{"entity": "researcher", "timestamp": "2026-07-15T16:14:36.372Z", "family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "affiliations": ["Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547"}}, "publications": [{"entity": "publication", "iuid": "97a9599da59641ebb05e5b7a8fe6ad45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45"}}, "title": "The expanded genome of Hexamita inflata, a free-living diplomonad.", "authors": [{"family": "Akdeniz", "given": "Zeynep", "initials": "Z", "orcid": "0000-0002-5279-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b6a7222e2d3487db2b50842f74e173e.json"}}, {"family": "Havelka", "given": "Michal", "initials": "M"}, {"family": "Stoklasa", "given": "Michal", "initials": "M"}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "\u017d\u00e1rsk\u00fd", "given": "Vojt\u011bch", "initials": "V"}, {"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}, {"family": "Kol\u00edsko", "given": "Martin", "initials": "M"}, {"family": "Provazn\u00edk", "given": "Jan", "initials": "J"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Tachezy", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2025-02-01", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "192", "issn-l": "2052-4463"}, "abstract": "Diplomonads are anaerobic, flagellated protists, being part of the Metamonada group of Eukaryotes. Diplomonads either live as endobionts (parasites and commensals) of animals or free-living in low-oxygen environments. Genomic information is available for parasitic diplomonads like Giardia intestinalis and Spironucleus salmonicida, while little is known about the genomic arrangements of free-living diplomonads. We have generated the first reference genome of a free-living diplomonad, Hexamita inflata. The final version of the genome assembly is fragmented (1241 contigs) but substantially larger (142 Mbp) than the parasitic diplomonad genomes (9.8-14.7 Mbp). It encodes 79,341 proteins; 29,874 have functional annotations and 49,467 are hypothetical proteins. Interspersed repeats comprise 34% of the genome (9617 Retroelements, 2676 DNA transposons). The large expansion of protein-encoding capacity and the interspersed repeats are the major reasons for the large genome size. This genome from a free-living diplomonad will be the basis for further studies of the Diplomonadida lineage and the evolution of parasitism-free living style transitions.", "doi": "10.1038/s41597-025-04514-x", "pmid": "39893204", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11787283"}, {"db": "pii", "key": "10.1038/s41597-025-04514-x"}], "notes": [], "created": "2025-03-07T09:59:16.550Z", "modified": "2025-04-03T08:27:54.918Z"}, {"entity": "publication", "iuid": "8aa299665472425e85321e47494115a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8aa299665472425e85321e47494115a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8aa299665472425e85321e47494115a3"}}, "title": "Macrophages support healing of ischemic injury by transdifferentiating towards mural cells and adopting functions important for vascular support", "authors": [{"family": "Parv", "given": "Kristel", "initials": "K"}, {"family": "Hidalgo", "given": "Carmen Herrera", "initials": "CH"}, {"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Amoedo-Leite", "given": "Catarina", "initials": "C", "orcid": "0000-0002-7556-4826", "researcher": {"href": "https://publications.scilifelab.se/researcher/09c63612668841df817c18ab93d6f4e4.json"}}, {"family": "Giraud", "given": "Antoine", "initials": "A", "orcid": "0000-0002-8559-5781", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d7d5e9c90a4dc8b798c366ce4aa6a7.json"}}, {"family": "Holl", "given": "Daniel", "initials": "D"}, {"family": "Seignez", "given": "Cedric", "initials": "C", "orcid": "0000-0002-6381-2968", "researcher": {"href": "https://publications.scilifelab.se/researcher/10cc35e368844041b36da62fa6dbc6a2.json"}}, {"family": "Goeritz", "given": "Christian", "initials": "C", "orcid": "0000-0003-0799-766X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3358941841740db8d22fd49e14bdea2.json"}}, {"family": "Christoffersson", "given": "Gustaf", "initials": "G", "orcid": "0000-0002-9640-9702", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4092dad56b342bca7a5ce9d8ed56dc2.json"}}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}], "type": "posted-content", "published": "2022-11-21", "journal": {"title": "res sq", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.21203/rs.3.rs-2263892/v1", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-27T22:00:49.724Z", "modified": "2025-12-22T07:57:42.057Z"}, {"entity": "publication", "iuid": "8a75948c51be42018169ce7fe05133b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a75948c51be42018169ce7fe05133b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a75948c51be42018169ce7fe05133b1"}}, "title": "A chromosome-scale reference genome for Spironucleus