{"entity": "researcher", "timestamp": "2026-07-12T08:34:22.921Z", "family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "affiliations": ["Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/cc1cd4d11f8d443e8ff305f923b8fbb0.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/cc1cd4d11f8d443e8ff305f923b8fbb0"}}, "publications": [{"entity": "publication", "iuid": "f03fa87b287c4a4dbe0102b0c98c9205", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f03fa87b287c4a4dbe0102b0c98c9205.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f03fa87b287c4a4dbe0102b0c98c9205"}}, "title": "Analysis-ready VCF at Biobank scale using Zarr.", "authors": [{"family": "Czech", "given": "Eric", "initials": "E", "orcid": "0000-0002-4254-4255", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0e21d447a9449239d9b86d7c914def4.json"}}, {"family": "Tyler", "given": "Will", "initials": "W"}, {"family": "White", "given": "Tom", "initials": "T"}, {"family": "Jeffery", "given": "Ben", "initials": "B", "orcid": "0000-0002-1982-6801", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78f19bbd831415888401c9da9f21afb.json"}}, {"family": "Millar", "given": "Timothy R", "initials": "TR", "orcid": "0000-0002-5142-8811", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cf1756a518a4c0ea81f84fbe7601fdf.json"}}, {"family": "Elsworth", "given": "Benjamin", "initials": "B", "orcid": "0000-0001-7328-4233", "researcher": {"href": "https://publications.scilifelab.se/researcher/79e783b811504d93bd5f9f62d367b6c8.json"}}, {"family": "Guez", "given": "J\u00e9r\u00e9my", "initials": "J", "orcid": "0009-0007-6406-5187", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc75ff112f094d18af6fe11837c0a785.json"}}, {"family": "Hancox", "given": "Jonny", "initials": "J", "orcid": "0009-0003-5799-5299", "researcher": {"href": "https://publications.scilifelab.se/researcher/c30408b6f07a484faf4548e2c1cfd924.json"}}, {"family": "Karczewski", "given": "Konrad J", "initials": "KJ", "orcid": "0000-0003-2878-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/096bfb156b54478e9a3f9c9d7730bc43.json"}}, {"family": "Miles", "given": "Alistair", "initials": "A", "orcid": "0000-0001-9018-4680", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a1ed566e4094bfbbd02125004b3b5ad.json"}}, {"family": "Tallman", "given": "Sam", "initials": "S", "orcid": "0000-0001-7183-6276", "researcher": {"href": "https://publications.scilifelab.se/researcher/1583d2c9f189432182094fff666f8dc5.json"}}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1cd4d11f8d443e8ff305f923b8fbb0.json"}}, {"family": "Wojdyla", "given": "Rafal", "initials": "R", "orcid": "0009-0005-0735-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/bba48e71bad248e7a13b11cac0ac1af7.json"}}, {"family": "Zabad", "given": "Shadi", "initials": "S", "orcid": "0000-0002-8003-9284", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f9abcfa26374c50977b281e85609ba6.json"}}, {"family": "Hammerbacher", "given": "Jeff", "initials": "J", "orcid": "0000-0001-6596-8563", "researcher": {"href": "https://publications.scilifelab.se/researcher/321413798f474d36adcb402eafd20d22.json"}}, {"family": "Kelleher", "given": "Jerome", "initials": "J", "orcid": "0000-0002-7894-5253", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd5258b200943949537f9b6c0dd24f5.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Gigascience", "issn": "2047-217X", "volume": "14", "issn-l": "2047-217X"}, "abstract": "Variant Call Format (VCF) is the standard file format for interchanging genetic variation data and associated quality control metrics. The usual row-wise encoding of the VCF data model (either as text or packed binary) emphasizes efficient retrieval of all data for a given variant, but accessing data on a field or sample basis is inefficient. The Biobank-scale datasets currently available consist of hundreds of thousands of whole genomes and hundreds of terabytes of compressed VCF. Row-wise data storage is fundamentally unsuitable and a more scalable approach is needed.\n\nZarr is a format for storing multidimensional data that is widely used across the sciences, and is ideally suited to massively parallel processing. We present the VCF Zarr specification, an encoding of the VCF data model using Zarr, along with fundamental software infrastructure for efficient and reliable conversion at scale. We show how this format is far more efficient than standard VCF-based approaches, and competitive with specialized methods for storing genotype data in terms of compression ratios and single-threaded calculation performance. We present case studies on subsets of 3 large human datasets (Genomics England: $n$=78,195; Our Future Health: $n$=651,050; All of Us: $n$=245,394) along with whole genome datasets for Norway Spruce ($n$=1,063) and SARS-CoV-2 ($n$=4,484,157). We demonstrate the potential for VCF Zarr to enable a new generation of high-performance and cost-effective applications via illustrative examples using cloud computing and GPUs.