{"entity": "researcher", "timestamp": "2026-09-23T15:03:20.459Z", "family": "Subramanian", "given": "Ayshwarya", "initials": "A", "orcid": "0000-0002-4134-7612", "affiliations": ["Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/dda9998955294a798208e67cac6baaea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/dda9998955294a798208e67cac6baaea"}}, "publications": [{"entity": "publication", "iuid": "0588b65dcdd14e4084e68dbbef556a0f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0588b65dcdd14e4084e68dbbef556a0f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0588b65dcdd14e4084e68dbbef556a0f"}}, "title": "The contribution of historical processes to contemporary extinction risk in placental mammals.", "authors": [{"family": "Wilder", "given": "Aryn P", "initials": "AP", "orcid": "0000-0003-4970-6891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b080282d4674df1bde072812bf448be.json"}}, {"family": "Supple", "given": "Megan A", "initials": "MA", "orcid": "0000-0002-0204-7852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/073a9fab924c4e96973f1e23accaa7ae.json"}}, {"family": "Subramanian", "given": "Ayshwarya", "initials": "A", "orcid": "0000-0002-4134-7612", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dda9998955294a798208e67cac6baaea.json"}}, {"family": "Mudide", "given": "Anish", "initials": "A", "orcid": "0000-0002-6174-2345", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1bf10150429a444186df7ddf697369e6.json"}}, {"family": "Swofford", "given": "Ross", "initials": "R", "orcid": "0000-0003-3676-8479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85b0174c633b417b933092763175bb1c.json"}}, {"family": "Serres-Armero", "given": "Aitor", "initials": "A"}, {"family": "Steiner", "given": "Cynthia", "initials": "C", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9386c16bd7e14ddca60e03e06f6808fe.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "KP"}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Munoz Fuentes", "given": "Violeta", "initials": "V", "orcid": "0000-0003-3574-546X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a5d067d41a846f9bee05b1bdacc1a7f.json"}}, {"family": "Foley", "given": "Kathleen", "initials": "K", "orcid": "0000-0003-0923-1326", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/907a734d325d4f76bf083c68202f2e05.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b1fba9de46a4c8c8cbbbec685a9b94c.json"}}, {"family": "Zoonomia Consortium\u2021", "given": "", "initials": ""}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f15a636469944ddb56489a74a75591b.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "380", "issue": "6643", "pages": "eabn5856", "issn-l": "0036-8075"}, "abstract": "Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.", "doi": "10.1126/science.abn5856", "pmid": "37104572", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1893031"}, {"db": "pmc", "key": "PMC10184782"}], "notes": [], "created": "2026-09-23T07:40:18.022Z", "modified": "2026-09-23T07:40:18.317Z"}, {"entity": "publication", "iuid": "62a9eb3d3e5f44599d66049c4227f50a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/62a9eb3d3e5f44599d66049c4227f50a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/62a9eb3d3e5f44599d66049c4227f50a"}}, "title": "Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.", "authors": [{"family": "Muus", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2779-0893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be8fbc93ed974a11b06a0e9837ec8c30.json"}}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/573854d96a9e4e21a3b96135c11c6efc.json"}}, {"family": "Eraslan", "given": "G\u00f6kcen", "initials": "G"}, {"family": "Sikkema", "given": "Lisa", "initials": "L", "orcid": "0000-0001-9686-6295", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/462d0024767146ebba699345e9deeb9e.json"}}, {"family": "Waghray", "given": "Avinash", "initials": "A"}, {"family": "Heimberg", "given": "Graham", "initials": "G"}, {"family": "Kobayashi", "given": "Yoshihiko", "initials": "Y"}, {"family": "Vaishnav", "given": "Eeshit