{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T17:42:51Z","timestamp":1791999771743,"version":"4.4.0"},"reference-count":130,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,3,14]],"date-time":"2025-03-14T00:00:00Z","timestamp":1741910400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,3,14]],"date-time":"2025-03-14T00:00:00Z","timestamp":1741910400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000038","name":"U.S. Food and Drug Administration","doi-asserted-by":"publisher","award":["HHSF223201810172C"],"award-info":[{"award-number":["HHSF223201810172C"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-027498"],"award-info":[{"award-number":["INV-027498"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R01 CA258776"],"award-info":[{"award-number":["R01 CA258776"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R01 HL129506-07"],"award-info":[{"award-number":["R01 HL129506-07"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Blood Clot Alliance","award":["PR200524P1"],"award-info":[{"award-number":["PR200524P1"]}]},{"DOI":"10.13039\/100016958","name":"Office of Research Infrastructure Programs, National Institutes of Health","doi-asserted-by":"publisher","award":["Massachusetts Life Sciences Center"],"award-info":[{"award-number":["Massachusetts Life Sciences Center"]}],"id":[{"id":"10.13039\/100016958","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["K08CA222663"],"award-info":[{"award-number":["K08CA222663"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R37CA258829"],"award-info":[{"award-number":["R37CA258829"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R21CA263381"],"award-info":[{"award-number":["R21CA263381"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U54CA225088"],"award-info":[{"award-number":["U54CA225088"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NIH Support Grant","award":["S10RR027050"],"award-info":[{"award-number":["S10RR027050"]}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["P30CA013696"],"award-info":[{"award-number":["P30CA013696"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The molecular underpinnings of organ dysfunction in severe COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we perform single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We identify hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells, and a central role in a pro-fibrotic TGF\u03b2 signaling cell\u2013cell communications network. Integrated analysis and comparisons with healthy controls reveal extensive changes in the cellular composition and expression states in COVID-19 liver, providing the underpinning of hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis characteristic of COVID-19 cholangiopathy. We also observe Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition is dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13059-025-03499-5","type":"journal-article","created":{"date-parts":[[2025,3,14]],"date-time":"2025-03-14T06:36:51Z","timestamp":1741934211000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients"],"prefix":"10.1186","volume":"26","author":[{"given":"Yered","family":"Pita-Juarez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimitra","family":"Karagkouni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikolaos","family":"Kalavros","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johannes C.","family":"Melms","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Niezen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toni M.","family":"Delorey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam L.","family":"Essene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga R.","family":"Brook","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deepti","family":"Pant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Disha","family":"Skelton-Badlani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pourya","family":"Naderi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pinzhu","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liuliu","family":"Pan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler","family":"Hether","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tallulah S.","family":"Andrews","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carly G. K.","family":"Ziegler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason","family":"Reeves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andriy","family":"Myloserdnyy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andy","family":"Nam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Phelan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Gregory","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanshan","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Patrick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tushar","family":"Rane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aster","family":"Wardhani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit Dipak","family":"Amin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"Biermann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanina","family":"Hibshoosh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Molly","family":"Veregge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary","family":"Kramer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Jacobs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yusuf","family":"Yalcin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devan","family":"Phillips","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michal","family":"Slyper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayshwarya","family":"Subramanian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orr","family":"Ashenberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zohar","family":"Bloom-Ackermann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria