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Jennifer M. Lee

Bio: Jennifer M. Lee is a academic researcher at National Institutes of Health who has co-authored 21 publication(s) receiving 6558 citation(s). The author has an hindex of 14. Previous affiliations of Jennifer M. Lee include Colorado State University & University of Washington. The author has done significant research in the topic(s): Nanocages & Phenotypic trait.

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Topics: Nanocages, Phenotypic trait, Nanoparticle ...read more
Papers
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Open accessJournal ArticleDOI: 10.1093/NAR/GKT1113
Abstract: ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/) provides a freely available archive of reports of relationships among medically important variants and phenotypes. ClinVar accessions submissions reporting human variation, interpretations of the relationship of that variation to human health and the evidence supporting each interpretation. The database is tightly coupled with dbSNP and dbVar, which maintain information about the location of variation on human assemblies. ClinVar is also based on the phenotypic descriptions maintained in MedGen (http://www.ncbi.nlm.nih.gov/medgen). Each ClinVar record represents the submitter, the variation and the phenotype, i.e. the unit that is assigned an accession of the format SCV000000000.0. The submitter can update the submission at any time, in which case a new version is assigned. To facilitate evaluation of the medical importance of each variant, ClinVar aggregates submissions with the same variation/phenotype combination, adds value from other NCBI databases, assigns a distinct accession of the format RCV000000000.0 and reports if there are conflicting clinical interpretations. Data in ClinVar are available in multiple formats, including html, download as XML, VCF or tab-delimited subsets. Data from ClinVar are provided as annotation tracks on genomic RefSeqs and are used in tools such as Variation Reporter (http://www.ncbi.nlm.nih.gov/variation/tools/reporter), which reports what is known about variation based on user-supplied locations.

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1,852 Citations


Open accessJournal ArticleDOI: 10.1093/NAR/GKV1222
Melissa J. Landrum1, Jennifer M. Lee1, Mark L. Benson1, Garth Brown1  +15 moreInstitutions (1)
Abstract: ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) at the National Center for Biotechnology Information (NCBI) is a freely available archive for interpretations of clinical significance of variants for reported conditions. The database includes germline and somatic variants of any size, type or genomic location. Interpretations are submitted by clinical testing laboratories, research laboratories, locus-specific databases, OMIM®, GeneReviews™, UniProt, expert panels and practice guidelines. In NCBI's Variation submission portal, submitters upload batch submissions or use the Submission Wizard for single submissions. Each submitted interpretation is assigned an accession number prefixed with SCV. ClinVar staff review validation reports with data types such as HGVS (Human Genome Variation Society) expressions; however, clinical significance is reported directly from submitters. Interpretations are aggregated by variant-condition combination and assigned an accession number prefixed with RCV. Clinical significance is calculated for the aggregate record, indicating consensus or conflict in the submitted interpretations. ClinVar uses data standards, such as HGVS nomenclature for variants and MedGen identifiers for conditions. The data are available on the web as variant-specific views; the entire data set can be downloaded via ftp. Programmatic access for ClinVar records is available through NCBI's E-utilities. Future development includes providing a variant-centric XML archive and a web page for details of SCV submissions.

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1,680 Citations


Open accessJournal ArticleDOI: 10.1093/NAR/GKX1153
Melissa J. Landrum1, Jennifer M. Lee1, Mark L. Benson1, Garth Brown1  +18 moreInstitutions (1)
Abstract: ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants). Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report. ClinVar recently started accepting submissions that are focused primarily on providing phenotypic information for individuals who have had genetic testing. Submissions may come from clinical providers providing their own interpretation of the variant ('provider interpretation') or from groups such as patient registries that primarily provide phenotypic information from patients ('phenotyping only'). ClinVar continues to make improvements to its search and retrieval functions. Several new fields are now indexed for more precise searching, and filters allow the user to narrow down a large set of search results.

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Topics: Variant Call Format (53%)

1,264 Citations


Open accessJournal ArticleDOI: 10.1101/GR.080531.108
Kim D. Pruitt1, Jennifer Harrow, Rachel A. Harte, Craig Wallin  +45 moreInstitutions (1)
01 Jul 2009-Genome Research
Abstract: Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers. Importantly, the project coordinates on manually reviewing inconsistent protein annotations between sites, as well as annotations for which new evidence suggests a revision is needed, to progressively converge on a complete protein-coding set for the human and mouse reference genomes, while maintaining a high standard of reliability and biological accuracy. To date, the project has identified 20,159 human and 17,707 mouse consensus coding regions from 17,052 human and 16,893 mouse genes. Three evaluation methods indicate that the entries in the CCDS set are highly likely to represent real proteins, more so than annotations from contributing groups not included in CCDS. The CCDS database thus centralizes the function of identifying well-supported, identically-annotated, protein-coding regions.