salmonicida.", "authors": [{"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "Kurt", "given": "Zeynep", "initials": "Z"}, {"family": "\u00c1stvaldsson", "given": "\u00c1sgeir", "initials": "\u00c1", "orcid": "0000-0002-0320-6974", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a3d973dc6d246b48426d2063eef8934.json"}}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "dataset", "published": "2022-09-24", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "9", "issue": "1", "pages": "585", "issn-l": "2052-4463"}, "abstract": "Spironucleus salmonicida is a diplomonad causing systemic infection in salmon. The first S. salmonicida genome assembly was published 2014 and has been a valuable reference genome in protist research. However, the genome assembly is fragmented without assignment of the sequences to chromosomes. In our previous Giardia genome study, we have shown how a fragmented genome assembly can be improved with long-read sequencing technology complemented with optical maps. Combining Pacbio long-read sequencing technology and optical maps, we are presenting here this new S. salmonicida genome assembly in nine near-complete chromosomes with only three internal gaps at long repeats. This new genome assembly is not only more complete sequence-wise but also more complete at annotation level, providing more details into gene families, gene organizations and chromosomal structure. This near-complete reference genome will aid comparative genomics at chromosomal level, and serve as a valuable resource for the diplomonad community and protist research.", "doi": "10.1038/s41597-022-01703-w", "pmid": "36153341", "labels": {"NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9509377"}, {"db": "pii", "key": "10.1038/s41597-022-01703-w"}], "notes": [], "created": "2022-11-28T10:42:49.061Z", "modified": "2022-11-28T10:42:49.118Z"}, {"entity": "publication", "iuid": "7f473288e3b642c59aced9e1c0a27093", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f473288e3b642c59aced9e1c0a27093.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f473288e3b642c59aced9e1c0a27093"}}, "title": "Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions.", "authors": [{"family": "W\u00e4neskog", "given": "Marcus", "initials": "M", "orcid": "0000-0003-2480-5631", "researcher": {"href": "https://publications.scilifelab.se/researcher/061c0a9720bc4c12936ae06e4cc34448.json"}}, {"family": "Halvorsen", "given": "Tiffany", "initials": "T", "orcid": "0000-0001-9845-7313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c43bcbbe9e440078b97b0a839ae8933.json"}}, {"family": "Filek", "given": "Klara", "initials": "K", "orcid": "0000-0003-2518-4494", "researcher": {"href": "https://publications.scilifelab.se/researcher/27050310845f4590bdcb3ba86ca0a8f2.json"}}, {"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Hammarl\u00f6f", "given": "Disa L", "initials": "DL", "orcid": "0000-0002-8077-7615", "researcher": {"href": "https://publications.scilifelab.se/researcher/88cfbc6e22a64030bd973295f6cd5972.json"}}, {"family": "Hayes", "given": "Christopher S", "initials": "CS", "orcid": "0000-0002-2216-6445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8098c48713b64fc1ab2ac333111af518.json"}}, {"family": "Braaten", "given": "Bruce A", "initials": "BA"}, {"family": "Low", "given": "David A", "initials": "DA"}, {"family": "Poole", "given": "Stephen J", "initials": "SJ", "orcid": "0000-0002-5504-0590", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa971b41ea8f47bc8895654c8cd7cfd6.json"}}, {"family": "Koskiniemi", "given": "Sanna", "initials": "S", "orcid": "0000-0002-3275-0936", "researcher": {"href": "https://publications.scilifelab.se/researcher/622e0bb6cb184df9b8788aa218174dac.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "7", "issue": "3", "pages": null, "issn-l": null}, "abstract": "The phenomenon of contact-dependent growth inhibition (CDI) and the genes required for CDI (cdiBAI) were identified and isolated in 2005 from an Escherichia coli isolate (EC93) from rats. Although the cdiBAI EC93 locus has been the focus of extensive research during the past 15 years, little is known about the EC93 isolate from which it originates. Here we sequenced the EC93 genome and find two complete and functional cdiBAI loci (including the previously identified cdi locus), both carried on a large 127 kb plasmid. These cdiBAI systems are differentially expressed in laboratory media, enabling EC93 to outcompete E. coli cells lacking cognate cdiI immunity genes. The two CDI systems deliver distinct effector peptides that each dissipate the membrane potential of target cells, although the two toxins display different toxic potencies. Despite the differential expression and toxic potencies of these CDI systems, both yielded similar competitive advantages against E. coli cells lacking immunity. This can be explained by the fact that the less expressed cdiBAI system (cdiBAIEC93-2) delivers a more potent toxin than the highly expressed cdiBAIEC93-1 system. Moreover, our results indicate that unlike most sequenced CDI+ bacterial isolates, the two cdi loci of E. coli EC93 are located on a plasmid and are expressed in laboratory