{"entity": "researcher", "timestamp": "2026-08-20T21:15:24.904Z", "family": "Xie", "given": "Duo", "initials": "D", "orcid": "0000-0001-7010-3601", "affiliations": ["BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.", "BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bee104c168a4a2994257ccca5a835ca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bee104c168a4a2994257ccca5a835ca"}}, "publications": [{"entity": "publication", "iuid": "3da2df3be502484dac135656b8bfb33c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3da2df3be502484dac135656b8bfb33c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3da2df3be502484dac135656b8bfb33c"}}, "title": "Cell transcriptomic atlas of the non-human primate Macaca fascicularis.", "authors": [{"family": "Han", "given": "Lei", "initials": "L", "orcid": "0000-0002-7535-7915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4789398978c486aa2dd35a73c57df31.json"}}, {"family": "Wei", "given": "Xiaoyu", "initials": "X"}, {"family": "Liu", "given": "Chuanyu", "initials": "C", "orcid": "0000-0003-2258-0897", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22b06d8b1d514c03b8efcb24ea922593.json"}}, {"family": "Volpe", "given": "Giacomo", "initials": "G", "orcid": "0000-0001-5000-6951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e230618482b4785838d1f68eca8d7c9.json"}}, {"family": "Zhuang", "given": "Zhenkun", "initials": "Z"}, {"family": "Zou", "given": "Xuanxuan", "initials": "X"}, {"family": "Wang", "given": "Zhifeng", "initials": "Z"}, {"family": "Pan", "given": "Taotao", "initials": "T"}, {"family": "Yuan", "given": "Yue", "initials": "Y"}, {"family": "Zhang", "given": "Xiao", "initials": "X"}, {"family": "Fan", "given": "Peng", "initials": "P"}, {"family": "Guo", "given": "Pengcheng", "initials": "P"}, {"family": "Lai", "given": "Yiwei", "initials": "Y", "orcid": "0000-0003-0733-812X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9477759581854828a0611c2f1dff041a.json"}}, {"family": "Lei", "given": "Ying", "initials": "Y"}, {"family": "Liu", "given": "Xingyuan", "initials": "X"}, {"family": "Yu", "given": "Feng", "initials": "F"}, {"family": "Shangguan", "given": "Shuncheng", "initials": "S"}, {"family": "Lai", "given": "Guangyao", "initials": "G"}, {"family": "Deng", "given": "Qiuting", "initials": "Q"}, {"family": "Liu", "given": "Ya", "initials": "Y"}, {"family": "Wu", "given": "Liang", "initials": "L"}, {"family": "Shi", "given": "Quan", "initials": "Q"}, {"family": "Yu", "given": "Hao", "initials": "H"}, {"family": "Huang", "given": "Yunting", "initials": "Y"}, {"family": "Cheng", "given": "Mengnan", "initials": "M"}, {"family": "Xu", "given": "Jiangshan", "initials": "J"}, {"family": "Liu", "given": "Yang", "initials": "Y"}, {"family": "Wang", "given": "Mingyue", "initials": "M"}, {"family": "Wang", "given": "Chunqing", "initials": "C"}, {"family": "Zhang", "given": "Yuanhang", "initials": "Y"}, {"family": "Xie", "given": "Duo", "initials": "D", "orcid": "0000-0001-7010-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bee104c168a4a2994257ccca5a835ca.json"}}, {"family": "Yang", "given": "Yunzhi", "initials": "Y"}, {"family": "Yu", "given": "Yeya", "initials": "Y"}, {"family": "Zheng", "given": "Huiwen", "initials": "H"}, {"family": "Wei", "given": "Yanrong", "initials": "Y"}, {"family": "Huang", "given": "Fubaoqian", "initials": "F"}, {"family": "Lei", "given": "Junjie", "initials": "J"}, {"family": "Huang", "given": "Waidong", "initials": "W"}, {"family": "Zhu", "given": "Zhiyong", "initials": "Z"}, {"family": "Lu", "given": "Haorong", "initials": "H"}, {"family": "Wang", "given": "Bo", "initials": "B"}, {"family": "Wei", "given": "Xiaofeng", "initials": "X"}, {"family": "Chen", "given": "Fengzhen", "initials": "F"}, {"family": "Yang", "given": "Tao", "initials": "T", "orcid": "0000-0003-4211-5183", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be647cbef7f347898d47f86e4403e242.json"}}, {"family": "Du", "given": "Wensi", "initials": "W"}, {"family": "Chen", "given": "Jing", "initials": "J"}, {"family": "Xu", "given": "Shibo", "initials": "S", "orcid": "0000-0001-9867-8757", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/797867c68bf94bd287e1514d7fe51898.json"}}, {"family": "An", "given": "Juan", "initials": "J"}, {"family": "Ward", "given": "Carl", "initials": "C", "orcid": "0000-0003-0889-9025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3312d4b42508424f992750161316d5bf.json"}}, {"family": "Wang", "given": "Zongren", "initials": "Z"}, {"family": "Pei", "given": "Zhong", "initials": "Z"}, {"family": "Wong", "given": "Chi-Wai", "initials": "CW"}, {"family": "Liu", "given": "Xiaolei", "initials": "X"}, {"family": "Zhang", "given": "Huafeng", "initials": "H"}, {"family": "Liu", "given": "Mingyuan", "initials": "M"}, {"family": "Qin", "given": "Baoming", "initials": "B", "orcid": "0000-0001-7652-161X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c14b215bed74e3aacdd3ea198dd6a6f.json"}}, {"family": "Schambach", "given": "Axel", "initials": "A", "orcid": "0000-0003-2743-0070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e762ac6206e4cef9b4545bb80c9ca7d.json"}}, {"family": "Isern", "given": "Joan", "initials": "J"}, {"family": "Feng", "given": "Liqiang", "initials": "L", "orcid": "0000-0001-6811-2074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a2908b020904ad0bee85061c3e83e07.json"}}, {"family": "Liu", "given": "Yan", "initials": "Y"}, {"family": "Guo", "given": "Xiangyu", "initials": "X"}, {"family": "Liu", "given": "Zhen", "initials": "Z"}, {"family": "Sun", "given": "Qiang", "initials": "Q"}, {"family": "Maxwell", "given": "Patrick H", "initials": "PH", "orcid": "0000-0002-0338-2679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03b83b6f6aaa44f194e004f416706052.json"}}, {"family": "Barker", "given": "Nick", "initials": "N", "orcid": "0000-0003-3566-4475", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31db89a6ce0c44aca9814adb782f5c0b.json"}}, {"family": "Mu\u00f1oz-C\u00e1noves", "given": "Pura", "initials": "P", "orcid": "0000-0002-7533-9047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbd9111ffb8b44cba269b0f04efcbeec.json"}}, {"family": "Gu", "given": "Ying", "initials": "Y", "orcid": "0000-0001-7822-0570", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2960e0123e5c40549d22941f72f7cbfb.