J
Johann A. Gagnon-Bartsch
Researcher at University of Michigan
Publications - 46
Citations - 1714
Johann A. Gagnon-Bartsch is an academic researcher from University of Michigan. The author has contributed to research in topics: Covariate & Randomized experiment. The author has an hindex of 13, co-authored 40 publications receiving 1355 citations. Previous affiliations of Johann A. Gagnon-Bartsch include University of California, Berkeley.
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Journal ArticleDOI
Using control genes to correct for unwanted variation in microarray data
TL;DR: A new method, intended for use in differential expression studies, that attempts to overcome the problem of unwanted variation by restricting the factor analysis to negative control genes, and finds that RUV-2 performs as well or better than other methods.
Journal ArticleDOI
Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas
Suling J. Lin,Johann A. Gagnon-Bartsch,Iain Beehuat Tan,Sophie Earle,Louise Ruff,Katherine J Pettinger,Bauke Ylstra,Nicole C.T. van Grieken,Sun Young Rha,Hyun Cheol Chung,Ju Seog Lee,Jae Ho Cheong,Sung Hoon Noh,Toru Aoyama,Yohei Miyagi,Akira Tsuburaya,Takaki Yoshikawa,Jaffer A. Ajani,Alex Boussioutas,Alex Boussioutas,Khay Guan Yeoh,Wei Peng Yong,Jimmy Bok Yan So,Jeeyun Lee,Won Ki Kang,Sung Joon Kim,Yoichi Kameda,Tomio Arai,Axel zur Hausen,Terence P. Speed,Terence P. Speed,Heike I. Grabsch,Heike I. Grabsch,Patrick Tan +33 more
TL;DR: It is suggested that Asian and non-Asian GCs exhibit distinct tumour immunity signatures related to T-cell function, and these differences may influence geographical differences in clinical outcome, and the design of future trials particularly in immuno-oncology.
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Skeletal muscle and plasma lipidomic signatures of insulin resistance and overweight/obesity in humans
Katherine T. Tonks,Adelle C.F. Coster,Adelle C.F. Coster,Michael J. Christopher,Rima Chaudhuri,A Xu,Johann A. Gagnon-Bartsch,Donald J. Chisholm,Donald J. Chisholm,David E. James,Peter J. Meikle,Dorit Samocha-Bonet,Dorit Samocha-Bonet +12 more
TL;DR: Alterations in lipids in muscle and plasma have been documented in insulin‐resistant people with obesity and whether these lipid alterations are a reflection of insulin resistance or obesity remains unclear.
Journal ArticleDOI
scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets
Yingxin Lin,Shila Ghazanfar,Kevin Wang,Johann A. Gagnon-Bartsch,Kitty Lo,Xianbin Su,Ze-Guang Han,John T. Ormerod,Terence P. Speed,Terence P. Speed,Pengyi Yang,Jean Yee Hwa Yang +11 more
TL;DR: This study presents scMerge, an algorithm that integrates multiple single-cell RNA-seq datasets using factor analysis of stably expressed genes and pseudoreplicates across datasets and demonstrates that it consistently provides improved cell type separation by removing unwanted factors.
Journal ArticleDOI
Statistical methods for handling unwanted variation in metabolomics data.
Alysha M De Livera,Marko Sysi-Aho,Laurent Jacob,Johann A. Gagnon-Bartsch,Sandra Castillo,Julie A. Simpson,Terence P. Speed,Terence P. Speed,Terence P. Speed +8 more
TL;DR: The causes of unwanted variation in metabolomics experiments are discussed, commonly used metabolomics approaches for handling this unwanted variation are reviewed, and a statistical approach for the removal of unwantedVariation to obtain normalized metabolomics data is presented.