{"entity": "researcher", "timestamp": "2026-08-11T14:52:43.034Z", "family": "Song", "given": "Gang", "initials": "G", "orcid": "0000-0002-0190-8315", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765"}}, "publications": [{"entity": "publication", "iuid": "6d6faf7279134df68f3e4160a4981f61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61"}}, "title": "The genomic landscape of relapsed infant and childhood KMT2A-rearranged acute leukemia.", "authors": [{"family": "Ahlgren", "given": "Louise", "initials": "L"}, {"family": "Pilheden", "given": "Mattias", "initials": "M"}, {"family": "Sturesson", "given": "Helena", "initials": "H"}, {"family": "Song", "given": "Guangchun", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Walsh", "given": "Michael P", "initials": "MP"}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Maillard", "given": "Maud", "initials": "M"}, {"family": "Zhao", "given": "Huanbin", "initials": "H", "orcid": "0009-0001-4418-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/02a78b74f32d4670b628a8e3fb78ea0a.json"}}, {"family": "Cheng", "given": "Zhongshan", "initials": "Z"}, {"family": "Singh", "given": "Varsha", "initials": "V"}, {"family": "Castor", "given": "Anders", "initials": "A", "orcid": "0009-0007-4634-0704", "researcher": {"href": 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"initials": "P"}, {"family": "Pieters", "given": "Rob", "initials": "R", "orcid": "0000-0003-2997-3570", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb567d1e17e0428c843c07682decb31c.json"}}, {"family": "Zhang", "given": "Jinghui", "initials": "J", "orcid": "0000-0003-3350-9682", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe8464634149a39bc8accf6077bac4.json"}}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}, {"family": "Yang", "given": "Jun J", "initials": "JJ", "orcid": "0000-0002-0770-9659", "researcher": {"href": "https://publications.scilifelab.se/researcher/023457113ddc4e3a8309d0b4936c097e.json"}}, {"family": "Gruber", "given": "Tanja A", "initials": "TA", "orcid": "0000-0003-1072-7257", "researcher": {"href": "https://publications.scilifelab.se/researcher/c16c5b66f56f40fd93a9f398b0487a64.json"}}, {"family": "Stam", "given": "Ronald W", "initials": "RW", "orcid": "0000-0003-4986-1656", "researcher": {"href": "https://publications.scilifelab.se/researcher/f528aaa6b3ba479f85619e1496e3f395.json"}}, {"family": "Ma", "given": "Jing", "initials": "J"}, {"family": "Hagstr\u00f6m-Andersson", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-2904-1311", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc93a87c663d471ba64fc3be63212a89.json"}}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "8964", "issn-l": "2041-1723"}, "abstract": "To study the mechanisms of relapse in KMT2A-rearranged (KMT2A-r) acute lymphoblastic (ALL) and acute myeloid leukemia (AML), we performed whole-genome and exome sequencing of infants and children with relapsed ALL/AML (n = 36), and longitudinal deep-sequencing of 257 samples in 30 patients. Somatic alterations in drug-response genes, most commonly in TP53 and IKZF1 (64%), were highly enriched in early relapse ALL (79%, 9-36 months after diagnosis), but rare in very early relapse ALL (<9 months, 9%). A marked chemotherapy-exposure signature was detected for mutations in early relapse ALL but not in very early ALL or AML relapse, in line with different mechanisms of relapse. Longitudinal analyses could track residual leukemia cells, clonal drug responses, and the upcoming relapse. These results highlight that KMT2A-r ALL and AML evade therapy differently and provide insights into the mechanisms of relapse in this highly lethal form of pediatric acute leukemia.", "doi": "10.1038/s41467-025-64190-8", "pmid": "41062506", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12508131"}, {"db": "pii", "key": "10.1038/s41467-025-64190-8"}], "notes": [], "created": "2025-10-28T09:43:15.594Z", "modified": "2025-11-07T07:22:38.375Z"}, {"entity": "publication", "iuid": "af1d860a40a54aff870af824f6fef807", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af1d860a40a54aff870af824f6fef807.