{"entity": "researcher", "timestamp": "2026-08-13T19:18:52.432Z", "family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "affiliations": ["Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.", "Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.", "Department of Laboratory Medicine, Lund University, Lund, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8"}}, "publications": [{"entity": "publication", "iuid": "dcfeee20dac44d149e7456edf098d297", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcfeee20dac44d149e7456edf098d297.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcfeee20dac44d149e7456edf098d297"}}, "title": "Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.", "authors": [{"family": "Brown", "given": "Thomas", "initials": "T"}, {"family": "Mishra", "given": "Ketan", "initials": "K"}, {"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Iarovenko", "given": "Svetlana", "initials": "S"}, {"family": "Subramanian", "given": "Elaiyaraja", "initials": "E"}, {"family": "Araus", "given": "Alberto Joven", "initials": "AJ"}, {"family": "Petzold", "given": "Andreas", "initials": "A"}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29dd3593b894c5e9d233da6049d59e8.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}, {"family": "Rikk", "given": "Lennart", "initials": "L"}, {"family": "Suzuki", "given": "Miyuki", "initials": "M"}, {"family": "Suzuki", "given": "Ken-Ichi T", "initials": "KT"}, {"family": "Hayashi", "given": "Toshinori", "initials": "T"}, {"family": "Toyoda", "given": "Atsushi", "initials": "A"}, {"family": "Oliveira", "given": "Catarina R", "initials": "CR"}, {"family": "Osipova", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-6769-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900.json"}}, {"family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}}, {"family": "Yun", "given": "Maximina H", "initials": "MH"}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "researcher": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}}], "type": "journal article", "published": "2025-02-12", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "issn-l": null, "volume": "5", "issue": "2", "pages": "100761"}, "abstract": "Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.3 Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. Utilizing this assembly, we demonstrate conserved synteny as well as genetic rearrangements, such as in the major histocompatibility complex locus. We provide evidence suggesting that intronic repeat elements drive newt-specific circular RNA (circRNA) biogenesis and show their regeneration-specific expression. We also present a comprehensive in-depth annotation and chromosomal mapping of microRNAs, highlighting genomic expansion profiles as well as a distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs, and adult regeneration and provide key resources for addressing developmental, regenerative, and evolutionary principles.", "doi": "10.1016/j.xgen.2025.100761", "pmid": "39874962", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11872487"}, {"db": "pii", "key": "S2666-979X(25)00017-5"}], "notes": [], "created": "2025-01-30T10:51:47.306Z", "modified": "2025-11-14T11:06:23.898Z"}, {"entity": "publication", "iuid": "953e70aba81b4127939f42ea17f61c21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/953e70aba81b4127939f42ea17f61c21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/953e70aba81b4127939f42ea17f61c21"}}, "title": "Evaluation of genetic demultiplexing of single-cell sequencing data from model species.", "authors": [{"family": "Cardiello", "given": "Joseph F", "initials": "JF", "orcid": "0000-0001-7212-6508", "researcher": {"href": "https://publications.scilifelab.se/researcher/f66dfd07566947b68638630de5b8e807.json"}}, {"family": "Joven Araus", "given": "Alberto", "initials": "A", "orcid": "0000-0002-0926-4665", "researcher": {"href": "https://publications.scilifelab.se/researcher/11c7df4727464e1c95bdaa9372ce7409.json"}}, {"family": "Giatrellis", "given": "Sarantis", "initials": "S"}, {"family": "Helsens", "given": "Clement", "initials": "C", "orcid": "0000-0002-9243-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c293306f5704b2eb524f1e195dc6113.json"}}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "researcher": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}}, {"family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "6", "issue": "8", "pages": "e202301979"}, "abstract": "Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address these problems is pooling cells from multiple individuals into one sc-seq library. In humans, genotype-based computational separation (i.e., demultiplexing) of pooled sc-seq samples is common. This approach would be instrumental for studying non-isogenic model organisms. We set out to determine whether genotype-based demultiplexing could be more broadly applied among species ranging from zebrafish to non-human primates. Using such non-isogenic species, we benchmark genotype-based demultiplexing of pooled sc-seq datasets against various ground truths. We demonstrate that genotype-based demultiplexing of pooled sc-seq samples can be used with confidence in several non-isogenic model organisms and uncover limitations of this method. Importantly, the only genomic resource required for this approach is sc-seq data and a de novo transcriptome. The incorporation of pooling into sc-seq study designs will decrease cost while simultaneously increasing the reproducibility and experimental options in non-isogenic model organisms.", "doi": "10.26508/lsa.202301979", "pmid": "37197983", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Single cell": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10192724"}, {"db": "pii", "key": "6/8/e202301979"}], "notes": [], "created": "2022-12-01T13:53:09.953Z", "modified": "2024-10-16T13:17:03.038Z"}, {"entity": "publication", "iuid": "1d8e4456081f4c1fa318ba451e997fe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d8e4456081f4c1fa318ba451e997fe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d8e4456081f4c1fa318ba451e997fe0"}}, "title": "Human Primary Airway Basal Cells Display a Continuum of Molecular Phases from Health to Disease in Chronic Obstructive Pulmonary Disease.", "authors": [{"family": "Wijk", "given": "Sofia