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
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Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
Yifu Ding,Daniel J. Vanselow,Maksim A Yakovlev,Spencer R Katz,Alex Y. Lin,Darin P. Clark,Phillip Vargas,Xuying Xin,Jean E. Copper,Victor A. Canfield,Khai C. Ang,Yuxin Wang,Xianghui Xiao,Francesco De Carlo,Damian B. van Rossum,Patrick J. La Riviere,Keith C. Cheng +16 more
TL;DR: The computational and visual insights into 3D cell and tissue architecture provided by histotomography are expected to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
Journal ArticleDOI
Putative cell type discovery from single-cell gene expression data.
Zhichao Miao,Pablo Moreno,Ni Huang,Ni Huang,Irene Papatheodorou,Alvis Brazma,Sarah A. Teichmann +6 more
TL;DR: The Single-Cell Clustering Assessment Framework (SCCAF) as mentioned in this paper is a method for the automated identification of putative cell types from single-cell RNA sequencing (scRNA-seq) data.
Journal ArticleDOI
Single-cell genomic approaches for developing the next generation of immunotherapies.
Ido Yofe,Rony Dahan,Ido Amit +2 more
TL;DR: How emerging single-cell genomic technologies can serve as an engine for target identification and drug development and improve the development of immunotherapies is discussed.
Journal ArticleDOI
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography.
Claire Walsh,Paul Tafforeau,Willi L. Wagner,Daniyal J. Jafree,Alexandre Bellier,Christopher Werlein,Mark Kühnel,Elodie Boller,Simon Walker-Samuel,J. L. Robertus,David A. Long,J. Jacob,Sebastian Marussi,E. Brown,Natalie A. Holroyd,Danny Jonigk,Maximilian Ackermann,Peter D. Lee +17 more
TL;DR: In this article, a hierarchical phase-contrast tomography (HiP-CT) was developed to image intact human organs from the organ to the cellular scale in 3D.
Journal ArticleDOI
Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas
David G.P. van IJzendoorn,Karoly Szuhai,Inge H. Briaire-de Bruijn,Marie Kostine,Marieke L. Kuijjer,Judith V.M.G. Bovée +5 more
TL;DR: Reconstruction of regulatory networks combined with data from the Connectivity Map showed that HDAC inhibitors could be a potential effective therapy for multiple soft tissue sarcoma subtypes and prognostic genes that are strong predictors of disease outcome when used in a k-nearest neighbor algorithm.
References
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