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
Multiplexed laser particles for spatially resolved single-cell analysis
Sheldon J. J. Kwok,Sheldon J. J. Kwok,Nicola Martino,Paul H. Dannenberg,Paul H. Dannenberg,Seok Hyun Yun,Seok Hyun Yun +6 more
TL;DR: Current methods for spatially resolved single-cell analysis are reviewed and the prospect of novel multiplexed imaging probes, called laser particles, which allow individual cells to be tagged in tissue and analyzed subsequently using high-throughput, comprehensive single- cell techniques are discussed.
Book ChapterDOI
Identification of Cell Types from Single-Cell Transcriptomic Data
TL;DR: This chapter outlines an instructive step-by-step example bioinformatic pipeline for researchers entering this field of cell-type identification, and introduces computational tools rooted in dimensionality reduction and clustering.
Journal ArticleDOI
The biology of the cell - insights from mass cytometry.
Petter Brodin,Petter Brodin +1 more
TL;DR: The different measurements possible by mass cytometry are discussed and its potential but also its limitations now and in the years to come are discussed.
Journal ArticleDOI
Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics
Christopher Cherry,David R. Maestas,Jin Han,James I. Andorko,Patrick Cahan,Elana J. Fertig,Lana X. Garmire,Jennifer H. Elisseeff +7 more
TL;DR: In this article, single-cell RNA-sequencing data from 42,156 cells collected from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss was used to reconstruct intercellular signalling networks from predictions of transcription-factor activation.
Posted ContentDOI
Learning interpretable latent autoencoder representations with annotations of feature sets
TL;DR: A framework for learning interpretable autoencoders based on regularized linear decoders that decomposes variation into interpretable components using prior knowledge in the form of annotated feature sets obtained from public databases is introduced.
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