Ericca Stamper
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View article: Exome sequencing shows same pattern of clonal tumor mutational burden, intratumor heterogenicity and clonal neoantigen between autologous tumor and Vigil product
Exome sequencing shows same pattern of clonal tumor mutational burden, intratumor heterogenicity and clonal neoantigen between autologous tumor and Vigil product Open
Retrospective data support overall survival (OS) advantage to high clonal tumor mutation burden (cTMB), high clonal neoantigen load (cNEO) and low intratumor heterogeneity (ITH) in cancer patients who receive immunotherapy. In order to exp…
View article: State-Threatened Gopher Tortoise (<i>Gopherus polyphemus</i>) Gut Microbiome Analysis Reveals Health Insights into Southeastern Florida Population
State-Threatened Gopher Tortoise (<i>Gopherus polyphemus</i>) Gut Microbiome Analysis Reveals Health Insights into Southeastern Florida Population Open
The gopher tortoise ( Gopherus polyphemus ), endemic to the southeastern part of the United States, is a keystone species that provides ecological support to over 350 species. Deforestation, urbanization, road mortality, and disease, over …
View article: Phosphoregulation of DSB-1 mediates control of meiotic double-strand break activity
Phosphoregulation of DSB-1 mediates control of meiotic double-strand break activity Open
In the first meiotic cell division, proper segregation of chromosomes in most organisms depends on chiasmata, exchanges of continuity between homologous chromosomes that originate from the repair of programmed double-strand breaks (DSBs) c…
View article: Author response: Phosphoregulation of DSB-1 mediates control of meiotic double-strand break activity
Author response: Phosphoregulation of DSB-1 mediates control of meiotic double-strand break activity Open
Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract In the first meiotic c…
View article: Phosphoregulation of DSB-1 mediates control of meiotic double-strand break activity
Phosphoregulation of DSB-1 mediates control of meiotic double-strand break activity Open
In the first meiotic cell division, proper segregation of chromosomes in most organisms depends on chiasmata, exchanges of continuity between homologous chromosomes that originate from the repair of programmed double-strand breaks (DSBs) c…
View article: Additional file 4 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Additional file 4 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions Open
Additional file 4: Table S5. RNA-seq mapping statistics. The number of sequenced, mapped, and multimapping RNA-seq reads for all libraries used in this study.
View article: Additional file 6 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Additional file 6 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions Open
Additional file 6: Table S7. Maintained regulatory regions in transposable elements. Counts of maintained regulatory regions overlapping different repeat groups used for enrichment analyses in Figure S10A.
View article: Additional file 7 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Additional file 7 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions Open
Additional file 7: Table S8. Multimapping reads. The percentage of quality controlled reads, i.e. MAPQ > 1 and duplicate removed, that map uniquely within non-repetitive genomic regions and LINE L1 and L2 genomic regions.
View article: Additional file 8 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Additional file 8 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions Open
Additional file 8: Table S9. Evolutionarily dynamic regulatory regions in transposable elements. Counts of evolutionarily dynamic regulatory regions overlapping different repeat groups use for enrichment analyses in Fig. 5e.
View article: Additional file 9 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Additional file 9 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions Open
Additional file 9: Data S1. The standalone ZIP file containing custom scripts and pipelines produced for this study.
View article: Additional file 5 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Additional file 5 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions Open
Additional file 5: Table S6. Recently evolved regulatory regions in transposable elements. Counts of recently evolved regulatory regions overlapping different repeat groups use for enrichment analyses in Fig. 5a.
View article: Additional file 2 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Additional file 2 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions Open
Additional file 2: Table S2. All tissues used in the study. Detailed description of all tissues samples used in the study, including the unique identifiers for three histone ChIP-seq libraries, the corresponding input libraries and RNA-seq…
View article: Additional file 3 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Additional file 3 of LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions Open
Additional file 3: Table S3. ChIP-seq mapping statistics. The number of reads sequenced, mapped, passing quality control and after duplicate removal for all ChIP-seq and input libraries used in this study.
View article: LINE elements are a reservoir of regulatory potential in mammalian genomes
LINE elements are a reservoir of regulatory potential in mammalian genomes Open
SUMMARY To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in liver, brain, muscle, and testis from ten diverse mammals. The regulatory landscape ar…