{"entity": "researcher", "timestamp": "2026-07-14T03:26:29.237Z", "family": "Heyn", "given": "Holger", "initials": "H", "orcid": "0000-0002-3276-1889", "affiliations": ["CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain. holger.heyn@cnag.crg.eu.", "Universitat Pompeu Fabra, Barcelona, Spain. holger.heyn@cnag.crg.eu."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/b7f8103bc9af4fb5a3bd1d544648e588.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/b7f8103bc9af4fb5a3bd1d544648e588"}}, "publications": [{"entity": "publication", "iuid": "d8caf32b4e914eb6bbeb6cba5fa922c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d8caf32b4e914eb6bbeb6cba5fa922c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d8caf32b4e914eb6bbeb6cba5fa922c5"}}, "title": "The emerging landscape of spatial profiling technologies.", "authors": [{"family": "Moffitt", "given": "Jeffrey R", "initials": "JR", "orcid": "0000-0002-3836-3101", "researcher": {"href": "https://publications.scilifelab.se/researcher/7949777899fc42ccb59205e2cdc22efd.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Heyn", "given": "Holger", "initials": "H", "orcid": "0000-0002-3276-1889", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f8103bc9af4fb5a3bd1d544648e588.json"}}], "type": "journal article", "published": "2022-12-00", "journal": {"title": "Nat. Rev. Genet.", "issn": "1471-0064", "volume": "23", "issue": "12", "pages": "741-759", "issn-l": "1471-0056"}, "abstract": "Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein profiling methods as a major pillar for cellular atlas building of complex samples, from tissues to full organisms. Emerging methods yield omics measurements at resolutions covering the nano- to microscale, enabling the charting of cellular heterogeneity, complex tissue architectures and dynamic changes during development and disease. We present an overview of the developing landscape of in situ spatial genome, transcriptome and proteome technologies, exemplify their impact on cell biology and translational research, and discuss current challenges for their community-wide adoption. Among many transformative applications, we envision that spatial methods will map entire organs and enable next-generation pathology.", "doi": "10.1038/s41576-022-00515-3", "pmid": "35859028", "labels": {"Spatial Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41576-022-00515-3"}], "notes": [], "created": "2022-11-29T06:31:50.361Z", "modified": "2022-11-29T06:31:50.411Z"}, {"entity": "publication", "iuid": "41bcf2ce98a54d95bd77cb57d287490b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41bcf2ce98a54d95bd77cb57d287490b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41bcf2ce98a54d95bd77cb57d287490b"}}, "title": "Building a high-quality Human Cell Atlas.", "authors": [{"family": "Rozenblatt-Rosen", "given": "Orit", "initials": "O"}, {"family": "Shin", "given": "Jay W", "initials": "JW", "orcid": "0000-0003-4037-3533", "researcher": {"href": "https://publications.scilifelab.se/researcher/d036e3b029d54dad9a678b47f138def3.json"}}, {"family": "Rood", "given": "Jennifer E", "initials": "JE"}, {"family": "Hupalowska", "given": "Anna", "initials": "A"}, {"family": "Human Cell Atlas Standards and Technology Working Group", "given": "", "initials": ""}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}}, {"family": "Heyn", "given": "Holger", "initials": "H", "orcid": "0000-0002-3276-1889", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f8103bc9af4fb5a3bd1d544648e588.json"}}], "type": "letter", "published": "2021-02-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "39", "issue": "2", "pages": "149-153", "issn-l": "1087-0156"}, "abstract": null, "doi": "10.1038/s41587-020-00812-4", "pmid": "33500565", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-00812-4"}], "notes": [], "created": "2021-12-09T09:50:46.803Z", "modified": "2021-12-09T09:50:46.886Z"}, {"entity": "publication", "iuid": "ed70a147175843f5a31852a576f105bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed70a147175843f5a31852a576f105bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed70a147175843f5a31852a576f105bc"}}, "title": "Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.", "authors": [{"family": "Mereu", "given": "Elisabetta", "initials": "E"}, {"family": "Lafzi", "given": "Atefeh", "initials": "A"}, {"family": "Moutinho", "given": "Catia", "initials": "C"}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "researcher": {"href": "https://publications.scilifelab.se/researcher/3297f21f1a174cd388ac586eda2b5177.json"}}, {"family": "McCarthy", "given": "Davis