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Topics: Ensembl (57%), Human genome (53%), Protein Annotation (50%)

555 Citations


Journal ArticleDOI: 10.1002/ADMA.200500833
Jingyi Chen1, Benjamin J. Wiley1, Zhi-Yuan Li2, Dean Campbell1  +6 moreInstitutions (2)
16 Sep 2005-Advanced Materials
Abstract: The galvanic replacement reaction between a Ag template and HAuCl4 in an aqueous solution transforms 30-200 mn Ag nanocubes into Au nanoboxes and nanocages (nanoboxes with porous walls). By controlling the molar ratio of Ag to HAuCl4, the extinction peak of resultant structures can be continuously tuned from the blue (400 nm) to the near-infrared (1200 nm) region of the electromagnetic spectrum. These hollow An nanostructures are characterized by extraordinarily large cross sections for both absorption and scattering. Optical coherence tomography measurements indicate that the 36 nm nanocage has a scattering cross-section of similar to 0.8 X 10(-15) m(2) and an absorption cross-section of similar to 7.3 X 10(-15) m(2). The absorption cross-section is more than five orders of magnitude larger than those of conventional organic dyes. Exposure of Au nanocages to a camera flash resulted in the melting and conversion of Au nanocages into spherical particles due to photothermal heating. Discrete-di poleapproximation calculations suggest that the magnitudes of both scattering and absorption cross-sections of An nanocages can be tailored by controlling their dimensions, as well as the thickness and porosity of their walls. This novel class of hollow nanostructures is expected to find use as both a contrast agent for optical imaging in early stage tumor detection and as a therapeutic agent for photothermal cancer treatment.

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Topics: Nanocages (72%), Photothermal therapy (51%), Absorption (electromagnetic radiation) (50%) ...read more

523 Citations


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Open accessJournal Article
Fumio Tajima1Institutions (1)
30 Oct 1989-Genomics
Abstract: The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method needs only the data of DNA polymorphism, namely the genetic variation within population at the DNA level. A simple method of computer simulation, that was used in order to obtain the distribution of a new statistic developed, is also presented. Applying this statistical method to the five regions of DNA sequences in Drosophila melanogaster, it is found that large insertion/deletion (greater than 100 bp) is deleterious. It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

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Topics: Neutral mutation (54%), Population (54%), Genetic variation (52%) ...read more

10,734 Citations


Journal ArticleDOI: 10.1021/NL052396O
01 Mar 2006-Nano Letters
Abstract: We investigated the intracellular uptake of different sized and shaped colloidal gold nanoparticles. We showed that kinetics and saturation concentrations are highly dependent upon the physical dimensions of the nanoparticles (e.g., uptake half-life of 14, 50, and 74 nm nanoparticles is 2.10, 1.90, and 2.24 h, respectively). The findings from this study will have implications in the chemical design of nanostructures for biomedical applications (e.g., tuning intracellular delivery rates and amounts by nanoscale dimensions and engineering complex, multifunctional nanostructures for imaging and therapeutics).

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Topics: Colloidal gold (56%), Nanoparticle (52%)

4,022 Citations


Open accessJournal ArticleDOI: 10.1101/GR.135350.111
01 Sep 2012-Genome Research
Abstract: The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

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Topics: GENCODE (77%), Ensembl (53%), Molecular Sequence Annotation (53%) ...read more

3,750 Citations


Open accessJournal ArticleDOI: 10.1021/JP057170O
Abstract: The selection of nanoparticles for achieving efficient contrast for biological and cell imaging applications, as well as for photothermal therapeutic applications, is based on the optical properties of the nanoparticles. We use Mie theory and discrete dipole approximation method to calculate absorption and scattering efficiencies and optical resonance wavelengths for three commonly used classes of nanoparticles: gold nanospheres, silica−gold nanoshells, and gold nanorods. The calculated spectra clearly reflect the well-known dependence of nanoparticle optical properties viz. the resonance wavelength, the extinction cross-section, and the ratio of scattering to absorption, on the nanoparticle dimensions. A systematic quantitative study of the various trends is presented. By increasing the size of gold nanospheres from 20 to 80 nm, the magnitude of extinction as well as the relative contribution of scattering to the extinction rapidly increases. Gold nanospheres in the size range commonly employed (∼40 nm)...

