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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Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis
Ruilin Tian,Anthony B. Abarientos,Jason Hong,Sayed Hadi Hashemi,Rui Yan,Mike A. Nalls,Andrew B. Singleton,Ke Xu,Faraz Faghri,Faraz Faghri,Martin Kampmann +10 more
TL;DR: The first genome-wide CRISPR interference andCRISPR activation screens in human neurons are presented and pathways controlling neuronal response to chronic oxidative stress are uncovered, which is implicated in neurodegenerative diseases.
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The evolving concept of cell identity in the single cell era.
TL;DR: This Spotlight explores emerging technologies that are enabling the systematic and unbiased quantification of cell identity, and how these efforts will enable the construction of high-resolution, dynamic cell atlases.
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Cell composition analysis of bulk genomics using single-cell data.
Amit Frishberg,Naama Peshes-Yaloz,Ofir Cohn,Diana Rosentul,Yael Steuerman,Liran Valadarsky,Gal Yankovitz,Michal Mandelboim,Michal Mandelboim,Fuad A. Iraqi,Ido Amit,Lior Mayo,Eran Bacharach,Irit Gat-Viks +13 more
TL;DR: Cell Population Mapping (CPM), a deconvolution algorithm in which reference scRNA-seq profiles are leveraged to infer the composition of cell types and states from bulk transcriptome data, demonstrates the power of CPM in reconstructing the continuous spectrum of cell states within heterogeneous tissues.
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Interplay of EMT and CSC in Cancer and the Potential Therapeutic Strategies.
TL;DR: The mechanism of cancer stem cell (CSC) population, EMT, regulation of EMT and CSCs by microRNAs and nanomedicine-based approaches to target CSC’s are focused on.
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Single-cell transcriptomics in cancer: computational challenges and opportunities.
TL;DR: In this paper, the authors highlight emerging themes in the computational analysis of single-cell transcriptomics data and their applications to cancer research, including how to perform unified analysis across many patients and disease states, distinguish neoplastic from nonneoplastic cells, infer communication with the tumor microenvironment, and delineate tumoral and microenvironmental evolution with trajectory and RNA velocity analysis.
References
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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
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