J", "initials": "DJ"}, {"family": "\u00c1lvarez-Varela", "given": "Adri\u00e1n", "initials": "A"}, {"family": "Batlle", "given": "Eduard", "initials": "E"}, {"family": "Gr\u00fcn", "given": "Dominic", "initials": "D", "orcid": "0000-0002-3364-5898", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ee67aea7fd94e56a66d33a92c32863b.json"}}, {"family": "Lau", "given": "Julia K", "initials": "JK"}, {"family": "Boutet", "given": "St\u00e9phane C", "initials": "SC"}, {"family": "Sanada", "given": "Chad", "initials": "C"}, {"family": "Ooi", "given": "Aik", "initials": "A"}, {"family": "Jones", "given": "Robert C", "initials": "RC", "orcid": "0000-0001-7235-9854", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fc0262d6f154970914dce5fa42fa83f.json"}}, {"family": "Kaihara", "given": "Kelly", "initials": "K"}, {"family": "Brampton", "given": "Chris", "initials": "C"}, {"family": "Talaga", "given": "Yasha", "initials": "Y"}, {"family": "Sasagawa", "given": "Yohei", "initials": "Y"}, {"family": "Tanaka", "given": "Kaori", "initials": "K"}, {"family": "Hayashi", "given": "Tetsutaro", "initials": "T"}, {"family": "Braeuning", "given": "Caroline", "initials": "C"}, {"family": "Fischer", "given": "Cornelius", "initials": "C", "orcid": "0000-0003-0329-2435", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dcb9bf2b11a45a9a95219a0e456388e.json"}}, {"family": "Sauer", "given": "Sascha", "initials": "S"}, {"family": "Trefzer", "given": "Timo", "initials": "T"}, {"family": "Conrad", "given": "Christian", "initials": "C"}, {"family": "Adiconis", "given": "Xian", "initials": "X"}, {"family": "Nguyen", "given": "Lan T", "initials": "LT"}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}}, {"family": "Levin", "given": "Joshua Z", "initials": "JZ", "orcid": "0000-0002-0170-3598", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aab17c0401f44df98fa2df56e8ddcae.json"}}, {"family": "Parekh", "given": "Swati", "initials": "S", "orcid": "0000-0002-4826-1651", "researcher": {"href": "https://publications.scilifelab.se/researcher/aeed2ef091514d25aa845563f9c41687.json"}}, {"family": "Janjic", "given": "Aleksandar", "initials": "A", "orcid": "0000-0001-7180-5381", "researcher": {"href": "https://publications.scilifelab.se/researcher/38aaef51d88e4c6795f38fb6e8cee5d5.json"}}, {"family": "Wange", "given": "Lucas E", "initials": "LE", "orcid": "0000-0002-3275-9156", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d25e9c8662444ecaad76339843df61e.json"}}, {"family": "Bagnoli", "given": "Johannes W", "initials": "JW"}, {"family": "Enard", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-4056-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc85b7ab2ce48408c3d9e00895a7cbf.json"}}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Nikaido", "given": "Itoshi", "initials": "I", "orcid": "0000-0002-7261-2570", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c5e9ef375146618fb7fbe1c95c2104.json"}}, {"family": "Gut", "given": "Ivo", "initials": "I", "orcid": "0000-0001-7219-632X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c14600c4e0d54a7aae393c728d9af088.json"}}, {"family": "Stegle", "given": "Oliver", "initials": "O"}, {"family": "Heyn", "given": "Holger", "initials": "H", "orcid": "0000-0002-3276-1889", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f8103bc9af4fb5a3bd1d544648e588.json"}}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "38", "issue": "6", "pages": "747-755", "issn-l": "1087-0156"}, "abstract": "Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands of cells and are being used to compile cell atlases of tissues, organs and organisms. However, the protocols differ substantially with respect to their RNA capture efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. In the present study, we generated benchmark datasets to systematically evaluate protocols in terms of their power to comprehensively describe cell types and states. We performed a multicenter study comparing 13 commonly used scRNA-seq and single-nucleus RNA-seq protocols applied to a heterogeneous reference sample resource. Comparative analysis revealed marked differences in protocol performance. The protocols differed in library complexity and their ability to detect cell-type markers, impacting their predictive value and suitability for integration into reference cell atlases. These results provide guidance both for individual researchers and for consortium projects such as the Human Cell Atlas.", "doi": "10.1038/s41587-020-0469-4", "pmid": "32518403", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-0469-4"}], "notes": [], "created": "2020-07-08T13:04:12.225Z", "modified": "2021-11-10T12:50:42.946Z"}]}