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40ed8170792444b491519e499d51c434.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Tan", "given": "Tao", "initials": "T", "orcid": "0000-0001-8650-0388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58cba43b8c29410bac79521f710805ee.json"}}, {"family": "Liu", "given": "Shiping", "initials": "S", "orcid": "0000-0003-0019-619X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9572f0eae17949d98dfaf6ab2566b330.json"}}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Hou", "given": "Yong", "initials": "Y", "orcid": "0000-0002-0420-0726", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3e6517875f14c98b700e9cf1dc83795.json"}}, {"family": "Xu", "given": "Xun", "initials": "X", "orcid": "0000-0002-5338-5173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a6e2e5d236148c7ba386c89941f2d41.json"}}, {"family": "Esteban", "given": "Miguel A", "initials": "MA", "orcid": "0000-0002-1426-6809", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf5feccf49c44d929ec7eb8295d60624.json"}}, {"family": "Liu", "given": "Longqi", "initials": "L", "orcid": "0000-0002-5828-5542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d69759c9d7f4a9a9bc512b2f5c7877f.json"}}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "604", "issue": "7907", "pages": "723-731", "issn-l": "0028-0836"}, "abstract": "Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.", "doi": "10.1038/s41586-022-04587-3", "pmid": "35418686", "labels": [], "xrefs": [{"db": "pii", "key": "10.1038/s41586-022-04587-3"}], "notes": [], "created": "2026-08-20T08:57:35.645Z", "modified": "2026-08-20T08:57:36.507Z"}, {"entity": "publication", "iuid": "1eefcae7314541e0a3860a83a1c16d84", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1eefcae7314541e0a3860a83a1c16d84.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1eefcae7314541e0a3860a83a1c16d84"}}, "title": "Progressive Cactus is a multiple-genome aligner for the thousand-genome era.", "authors": [{"family": "Armstrong", "given": "Joel", "initials": "J", "orcid": "0000-0003-2077-4671", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e05c7c5e78e448cdb7d94bae26e7bcb1.json"}}, {"family": "Hickey", "given": "Glenn", "initials": "G"}, {"family": "Diekhans", "given": "Mark", "initials": "M", "orcid": "0000-0002-0430-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7999277bf08b4dbdbcc7d5e78cafcb00.json"}}, {"family": "Fiddes", "given": "Ian T", "initials": "IT"}, {"family": "Novak", "given": "Adam M", "initials": "AM", "orcid": "0000-0001-5828-047X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cc29a94bc2347e0a4d64bdb105b29c0.json"}}, {"family": "Deran", "given": "Alden", "initials": "A"}, {"family": "Fang", "given": "Qi", "initials": "Q", "orcid": "0000-0002-9181-8689", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a04a244840c248c4a7515c427ffdc5de.json"}}, {"family": "Xie", "given": "Duo", "initials": "D", "orcid": "0000-0001-7010-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bee104c168a4a2994257ccca5a835ca.json"}}, {"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/458d41da2844484a82fb7b21231a567e.json"}}, {"family": "Stiller", "given": "Josefin", "initials": "J", "orcid": "0000-0001-6009-9581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c58298dbc8ef46a086a0f74bdded4a6b.json"}}, {"family": "Genereux", "given": "Diane", "initials": "D"}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Marinescu", "given": "Voichita Dana", "initials": "VD"}, {"family": "Alf\u00f6ldi", "given": "Jessica", "initials": "J"}, {"family": "Harris", "given": "Robert S", "initials": "RS"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Haussler", "given": "David", "initials": "D", "orcid": "0000-0003-1533-4575", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4b918ad2e1c4544a4a52dfd64f6ebba.json"}}, {"family": "Karlsson", "given": "Elinor", "initials": "E", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c916e24b35f2459480cf87e27bb21ee1.json"}}], "type": "comparative study", "published": "2020-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "587", "issue": "7833", "pages": "246-251", "issn-l": "0028-0836"}, "abstract": "New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1-3. For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database4 increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies5 are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus6, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far.", "doi": "10.1038/s41586-020-2871-y", "pmid": "33177663", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1615919"}, {"db": "pmc", "key": "PMC7673649"}, {"db": "pii", "key": "10.1038/s41586-020-2871-y"}], "notes": [], "created": "2026-08-20T08:56:20.261Z", "modified": "2026-08-20T08:56:56.935Z"}]}