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Xiaoxi Megan Cao
Researcher at ICF International
Publications - 4
Citations - 2431
Xiaoxi Megan Cao is an academic researcher from ICF International. The author has contributed to research in topics: Gene & Comparative genomics. The author has an hindex of 4, co-authored 4 publications receiving 2376 citations.
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Journal ArticleDOI
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
Leming Shi,Laura H. Reid,Wendell D. Jones,Richard Shippy,Janet A. Warrington,Shawn C. Baker,Patrick J. Collins,Francoise de Longueville,Ernest S. Kawasaki,Kathleen Y. Lee,Yuling Luo,Yongming Andrew Sun,James C. Willey,Robert Setterquist,Gavin M. Fischer,Weida Tong,Yvonne P. Dragan,David J. Dix,Felix W. Frueh,Federico Goodsaid,Damir Herman,Roderick V. Jensen,Charles D. Johnson,Edward K. Lobenhofer,Raj K. Puri,Uwe Scherf,Jean Thierry-Mieg,Charles Wang,Michael A Wilson,Paul K. Wolber,Lu Zhang,William Slikker,Shashi Amur,Wenjun Bao,Catalin Barbacioru,Anne Bergstrom Lucas,Vincent Bertholet,Cecilie Boysen,Bud Bromley,Donna Brown,Alan Brunner,Roger D. Canales,Xiaoxi Megan Cao,Thomas A. Cebula,James J. Chen,Jing Cheng,Tzu Ming Chu,Eugene Chudin,John F. Corson,J. Christopher Corton,Lisa J. Croner,Christopher Davies,Timothy Davison,Glenda C. Delenstarr,Xutao Deng,David Dorris,Aron Charles Eklund,Xiaohui Fan,Hong Fang,Stephanie Fulmer-Smentek,James C. Fuscoe,Kathryn Gallagher,Weigong Ge,Lei Guo,Xu Guo,Janet Hager,Paul K. Haje,Jing Han,Tao Han,Heather Harbottle,Stephen C. Harris,Eli Hatchwell,Craig A. Hauser,Susan D. Hester,Huixiao Hong,Patrick Hurban,Scott A. Jackson,Hanlee P. Ji,Charles R. Knight,Winston Patrick Kuo,J. Eugene LeClerc,Shawn Levy,Quan Zhen Li,Chunmei Liu,Ying Liu,Michael Lombardi,Yunqing Ma,Scott R. Magnuson,Botoul Maqsodi,Timothy K. McDaniel,Nan Mei,Ola Myklebost,Baitang Ning,Natalia Novoradovskaya,Michael S. Orr,Terry Osborn,Adam Papallo,Tucker A. Patterson,Roger Perkins,Elizabeth Herness Peters,Ron L. Peterson,Kenneth L. Philips,P. Scott Pine,Lajos Pusztai,Feng Qian,Hongzu Ren,Mitch Rosen,Barry A. Rosenzweig,Raymond R. Samaha,Mark Schena,Gary P. Schroth,Svetlana Shchegrova,Dave D. Smith,Frank Staedtler,Zhenqiang Su,Hongmei Sun,Zoltan Szallasi,Zivana Tezak,Danielle Thierry-Mieg,Karol L. Thompson,Irina Tikhonova,Yaron Turpaz,Beena Vallanat,Christophe Van,Stephen J. Walker,Sue Jane Wang,Yonghong Wang,Russell D. Wolfinger,Alexander Wong,Jie Wu,Chunlin Xiao,Qian Xie,Jun Xu,Wen Yang,Liang Zhang,Sheng Zhong,Yaping Zong +136 more
TL;DR: This study describes the experimental design and probe mapping efforts behind the MicroArray Quality Control project and shows intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed.
Journal ArticleDOI
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
Leming Shi,Wendell D. Jones,Roderick V. Jensen,Stephen C. Harris,Roger Perkins,Federico Goodsaid,Lei Guo,Lisa J. Croner,Cecilie Boysen,Hong Fang,Feng Qian,Shashi Amur,Wenjun Bao,Catalin Barbacioru,Vincent Bertholet,Xiaoxi Megan Cao,Tzu Ming Chu,Patrick J. Collins,Xiaohui Fan,Xiaohui Fan,Felix W. Frueh,James C. Fuscoe,Xu Guo,Jing Han,Damir Herman,Huixiao Hong,Ernest S. Kawasaki,Quan Zhen Li,Yuling Luo,Yunqing Ma,Nan Mei,Ron L. Peterson,Raj K. Puri,Richard Shippy,Zhenqiang Su,Yongming Andrew Sun,Hongmei Sun,Brett T. Thorn,Yaron Turpaz,Charles Wang,Sue Jane Wang,Janet A. Warrington,James C. Willey,Jie Wu,Qian Xie,Liang Zhang,Lu Zhang,Sheng Zhong,Russell D. Wolfinger,Weida Tong +49 more
TL;DR: The results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs and recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists.
Journal ArticleDOI
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling
Hong Fang,Weida Tong,Roger Perkins,Leming Shi,Huixiao Hong,Xiaoxi Megan Cao,Qian Xie,Sun Hee Yim,Jerrold M. Ward,Henry C. Pitot,Yvonne P. Dragan +10 more
TL;DR: The study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer.
Journal ArticleDOI
The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies
Leming Shi,Wendell D. Jones,Roderick V. Jensen,Stephen C. Harris,Roger Perkins,Federico Goodsaid,Lei Guo,Lisa J. Croner,Cecilie Boysen,Hong Fang,Shashi Amur,Wenjun Bao,Catalin Barbacioru,Vincent Bertholet,Xiaoxi Megan Cao,Tzu-Ming Chu,Patrick J. Collins,Xiaohui Fan,Felix W. Frueh,James C. Fuscoe,Xu Guo,Jing Han,Damir Herman,Huixiao Hong,Ernest S. Kawasaki,Quan Zhen Li,Yuling Luo,Nan Mei,Ron L. Peterson,Raj K. Puri,Feng Qian,Richard Shippy,Zhenqiang Su,Yongming Andrew Sun,Hongmei Sun,Brett T. Thorn,Yaron Turpaz,Charles Wang,Jane Wang,Janet A. Warrington,James C. Willey,Jie Wu,Qian Xie,Liang Zhang,Sheng Zhong,James J. Chen,Russell D. Wolfinger,Weida Tong,Meridian Parkway,Harry Hines Boulevard,David Geffen +50 more
TL;DR: This study demonstrates that discordance in lists of differentially expressed genes may stem from ranking and selecting DEGs solely by statistical significance derived from widely used simple t-tests and recommends the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists.