{"entity": "researcher", "timestamp": "2026-08-20T20:57:51.299Z", "family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "affiliations": ["Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df"}}, "publications": [{"entity": "publication", "iuid": "72a59460db0b4dbeb14e1dd17cc8da39", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/72a59460db0b4dbeb14e1dd17cc8da39.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/72a59460db0b4dbeb14e1dd17cc8da39"}}, "title": "A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract.", "authors": [{"family": "Monasterio", "given": "Gustavo", "initials": "G", "orcid": "0000-0001-6336-132X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce06c970b0f84b749499513116913eb6.json"}}, {"family": "Morales", "given": "Rodrigo A", "initials": "RA", "orcid": "0000-0003-4382-5777", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/32b43121030e4531b11e3b04938e765e.json"}}, {"family": "Bejarano", "given": "David A", "initials": "DA", "orcid": "0000-0001-7804-0131", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78885dd0abe24535993f60bd2e6b9829.json"}}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df.json"}}, {"family": "Fransson", "given": "Jennifer", "initials": "J"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Schlitzer", "given": "Andreas", "initials": "A", "orcid": "0000-0001-7662-3712", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/79413d89067d43b292f2ca4b8a4d66f1.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c90ee0c3d1904ae0933efe3631a651e0.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "volume": "19", "issue": "10", "pages": "3085-3137", "issn-l": null}, "abstract": "Tissues are dynamic and complex biological systems composed of specialized cell types that interact with each other for proper biological function. To comprehensively characterize and understand the cell circuitry underlying biological processes within tissues, it is crucial to preserve their spatial information. Here we report a simple mounting technique to maximize the area of the tissue to be analyzed, encompassing the whole length of the murine gastrointestinal (GI) tract, from mouth to rectum. Using this method, analysis of the whole murine GI tract can be performed in a single slide not only by means of histological staining, immunohistochemistry and in situ hybridization but also by multiplexed antibody staining and spatial transcriptomic approaches. We demonstrate the utility of our method in generating a comprehensive gene and protein expression profile of the whole GI tract by combining the versatile tissue-rolling technique with a cutting-edge transcriptomics method (Visium) and two cutting-edge proteomics methods (ChipCytometry and CODEX-PhenoCycler) in a systematic and easy-to-follow step-by-step procedure. The entire process, including tissue rolling, processing and sectioning, can be achieved within 2-3 d for all three methods. For Visium spatial transcriptomics, an additional 2 d are needed, whereas for spatial proteomics assays (ChipCytometry and CODEX-PhenoCycler), another 3-4 d might be considered. The whole process can be accomplished by researchers with skills in performing murine surgery, and standard histological and molecular biology methods.", "doi": "10.1038/s41596-024-01001-2", "pmid": "38906985", "labels": [], "xrefs": [{"db": "pii", "key": "10.1038/s41596-024-01001-2"}, {"db": "GEO", "key": "GSE169749"}], "notes": [], "created": "2026-08-20T09:04:01.223Z", "modified": "2026-08-20T09:04:01.475Z"}, {"entity": "publication", "iuid": "3adaf7e2d1d14eb7bb027bb18463c836", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3adaf7e2d1d14eb7bb027bb18463c836.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3adaf7e2d1d14eb7bb027bb18463c836"}}, "title": "Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples.", "authors": [{"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ad34c94b64432ab74d61fbc6d16905.json"}}, {"family": "Newton", "given": "Phillip T", "initials": "PT", "orcid": "0000-0003-2142-1798", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e490d4b3da4741b490395399f1b8c1.json"}}, {"family": "Galicia", "given": "Leire Alonso", "initials": "LA"}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df.json"}}, {"family": "Avijgan", "given": "Mahtab", "initials": "M"}, {"family": "Kvastad", "given": "Linda", "initials": "L", "orcid": "0000-0001-5869-3485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/384e05b0be164cabb26bc3ce544742db.json"}}, {"family": "Denadai-Souza", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-0385-1321", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4f2a0f8d4d6470d8cf48d3a27b19b78.json"}}, {"family": "Stakenborg", "given": "Nathalie", "initials": "N", "orcid": "0000-0002-6229-0045", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d107940932374682934e1ee3860c20f2.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB"}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Jurek", "given": "Aleksandra", "initials": "A"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ff9fe255d640c0a2bbed0913fe208d.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C"}, {"family": "Boeckxstaens", "given": "Guy", "initials": "G", "orcid": "0000-0001-8267-5797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a5224f2c1014dab80a2e50af25d7a18.