Dhaval", "initials": "ED", "orcid": "0000-0003-3720-8051", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94b333bc8cff4a5689fad676abf84be8.json"}}, {"family": "Subramanian", "given": "Ayshwarya", "initials": "A", "orcid": "0000-0002-4134-7612", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dda9998955294a798208e67cac6baaea.json"}}, {"family": "Smillie", "given": "Christopher", "initials": "C"}, {"family": "Jagadeesh", "given": "Karthik A", "initials": "KA"}, {"family": "Duong", "given": "Elizabeth Thu", "initials": "ET", "orcid": "0000-0001-7122-4448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d28730373f248979f8c376d6d2203c6.json"}}, {"family": "Fiskin", "given": "Evgenij", "initials": "E"}, {"family": "Torlai Triglia", "given": "Elena", "initials": "E", "orcid": "0000-0002-6059-0116", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78e6c84e6c1744fa8d3d21244c875413.json"}}, {"family": "Ansari", "given": "Meshal", "initials": "M", "orcid": "0000-0002-8819-7965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6da554c21aeb4ffc919206424a5e72a5.json"}}, {"family": "Cai", "given": "Peiwen", "initials": "P"}, {"family": "Lin", "given": "Brian", "initials": "B", "orcid": "0000-0002-8851-3534", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fc4d1ec62fd4806bcb1d37185fd2922.json"}}, {"family": "Buchanan", "given": "Justin", "initials": "J"}, {"family": "Chen", "given": "Sijia", "initials": "S"}, {"family": "Shu", "given": "Jian", "initials": "J"}, {"family": "Haber", "given": "Adam L", "initials": "AL"}, {"family": "Chung", "given": "Hattie", "initials": "H"}, {"family": "Montoro", "given": "Daniel T", "initials": "DT"}, {"family": "Adams", "given": "Taylor", "initials": "T"}, {"family": "Aliee", "given": "Hananeh", "initials": "H"}, {"family": "Allon", "given": "Samuel J", "initials": "SJ"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Angelidis", "given": "Ilias", "initials": "I"}, {"family": "Ashenberg", "given": "Orr", "initials": "O"}, {"family": "Bassler", "given": "Kevin", "initials": "K"}, {"family": "B\u00e9cavin", "given": "Christophe", "initials": "C"}, {"family": "Benhar", "given": "Inbal", "initials": "I"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L"}, {"family": "Bolt", "given": "Liam", "initials": "L"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Bui", "given": "Linh T", "initials": "LT"}, {"family": "Callori", "given": "Steven", "initials": "S"}, {"family": "Chaffin", "given": "Mark", "initials": "M"}, {"family": "Chichelnitskiy", "given": "Evgeny", "initials": "E"}, {"family": "Chiou", "given": "Joshua", "initials": "J"}, {"family": "Conlon", "given": "Thomas M", "initials": "TM"}, {"family": "Cuoco", "given": "Michael S", "initials": "MS"}, {"family": "Cuomo", "given": "Anna S E", "initials": "ASE"}, {"family": "Deprez", "given": "Marie", "initials": "M"}, {"family": "Duclos", "given": "Grant", "initials": "G"}, {"family": "Fine", "given": "Denise", "initials": "D"}, {"family": "Fischer", "given": "David S", "initials": "DS"}, {"family": "Ghazanfar", "given": "Shila", "initials": "S"}, {"family": "Gillich", "given": "Astrid", "initials": "A"}, {"family": "Giotti", "given": "Bruno", "initials": "B"}, {"family": "Gould", "given": "Joshua", "initials": "J"}, {"family": "Guo", "given": "Minzhe", "initials": "M"}, {"family": "Gutierrez", "given": "Austin J", "initials": "AJ"}, {"family": "Habermann", "given": "Arun