M.","family":"Tran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Gomez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Sturm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuting","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J.","family":"Fleming","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Warren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph","family":"Beechem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah","family":"Hung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mehrtash","family":"Babadi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr.","given":"Robert F.","family":"Padera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonya A.","family":"MacParland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary D.","family":"Bader","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nasser","family":"Imad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isaac H.","family":"Solomon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Riedel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline B. M.","family":"Porter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra-Chlo\u00e9","family":"Villani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linus T.-Y.","family":"Tsai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Winston","family":"Hide","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gyongyi","family":"Szabo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Hecht","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orit","family":"Rozenblatt-Rosen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex K.","family":"Shalek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Izar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aviv","family":"Regev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yury V.","family":"Popov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Z. Gordon","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8849-808X","authenticated-orcid":false,"given":"Ioannis S.","family":"Vlachos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,3,14]]},"reference":[{"key":"3499_CR1","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1056\/NEJMoa2001017","volume":"382","author":"N Zhu","year":"2020","unstructured":"Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382:727\u201333.","journal-title":"N Engl J Med"},{"key":"3499_CR2","doi-asserted-by":"publisher","first-page":"1169","DOI":"10.1002\/hep.31487","volume":"72","author":"MA Hundt","year":"2020","unstructured":"Hundt MA, Deng Y, Ciarleglio MM, Nathanson MH, Lim JK. Abnormal liver tests in COVID-19: a retrospective observational cohort study of 1,827 patients in a major U.S. hospital network. Hepatology. 2020;72:1169\u201376.","journal-title":"Hepatology."},{"key":"3499_CR3","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1038\/s41575-021-00426-4","volume":"18","author":"T Marjot","year":"2021","unstructured":"Marjot T, Webb GJ, Barritt AS 4th, Moon AM, Stamataki Z, Wong VW, et al. COVID-19 and liver disease: mechanistic and clinical perspectives. Nat Rev Gastroenterol Hepatol. 2021;18:348\u201364.","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"3499_CR4","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1038\/s42255-022-00552-6","volume":"4","author":"N Wanner","year":"2022","unstructured":"Wanner N, Andrieux G, Badia-I-Mompel P, Edler C, Pfefferle S, Lindenmeyer MT, et al. Molecular consequences of SARS-CoV-2 liver tropism. Nat Metab. 2022;4:310\u20139.","journal-title":"Nat Metab"},{"key":"3499_CR5","doi-asserted-by":"publisher","first-page":"n1648","DOI":"10.1136\/bmj.n1648","volume":"374","author":"H Crook","year":"2021","unstructured":"Crook H, Raza S, Nowell J, Young M, Edison P. Long covid-mechanisms, risk factors, and management. BMJ. 2021;374:n1648.","journal-title":"BMJ"},{"key":"3499_CR6","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.14309\/ajg.0000000000001154","volume":"116","author":"NC Roth","year":"2021","unstructured":"Roth NC, Kim A, Vitkovski T, Xia J, Ramirez G, Bernstein D, et al. Post-COVID-19 cholangiopathy: a novel entity. Am J Gastroenterol. 2021;116:1077\u201382.","journal-title":"Am J Gastroenterol"},{"key":"3499_CR7","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1038\/s41586-021-03570-8","volume":"595","author":"TM Delorey","year":"2021","unstructured":"Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe \u00c5, et al. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 2021;595:107\u201313.","journal-title":"Nature"},{"key":"3499_CR8","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1038\/s41586-021-03569-1","volume":"595","author":"JC Melms","year":"2021","unstructured":"Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, et al. A molecular single-cell lung atlas of lethal COVID-19. Nature. 2021;595:114\u20139.","journal-title":"Nature"},{"key":"3499_CR9","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1038\/s41591-020-01227-z","volume":"27","author":"C Muus","year":"2021","unstructured":"Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, et al. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med. 2021;27:546\u201359.","journal-title":"Nat Med"},{"key":"3499_CR10","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1016\/j.jhep.2020.05.030","volume":"73","author":"V De Smet","year":"2020","unstructured":"De Smet V, Verhulst S, van Grunsven LA. Single cell RNA sequencing analysis did not predict hepatocyte infection by SARS-CoV-2. J Hepatol. 