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}], "type": "journal article", "published": "2023-01-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "509", "issn-l": "2041-1723"}, "abstract": "Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins.", "doi": "10.1038/s41467-023-36071-5", "pmid": "36720873", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9889806"}, {"db": "pii", "key": "10.1038/s41467-023-36071-5"}], "notes": [], "created": "2026-08-20T08:52:29.319Z", "modified": "2026-08-20T08:52:29.623Z"}, {"entity": "publication", "iuid": "9ef1a1c67d104a3ba0cc7461f0d1f2a7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9ef1a1c67d104a3ba0cc7461f0d1f2a7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9ef1a1c67d104a3ba0cc7461f0d1f2a7"}}, "title": "Ancient multiplicity in cyclic nucleotide-gated (CNG) cation channel repertoire was reduced in the ancestor of Olfactores before re-expansion by whole genome duplications in vertebrates.", "authors": [{"family": "Lagman", "given": "David", "initials": "D", "orcid": "0000-0001-7600-5287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/274e2232c3ae463d8d004c533dd3cd24.json"}}, {"family": "Haines", "given": "Helen J", "initials": "HJ"}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df.json"}}, {"family": "Larhammar", "given": "Dan", "initials": "D"}], "type": "journal article", "published": "2022-12-30", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "17", "issue": "12", "pages": "e0279548", "issn-l": "1932-6203"}, "abstract": "Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the retina, with different subunit composition in cone and rod photoreceptor cells: three CNGA3 and one CNGB3 in cones and three CNGA1 and one CNGB1 in rods. CNGA and CNGB subunits form separate subfamilies. We have analyzed the evolution of the CNG gene family in metazoans, with special focus on vertebrates by using sequence-based phylogeny and conservation of chromosomal synteny to deduce paralogons resulting from the early vertebrate whole genome duplications (WGDs). Our analyses show, unexpectedly, that the CNGA subfamily had four sister subfamilies in the ancestor of bilaterians and cnidarians that we named CNGC, CNGD, CNGE and CNGF. Of these, CNGC, CNGE and CNGF were lost in the ancestor of Olfactores while CNGD was lost in the vertebrate ancestor. The remaining CNGA and CNGB genes were expanded by a local duplication of CNGA and the subsequent chromosome duplications in the basal vertebrate WGD events. Upon some losses, this resulted in the gnathostome ancestor having three members in the visual CNGA subfamily (CNGA1-3), a single CNGA4 gene, and two members in the CNGB subfamily (CNGB1 and CNGB3). The nature of chromosomal rearrangements in the vertebrate CNGA paralogon was resolved by including the genomes of a non-teleost actinopterygian and an elasmobranch. After the teleost-specific WGD, additional duplicates were generated and retained for CNGA1, CNGA2, CNGA3 and CNGB1. Furthermore, teleosts retain a local duplicate of CNGB3. The retention of duplicated CNG genes is explained by their subfunctionalisation and photoreceptor-specific expression. In conclusion, this study provides evidence for four previously unknown CNG subfamilies in metazoans and further evidence that the early vertebrate WGD events were instrumental in the evolution of the vertebrate visual and central nervous systems.", "doi": "10.1371/journal.pone.0279548", "pmid": "36584110", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9803222"}, {"db": "pii", "key": "PONE-D-22-27051"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.6170824.v1"}], "notes": [], "created": "2026-08-20T12:44:18.773Z", "modified": "2026-08-20T12:44:18.854Z"}, {"entity": "publication", "iuid": "5d33f9d184034a6fba14ac0d80c62812", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5d33f9d184034a6fba14ac0d80c62812.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5d33f9d184034a6fba14ac0d80c62812"}}, "title": "Super-resolved spatial transcriptomics by deep data fusion.", "authors": [{"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L", "orcid": "0000-0002-5108-4481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60ea7a079ae04b8896196dafec84a6fc.json"}}, {"family": "He", "given": "Bryan", "initials": "B", "orcid": "0000-0002-6150-761X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/939849332f874f1cb13709938bc10e17.json"}}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Abalo", "given": "Xes\u00fas", "initials": "X", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df.json"}}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Ji", "given": "Andrew L", "initials": "AL", "orcid": "0000-0001-9688-5680", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/277ab9d989dc415b8b4a23f929bee180.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ad34c94b64432ab74d61fbc6d16905.json"}}, {"family": "Stakenborg", "given": "Nathalie", "initials": "N", "orcid": "0000-0002-6229-0045", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d107940932374682934e1ee3860c20f2.json"}}, {"family": "Boeckxstaens", "given": "Guy", "initials": "G"}, {"family": "Khavari", "given": "Paul", "initials": "P", "orcid": "0000-0003-0098-4989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94c287c0a13b42c6b2de95fc4138e821.json"}}, {"family": "Zou", "given": "James", "initials": "J", "orcid": "0000-0001-8880-4764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bee507e18338496f812ab20fd8e4c302.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Maaskola", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "40", "issue": "4", "pages": "476-479", "issn-l": "1087-0156"}, "abstract": "Current methods for spatial transcriptomics are limited by low spatial resolution. Here we introduce a method that integrates spatial gene expression data with histological image data from the same tissue section to infer higher-resolution expression maps. Using a deep generative model, our method characterizes the transcriptome of micrometer-scale anatomical features and can predict spatial gene expression from histology images alone.", "doi": "10.1038/s41587-021-01075-3", "pmid": "34845373", "labels": [], "xrefs": [{"db": "pii", "key": "10.1038/s41587-021-01075-3"}], "notes": [], "created": "2026-08-20T08:59:26.295Z", "modified": "2026-08-20T08:59:26.538Z"}]}