C", "initials": "SC"}, {"family": "Prabhala", "given": "Pavan", "initials": "P", "orcid": "0000-0002-8495-6274", "researcher": {"href": "https://publications.scilifelab.se/researcher/aec8f122bfdb42c7b64fa6adfb51cf1e.json"}}, {"family": "Michalikov\u00e1", "given": "Barbora", "initials": "B"}, {"family": "Sommarin", "given": "Mikael", "initials": "M", "orcid": "0000-0002-2581-5543", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdeebff543c249689f31f956ca071905.json"}}, {"family": "Doyle", "given": "Alexander", "initials": "A"}, {"family": "Lang", "given": "Stefan", "initials": "S"}, {"family": "Kanzenbach", "given": "Karina", "initials": "K"}, {"family": "Tufvesson", "given": "Ellen", "initials": "E", "orcid": "0000-0002-4941-332X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ca6d27ac44744739ceeb6c0494ae09b.json"}}, {"family": "Lindstedt", "given": "Sandra", "initials": "S"}, {"family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-8197-754X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77c85732b1a84a02b1812a384795a1bc.json"}}, {"family": "Bjermer", "given": "Leif", "initials": "L"}, {"family": "Westergren-Thorsson", "given": "Gunilla", "initials": "G", "orcid": "0000-0001-5327-8805", "researcher": {"href": "https://publications.scilifelab.se/researcher/08bbfee41c5545779fa88211baeeb216.json"}}, {"family": "Magnusson", "given": "Mattias", "initials": "M", "orcid": "0000-0002-7913-5623", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4666145595e4843a3b662abf6530e19.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Am J Respir Cell Mol Biol", "issn": "1535-4989", "volume": "65", "issue": "1", "pages": "103-113", "issn-l": null}, "abstract": "Airway basal cells are crucial for regeneration of the human lung airway epithelium and are believed to be important contributors to chronic obstructive pulmonary disease (COPD) and other lung disorders. To reveal how basal cells contribute to disease and to discover novel therapeutic targets, these basal cells need to be further characterized. In this study, we optimized a flow cytometry-based cell sorting protocol for primary human airway basal cells dependent on cell size and NGFR (nerve-growth factor receptor) expression. The basal cell population was found to be molecularly and functionally heterogeneous, in contrast to cultured basal cells. In addition, significant differences were found, such as KRT14 expression exclusively existing in cultured cells. Also, colony-forming capacity was significantly increased in cultured cells showing a clonal enrichment in vitro. Next, by single-cell RNA sequencing on primary basal cells from healthy donors and patients with Global Initiative for Chronic Obstructive Lung Disease stage IV COPD, the gene expression revealed a continuum ranging from healthy basal cell signatures to diseased basal cell phenotypes. We identified several upregulated genes that may indicate COPD, such as stress response-related genes GADD45B and AHSA1, together with with genes involved in the response to hypoxia, such as CITED2 and SOD1. Taken together, the presence of healthy basal cells in stage IV COPD demonstrates the potential for regeneration through the discovery of novel therapeutic targets. In addition, we show the importance of studying primary basal cells when investigating disease mechanisms as well as for developing future cell-based therapies in the human lung.", "doi": "10.1165/rcmb.2020-0464OC", "pmid": "33789072", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2022-01-13T12:01:38.377Z", "modified": "2022-01-13T12:01:38.595Z"}, {"entity": "publication", "iuid": "3adfb48e02604b2ba757fbc5eb5fa1c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3adfb48e02604b2ba757fbc5eb5fa1c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3adfb48e02604b2ba757fbc5eb5fa1c3"}}, "title": "Isolation of high-yield and -quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts.", "authors": [{"family": "Stegmayr", "given": "John", "initials": "J", "orcid": "0000-0002-8167-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c4ae88fd45a4690b0d9d47bd5e9b3d3.json"}}, {"family": "Alsafadi", "given": "Hani N", "initials": "HN", "orcid": "0000-0002-1186-2517", "researcher": {"href": "https://publications.scilifelab.se/researcher/f196e12b6b9e48e2a2c9099cc0b1dc26.json"}}, {"family": "Langwi\u0144ski", "given": "Wojciech", "initials": "W"}, {"family": "Niroomand", "given": "Anna", "initials": "A"}, {"family": "Lindstedt", "given": "Sandra", "initials": "S", "orcid": "0000-0003-4484-6473", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1eb6cdf462148de80a94cbc0389d68e.json"}}, {"family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}}, {"family": "Wagner", "given": "Darcy E", "initials": "DE", "orcid": "0000-0003-3794-1309", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4f4c5ba44e3428186b5e6b73d745c34.json"}}], "type": "journal article", "published": "2021-02-01", "journal": {"title": "Am J Physiol Lung Cell Mol Physiol", "issn": "1522-1504", "volume": "320", "issue": "2", "pages": "L232-L240", "issn-l": null}, "abstract": "Precision-cut lung slices (PCLS) have gained increasing interest as a model to study lung biology/disease and screening novel therapeutics. In particular, PCLS derived from human tissue can better recapitulate some aspects of lung biology/disease as compared with animal models. Several experimental readouts have been established for use with PCLS, but obtaining high-yield and -quality RNA for downstream analysis has remained challenging. This is particularly problematic for utilizing the power of next-generation sequencing techniques, such as RNA-sequencing (RNA-seq), for nonbiased and high-throughput analysis of PCLS human cohorts. In the current study, we present a novel approach for isolating high-quality RNA from a small amount of tissue, including diseased human tissue, such as idiopathic pulmonary fibrosis. We show that the RNA isolated using this method has sufficient quality for RT-qPCR and RNA-seq analysis. Furthermore, the RNA-seq data from human PCLS could be used in several established computational pipelines, including deconvolution of bulk RNA-seq data using publicly available single-cell RNA-seq data. Deconvolution using Bisque revealed a diversity of cell populations in human PCLS, including several immune cell populations, which correlated with cell populations known to be present and aberrant in human disease.", "doi": "10.1152/ajplung.00401.2020", "pmid": "33112185", "labels": {"Clinical Genomics Lund": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2021-11-23T13:49:53.813Z", "modified": "2024-01-16T13:48:40.784Z"}]}