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Akademický článek

Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data

Autor: Rui Hong, Yusuke Koga, Shruthi Bandyadka, Anastasia Leshchyk, Yichen Wang, Vidya Akavoor, Xinyun Cao, Irzam Sarfraz, Zhe Wang, Salam Alabdullatif, Frederick Jansen, Masanao Yajima, W. Evan Johnson, Joshua D. Campbell

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-9 (2022)

Quality control (QC) is a crucial step in single-cell RNA-seq data analysis. Here, the authors present the SCTK-QC pipeline which generates and visualizes a comprehensive set of QC metrics to streamline the process of detecting and removing poor qual

Externí odkaz: https://doaj.org/article/3b9c0a0a78f74f97957e4f3059d88d39

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Akademický článek

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Autor: Shiyi Yang, Sean E. Corbett, Yusuke Koga, Zhe Wang, W Evan Johnson, Masanao Yajima, Joshua D. Campbell

Publikováno v: Genome Biology, Vol 21, Iss 1, Pp 1-15 (2020)

Abstract Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s native mRNA and result in cross

Externí odkaz: https://doaj.org/article/eb723902385c482f96dc28348751ae7c

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Akademický článek

Elevated T cell repertoire diversity is associated with progression of lung squamous cell premalignant lesions

Autor: Gang Liu, Asaf Maoz, Christopher Stevenson, Mary E Reid, Avrum Spira, Marc E Lenburg, Joshua D Campbell, Carter Merenstein, Yusuke Koga, Austin Potter, Adam C Gower, Sherry Zhang, Hanqiao Liu, Sarah A Mazzilli, Jennifer Beane

Publikováno v: Journal for ImmunoTherapy of Cancer, Vol 9, Iss 9 (2021)

Externí odkaz: https://doaj.org/article/1a370bde366f4973b623356a8d390ced

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Akademický článek

Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines

Autor: Anthony Federico, Tanya Karagiannis, Kritika Karri, Dileep Kishore, Yusuke Koga, Joshua D. Campbell, Stefano Monti

Publikováno v: Frontiers in Genetics, Vol 10 (2019)

The advent of high-throughput sequencing technologies has led to the need for flexible and user-friendly data preprocessing platforms. The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data. It com

Externí odkaz: https://doaj.org/article/5055b186eb674ffebf7e3205b1fe7bf3

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Akademický článek

Changes in Plasma Constituents of Crossbred (Aigamo) Ducks During the Winter Season

Autor: Yusuke Koga, Shin Saito, Kunio Kaneko, Yasuhiro Kido, Mitsuhiro Furuse

Publikováno v: The Journal of Poultry Science, Vol 41, Iss 2, Pp 131-139 (2004)

Changes in plasma constituents in the crossbred (aigamo) duck (female Japanese mallard duck × male mallard) were successively investigated at two-week intervals during winter from December to March. The pattern of changes in plasma triacylglycerol a

Externí odkaz: https://doaj.org/article/0e3ab5d0fadc44c8abf9fb92b6644506

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Akademický článek

Association between reduction of plasma adiponectin levels and risk of bacterial infection after gastric cancer surgery.

Autor: Hiroshi Yamamoto, Kazuhisa Maeda, Yoshitaka Uji, Hiroshi Tsuchihashi, Tsuyoshi Mori, Tomoharu Shimizu, Yoshihiro Endo, Aya Kadota, Katsuyuki Miura, Yusuke Koga, Toshinori Ito, Tohru Tani

Publikováno v: PLoS ONE, Vol 8, Iss 3, p e56129 (2013)

BACKGROUND AND PURPOSE: Infections are important causes of postoperative morbidity after gastric surgery; currently, no factors have been identified that can predict postoperative infection. Adiponectin (ADN) mediates energy metabolism and functions

Externí odkaz: https://doaj.org/article/1884f9ef1ab84b618fa9fe1043c88349

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