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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Systems Immunology: Learning the Rules of the Immune System
TL;DR: This work focuses on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts the authors' ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors.
Posted ContentDOI
Interpretable dimensionality reduction of single cell transcriptome data with deep generative models
TL;DR: A robust statistical model, scvis, is presented, to capture and visualize the low-dimensional structures in single-cell gene expression data and is robust to the number of data points and learns a probabilistic parametric mapping function to add new data points to an existing embedding.
Journal ArticleDOI
Advances and Opportunities in Single-Cell Transcriptomics for Plant Research
Carolin Seyfferth,Jim Renema,Jos R. Wendrich,Thomas Eekhout,Ruth Seurinck,Niels Vandamme,Bernhard Blob,Bernhard Blob,Yvan Saeys,Yrjö Helariutta,Yrjö Helariutta,Kenneth D. Birnbaum,Bert De Rybel +12 more
TL;DR: The field of plant biology has fully embraced single-cell transcriptomics and is rapidly expanding the portfolio of available technologies and applications as mentioned in this paper, which is changing our view on biological systems by increasing the spatiotemporal resolution of our analyses to the level of the individual cell.
Posted ContentDOI
Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models
Chenling Xu,Romain Lopez,Edouard Mehlman,Edouard Mehlman,Jeffrey Regier,Michael I. Jordan,Nir Yosef +6 more
TL;DR: It is demonstrated that scVI and scANVI represent the integrated datasets with a single generative model that can be directly used for any probabilistic decision making task, using differential expression as a case study.
Posted ContentDOI
High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes
Mandeep Singh,Ghamdan Al-Eryani,Shaun Carswell,James Ferguson,James Blackburn,Kirston Barton,Daniel L. Roden,Fabio Luciani,Tri Giang Phan,Simon Junankar,Katherine J. L. Jackson,Christopher C. Goodnow,Martin A. Smith,Alexander Swarbrick +13 more
TL;DR: This work uses Repertoire And Gene Expression sequencing (RAGE-seq) to accurately characterize full-length T cell (TCR) and B cell (BCR) receptor sequences and transcriptional profiles of more than 7,138 lymphocytes sampled from the primary tumour and draining lymph node of a breast cancer patient.
References
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Fast unfolding of communities in large networks
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Tissue-based map of the human proteome
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