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af1d860a40a54aff870af824f6fef807"}}, "title": "The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.", "authors": [{"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}, {"family": "Chen", "given": "Chunhai", "initials": "C", "orcid": "0000-0002-2882-4517", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd523248fd54ae299c069b960312115.json"}}, {"family": "Chen", "given": "Xiumin", "initials": "X"}, {"family": "Hao", "given": "Yan", "initials": "Y", "orcid": "0000-0002-1415-7610", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c1a42ec6cf4f3f990220e6b4735bec.json"}}, {"family": "She", "given": "Huishang", "initials": "H", "orcid": "0000-0001-6259-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/a02a8db02a40437a87bd000b995d10c8.json"}}, {"family": "Wang", "given": "Mengxia", "initials": "M"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Lin", "given": "Haiyan", "initials": "H", "orcid": "0000-0002-1623-9361", "researcher": {"href": "https://publications.scilifelab.se/researcher/e54d1bf82275458794a989de37b58480.json"}}, {"family": "Cai", "given": "Tianlong", "initials": "T"}, {"family": "Song", "given": "Gang", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Jia", "given": "Chenxi", "initials": "C"}, {"family": "Chen", "given": "Chunyan", "initials": "C", "orcid": "0000-0002-2882-4517", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd523248fd54ae299c069b960312115.json"}}, {"family": "Zhang", "given": "Hailin", "initials": "H"}, {"family": "Li", "given": "Jiang", "initials": "J", "orcid": "0000-0003-2099-8165", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64bd87a57e0468b879e6361e79e3000.json"}}, {"family": "Liang", "given": "Liping", "initials": "L"}, {"family": "Wu", "given": "Tianyu", "initials": "T"}, {"family": "Zhao", "given": "Jinyang", "initials": "J", "orcid": "0000-0002-8150-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d41f239fe612446194498f9e5ed06321.json"}}, {"family": "Gao", "given": "Qiang", "initials": "Q", "orcid": "0000-0001-9880-4944", "researcher": {"href": "https://publications.scilifelab.se/researcher/faf3d20ec8344174a8c001bac7464421.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}, {"family": "Zhai", "given": "Weiwei", "initials": "W", "orcid": "0000-0001-7938-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/e33e2ebb818449b9b95ba2484fccaa86.json"}}, {"family": "Zhang", "given": "Chi", "initials": "C"}, {"family": "Zhang", "given": "Yong E", "initials": "YE", "orcid": "0000-0003-3770-2383", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c91998c67674b75891a4473451916d6.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}], "type": "journal article", "published": "2021-03-30", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "13", "pages": "e2012398118", "issn-l": "0027-8424"}, "abstract": "Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai-Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.", "doi": "10.1073/pnas.2012398118", "pmid": "33753478", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2012398118"}, {"db": "pmc", "key": "PMC8020664"}], "notes": [], "created": "2021-06-09T12:15:45.569Z", "modified": "2024-01-16T13:48:40.345Z"}, {"entity": "publication", "iuid": "0cd1833de8764e41812f14260f5961b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5"}}, "title": "Dense sampling of bird diversity increases power of comparative genomics.", "authors": [{"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/92ad360b09004877aee9cfde491c76a3.json"}}, {"family": "Stiller", "given": "Josefin", "initials": "J", "orcid": "0000-0001-6009-9581", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e54e7b719bb422aa18ccd99d6c2edf6.json"}}, {"family": "Deng", "given": "Yuan", "initials": "Y"}, {"family": "Armstrong", "given": "Joel", "initials": "J", "orcid": "0000-0003-2077-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/63cfeea6ae9942b8a48e6e13ecf4bf0d.json"}}, {"family": "Fang", "given": "Qi", "initials": "Q", "orcid": "0000-0002-9181-8689", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9ff76a9a8bb42c8973d968c7e39a216.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Xie", "given": "Duo", "initials": "D", "orcid": "0000-0001-7010-3601", "researcher": {"href": "https://publications.scilifelab.se/researcher/9258a952a3c54596add7d930e1432ebe.json"}}, {"family": "Chen", "given": "Guangji", "initials": "G", "orcid": "0000-0002-9441-1155", "researcher": {"href": "https://publications.scilifelab.se/researcher/19514f67b1504dc6b4b7d393e97f8cc0.json"}}, {"family": "Guo", "given": "Chunxue", "initials": "C"}, {"family": "Faircloth", "given": "Brant C", "initials": "BC", "orcid": "0000-0002-1943-0217", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df01b37d97a44ffb6f4d069085d7b64.