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      The Human Cell Atlas

      , 1 , 2 , 3 , , 4 , 5 , 6 , , 1 , 2 , 7 , 8 , 9 , 5 , 5 , 10 , 4 , 11 , 6 , 12 , 13 , 14 , 15 , 5 , 16 , 17 , 18 , 19 , 20 , 21 , 11 , 22 , 1 , 23 , 24 , 4 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 4 , 5 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 1 , 42 , 43 , 44 , 4 , 45 , 46 , 1 , 47 , 48 , 49 , 50 , 1 , 51 , 52 , 53 , 54 , 12 , 5 , 4 , 4 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 3 , 62 , 63 , 64 , 65 , 1 , 66 , 67 , 68 , 52 , 60 , Human Cell Atlas Meeting Participants

      eLife

      eLife Sciences Publications, Ltd

      single-cell genomics, lineage, cell atlas, science forum, Human, Mouse

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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.

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          Most cited references 94

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          Fast unfolding of communities in large networks

          We propose a simple method to extract the community structure of large networks. Our method is a heuristic method that is based on modularity optimization. It is shown to outperform all other known community detection method in terms of computation time. Moreover, the quality of the communities detected is very good, as measured by the so-called modularity. This is shown first by identifying language communities in a Belgian mobile phone network of 2.6 million customers and by analyzing a web graph of 118 million nodes and more than one billion links. The accuracy of our algorithm is also verified on ad-hoc modular networks. .
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            Maps of random walks on complex networks reveal community structure

            To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network into modules by optimally compressing a description of information flows on the network. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of more than 6000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network -- including physics, chemistry, molecular biology, and medicine -- information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.
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              Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex.

              Neuroscience produces a vast amount of data from an enormous diversity of neurons. A neuronal classification system is essential to organize such data and the knowledge that is derived from them. Classification depends on the unequivocal identification of the features that distinguish one type of neuron from another. The problems inherent in this are particularly acute when studying cortical interneurons. To tackle this, we convened a representative group of researchers to agree on a set of terms to describe the anatomical, physiological and molecular features of GABAergic interneurons of the cerebral cortex. The resulting terminology might provide a stepping stone towards a future classification of these complex and heterogeneous cells. Consistent adoption will be important for the success of such an initiative, and we also encourage the active involvement of the broader scientific community in the dynamic evolution of this project.
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                Author and article information