\n\nLarge row-encoded VCF files are a major bottleneck for current research, and storing and processing these files incurs a substantial cost. The VCF Zarr specification, building on widely used, open-source technologies, has the potential to greatly reduce these costs, and may enable a diverse ecosystem of next-generation tools for analysing genetic variation data directly from cloud-based object stores, while maintaining compatibility with existing file-oriented workflows.", "doi": "10.1093/gigascience/giaf049", "pmid": "40451243", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12127038"}, {"db": "pii", "key": "8154315"}], "notes": [], "created": "2025-11-03T11:31:25.593Z", "modified": "2025-11-03T11:31:27.796Z"}, {"entity": "publication", "iuid": "eb29b09a66a84e1081cbd8cf6eb5333a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb29b09a66a84e1081cbd8cf6eb5333a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb29b09a66a84e1081cbd8cf6eb5333a"}}, "title": "Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins.", "authors": [{"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1cd4d11f8d443e8ff305f923b8fbb0.json"}}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0002-7855-9539", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c626e0c08ca449899cebece751e79cf.json"}}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Papetti", "given": "Chiara", "initials": "C", "orcid": "0000-0002-4567-459X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1a151631ac04ec0bfd9f952781bc973.json"}}, {"family": "Gislason", "given": "Astthor", "initials": "A"}, {"family": "Glenner", "given": "Henrik", "initials": "H"}, {"family": "Cartes", "given": "Joan E", "initials": "JE"}, {"family": "Blanco-Bercial", "given": "Leocadio", "initials": "L", "orcid": "0000-0003-0658-7183", "researcher": {"href": "https://publications.scilifelab.se/researcher/5077c59ccfe8496eb534c1ef6d725e06.json"}}, {"family": "Eriksen", "given": "Elena", "initials": "E"}, {"family": "Meyer", "given": "Bettina", "initials": "B", "orcid": "0000-0001-6804-9896", "researcher": {"href": "https://publications.scilifelab.se/researcher/9347bf907b1c4b258495153b5550f3dc.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}], "type": "journal article", "published": "2024-08-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "6297"}, "abstract": "Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change.", "doi": "10.1038/s41467-024-50239-7", "pmid": "39090106", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11294593"}, {"db": "pii", "key": "10.1038/s41467-024-50239-7"}], "notes": [], "created": "2024-08-02T12:21:47.326Z", "modified": "2024-11-25T10:17:04.308Z"}, {"entity": "publication", "iuid": "30653c13c25141e2995dd5ba6d7d7e07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30653c13c25141e2995dd5ba6d7d7e07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30653c13c25141e2995dd5ba6d7d7e07"}}, "title": "The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich.", "authors": [{"family": "Yazdi", "given": "Homa Papoli", "initials": "HP", "orcid": "0000-0001-8667-6279", "researcher": {"href": "https://publications.scilifelab.se/researcher/608729115444421b8c6db7eb852a059a.json"}}, {"family": "Olito", "given": "Colin", "initials": "C", "orcid": "0000-0001-6883-0367", "researcher": {"href": "https://publications.scilifelab.se/researcher/458a918560b048d68236db4b00cec58d.json"}}, {"family": "Kawakami", "given": "Takeshi", "initials": "T", "orcid": "0000-0002-9204-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/424031a0011f4e77bbb6f64a1d369b8b.json"}}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1cd4d11f8d443e8ff305f923b8fbb0.json"}}, {"family": "Schou", "given": "Mads F", "initials": "MF", "orcid": "0000-0001-5521-5269", "researcher": {"href": "https://publications.scilifelab.se/researcher/6efaf36be9d14564bd6e18344d55832e.json"}}, {"family": "Cloete", "given": "Schalk W P", "initials": "SWP", "orcid": "0000-0002-4548-5633", "researcher": {"href": "https://publications.scilifelab.se/researcher/034596fb7f8b427f9f153ebb55ef1850.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}, {"family": "Cornwallis", "given": "Charlie K", "initials": "CK", "orcid": "0000-0003-1308-3995", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d766d021df4fbeba0d52a624df866d.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "19", "issue": "6", "pages": "e1010801", "issn-l": "1553-7390"}, "abstract": "Sex chromosomes have evolved repeatedly across the tree of life and often exhibit extreme size dimorphism due to genetic degeneration of the sex-limited chromosome (e.g. the W chromosome of some birds and Y chromosome of mammals). However, in some lineages, ancient sex-limited chromosomes have escaped degeneration. Here, we study the evolutionary maintenance of sex chromosomes in the ostrich (Struthio camelus), where the W remains 65% the size of the Z chromosome, despite being more than 100 million years old. Using genome-wide resequencing data, we show that the population scaled recombination rate of the pseudoautosomal region (PAR) is higher than similar sized autosomes and is correlated with pedigree-based recombination rate in the heterogametic females, but not homogametic males. Genetic variation within the sex-linked region (SLR) (\u03c0 = 0.001) was significantly lower than in the PAR, consistent with recombination cessation. Conversely, genetic variation across the PAR (\u03c0 = 0.0016) was similar to that of autosomes and dependent on local recombination rates, GC content and to a lesser extent, gene density. In particular, the region close to the SLR was as genetically diverse as autosomes, likely due to high recombination rates around the PAR boundary restricting genetic linkage with the SLR to only ~50Kb. The potential for alleles with antagonistic fitness effects in males and females to drive chromosome degeneration is therefore limited. While some regions of the PAR had divergent male-female allele frequencies, suggestive of sexually antagonistic alleles, coalescent simulations showed this was broadly consistent with neutral genetic processes. Our results indicate that the degeneration of the large and ancient sex chromosomes of the ostrich may have been slowed by high recombination in the female PAR, reducing the scope for the accumulation of sexually antagonistic variation to generate selection for recombination cessation.", "doi": "10.1371/journal.pgen.1010801", "pmid": "37390104", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10343094"}, {"db": "pii", "key": "PGENETICS-D-22-01416"}], "notes": [], "created": "2023-08-15T09:51:56.763Z", "modified": "2024-01-16T13:48:33.279Z"}]}