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  • Figure 3. Calculated spectra of the efficiency of absorptionQabs (red triangles), scatteringQsca (black circles), and extinctionQext (green squares) for gold nanorods (a) with fixed aspect ratioR ) 3.9 andreff ) 8.74, 11.43, 17.90, and 21.86 nm, and (b) with fixed effective radiusreff ) 11.43 nm andR ) 3.1, 3.9, and 4.6. Note the solid curves are Lorentzian fits to the calculated data points.
    Figure 3. Calculated spectra of the efficiency of absorptionQabs (red triangles), scatteringQsca (black circles), and extinctionQext (green squares) for gold nanorods (a) with fixed aspect ratioR ) 3.9 andreff ) 8.74, 11.43, 17.90, and 21.86 nm, and (b) with fixed effective radiusreff ) 11.43 nm andR ) 3.1, 3.9, and 4.6. Note the solid curves are Lorentzian fits to the calculated data points.
  • Figure 4. Tunability of the plasmon resonance maximum in nanoparticles. Variation of surface plasmon extinction maximumλmax with (a) nanosphere diameterD, (b) nanoshell total radiusR2 at fixed R1/R2 ) 0.857, (c) nanoshell core/shell ratioR1/R2 at fixed R2 ) 70 nm, (d) nanorod effective radiusreff at fixed aspect ratioR ) 3.9, and (e) nanorod aspect ratioR at fixed reff ) 11.43 nm (and straight line fit).
    Figure 4. Tunability of the plasmon resonance maximum in nanoparticles. Variation of surface plasmon extinction maximumλmax with (a) nanosphere diameterD, (b) nanoshell total radiusR2 at fixed R1/R2 ) 0.857, (c) nanoshell core/shell ratioR1/R2 at fixed R2 ) 70 nm, (d) nanorod effective radiusreff at fixed aspect ratioR ) 3.9, and (e) nanorod aspect ratioR at fixed reff ) 11.43 nm (and straight line fit).
  • TABLE 1: Calculated Extinction Wavelength Maximum λmax (nm), Per Micron Absorption Coefficient µa (at absorption wavelength maximumλa), Per Micron Scattering Coefficient µs (at scattering maximum wavelengthλs), and Ratio of Scattering to Absorption Component of the Extinction µs/µa for Gold Nanospheres, Gold Nanorods, and Silica-Gold Nanoshells of Different Dimensions
    TABLE 1: Calculated Extinction Wavelength Maximum λmax (nm), Per Micron Absorption Coefficient µa (at absorption wavelength maximumλa), Per Micron Scattering Coefficient µs (at scattering maximum wavelengthλs), and Ratio of Scattering to Absorption Component of the Extinction µs/µa for Gold Nanospheres, Gold Nanorods, and Silica-Gold Nanoshells of Different Dimensions
  • Figure 5. Tunability of the extinction cross-section of nanoparticles. Variation ofCext with (a) nanosphere diameterD, (b) nanoshell total radius R2 at fixed R1/R2 ) 0.857, (c) nanoshell core/shell ratioR1/R2 at fixed R2 ) 70 nm, (d) nanorod effective radiusreff at fixed aspect ratioR ) 3.9, and (e) nanorod aspect ratioR at fixed reff ) 11.43 nm.
    Figure 5. Tunability of the extinction cross-section of nanoparticles. Variation ofCext with (a) nanosphere diameterD, (b) nanoshell total radius R2 at fixed R1/R2 ) 0.857, (c) nanoshell core/shell ratioR1/R2 at fixed R2 ) 70 nm, (d) nanorod effective radiusreff at fixed aspect ratioR ) 3.9, and (e) nanorod aspect ratioR at fixed reff ) 11.43 nm.
  • Figure 1. Calculated spectra of the efficiency of absorptionQabs (red dashed), scatteringQsca (black dotted), and extinctionQext (green solid) for gold nanospheres (a)D ) 20 nm, (b)D ) 40 nm, (c)D ) 80 nm, and polystyrene nanospheres (d)D 300 nm.
    Figure 1. Calculated spectra of the efficiency of absorptionQabs (red dashed), scatteringQsca (black dotted), and extinctionQext (green solid) for gold nanospheres (a)D ) 20 nm, (b)D ) 40 nm, (c)D ) 80 nm, and polystyrene nanospheres (d)D 300 nm.
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Topics: Colloidal gold (56%), Scattering (55%), Discrete dipole approximation (54%) ...read more

3,694 Citations


Open accessJournal ArticleDOI: 10.1186/S13059-016-0974-4
06 Jun 2016-Genome Biology
Abstract: The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.

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Topics: Ensembl (64%)

2,941 Citations


Performance
Metrics

Author's H-index: 14

No. of papers from the Author in previous years
YearPapers
20211
20201
20192
20181
20163
20151

Top Attributes

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Author's top 5 most impactful journals

Nucleic Acids Research

4 papers, 4.9K citations

Genetics

2 papers, 153 citations

Angewandte Chemie

2 papers, 8 citations

ACS Nano

1 papers, 35 citations

Arthritis Research & Therapy

1 papers, 94 citations

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