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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Integrated analysis of single cell transcriptomic data across conditions, technologies, and species
Andrew Butler,Rahul Satija +1 more
TL;DR: A new computational strategy for scRNA-seq alignment is introduced, utilizing common sources of variation to identify shared subpopulations between datasets as part of the R toolkit Seurat, potentially deepening the understanding of how distinct cell states respond to perturbation, disease, and evolution.
Journal ArticleDOI
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
Samuel W. Kazer,Toby Aicher,Toby Aicher,Toby Aicher,Daniel M. Muema,Shaina L. Carroll,Jose Ordovas-Montanes,Vincent N. Miao,Ang A. Tu,Ang A. Tu,Carly G. K. Ziegler,Sarah K. Nyquist,Emily B. Wong,Nasreen Ismail,Mary Dong,Amber Moodley,Bonnie Berger,J. Christopher Love,J. Christopher Love,Krista L. Dong,Alasdair Leslie,Zaza M. Ndhlovu,Thumbi Ndung'u,Bruce D. Walker,Bruce D. Walker,Bruce D. Walker,Alex K. Shalek +26 more
TL;DR: An experimental and computational methodology that uses scRNA-seq to characterize dynamic cellular programs and their molecular drivers, and applies it to HIV infection provides insights into the initial immune responses during early infection that might shape future outcomes.
Posted ContentDOI
A Systematic Evaluation of Single-cell RNA-sequencing Imputation Methods
TL;DR: While most scRNA-seq imputation methods recover biological expression observed in bulk RNA-seq data, the majority of the methods do not improve performance in downstream analyses compared to no imputation, in particular for clustering and trajectory analysis, and thus should be used with caution.
Journal ArticleDOI
Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants
TL;DR: This study provides a framework to estimate the cellular composition of GTEx tissues enabling the functional characterization of human genetic variation that impacts gene expression in cell-type-specific manners and shows the power of using cell populations in eQTL analyses to identify disease and cell- type-associated regulatory variants.
Journal ArticleDOI
Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets.
TL;DR: Single-Cell_Signature_Explorer is presented, the first method for qualitative and high-throughput scoring of any gene set-based signature at the single cell level and its visualization using t-SNE or UMAP.
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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TL;DR: In this paper, a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level.
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