Jonathan Ogata
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View article: Quantitative proteomics identifies conserved proteins and altered regulation of mucin-16 in low grade serous ovarian cancers
Quantitative proteomics identifies conserved proteins and altered regulation of mucin-16 in low grade serous ovarian cancers Open
Our efforts define highly conserved protein alterations distinguishing LGSOC from HGSOC tumors, including CD73, as well as the novel identification that MUC16 is elevated and exhibits more apical staining pattern in LGSOC tumor tissues. Th…
View article: Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches
Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches Open
Short-read sequencing data can be affected by alignment artifacts in certain genomic regions. Removing reads overlapping these exclusion regions, previously known as Blacklists, help to potentially improve biological signal. Tools like the…
View article: Deep Quantitative Proteomics Identifies Conserved Proteome Alterations in Low and High-Grade Serous Ovarian Cancers
Deep Quantitative Proteomics Identifies Conserved Proteome Alterations in Low and High-Grade Serous Ovarian Cancers Open
Low-grade serous ovarian carcinoma (LGSOC) is a rare and largely chemoresistant subtype of epithelial ovarian cancer. Unlike treatment for high-grade serous ovarian cancer (HGSOC), management options for LGSOC patients are limited, in part…
View article: excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies
excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies Open
Summary Exclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settin…
View article: excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies
excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies Open
Summary Exclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settin…
View article: Are the Double-mode Bulge RR Lyrae Stars with Identical Period Ratios the Relic of a Disrupted Stellar System?
Are the Double-mode Bulge RR Lyrae Stars with Identical Period Ratios the Relic of a Disrupted Stellar System? Open
Radial velocities of 15 double-mode bulge RR Lyrae (RR01) stars are presented, 6 of which belong to a compact group of RR01 stars in pulsation space, with the ratio of first-overtone period to fundamental mode period, P fo / P f ∼ 0.74, an…