2020;73:993\u20135.","journal-title":"J Hepatol"},{"key":"3499_CR11","doi-asserted-by":"publisher","first-page":"2576","DOI":"10.3748\/wjg.v27.i20.2576","volume":"27","author":"A Signorello","year":"2021","unstructured":"Signorello A, Lenci I, Milana M, Grassi G, Baiocchi L. COVID-19 in normal, diseased and transplanted liver. World J Gastroenterol. 2021;27:2576\u201385.","journal-title":"World J Gastroenterol"},{"key":"3499_CR12","doi-asserted-by":"publisher","first-page":"2110","DOI":"10.1111\/liv.14601","volume":"40","author":"A Sonzogni","year":"2020","unstructured":"Sonzogni A, Previtali G, Seghezzi M, Grazia Alessio M, Gianatti A, Licini L, et al. Liver histopathology in severe COVID 19 respiratory failure is suggestive of vascular alterations. Liver Int. 2020;40:2110\u20136.","journal-title":"Liver Int"},{"key":"3499_CR13","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1038\/s41575-019-0134-x","volume":"16","author":"S Ben-Moshe","year":"2019","unstructured":"Ben-Moshe S, Itzkovitz S. Spatial heterogeneity in the mammalian liver. Nat Rev Gastroenterol Hepatol. 2019;16:395\u2013410.","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"3499_CR14","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1016\/j.cgh.2017.02.030","volume":"16","author":"JA Africa","year":"2018","unstructured":"Africa JA, Behling CA, Brunt EM, Zhang N, Luo Y, Wells A, et al. In children with nonalcoholic fatty liver disease, zone 1 steatosis is associated with advanced fibrosis. Clin Gastroenterol Hepatol. 2018;16:438-446.e1.","journal-title":"Clin Gastroenterol Hepatol"},{"key":"3499_CR15","doi-asserted-by":"publisher","first-page":"1263","DOI":"10.1007\/s00261-020-02753-7","volume":"46","author":"OR Brook","year":"2021","unstructured":"Brook OR, Piper KG, Mercado NB, Gebre MS, Barouch DH, Busman-Sahay K, et al. Feasibility and safety of ultrasound-guided minimally invasive autopsy in COVID-19 patients. Abdom Radiol (NY). 2021;46:1263\u201371.","journal-title":"Abdom Radiol (NY)"},{"key":"3499_CR16","doi-asserted-by":"publisher","DOI":"10.1002\/hep4.1854","author":"TS Andrews","year":"2021","unstructured":"Andrews TS, Atif J, Liu JC, Perciani CT, Ma X-Z, Thoeni C, et al. Single-cell, single-nucleus, and spatial RNA sequencing of the human liver identifies cholangiocyte and mesenchymal heterogeneity. Hepatol Commun. 2021. https:\/\/doi.org\/10.1002\/hep4.1854.","journal-title":"Hepatol Commun"},{"key":"3499_CR17","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s13059-019-1850-9","volume":"21","author":"HTN Tran","year":"2020","unstructured":"Tran HTN, Ang KS, Chevrier M, Zhang X, Lee NYS, Goh M, et al. A benchmark of batch-effect correction methods for single-cell RNA sequencing data. Genome Biol. 2020;21:12.","journal-title":"Genome Biol"},{"key":"3499_CR18","doi-asserted-by":"publisher","first-page":"lqaa078","DOI":"10.1093\/nargab\/lqaa078","volume":"2","author":"Y Zhang","year":"2020","unstructured":"Zhang Y, Parmigiani G, Johnson WE. batch effect adjustment for RNA-seq count data. NAR Genom Bioinform. 2020;2:lqaa078.","journal-title":"NAR Genom Bioinform."},{"key":"3499_CR19","doi-asserted-by":"publisher","first-page":"5701","DOI":"10.1093\/bioinformatics\/btaa1009","volume":"36","author":"C Ahlmann-Eltze","year":"2021","unstructured":"Ahlmann-Eltze C, Huber W. glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data. Bioinformatics. 2021;36:5701\u20132.","journal-title":"Bioinformatics"},{"key":"3499_CR20","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1038\/nature21065","volume":"542","author":"KB Halpern","year":"2017","unstructured":"Halpern KB, Shenhav R, Matcovitch-Natan O, Toth B, Lemze D, Golan M, et al. Single-cell spatial reconstruction reveals global division of labour in the mammalian liver. Nature. 2017;542:352\u20136.","journal-title":"Nature"},{"key":"3499_CR21","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1038\/s41586-019-1373-2","volume":"572","author":"N Aizarani","year":"2019","unstructured":"Aizarani N, Saviano A, Sagar N, Mailly L, Durand S, Herman JS, et al. A human liver cell atlas reveals heterogeneity and epithelial progenitors. Nature. 2019;572:199\u2013204.","journal-title":"Nature."},{"key":"3499_CR22","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/s41575-020-0304-x","volume":"17","author":"P Ramachandran","year":"2020","unstructured":"Ramachandran P, Matchett KP, Dobie R, Wilson-Kanamori JR, Henderson NC. Single-cell technologies in hepatology: new insights into liver biology and disease pathogenesis. Nat Rev Gastroenterol Hepatol. 2020;17:457\u201372.","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"3499_CR23","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1053\/j.gastro.2014.07.056","volume":"147","author":"MM Yeh","year":"2014","unstructured":"Yeh MM, Brunt EM. Pathological features of fatty liver disease. Gastroenterology. 2014;147:754\u201364.","journal-title":"Gastroenterology"},{"key":"3499_CR24","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1111\/liv.14006","volume":"39","author":"CA Hudert","year":"2019","unstructured":"Hudert CA, Selinski S, Rudolph B, Bl\u00e4ker H, Loddenkemper C, Thielhorn R, et al. Genetic determinants of steatosis and fibrosis progression in paediatric non-alcoholic fatty liver disease. Liver Int. 2019;39:540\u201356.","journal-title":"Liver Int"},{"key":"3499_CR25","doi-asserted-by":"publisher","unstructured":"Chembazhi UV, Bangru S, Hernaez M, Kalsotra A. Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver. bioRxiv. bioRxiv; 2020. https:\/\/doi.org\/10.1101\/2020.05.29.124263.","DOI":"10.1101\/2020.05.29.124263"},{"key":"3499_CR26","doi-asserted-by":"publisher","first-page":"6103","DOI":"10.1073\/pnas.1912146117","volume":"117","author":"M Liu","year":"2020","unstructured":"Liu M, Yan Q, Sun Y, Nam Y, Hu L, Loong JH, et al. A hepatocyte differentiation model reveals two subtypes of liver cancer with different oncofetal properties and therapeutic targets. Proc Natl Acad Sci U S A. 2020;117:6103\u201313.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"3499_CR27","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1038\/s41575-020-0342-4","volume":"18","author":"GK Michalopoulos","year":"2021","unstructured":"Michalopoulos GK, Bhushan B. Liver regeneration: biological and pathological mechanisms and implications. Nat Rev Gastroenterol Hepatol. 2021;18:40\u201355.","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"3499_CR28","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1053\/j.gastro.2009.05.044","volume":"137","author":"AW Duncan","year":"2009","unstructured":"Duncan AW, Dorrell C, Grompe M. Stem cells and liver regeneration. Gastroenterology. 2009;137:466\u201381.","journal-title":"Gastroenterology"},{"key":"3499_CR29","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1016\/j.stem.2014.09.008","volume":"15","author":"BD Tarlow","year":"2014","unstructured":"Tarlow BD, Pelz C, Naugler WE, Wakefield L, Wilson EM, Finegold MJ, et al. Bipotential adult liver progenitors are derived from chronically injured mature hepatocytes. Cell Stem Cell. 2014;15:605\u201318.","journal-title":"Cell Stem Cell"},{"key":"3499_CR30","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1101\/gr.146399.112","volume":"23","author":"JS Jakobsen","year":"2013","unstructured":"Jakobsen JS, Waage J, Rapin N, Bisgaard HC, Larsen FS, Porse BT. Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Genome Res. 2013;23:592\u2013603.","journal-title":"Genome Res"},{"key":"3499_CR31","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.1038\/s42255-022-00652-3","volume":"4","author":"CS Palmer","year":"2022","unstructured":"Palmer CS. Innate metabolic responses against viral infections. Nat Metab. 2022;4:1245\u201359.","journal-title":"Nat Metab"},{"key":"3499_CR32","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1016\/j.cell.2021.01.004","volume":"184","author":"X Nie","year":"2021","unstructured":"Nie X, Qian L, Sun R, Huang B, Dong X, Xiao Q, et al. Multi-organ proteomic landscape of COVID-19 autopsies. Cell. 2021;184:775\u2013791.e14.","journal-title":"Cell"},{"key":"3499_CR33","doi-asserted-by":"publisher","first-page":"e1009128","DOI":"10.1371\/journal.ppat.1009128","volume":"16","author":"T Patra","year":"2020","unstructured":"Patra T, Meyer K, Geerling L, Isbell TS, Hoft DF, Brien J, et al. SARS-CoV-2 spike protein promotes IL-6 trans-signaling by activation of angiotensin II receptor signaling in epithelial cells. PLoS Pathog. 2020;16:e1009128.","journal-title":"PLoS Pathog"},{"key":"3499_CR34","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1016\/j.jhep.2013.09.024","volume":"60","author":"A Qu","year":"2014","unstructured":"Qu A, Jiang C, Cai Y, Kim J-H, Tanaka N, Ward JM, et al. Role of Myc in hepatocellular proliferation and hepatocarcinogenesis. J Hepatol. 2014;60:331\u20138.","journal-title":"J Hepatol"},{"key":"3499_CR35","doi-asserted-by":"publisher","first-page":"1765","DOI":"10.1016\/j.bbadis.2013.06.001","volume":"1832","author":"YA Nevzorova","year":"2013","unstructured":"Nevzorova YA, Hu W, Cubero FJ, Haas U, Freimuth J, Tacke F, et al. Overexpression of c-myc in hepatocytes promotes activation of hepatic stellate cells and facilitates the onset of liver fibrosis. Biochim Biophys Acta. 2013;1832:1765\u201375.","journal-title":"Biochim Biophys Acta"},{"key":"3499_CR36","doi-asserted-by":"publisher","first-page":"7288","DOI":"10.1073\/pnas.1304285110","volume":"110","author":"D Fu","year":"2013","unstructured":"Fu D, Mitra K, Sengupta P, Jarnik M, Lippincott-Schwartz J, Arias IM. Coordinated elevation of mitochondrial oxidative phosphorylation and autophagy help drive hepatocyte polarization. Proc Natl Acad Sci U S A. 2013;110:7288\u201393.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"3499_CR37","doi-asserted-by":"publisher","first-page":"490","DOI":"10.18632\/oncotarget.6357","volume":"7","author":"F Santacatterina","year":"2016","unstructured":"Santacatterina F, S\u00e1nchez-Cenizo L, Formentini L, Mobasher MA, Casas E, Rueda CB, et al. Down-regulation of oxidative phosphorylation in the liver by expression of the ATPase inhibitory factor 1 induces a tumor-promoter metabolic state. Oncotarget. 2016;7:490\u2013508.","journal-title":"Oncotarget"},{"key":"3499_CR38","doi-asserted-by":"publisher","first-page":"109659","DOI":"10.1016\/j.celrep.2021.109659","volume":"36","author":"X Bai","year":"2021","unstructured":"Bai X, Liao Y, Sun F, Xiao X, Fu S. Diurnal regulation of oxidative phosphorylation restricts hepatocyte proliferation and inflammation. Cell Rep. 2021;36:109659.","journal-title":"Cell Rep"},{"key":"3499_CR39","doi-asserted-by":"publisher","unstructured":"Buchynskyi M, Kamyshna I, Oksenych V, Zavidniuk N, Kamyshnyi A. The intersection of COVID-19 and metabolic-associated fatty liver disease: an overview of the current evidence. Viruses. 2023;15. https:\/\/doi.org\/10.3390\/v15051072.","DOI":"10.3390\/v15051072"},{"key":"3499_CR40","doi-asserted-by":"publisher","unstructured":"W\u00f6lfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, M\u00fcller MA, et al. Virological assessment of hospitalized patients with COVID-2019. Nature. 