Integrated analysis of multimodal single-cell data
Yuhan Hao,Stephanie Hao,Erica Andersen-Nissen,William M. Mauck,Shiwei Zheng,Andrew Butler,Maddie Jane Lee,Aaron J. Wilk,Charlotte A. Darby,Michael Zager,Paul Hoffman,Marlon Stoeckius,Efthymia Papalexi,Eleni P. Mimitou,Jaison Jain,Avi Srivastava,Tim Stuart,Lamar M. Fleming,Bertrand Z. Yeung,Angela J. Rogers,Juliana M. McElrath,Catherine A. Blish,Raphael Gottardo,Peter Smibert,Rahul Satija +24 more
TLDR
Weighted-nearest neighbor analysis as mentioned in this paper is an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities.About:
This article is published in Cell.The article was published on 2021-06-24 and is currently open access. It has received 3369 citations till now.read more
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BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection
Yunlong Cao,Ayijiang Yisimayi,F. Jian,Weiliang Song,T. Xiao,Lei Wang,Shuo Du,Qianqian Li,Xiao-song Chen,Yuanling Yu,Peng Wang,Zhiying Zhang,Pulan Liu,Ran An,Xiaohua Hao,Yao Wang,Jing Wang,Rui Feng,Haiyan Sun,Li-Jin Zhao,Wen Zhang,Dong Zhao,Jiang Zheng,Lingling Yu,Can Li,Na Zhang,Rui Wang,Xiaowei Niu,Siyuan Yang,Xuetao Song,Yangyang Chai,Ye Hu,Yansong Shi,Lin-Sheng Zheng,Zhiqiang Li,Qingqing Gu,Fei Shao,Weijin Huang,Ronghua Jin,Zhong-yang Shen,Youchun Wang,Xiangxi Wang,Junyu Xiao,Xiaoliang Sunney Xie +43 more
TL;DR: In this paper , the authors show that BA.4/BA.5 exhibit higher transmissibility than BA.2.1, BA.12.1 and BA.1.
Journal ArticleDOI
BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection
Yunlong Cao,Ayijiang Yisimayi,F. Jian,Weiliang Song,T. Xiao,Lei Wang,Shuo Du,Jing Wang,Qianqian Li,Xiao-song Chen,Yuanling Yu,Peng Wang,Zhiying Zhang,Pulan Liu,Ran An,Xiaohua Hao,Yao Wang,Rui Feng,Haiyan Sun,Li-Jin Zhao,Wen Zhang,Dong Zhao,Jiang Zheng,Ling-li Yu,Can Li,Na Zhang,Rui Wang,Xiaowei Niu,Siyuan Yang,Xuetao Song,Yangyang Chai,Yeping Hu,Yansong Shi,Lin-Sheng Zheng,Zhiqiang Li,Qingqing Gu,Fei Shao,Weijin Huang,Ronghua Jin,Zhong-yang Shen,Youchun Wang,Xiangxi Wang,Junyu Xiao,Xiaoliang Sunney Xie +43 more
TL;DR: In this article , the authors show that BA.4/BA.5 exhibit higher transmissibility than BA.2.1, BA.12.1 and BA.1.
Journal ArticleDOI
Single-cell chromatin state analysis with Signac.
TL;DR: Signac as mentioned in this paper is a comprehensive toolkit for the analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with singlecell gene expression datasets, DNA motif analysis and interactive visualization.
Journal ArticleDOI
GD2-CAR T cell therapy for H3K27M-mutated diffuse midline gliomas
Robbie G. Majzner,Sneha Ramakrishna,Kristen W. Yeom,Shabnum Patel,Harshini Chinnasamy,Liora M. Schultz,Rebecca Richards,Li Jiang,Valentin Barsan,Rebecca A Mancusi,Anna Geraghty,Zina Good,Aaron Mochizuki,Shawn M. Gillespie,Angus Toland,Jasia Mahdi,Agnes Reschke,Esther H Nie,Isabelle J. Chau,Maria Caterina Rotiroti,Christopher Mount,Christina Baggott,Sharon Mavroukakis,Emily Egeler,Jennifer Moon,Courtney Erickson,Sean Green,Michael Kunicki,Michelle Fujimoto,Zach Ehlinger,Warren D. Reynolds,Sreevidya Kurra,Katherine E. Warren,Snehit Prabhu,Hannes Vogel,Lindsey Rasmussen,Timothy T. Cornell,Sonia Partap,Paul B. Fisher,Cynthia J. Campen,Mariella G. Filbin,Gerald A. Grant,Bita Sahaf,Kara L. Davis,Steven R. Feldman,Crystal L. Mackall,Michelle Monje +46 more
TL;DR: In this paper , the clinical experience from the first four patients with H3K27M-mutated diffuse midline glioma (DIPG) or spinal cord DMG treated with GD2-CAR T cells at dose level 1 (1 × 106 GD2 CAR T cells per kg administered intravenously).
Journal ArticleDOI
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
TL;DR: Pijuan-Sala et al. as discussed by the authors combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq).
References
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R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
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Comprehensive Integration of Single-Cell Data.
Tim Stuart,Andrew Butler,Paul J. Hoffman,Christoph Hafemeister,Efthymia Papalexi,William M. Mauck,Yuhan Hao,Marlon Stoeckius,Peter Smibert,Rahul Satija +9 more
TL;DR: A strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities.
Posted Content
UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
Leland McInnes,John Healy +1 more
TL;DR: The UMAP algorithm is competitive with t-SNE for visualization quality, and arguably preserves more of the global structure with superior run time performance.
Journal ArticleDOI
The orphan nuclear receptor RORgammat directs the differentiation program of proinflammatory IL-17+ T helper cells.
Ivaylo I. Ivanov,Brent S. McKenzie,Liang Zhou,Carlos E. Tadokoro,Alice Lepelley,Juan J. Lafaille,Daniel J. Cua,Dan R. Littman +7 more
TL;DR: It is shown that the orphan nuclear receptor RORgammat is the key transcription factor that orchestrates the differentiation of this effector cell lineage of proinflammatory T helper cells and its potential as a therapeutic target in inflammatory diseases is highlighted.
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