                Contributors
                Role: Reviewing Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                05 December 2017
                2017
                : 6
                Affiliations
                [1 ]Broad Institute of MIT and Harvard CambridgeUnited States
                [2 ]deptDepartment of Biology Massachusetts Institute of Technology CambridgeUnited States
                [3 ]Howard Hughes Medical Institute Chevy ChaseUnited States
                [4 ]Wellcome Trust Sanger Institute, Wellcome Genome Campus HinxtonUnited Kingdom
                [5 ]deptEMBL-European Bioinformatics Institute Wellcome Genome Campus HinxtonUnited Kingdom
                [6 ]deptCavendish Laboratory, Department of Physics University of Cambridge CambridgeUnited Kingdom
                [7 ]deptDepartment of Systems Biology Harvard Medical School BostonUnited States
                [8 ]deptDepartment of Immunology Weizmann Institute of Science RehovotIsrael
                [9 ]deptDivision of Immunology, Department of Microbiology and Immunobiology Harvard Medical School BostonUnited States
                [10 ]deptInstitute of Molecular Life Sciences University of Zürich ZürichSwitzerland
                [11 ]deptDepartment of Haematology University of Cambridge CambridgeUnited Kingdom
                [12 ]deptDivision of Genomic Technologies RIKEN Center for Life Science Technologies YokohamaJapan
                [13 ]deptMolecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology University of Cambridge CambridgeUnited Kingdom
                [14 ]Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center Utrecht UtrechtThe Netherlands
                [15 ]deptInstitute of Bioengineering, School of Life Sciences Swiss Federal Institute of Technology (EPFL) LausanneSwitzerland
                [16 ]deptDepartment of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania PhiladelphiaUnited States
                [17 ]deptDivision of Theoretical Bioinformatics (B080) German Cancer Research Center (DKFZ) HeidelbergGermany
                [18 ]deptDepartment for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Heidelberg University HeidelbergGermany
                [19 ]deptDepartment of Biology II Ludwig Maximilian University Munich MartinsriedGermany
                [20 ]Takara Bio United States, Inc. Mountain ViewUnited States
                [21 ]deptOxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine John Radcliffe Hospital, University of Oxford OxfordUnited Kingdom
                [22 ]deptWellcome Trust-MRC Cambridge Stem Cell Institute University of Cambridge CambridgeUnited Kingdom
                [23 ]Massachusetts General Hospital Cancer Center BostonUnited States
                [24 ]deptInstitute of Cellular Medicine Newcastle University Newcastle upon TyneUnited Kingdom
                [25 ]deptDepartments of Developmental Biology and of Medicine Stanford University School of Medicine StanfordUnited States
                [26 ]deptPeter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine University of Oxford OxfordUnited Kingdom
                [27 ]deptOxford NIHR Biomedical Research Centre John Radcliffe Hospital OxfordUnited Kingdom
                [28 ]deptEli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research University of California, San Francisco San FranciscoUnited States
                [29 ]Allen Institute for Brain Science SeattleUnited States
                [30 ]deptLaboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics Karolinska Institutet StockholmSweden
                [31 ]deptScience for Life Laboratory, School of Biotechnology KTH Royal Institute of Technology StockholmSweden
                [32 ]deptDepartment of Genetics Stanford University StanfordUnited States
                [33 ]deptScience for Life Laboratory, Department of Gene Technology KTH Royal Institute of Technology StockholmSweden
                [34 ]National Institute of Biomedical Genomics KalyaniIndia
                [35 ]deptCancer Research UK Cambridge Institute University of Cambridge CambridgeUnited Kingdom
                [36 ]deptPrecision Immunology Institute Icahn School of Medicine at Mount Sinai New YorkUnited States
                [37 ]deptDivision of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences University of Cape Town Cape TownSouth Africa
                [38 ]deptDepartment of Pathology and Medical Biology, GRIAC Research Institute University of Groningen, University Medical Center Groningen GroningenThe Netherlands
                [39 ]deptDepartment of Internal Medicine and Radboud Center for Infectious Diseases Radboud University Medical Center NijmegenThe Netherlands
                [40 ]deptDepartment of Microbiology and Immunology Stanford University StanfordUnited States
                [41 ]deptComputational and Systems Biology Program Sloan Kettering Institute New YorkUnited States
                [42 ]deptMRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine University of Edinburgh EdinburghUnited Kingdom
                [43 ]deptDepartment of Applied Physics and Department of Bioengineering Stanford University StanfordUnited States
                [44 ]Chan Zuckerberg Biohub San FranciscoUnited States
                [45 ]deptEpigenetics Programme The Babraham Institute CambridgeUnited Kingdom
                [46 ]deptCentre for Trophoblast Research University of Cambridge CambridgeUnited Kingdom
                [47 ]deptCenter for Brain Science and Department of Molecular and Cellular Biology Harvard University CambridgeUnited States
                [48 ]deptDepartment of Biology New York University New YorkUnited States
                [49 ]deptNew York Genome Center New York University New YorkUnited States
                [50 ]deptDivision of Immunology The Netherlands Cancer Institute AmsterdamThe Netherlands
                [51 ]deptInstitute for Medical Engineering & Science (IMES) and Department of Chemistry Massachusetts Institute of Technology CambridgeUnited States
                [52 ]Ragon Institute of MGH, MIT and Harvard CambridgeUnited States
                [53 ]deptDepartment of Computer Science and Department of Biomolecular Sciences Weizmann Institute of Science RehovotIsrael
                [54 ]deptDepartment of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer Center University of Texas HoustonUnited States
                [55 ]deptInstitute of Computational Biology German Research Center for Environmental Health, Helmholtz Center Munich NeuherbergGermany
                [56 ]deptDepartment of Mathematics Technical University of Munich GarchingGermany
                [57 ]deptScience for Life Laboratory and Department of Proteomics KTH Royal Institute of Technology StockholmSweden
                [58 ]deptNovo Nordisk Foundation Center for Biosustainability Danish Technical University LyngbyDenmark
                [59 ]Hubrecht Institute and University Medical Center Utrecht UtrechtThe Netherlands
                [60 ]deptDepartment of Electrical Engineering and Computer Science and the Center for Computational Biology University of California, Berkeley BerkeleyUnited States
                [61 ]deptCentre for Stem Cells and Regenerative Medicine King's College London LondonUnited Kingdom
                [62 ]deptDepartment of Cellular & Molecular Pharmacology University of California, San Francisco San FranciscoUnited States
                [63 ]deptCalifornia Institute for Quantitative Biomedical Research University of California, San Francisco San FranciscoUnited States
                [64 ]deptCenter for RNA Systems Biology University of California, San Francisco San FranciscoUnited States
                [65 ]deptDivision of Biology and Biological Engineering California Institute of Technology PasadenaUnited States
                [66 ]deptCenter for Computational and Integrative Biology Massachusetts General Hospital BostonUnited States
                [67 ]deptGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease Massachusetts General Hospital BostonUnited States
                [68 ]deptCenter for Microbiome Informatics and Therapeutics Massachusetts Institute of Technology CambridgeUnited States
                Cold Spring Harbor Laboratory United States
                Cold Spring Harbor Laboratory United States
                Article
                27041
                10.7554/eLife.27041
                5762154
                29206104
                © 2017, Regev et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                Product
                Funding
                The authors declare that there was no funding for this work
                Categories
                Feature Article
                Cell Biology
                Computational and Systems Biology
                Science Forum
                Custom metadata
                Advances in techniques for analysing single cells and tissues have inspired an international effort to create comprehensive reference maps of all human cells - the fundamental units of life - as a basis for both understanding human health and diagnosing, monitoring and treating disease.

                Life sciences

                mouse, single-cell genomics, lineage, cell atlas, science forum, human

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