2020:465\u2013469. https:\/\/doi.org\/10.1038\/s41586-020-2196-x","DOI":"10.1038\/s41586-020-2196-x"},{"key":"3499_CR41","doi-asserted-by":"publisher","first-page":"2439","DOI":"10.1056\/NEJMoa2027906","volume":"383","author":"EE Walsh","year":"2020","unstructured":"Walsh EE, Frenck RW Jr, Falsey AR, Kitchin N, Absalon J, Gurtman A, et al. Safety and immunogenicity of two RNA-based covid-19 vaccine candidates. N Engl J Med. 2020;383:2439\u201350.","journal-title":"N Engl J Med"},{"key":"3499_CR42","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1002\/cphy.c120019","volume":"3","author":"JH Tabibian","year":"2013","unstructured":"Tabibian JH, Masyuk AI, Masyuk TV, O\u2019Hara SP, LaRusso NF. Physiology of cholangiocytes. Compr Physiol. 2013;3:541\u201365.","journal-title":"Compr Physiol"},{"key":"3499_CR43","first-page":"259","volume":"15","author":"T Roskams","year":"1998","unstructured":"Roskams T, Desmet V. Ductular reaction and its diagnostic significance. Semin Diagn Pathol. 1998;15:259\u201369.","journal-title":"Semin Diagn Pathol"},{"key":"3499_CR44","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.1002\/hep.25758","volume":"56","author":"J Pritchett","year":"2012","unstructured":"Pritchett J, Harvey E, Athwal V, Berry A, Rowe C, Oakley F, et al. Osteopontin is a novel downstream target of SOX9 with diagnostic implications for progression of liver fibrosis in humans. Hepatology. 2012;56:1108\u201316.","journal-title":"Hepatology"},{"key":"3499_CR45","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1111\/j.1478-3231.2009.02024.x","volume":"29","author":"BA Schotanus","year":"2009","unstructured":"Schotanus BA, van den Ingh TSGAM, Penning LC, Rothuizen J, Roskams TA, Spee B. Cross-species immunohistochemical investigation of the activation of the liver progenitor cell niche in different types of liver disease. Liver Int. 2009;29:1241\u201352.","journal-title":"Liver Int."},{"key":"3499_CR46","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1053\/j.gastro.2006.07.023","volume":"132","author":"D Alvaro","year":"2007","unstructured":"Alvaro D, Mancino MG, Glaser S, Gaudio E, Marzioni M, Francis H, et al. Proliferating cholangiocytes: a neuroendocrine compartment in the diseased liver. Gastroenterology. 2007;132:415\u201331.","journal-title":"Gastroenterology"},{"key":"3499_CR47","doi-asserted-by":"publisher","unstructured":"S\u00e1nchez-Taltavull D, Brodie T, Zindel J, Dommann N, Surewaard BGJ, Keogh A, et al. Single cell chronoatlas of regenerating mouse livers reveals early Kupffer cell proliferation. https:\/\/doi.org\/10.1101\/2021.06.09.447699.","DOI":"10.1101\/2021.06.09.447699"},{"key":"3499_CR48","doi-asserted-by":"publisher","first-page":"177","DOI":"10.14218\/JCTH.2019.00031","volume":"8","author":"L Yang","year":"2020","unstructured":"Yang L, Lewis K. Erythroid lineage cells in the liver: novel immune regulators and beyond. J Clin Transl Hepatol. 2020;8:177\u201383.","journal-title":"J Clin Transl Hepatol"},{"key":"3499_CR49","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.exphem.2021.02.012","volume":"97","author":"A Bapat","year":"2021","unstructured":"Bapat A, Schippel N, Shi X, Jasbi P, Gu H, Kala M, et al. Hypoxia promotes erythroid differentiation through the development of progenitors and proerythroblasts. Exp Hematol. 2021;97:32\u201346.e35.","journal-title":"Exp Hematol"},{"key":"3499_CR50","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1038\/nature12681","volume":"505","author":"B-S Ding","year":"2014","unstructured":"Ding B-S, Cao Z, Lis R, Nolan DJ, Guo P, Simons M, et al. Divergent angiocrine signals from vascular niche balance liver regeneration and fibrosis. Nature. 2014;505:97\u2013102.","journal-title":"Nature"},{"key":"3499_CR51","doi-asserted-by":"publisher","first-page":"e13325","DOI":"10.1111\/apha.13325","volume":"228","author":"PM Benz","year":"2020","unstructured":"Benz PM, Ding Y, Stingl H, Loot AE, Zink J, Wittig I, et al. AKAP12 deficiency impairs VEGF-induced endothelial cell migration and sprouting. Acta Physiol. 2020;228:e13325.","journal-title":"Acta Physiol"},{"key":"3499_CR52","doi-asserted-by":"publisher","first-page":"529179","DOI":"10.1155\/2012\/529179","volume":"2012","author":"S Akakura","year":"2012","unstructured":"Akakura S, Gelman IH. Pivotal role of AKAP12 in the regulation of cellular adhesion dynamics: control of cytoskeletal architecture, cell migration, and mitogenic signaling. J Signal Transduct. 2012;2012:529179.","journal-title":"J Signal Transduct"},{"key":"3499_CR53","doi-asserted-by":"publisher","unstructured":"Seo JH, Maki T, Miyamoto N, Choi YK, Chung KK, Hamanaka G, et al. AKAP12 Supports Blood-Brain Barrier Integrity against Ischemic Stroke. Int J Mol Sci. 2020;21. https:\/\/doi.org\/10.3390\/ijms21239078.","DOI":"10.3390\/ijms21239078"},{"key":"3499_CR54","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s12276-018-0187-x","volume":"50","author":"HS Lee","year":"2018","unstructured":"Lee HS, Choi J, Son T, Wee H-J, Bae S-J, Seo JH, et al. Altered AKAP12 expression in portal fibroblasts and liver sinusoids mediates transition from hepatic fibrogenesis to fibrosis resolution. Exp Mol Med. 2018;50:1\u201313.","journal-title":"Exp Mol Med"},{"key":"3499_CR55","doi-asserted-by":"publisher","first-page":"3640","DOI":"10.1182\/blood-2008-03-146472","volume":"113","author":"F Bossi","year":"2009","unstructured":"Bossi F, Rizzi L, Bulla R, Debeus A, Tripodo C, Picotti P, et al. C7 is expressed on endothelial cells as a trap for the assembling terminal complement complex and may exert anti-inflammatory function. Blood. 