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Xiaojie Qiu
Researcher at University of Washington
Publications - 36
Citations - 8145
Xiaojie Qiu is an academic researcher from University of Washington. The author has contributed to research in topics: Biology & Medicine. The author has an hindex of 18, co-authored 27 publications receiving 4683 citations. Previous affiliations of Xiaojie Qiu include Institute for Systems Biology & University of California, San Francisco.
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Journal ArticleDOI
Reversed graph embedding resolves complex single-cell trajectories.
TL;DR: Monocle 2, an algorithm that uses reversed graph embedding to describe multiple fate decisions in a fully unsupervised manner, is applied to two studies of blood development and found that mutations in the genes encoding key lineage transcription factors divert cells to alternative fates.
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The single-cell transcriptional landscape of mammalian organogenesis
Junyue Cao,Malte Spielmann,Xiaojie Qiu,Xingfan Huang,Daniel M. Ibrahim,Daniel M. Ibrahim,Andrew J. Hill,Fan Zhang,Stefan Mundlos,Stefan Mundlos,Lena Christiansen,Frank J. Steemers,Cole Trapnell,Jay Shendure +13 more
TL;DR: A cell atlas of mouse organogenesis provides a global view of developmental processes occurring during this critical period, including focused analyses of the apical ectodermal ridge, limb mesenchyme and skeletal muscle.
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Single-cell mRNA quantification and differential analysis with Census
TL;DR: The Census algorithm is introduced to convert relative RNA-seq expression levels into relative transcript counts without the need for experimental spike-in controls and it is demonstrated that Census enabled robust analysis at multiple layers of gene regulation.
Journal ArticleDOI
Comprehensive single-cell transcriptional profiling of a multicellular organism
Junyue Cao,Jonathan S. Packer,Vijay Ramani,Darren A. Cusanovich,Chau Huynh,Ray A. M. Daza,Xiaojie Qiu,Choli Lee,Scott N. Furlan,Scott N. Furlan,Scott N. Furlan,Frank J. Steemers,Andrew Adey,Andrew Adey,Robert H. Waterston,Cole Trapnell,Jay Shendure,Jay Shendure +17 more
TL;DR: The authors profiled almost 50,000 single cells from an individual Caenorhabditis elegans larval stage and were able to identify and recover information from different, even rare, cell types and develop combinatorial indexing strategies to profile the transcriptomes of single cells or nuclei.
Journal ArticleDOI
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.
Hannah A. Pliner,Jonathan S. Packer,José L. McFaline-Figueroa,Darren A. Cusanovich,Riza M. Daza,Delasa Aghamirzaie,Sanjay Srivatsan,Xiaojie Qiu,Dana Jackson,Anna Minkina,Andrew Adey,Frank J. Steemers,Jay Shendure,Jay Shendure,Cole Trapnell +14 more
TL;DR: Cicero is introduced, an algorithm that identifies co-accessible pairs of DNA elements using single-cell chromatin accessibility data and so connects regulatory elements to their putative target genes and is applied to investigate how dynamically accessible elements orchestrate gene regulation in differentiating myoblasts.