C", "initials": "AC"}, {"family": "Harvey", "given": "Tyler", "initials": "T"}, {"family": "He", "given": "Peng", "initials": "P"}, {"family": "Hou", "given": "Xiaomeng", "initials": "X"}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Hu", "given": "Yan", "initials": "Y"}, {"family": "Jaiswal", "given": "Alok", "initials": "A"}, {"family": "Ji", "given": "Lu", "initials": "L"}, {"family": "Jiang", "given": "Peiyong", "initials": "P"}, {"family": "Kapellos", "given": "Theodoros S", "initials": "TS"}, {"family": "Kuo", "given": "Christin S", "initials": "CS"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Leney-Greene", "given": "Michael A", "initials": "MA"}, {"family": "Lim", "given": "Kyungtae", "initials": "K"}, {"family": "Litvi\u0148ukov\u00e1", "given": "Monika", "initials": "M"}, {"family": "Ludwig", "given": "Leif S", "initials": "LS"}, {"family": "Lukassen", "given": "Soeren", "initials": "S"}, {"family": "Luo", "given": "Wendy", "initials": "W"}, {"family": "Maatz", "given": "Henrike", "initials": "H"}, {"family": "Madissoon", "given": "Elo", "initials": "E"}, {"family": "Mamanova", "given": "Lira", "initials": "L"}, {"family": "Manakongtreecheep", "given": "Kasidet", "initials": "K"}, {"family": "Leroy", "given": "Sylvie", "initials": "S"}, {"family": "Mayr", "given": "Christoph H", "initials": "CH"}, {"family": "Mbano", "given": "Ian M", "initials": "IM"}, {"family": "McAdams", "given": "Alexi M", "initials": "AM"}, {"family": "Nabhan", "given": "Ahmad N", "initials": "AN"}, {"family": "Nyquist", "given": "Sarah K", "initials": "SK"}, {"family": "Penland", "given": "Lolita", "initials": "L"}, {"family": "Poirion", "given": "Olivier B", "initials": "OB"}, {"family": "Poli", "given": "Sergio", "initials": "S"}, {"family": "Qi", "given": "CanCan", "initials": "C"}, {"family": "Queen", "given": "Rachel", "initials": "R"}, {"family": "Reichart", "given": "Daniel", "initials": "D"}, {"family": "Rosas", "given": "Ivan", "initials": "I"}, {"family": "Schupp", "given": "Jonas C", "initials": "JC"}, {"family": "Shea", "given": "Conor V", "initials": "CV"}, {"family": "Shi", "given": "Xingyi", "initials": "X"}, {"family": "Sinha", "given": "Rahul", "initials": "R"}, {"family": "Sit", "given": "Rene V", "initials": "RV"}, {"family": "Slowikowski", "given": "Kamil", "initials": "K"}, {"family": "Slyper", "given": "Michal", "initials": "M"}, {"family": "Smith", "given": "Neal P", "initials": "NP"}, {"family": "Sountoulidis", "given": "Alex", "initials": "A"}, {"family": "Strunz", "given": "Maximilian", "initials": "M"}, {"family": "Sullivan", "given": "Travis B", "initials": "TB"}, {"family": "Sun", "given": "Dawei", "initials": "D"}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Tan", "given": "Peng", "initials": "P"}, {"family": "Tantivit", "given": "Jessica", "initials": "J"}, {"family": "Travaglini", "given": "Kyle J", "initials": "KJ"}, {"family": "Tucker", "given": "Nathan R", "initials": "NR"}, {"family": "Vernon", "given": "Katherine A", "initials": "KA"}, {"family": "Wadsworth", "given": "Marc H", "initials": "MH"}, {"family": "Waldman", "given": "Julia", "initials": "J"}, {"family": "Wang", "given": "Xiuting", "initials": "X"}, {"family": "Xu", "given": "Ke", "initials": "K"}, {"family": "Yan", "given": "Wenjun", "initials": "W"}, {"family": "Zhao", "given": "William", "initials": "W"}, {"family": "Ziegler", "given": "Carly G K", "initials": "CGK"}, {"family": "NHLBI LungMap Consortium", "given": "", "initials": ""}, {"family": "Human Cell Atlas Lung Biological Network", "given": "", "initials": ""}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "volume": "27", "issue": "3", "pages": "546-559", "issn-l": "1078-8956"}, "abstract": "Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.", "doi": "10.1038/s41591-020-01227-z", "pmid": "33654293", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1757283"}, {"db": "pmc", "key": "PMC9469728"}, {"db": "pii", "key": "10.1038/s41591-020-01227-z"}], "notes": [], "created": "2026-09-23T06:35:23.181Z", "modified": "2026-09-23T06:35:23.526Z"}]}