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Wang", "given": "Zongji", "initials": "Z", "orcid": "0000-0002-5107-6246", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a18bde0ee684560ae3217db4b30a920.json"}}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Diekhans", "given": "Mark", "initials": "M", "orcid": "0000-0002-0430-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/da3441938f7b437b81cc92068bea158c.json"}}, {"family": "Chen", "given": "Wanjun", "initials": "W", "orcid": "0000-0002-4418-7650", "researcher": {"href": "https://publications.scilifelab.se/researcher/992e7029a2704d039ce578df2806f57f.json"}}, {"family": "Andreu-S\u00e1nchez", "given": "Sergio", "initials": "S"}, {"family": "Margaryan", "given": "Ashot", "initials": "A", "orcid": "0000-0002-2576-2429", "researcher": {"href": "https://publications.scilifelab.se/researcher/487f29e4a666414a8437f964e2052be7.json"}}, {"family": "Howard", "given": "Jason Travis", "initials": "JT"}, {"family": "Parent", "given": "Carole", "initials": "C"}, {"family": "Pacheco", "given": "George", "initials": "G", "orcid": "0000-0002-9367-6813", "researcher": {"href": "https://publications.scilifelab.se/researcher/449f532c61df4157b9bd1dc15deab965.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Puetz", "given": "Lara", "initials": "L", "orcid": "0000-0002-0323-799X", "researcher": {"href": "https://publications.scilifelab.se/researcher/986da811e11341379e73f5382b0f69ad.json"}}, {"family": "Cavill", "given": "Emily", "initials": "E", "orcid": "0000-0003-2198-8102", "researcher": {"href": "https://publications.scilifelab.se/researcher/eacd61b411f046d88c1e8942eb46cfff.json"}}, {"family": "Ribeiro", "given": "\u00c2ngela M", "initials": "\u00c2M"}, {"family": "Eckhart", "given": "Leopold", "initials": "L", "orcid": "0000-0002-5645-2036", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a24adae52741698457e9a733f36f6c.json"}}, {"family": "Fjelds\u00e5", "given": "Jon", "initials": "J", "orcid": "0000-0003-0790-3600", "researcher": {"href": "https://publications.scilifelab.se/researcher/f280ada51dfb41b2a3d035676a27ffb6.json"}}, {"family": "Hosner", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-7499-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a4c8cd6229436d9a39761aa77eeec2.json"}}, {"family": "Brumfield", "given": "Robb T", "initials": "RT", "orcid": "0000-0003-2307-0688", "researcher": {"href": "https://publications.scilifelab.se/researcher/71a3a36f83154d3dbe14e1a5290f425f.json"}}, {"family": 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"initials": "B"}, {"family": "Taylor", "given": "Scott A", "initials": "SA", "orcid": "0000-0001-9580-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/36c6baa1b23242e0bfd586d7e42c0cb9.json"}}, {"family": "Del-Rio", "given": "Glaucia", "initials": "G"}, {"family": "Aleixo", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-7816-9725", "researcher": {"href": "https://publications.scilifelab.se/researcher/b397ed6da07246caa50a438c233820ab.json"}}, {"family": "Vasconcelos", "given": "Ana Tereza Ribeiro", "initials": "ATR", "orcid": "0000-0002-4632-2086", "researcher": {"href": "https://publications.scilifelab.se/researcher/69b1022e72a84534850b8d650ba2c1be.json"}}, {"family": "Mello", "given": "Claudio V", "initials": "CV", "orcid": "0000-0002-9826-8421", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9715cacaf7d45bda2337a32ea0ec526.json"}}, {"family": "Weir", "given": "Jason T", "initials": "JT", "orcid": "0000-0001-8372-9937", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c77b745d8b044d4aed9478d056be226.json"}}, {"family": "Haussler", "given": "David", "initials": "D", "orcid": "0000-0003-1533-4575", "researcher": {"href": "https://publications.scilifelab.se/researcher/de140026a4f24291be768e713e4881bb.json"}}, {"family": "Li", "given": "Qiye", "initials": "Q", "orcid": "0000-0002-5993-0312", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807a3a13669425c9b00e4a2b7db672a.json"}}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Rahbek", "given": "Carsten", "initials": "C"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Graves", "given": "Gary R", "initials": "GR", "orcid": "0000-0003-1406-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3b9edee185456d971f5b596c3086fe.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "587", "issue": "7833", "pages": "252-257", "issn-l": "0028-0836"}, "abstract": "Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.", "doi": "10.1038/s41586-020-2873-9", "pmid": "33177665", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-020-2873-9"}, {"db": "pmc", "key": "PMC7759463"}], "notes": [], "created": "2020-12-07T16:36:44.079Z", "modified": "2021-11-10T12:45:51.851Z"}]}