media.", "doi": "10.1099/mgen.0.000534", "pmid": "33646095", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8190604"}], "notes": [], "created": "2021-03-13T09:59:02.922Z", "modified": "2024-01-16T13:48:40.610Z"}, {"entity": "publication", "iuid": "ba8e61b15fdf4091b7ee12bca3608e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba8e61b15fdf4091b7ee12bca3608e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba8e61b15fdf4091b7ee12bca3608e26"}}, "title": "The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.", "authors": [{"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "Einarsson", "given": "Elin", "initials": "E", "orcid": "0000-0002-1242-5263", "researcher": {"href": "https://publications.scilifelab.se/researcher/be89fa4c7f9d484c858a0bf385f06c61.json"}}, {"family": "\u00c1stvaldsson", "given": "\u00c1sgeir", "initials": "\u00c1", "orcid": "0000-0002-0320-6974", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a3d973dc6d246b48426d2063eef8934.json"}}, {"family": "Peirasmaki", "given": "Dimitra", "initials": "D", "orcid": "0000-0001-5376-626X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94231cbd0cab4644b42c3fab58cea9aa.json"}}, {"family": "Eckmann", "given": "Lars", "initials": "L"}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "6", "issue": "8", "issn-l": null}, "abstract": "Diplomonad parasites of the genus Giardia have adapted to colonizing different hosts, most notably the intestinal tract of mammals. The human-pathogenic Giardia species, Giardia intestinalis, has been extensively studied at the genome and gene expression level, but no such information is available for other Giardia species. Comparative data would be particularly valuable for Giardia muris, which colonizes mice and is commonly used as a prototypic in vivo model for investigating host responses to intestinal parasitic infection. Here we report the draft-genome of G. muris. We discovered a highly streamlined genome, amongst the most densely encoded ever described for a nuclear eukaryotic genome. G. muris and G. intestinalis share many known or predicted virulence factors, including cysteine proteases and a large repertoire of cysteine-rich surface proteins involved in antigenic variation. Different to G. intestinalis, G. muris maintains tandem arrays of pseudogenized surface antigens at the telomeres, whereas intact surface antigens are present centrally in the chromosomes. The two classes of surface antigens engage in genetic exchange. Reconstruction of metabolic pathways from the G. muris genome suggest significant metabolic differences to G. intestinalis. Additionally, G. muris encodes proteins that might be used to modulate the prokaryotic microbiota. The responsible genes have been introduced in the Giardia genus via lateral gene transfer from prokaryotic sources. Our findings point to important evolutionary steps in the Giardia genus as it adapted to different hosts and it provides a powerful foundation for mechanistic exploration of host-pathogen interaction in the G. muris-mouse pathosystem.", "doi": "10.1099/mgen.0.000402", "pmid": "32618561", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7641422"}], "notes": [], "created": "2021-01-08T16:29:45.383Z", "modified": "2021-11-10T12:48:32.906Z"}, {"entity": "publication", "iuid": "53fc32e0ae72487f9138a071ec3fdaba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53fc32e0ae72487f9138a071ec3fdaba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53fc32e0ae72487f9138a071ec3fdaba"}}, "title": "A chromosome-scale reference genome for Giardia intestinalis WB.", "authors": [{"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Jex", "given": "Aaron", "initials": "A"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "dataset", "published": "2020-02-04", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "7", "issue": "1", "pages": "38", "issn-l": "2052-4463"}, "abstract": "Giardia intestinalis is a protist causing diarrhea in humans. The first G. intestinalis genome, from the WB isolate, was published more than ten years ago, and has been widely used as the reference genome for Giardia research. However, the genome is fragmented, thus hindering research at the chromosomal level. We re-sequenced the Giardia genome with Pacbio long-read sequencing technology and obtained a new reference genome, which was assembled into near-complete chromosomes with only four internal gaps at long repeats. This new genome is not only more complete but also better annotated at both structural and functional levels, providing more details about gene families, gene organizations and chromosomal structure. This near-complete reference genome will be a valuable resource for the Giardia community and protist research. It also showcases how a fragmented genome can be improved with long-read sequencing technology completed with optical maps.", "doi": "10.1038/s41597-020-0377-y", "pmid": "32019935", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-020-0377-y"}, {"db": "pmc", "key": "PMC7000408"}], "notes": [], "created": "2020-02-11T18:48:52.944Z", "modified": "2021-11-10T12:54:10.933Z"}]}