{"entity": "researcher", "timestamp": "2026-07-22T17:31:02.673Z", "family": "Schirman", "given": "Dvir", "initials": "D", "orcid": "0000-0001-5175-0176", "affiliations": ["Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/02550d8122ed486fb67691b456926aed.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/02550d8122ed486fb67691b456926aed"}}, "publications": [{"entity": "publication", "iuid": "87a87989503945b7842ab3f695a22318", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87a87989503945b7842ab3f695a22318.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87a87989503945b7842ab3f695a22318"}}, "title": "Pooled optical screening in bacteria using chromosomally expressed barcodes.", "authors": [{"family": "Soares", "given": "Ruben R G", "initials": "RRG", "orcid": "0000-0001-5958-5232", "researcher": {"href": "https://publications.scilifelab.se/researcher/88ea8e0d81284c35a271f05187289390.json"}}, {"family": "Garc\u00eda-Soriano", "given": "Daniela A", "initials": "DA", "orcid": "0000-0003-2849-8528", "researcher": {"href": "https://publications.scilifelab.se/researcher/2aeeed6de99647a1878352e0da2220af.json"}}, {"family": "Larsson", "given": "Jimmy", "initials": "J"}, {"family": "Fange", "given": "David", "initials": "D", "orcid": "0009-0006-3981-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/195ab3e1f94e4ad39b4aa32da6b3e217.json"}}, {"family": "Schirman", "given": "Dvir", "initials": "D", "orcid": "0000-0001-5175-0176", "researcher": {"href": "https://publications.scilifelab.se/researcher/02550d8122ed486fb67691b456926aed.json"}}, {"family": "Grillo", "given": "Marco", "initials": "M", "orcid": "0000-0003-2155-0645", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd8bec6567444558acbcbd1b3d28f7a.json"}}, {"family": "Kn\u00f6ppel", "given": "Anna", "initials": "A"}, {"family": "Sen", "given": "Beer Chakra", "initials": "BC"}, {"family": "Svahn", "given": "Fabian", "initials": "F", "orcid": "0000-0002-5914-520X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f015b5855854d40b853c17a31d3d632.json"}}, {"family": "Zikrin", "given": "Spartak", "initials": "S", "orcid": "0000-0002-7802-8869", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a82f27ea7bf43deaded33d359270820.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.json"}}], "type": "journal article", "published": "2025-06-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "851", "issn-l": "2399-3642"}, "abstract": "Optical pooled screening is an important tool to study dynamic phenotypes for libraries of genetically engineered cells. However, the desired engineering often requires that the barcodes used for in situ genotyping are expressed from the chromosome. This has not previously been achieved in bacteria. Here we describe a method for in situ genotyping of libraries with genomic barcodes in Escherichia coli. The method is applied to measure the intracellular maturation time of 84 red fluorescent proteins.", "doi": "10.1038/s42003-025-08268-5", "pmid": "40461651", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12134211"}, {"db": "pii", "key": "10.1038/s42003-025-08268-5"}], "notes": [], "created": "2025-11-28T10:47:35.410Z", "modified": "2025-11-28T10:47:35.689Z"}, {"entity": "publication", "iuid": "f4ecf70c0f124d118f067a49621b872e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4ecf70c0f124d118f067a49621b872e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4ecf70c0f124d118f067a49621b872e"}}, "title": "Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle.", "authors": [{"family": "Karempudi", "given": "Praneeth", "initials": "P", "orcid": "0000-0002-5925-8669", "researcher": {"href": "https://publications.scilifelab.se/researcher/660b0381d6d248e7a3fc1737d88539b0.json"}}, {"family": "Gras", "given": "Konrad", "initials": "K"}, {"family": "Amselem", "given": "Elias", "initials": "E", "orcid": "0000-0003-2846-9225", "researcher": {"href": "https://publications.scilifelab.se/researcher/b36dcc99173f461e84941241665eaedf.json"}}, {"family": "Zikrin", "given": "Spartak", "initials": "S"}, {"family": "Schirman", "given": "Dvir", "initials": "D", "orcid": "0000-0001-5175-0176", "researcher": {"href": "https://publications.scilifelab.se/researcher/02550d8122ed486fb67691b456926aed.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8c05ef8453040a794cb9c716f0ef8d6.json"}}], "type": "journal article", "published": "2024-11-05", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "1443", "issn-l": "2399-3642"}, "abstract": "The intracellular position of genes may impact their expression, but it has not been possible to accurately measure the 3D position of chromosomal loci. In 2D, loci can be tracked using arrays of DNA-binding sites for transcription factors (TFs) fused with fluorescent proteins. However, the same 2D data can result from different 3D trajectories. Here, we have developed a deep learning method for super-resolved astigmatism-based 3D localization of chromosomal loci in live E. coli cells which enables a precision better than 61 nm at a signal-to-background ratio of ~4 on a heterogeneous cell background. Determining the spatial localization of chromosomal loci, we find that some loci are at the periphery of the nucleoid for large parts of the cell cycle. Analyses of individual trajectories reveal that these loci are subdiffusive both longitudinally (x) and radially (r), but that individual loci explore the full radial width on a minute time scale.", "doi": "10.1038/s42003-024-07155-9", "pmid": "39501081", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11538341"}, {"db": "pii", "key": "10.1038/s42003-024-07155-9"}], "notes": [], "created": "2024-11-25T10:21:54.835Z", "modified": "2025-02-28T14:16:15.992Z"}]}