2009;113:3640\u20138.","journal-title":"Blood"},{"key":"3499_CR56","doi-asserted-by":"publisher","unstructured":"Niethamer TK, Stabler CT, Leach JP, Zepp JA, Morley MP, Babu A, et al. Defining the role of pulmonary endothelial cell heterogeneity in the response to acute lung injury. Elife. 2020;9. https:\/\/doi.org\/10.7554\/eLife.53072.","DOI":"10.7554\/eLife.53072"},{"key":"3499_CR57","first-page":"34","volume":"4","author":"J Xu","year":"2015","unstructured":"Xu J, Cong M, Park TJ, Scholten D, Brenner DA, Kisseleva T. Contribution of bone marrow-derived fibrocytes to liver fibrosis. Hepatobiliary Surg Nutr. 2015;4:34\u201347.","journal-title":"Hepatobiliary Surg Nutr"},{"key":"3499_CR58","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1053\/j.gastro.2014.05.001","volume":"147","author":"RG Wells","year":"2014","unstructured":"Wells RG. The portal fibroblast: not just a poor man\u2019s stellate cell. Gastroenterology. 2014;147:41\u20137.","journal-title":"Gastroenterology"},{"key":"3499_CR59","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/j.diff.2016.07.001","volume":"92","author":"D Karin","year":"2016","unstructured":"Karin D, Koyama Y, Brenner D, Kisseleva T. The characteristics of activated portal fibroblasts\/myofibroblasts in liver fibrosis. Differentiation. 2016;92:84\u201392.","journal-title":"Differentiation"},{"key":"3499_CR60","doi-asserted-by":"publisher","first-page":"2823","DOI":"10.1038\/ncomms3823","volume":"4","author":"I Mederacke","year":"2013","unstructured":"Mederacke I, Hsu CC, Troeger JS, Huebener P, Mu X, Dapito DH, et al. Fate tracing reveals hepatic stellate cells as dominant contributors to liver fibrosis independent of its aetiology. Nat Commun. 2013;4:2823.","journal-title":"Nat Commun"},{"key":"3499_CR61","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/nrendo.2016.12","volume":"12","author":"VS Salazar","year":"2016","unstructured":"Salazar VS, Gamer LW, Rosen V. BMP signalling in skeletal development, disease and repair. Nat Rev Endocrinol. 2016;12:203\u201321.","journal-title":"Nat Rev Endocrinol"},{"key":"3499_CR62","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/nrm1962","volume":"7","author":"A Citri","year":"2006","unstructured":"Citri A, Yarden Y. EGF-ERBB signalling: towards the systems level. Nat Rev Mol Cell Biol. 2006;7:505\u201316.","journal-title":"Nat Rev Mol Cell Biol"},{"key":"3499_CR63","doi-asserted-by":"publisher","first-page":"939","DOI":"10.1136\/gutjnl-2016-313314","volume":"66","author":"K Breitkopf-Heinlein","year":"2017","unstructured":"Breitkopf-Heinlein K, Meyer C, K\u00f6nig C, Gaitantzi H, Addante A, Thomas M, et al. BMP-9 interferes with liver regeneration and promotes liver fibrosis. Gut. 2017;66:939\u201354.","journal-title":"Gut"},{"key":"3499_CR64","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.abb.2014.07.011","volume":"561","author":"AC Carreira","year":"2014","unstructured":"Carreira AC, Alves GG, Zambuzzi WF, Sogayar MC, Granjeiro JM. Bone Morphogenetic Proteins: structure, biological function and therapeutic applications. Arch Biochem Biophys. 2014;561:64\u201373.","journal-title":"Arch Biochem Biophys"},{"key":"3499_CR65","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1007\/s00535-013-0907-x","volume":"49","author":"C Berasain","year":"2014","unstructured":"Berasain C, Avila MA. The EGFR signalling system in the liver: from hepatoprotection to hepatocarcinogenesis. J Gastroenterol. 2014;49:9\u201323.","journal-title":"J Gastroenterol"},{"key":"3499_CR66","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1002\/emmm.201000085","volume":"2","author":"F B\u00f6hm","year":"2010","unstructured":"B\u00f6hm F, K\u00f6hler UA, Speicher T, Werner S. Regulation of liver regeneration by growth factors and cytokines. EMBO Mol Med. 2010;2:294\u2013305.","journal-title":"EMBO Mol Med"},{"key":"3499_CR67","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1016\/j.jss.2006.07.027","volume":"138","author":"M Bockhorn","year":"2007","unstructured":"Bockhorn M, Goralski M, Prokofiev D, Dammann P, Gr\u00fcnewald P, Trippler M, et al. VEGF is important for early liver regeneration after partial hepatectomy. J Surg Res. 2007;138:291\u20139.","journal-title":"J Surg Res"},{"key":"3499_CR68","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1053\/j.gastro.2011.12.017","volume":"142","author":"G Xie","year":"2012","unstructured":"Xie G, Wang X, Wang L, Wang L, Atkinson RD, Kanel GC, et al. Role of differentiation of liver sinusoidal endothelial cells in progression and regression of hepatic fibrosis in rats. Gastroenterology. 2012;142:918\u2013927.e6.","journal-title":"Gastroenterology"},{"key":"3499_CR69","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1038\/nrm1911","volume":"7","author":"A-K Olsson","year":"2006","unstructured":"Olsson A-K, Dimberg A, Kreuger J, Claesson-Welsh L. VEGF receptor signalling - in control of vascular function. Nat Rev Mol Cell Biol. 2006;7:359\u201371.","journal-title":"Nat Rev Mol Cell Biol"},{"key":"3499_CR70","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1038\/s12276-021-00574-2","volume":"53","author":"Q-S Liang","year":"2021","unstructured":"Liang Q-S, Xie J-G, Yu C, Feng Z, Ma J, Zhang Y, et al. Splenectomy improves liver fibrosis via tumor necrosis factor superfamily 14 (LIGHT) through the JNK\/TGF-\u03b21 signaling pathway. Exp Mol Med. 2021;53:393\u2013406.","journal-title":"Exp Mol Med"},{"key":"3499_CR71","first-page":"1844","volume":"19","author":"F Li","year":"2020","unstructured":"Li F, Xu X, Geng J, Wan X, Dai H. The autocrine CXCR4\/CXCL12 axis contributes to lung fibrosis through modulation of lung fibroblast activity. Exp Ther Med. 2020;19:1844\u201354.","journal-title":"Exp Ther Med"},{"key":"3499_CR72","doi-asserted-by":"publisher","first-page":"1961","DOI":"10.1038\/s41467-021-22210-3","volume":"12","author":"M Ferreira-Gomes","year":"2021","unstructured":"Ferreira-Gomes M, Kruglov A, Durek P, Heinrich F, Tizian C, Heinz GA, et al. SARS-CoV-2 in severe COVID-19 induces a TGF-\u03b2-dominated chronic immune response that does not target itself. Nat Commun. 