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 Biochemistry Approaches to Defining Mitochondrial Protein Function
TL;DR: Recent systems biochemistry approaches have accelerated the identification of new disease-related mitochondrial proteins and of long-sought "missing" proteins that fulfill key functions, moving us toward a more complete understanding of mitochondrial activities and providing a molecular framework for the investigation of mitochondrial pathogenesis.
Journal ArticleDOI
Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data
Junlin Xu,Jielin Xu,Yajie Meng,Changcheng Lu,Lijun Cai,Xiangxiang Zeng,Ruth Nussinov,Feixiong Cheng +7 more
TL;DR: AutoCell as discussed by the authors is a variational autoencoding network that combines graph embedding and a probabilistic depth Gaussian mixture model to infer the distribution of high-dimensional, sparse scRNA-seq data.
Posted ContentDOI
Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR software
TL;DR: ASHLAR as mentioned in this paper coordinates stitching and registration and scales to 103 or more image tiles over many imaging cycles to generate accurate, high-plex image mosaics, the key type of data for downstream visualization and computational analysis.
Posted ContentDOI
The cell type composition of the adult mouse brain revealed by single cell and spatial genomics
Jonah Langlieb,Nina Sachdev,Karol S. Balderrama,Naeem Nadaf,Mukund Raj,Evan Murray,James Weber,Charles R. Vanderburg,Vahid H. Gazestani,Daniel Tward,Chris Mezias,Xu Li,Dylan M. Cable,Tabitha Norton,Partha P. Mitra,Fei Chen,Evan Z. Macosko +16 more
TL;DR: In this article , the authors constructed a comprehensive atlas of cell types in each brain structure, paired high-throughput single-nucleus RNA-seq with Slide-seq-a recently developed spatial transcriptomics method with near-cellular resolution.
Journal ArticleDOI
Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types.
Meng Yuan,Xujiang Yang,Jinghua Lin,Xiaolong Cao,Feng Chen,Xiaoyu Zhang,Zizhang Li,Guifeng Zheng,Xueqin Wang,Xiaoshu Chen,Jian-Rong Yang +10 more
TL;DR: Quantified phenotypic similarity between CLTs using a novel computational method that exhaustively searches for optimal correspondence between individual cells meanwhile retaining their topological relationships to help answer the myriad of questions surrounding the developmental process.
References
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TL;DR: The derivation of a number of tissue culture cell lines which secrete anti-sheep red blood cell (SRBC) antibodies is described here, made by fusion of a mouse myeloma and mouse spleen cells from an immunised donor.
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Journal ArticleDOI
Fast unfolding of communities in large networks
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TL;DR: In this paper, the authors proposed a simple method to extract the community structure of large networks based on modularity optimization, which is shown to outperform all other known community detection methods in terms of computation time.
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Tissue-based map of the human proteome
Mathias Uhlén,Mathias Uhlén,Linn Fagerberg,Björn M. Hallström,Cecilia Lindskog,Per Oksvold,Adil Mardinoglu,Åsa Sivertsson,Caroline Kampf,Evelina Sjöstedt,Evelina Sjöstedt,Anna Asplund,IngMarie Olsson,Karolina Edlund,Emma Lundberg,Sanjay Navani,Cristina Al-Khalili Szigyarto,Jacob Odeberg,Dijana Djureinovic,Jenny Ottosson Takanen,Sophia Hober,Tove Alm,Per-Henrik Edqvist,Holger Berling,Hanna Tegel,Jan Mulder,Johan Rockberg,Peter Nilsson,Jochen M. Schwenk,Marica Hamsten,Kalle von Feilitzen,Mattias Forsberg,Lukas Persson,Fredric Johansson,Martin Zwahlen,Gunnar von Heijne,Jens Nielsen,Jens Nielsen,Fredrik Pontén +38 more
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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