus horse. Major additions improvements to since our previous report extensive functional genomics data form specialized database,...
We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists three fully integrated parts, reference 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, visualization tool that has been with the Ensembl genome browser new algorithm analysis immunoprecipitation-based demonstrate utility our by identifying first comprehensive set differentially methylated regions (tDMRs) may play role in...
Identifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem an important step toward integrating WGS into precision medicine. We developed a software tool called ExpansionHunter that, using PCR-free data, can genotype at the locus interest, even if expanded repeat larger than read length. applied our algorithm data...
Ensembl(http://www.ensembl.org)integrates genomic information for a comprehensive set of chordate genomes with particular focus on resources human, mouse, rat, zebrafish and other high-value sequenced genomes.We provide complete gene annotations all supported species in addition to specific that target genome variation, function evolution.Ensembl data is accessible variety formats including via our browser, API BioMart.This year marks the tenth anniversary Ensembl time project has grown...
Abstract Motivation: Using high-throughput sequencing, researchers are now generating hundreds of whole-genome assays to measure various features such as transcription factor binding, histone marks, DNA methylation or RNA transcription. Displaying so much data generally leads a confusing accumulation plots. We describe here multithreaded library that computes statistics on large numbers datasets (Wiggle, BigWig, Bed, BigBed and BAM), statistical summaries within minutes with limited memory...
New experimental techniques in epigenomics allow researchers to assay a diversity of highly dynamic features such as histone marks, DNA modifications or chromatin structure. The study their fluctuations should provide insights into gene expression regulation, cell differentiation and disease. Ensembl project collects maintains the regulation data resources on epigenetic transcription factor binding methylation for human mouse, well microarray probe mappings annotations variety chordate...
Molecular profiling with next generation sequencing (NGS) delivers key information on mutant gene sequences, copy number alterations, gene-fusions, and immunohistochemistry (IHC), is a valuable tool in clinical decision making for patients entering investigational agent trials. Our objective was to elucidate mutational profiles from primary versus metastatic sites advanced cancer guide rational therapy. All phase I (n = 203) were profiled by commercially available NGS platforms. The samples...
Abstract Background Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial attempt to measure the level of all genes in genome. Effectively translating results from microarray into a biological interpretation requires an accurate mapping between probesets on array that they targeting. Although major manufacturers provide annotations their gene arrays, methods by various different difficult keep up date rapidly changing world sequence databases....
Burkholderia pseudomallei and mallei are biological agents of military significance. There has been significant research in recent years to develop medical countermeasures for these organisms. This review summarizes work which details aspects the pathogenesis B. discusses key scientific questions directions future research.
Trumbo’s (1981) ideas on bivariate choropleth design have been underexplored and underutilized. He noted that effective map (including color selection) is directly informed by the intended goal or use of (i.e., what questions might answer), he identified three common spatial relationships can be displayed a choropleth: inverse relationships, range one variable within another, direct relationships. Each best suited to answering different readers’ questions. Trumbo also suggested sample...