2021;12:1961.","journal-title":"Nat Commun"},{"key":"3499_CR73","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1038\/ng1599","volume":"37","author":"S Hillebrandt","year":"2005","unstructured":"Hillebrandt S, Wasmuth HE, Weiskirchen R, Hellerbrand C, Keppeler H, Werth A, et al. Complement factor 5 is a quantitative trait gene that modifies liver fibrogenesis in mice and humans. Nat Genet. 2005;37:835\u201343.","journal-title":"Nat Genet"},{"key":"3499_CR74","doi-asserted-by":"publisher","first-page":"2041","DOI":"10.1053\/gast.2002.37069","volume":"123","author":"S Hillebrandt","year":"2002","unstructured":"Hillebrandt S, Goos C, Matern S, Lammert F. Genome-wide analysis of hepatic fibrosis in inbred mice identifies the susceptibility locus Hfib1 on chromosome 15. Gastroenterology. 2002;123:2041\u201351.","journal-title":"Gastroenterology"},{"key":"3499_CR75","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1080\/19336918.2016.1215785","volume":"10","author":"D Ito","year":"2016","unstructured":"Ito D, Kumanogoh A. The role of Sema4A in angiogenesis, immune responses, carcinogenesis, and retinal systems. Cell Adh Migr. 2016;10:692\u20139.","journal-title":"Cell Adh Migr"},{"key":"3499_CR76","doi-asserted-by":"publisher","first-page":"1517","DOI":"10.1016\/S0140-6736(20)30920-X","volume":"395","author":"H Li","year":"2020","unstructured":"Li H, Liu L, Zhang D, Xu J, Dai H, Tang N, et al. SARS-CoV-2 and viral sepsis: observations and hypotheses. Lancet. 2020;395:1517\u201320.","journal-title":"Lancet"},{"key":"3499_CR77","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1097\/SHK.0b013e31824a670b","volume":"37","author":"FA Gonnert","year":"2012","unstructured":"Gonnert FA, Kunisch E, Gajda M, Lambeck S, Weber M, Claus RA, et al. Hepatic fibrosis in a long-term murine model of sepsis. Shock. 2012;37:399\u2013407.","journal-title":"Shock"},{"key":"3499_CR78","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1007\/s13238-020-00718-6","volume":"11","author":"B Zhao","year":"2020","unstructured":"Zhao B, Ni C, Gao R, Wang Y, Yang L, Wei J, et al. Recapitulation of SARS-CoV-2 infection and cholangiocyte damage with human liver ductal organoids. Protein Cell. 2020;11:771\u20135.","journal-title":"Protein Cell"},{"key":"3499_CR79","doi-asserted-by":"publisher","first-page":"13464","DOI":"10.1038\/s41598-021-92941-2","volume":"11","author":"C-M Su","year":"2021","unstructured":"Su C-M, Wang L, Yoo D. Activation of NF-\u03baB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. Sci Rep. 2021;11:13464.","journal-title":"Sci Rep"},{"key":"3499_CR80","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1016\/j.abb.2019.07.013","volume":"671","author":"L Perez","year":"2019","unstructured":"Perez L. Acute phase protein response to viral infection and vaccination. Arch Biochem Biophys. 2019;671:196\u2013202.","journal-title":"Arch Biochem Biophys"},{"key":"3499_CR81","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1038\/s41579-018-0003-6","volume":"16","author":"Y Choi","year":"2018","unstructured":"Choi Y, Bowman JW, Jung JU. Autophagy during viral infection - a double-edged sword. Nat Rev Microbiol. 2018;16:341\u201354.","journal-title":"Nat Rev Microbiol"},{"key":"3499_CR82","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1186\/s12985-023-02069-0","volume":"20","author":"T Shan","year":"2023","unstructured":"Shan T, Li L-Y, Yang J-M, Cheng Y. Role and clinical implication of autophagy in COVID-19. Virol J. 2023;20:125.","journal-title":"Virol J"},{"key":"3499_CR83","doi-asserted-by":"publisher","unstructured":"Hartl L, Haslinger K, Angerer M, Semmler G, Schneeweiss-Gleixner M, Jachs M, et al. Progressive cholestasis and associated sclerosing cholangitis are frequent complications of COVID-19 in patients with chronic liver disease. Hepatology. 2022. https:\/\/doi.org\/10.1002\/hep.32582.","DOI":"10.1002\/hep.32582"},{"key":"3499_CR84","doi-asserted-by":"publisher","unstructured":"Rela M, Rajakannu M, Veerankutty FH, Vij M, Rammohan A. First report of auxiliary liver transplantation for severe cholangiopathy after SARS-CoV-2 respiratory infection. Am J Transplant. 2022.https:\/\/doi.org\/10.1111\/ajt.17165.","DOI":"10.1111\/ajt.17165"},{"key":"3499_CR85","doi-asserted-by":"publisher","first-page":"102328","DOI":"10.1016\/j.redox.2022.102328","volume":"53","author":"X Wu","year":"2022","unstructured":"Wu X, Luo Y, Wang S, Li Y, Bao M, Shang Y, et al. AKAP12 ameliorates liver injury via targeting PI3K\/AKT\/PCSK6 pathway. Redox Biol. 2022;53:102328.","journal-title":"Redox Biol"},{"key":"3499_CR86","doi-asserted-by":"publisher","first-page":"C469","DOI":"10.1152\/ajpcell.00452.2010","volume":"301","author":"N Lin","year":"2011","unstructured":"Lin N, Chen S, Pan W, Xu L, Hu K, Xu R. NP603, a novel and potent inhibitor of FGFR1 tyrosine kinase, inhibits hepatic stellate cell proliferation and ameliorates hepatic fibrosis in rats. Am J Physiol Cell Physiol. 