The Human Cell Atlas
Aviv Regev,Aviv Regev,Aviv Regev,Sarah A. Teichmann,Sarah A. Teichmann,Sarah A. Teichmann,Eric S. Lander,Eric S. Lander,Eric S. Lander,Ido Amit,Christophe Benoist,Ewan Birney,Bernd Bodenmiller,Bernd Bodenmiller,Peter J. Campbell,Peter J. Campbell,Piero Carninci,Menna R. Clatworthy,Hans Clevers,Bart Deplancke,Ian Dunham,James Eberwine,Roland Eils,Roland Eils,Wolfgang Enard,Andrew Farmer,Lars Fugger,Berthold Göttgens,Nir Hacohen,Nir Hacohen,Muzlifah Haniffa,Martin Hemberg,Seung K. Kim,Paul Klenerman,Paul Klenerman,Arnold R. Kriegstein,Ed S. Lein,Sten Linnarsson,Emma Lundberg,Emma Lundberg,Joakim Lundeberg,Partha P. Majumder,John C. Marioni,John C. Marioni,John C. Marioni,Miriam Merad,Musa M. Mhlanga,Martijn C. Nawijn,Mihai G. Netea,Garry P. Nolan,Dana Pe'er,Anthony Phillipakis,Chris P. Ponting,Stephen R. Quake,Wolf Reik,Wolf Reik,Wolf Reik,Orit Rozenblatt-Rosen,Joshua R. Sanes,Rahul Satija,Ton N. Schumacher,Alex K. Shalek,Alex K. Shalek,Alex K. Shalek,Ehud Shapiro,Padmanee Sharma,Jay W. Shin,Oliver Stegle,Michael R. Stratton,Michael J. T. Stubbington,Fabian J. Theis,Matthias Uhlen,Matthias Uhlen,Alexander van Oudenaarden,Allon Wagner,Fiona M. Watt,Jonathan S. Weissman,Barbara J. Wold,Ramnik J. Xavier,Nir Yosef,Nir Yosef,Human Cell Atlas Meeting Participants +81 more
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TLDR
An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease.Abstract:
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.read more
Citations
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Journal ArticleDOI
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.
Journal ArticleDOI
Integrating single-cell transcriptomic data across different conditions, technologies, and species.
TL;DR: An analytical strategy for integrating scRNA-seq data sets based on common sources of variation is introduced, enabling the identification of shared populations across data sets and downstream comparative analysis.
Journal ArticleDOI
SCANPY: large-scale single-cell gene expression data analysis
TL;DR: This work presents Scanpy, a scalable toolkit for analyzing single-cell gene expression data that includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks, and AnnData, a generic class for handling annotated data matrices.
Journal ArticleDOI
Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky,Nghia Millard,Jean Fan,Kamil Slowikowski,Fan Zhang,Kevin Wei,Yuriy Baglaenko,Michael B. Brenner,Po-Ru Loh,Po-Ru Loh,Po-Ru Loh,Soumya Raychaudhuri +11 more
TL;DR: Harmony, for the integration of single-cell transcriptomic data, identifies broad and fine-grained populations, scales to large datasets, and can integrate sequencing- and imaging-based data.
Journal ArticleDOI
SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar,Carmen Bravo González-Blas,Thomas Moerman,Vân Anh Huynh-Thu,Hana Imrichova,Gert Hulselmans,Florian Rambow,Jean-Christophe Marine,Pierre Geurts,Jan Aerts,Joost van den Oord,Zeynep Kalender Atak,Jasper Wouters,Stein Aerts +13 more
TL;DR: On a compendium of single-cell data from tumors and brain, it is demonstrated that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states.
References
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Posted Content
Quasi-potential landscape in complex multi-stable systems
Joseph X. Zhou,Joseph X. Zhou,Joseph X. Zhou,M. D. S. Aliyu,Erik Aurell,Erik Aurell,Sui Huang,Sui Huang,Sui Huang +8 more
TL;DR: In this article, a new decomposition of vector fields that permits the computation of a quasi-potential function that is equivalent to the Freidlin-Wentzell potential but is not limited to two attractors is proposed.
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