2011;301:C469\u201377.","journal-title":"Am J Physiol Cell Physiol"},{"key":"3499_CR87","doi-asserted-by":"publisher","first-page":"eabl5197","DOI":"10.1126\/science.abl5197","volume":"376","author":"C Dom\u00ednguez Conde","year":"2022","unstructured":"Dom\u00ednguez Conde C, Xu C, Jarvis LB, Rainbow DB, Wells SB, Gomes T, et al. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science. 2022;376:eabl5197.","journal-title":"Science."},{"key":"3499_CR88","doi-asserted-by":"publisher","first-page":"1346520","DOI":"10.3389\/fimmu.2024.1346520","volume":"15","author":"L Van Melkebeke","year":"2024","unstructured":"Van Melkebeke L, Verbeek J, Bihary D, Boesch M, Boeckx B, Feio-Azevedo R, et al. Comparison of the single-cell and single-nucleus hepatic myeloid landscape within decompensated cirrhosis patients. Front Immunol. 2024;15:1346520.","journal-title":"Front Immunol"},{"key":"3499_CR89","doi-asserted-by":"publisher","first-page":"753","DOI":"10.1038\/s41588-023-01375-1","volume":"55","author":"R Edahiro","year":"2023","unstructured":"Edahiro R, Shirai Y, Takeshima Y, Sakakibara S, Yamaguchi Y, Murakami T, et al. Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity. Nat Genet. 2023;55:753\u201367.","journal-title":"Nat Genet"},{"key":"3499_CR90","doi-asserted-by":"publisher","first-page":"5838","DOI":"10.1016\/j.cell.2021.10.023","volume":"184","author":"X Ren","year":"2021","unstructured":"Ren X, Wen W, Fan X, Hou W, Su B, Cai P, et al. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell. 2021;184:5838.","journal-title":"Cell"},{"key":"3499_CR91","doi-asserted-by":"publisher","first-page":"e247","DOI":"10.1016\/S2666-5247(23)00368-3","volume":"5","author":"S Feys","year":"2024","unstructured":"Feys S, Vanmassenhove S, Kraisin S, Yu K, Jacobs C, Boeckx B, et al. Lower respiratory tract single-cell RNA sequencing and neutrophil extracellular trap profiling of COVID-19-associated pulmonary aspergillosis: a single centre, retrospective, observational study. Lancet Microbe. 2024;5:e247\u201360.","journal-title":"Lancet Microbe"},{"key":"3499_CR92","doi-asserted-by":"publisher","first-page":"792","DOI":"10.1038\/s41591-020-0844-1","volume":"26","author":"M Slyper","year":"2020","unstructured":"Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, et al. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med. 2020;26:792\u2013802.","journal-title":"Nat Med"},{"key":"3499_CR93","doi-asserted-by":"publisher","first-page":"1606","DOI":"10.1016\/j.cell.2020.08.003","volume":"182","author":"E Drokhlyansky","year":"2020","unstructured":"Drokhlyansky E, Smillie CS, Van Wittenberghe N, Ericsson M, Griffin GK, Eraslan G, et al. The Human and Mouse Enteric Nervous System at Single-Cell Resolution. Cell. 2020;182:1606\u20131622.e23.","journal-title":"Cell"},{"key":"3499_CR94","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10.","journal-title":"EMBnet J"},{"key":"3499_CR95","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1038\/s41592-020-0905-x","volume":"17","author":"B Li","year":"2020","unstructured":"Li B, Gould J, Yang Y, Sarkizova S, Tabaka M, Ashenberg O, et al. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq. Nat Methods. 2020;17:793\u20138.","journal-title":"Nat Methods"},{"key":"3499_CR96","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1016\/j.cell.2020.04.011","volume":"181","author":"D Kim","year":"2020","unstructured":"Kim D, Lee J-Y, Yang J-S, Kim JW, Kim VN, Chang H. The Architecture of SARS-CoV-2 Transcriptome. Cell. 2020;181:914\u2013921.e10.","journal-title":"Cell"},{"key":"3499_CR97","doi-asserted-by":"publisher","unstructured":"Fleming SJ, Marioni JC, Babadi M. CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. bioRxiv. bioRxiv. 2019. https:\/\/doi.org\/10.1101\/791699.","DOI":"10.1101\/791699"},{"key":"3499_CR98","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","volume":"184","author":"Y Hao","year":"2021","unstructured":"Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184:3573\u20133587.e29.","journal-title":"Cell"},{"key":"3499_CR99","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","volume":"177","author":"T Stuart","year":"2019","unstructured":"Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, et al. comprehensive integration of single-cell data. Cell. 2019;177:1888\u20131902.e21.","journal-title":"Cell"},{"key":"3499_CR100","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/nbt.4096","volume":"36","author":"A Butler","year":"2018","unstructured":"Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36:411\u201320.","journal-title":"Nat Biotechnol"},{"key":"3499_CR101","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky I, Millard N, Fan J, Slowikowski K, Zhang F, Wei K, et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods. 2019;16:1289\u201396.","journal-title":"Nat Methods"},{"key":"3499_CR102","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","volume":"8","author":"SL Wolock","year":"2019","unstructured":"Wolock SL, Lopez R, Klein AM. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 2019;8:281\u2013291.e9.","journal-title":"Cell Syst"},{"key":"3499_CR103","doi-asserted-by":"publisher","unstructured":"Townes FW, William Townes F, Hicks SC, Aryee MJ, Irizarry RA. Feature selection and dimension reduction for single cell RNA-seq based on a multinomial model. https:\/\/doi.org\/10.1101\/574574.","DOI":"10.1101\/574574"},{"key":"3499_CR104","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1186\/s13059-019-1874-1","volume":"20","author":"C Hafemeister","year":"2019","unstructured":"Hafemeister C, Satija R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 2019;20:296.","journal-title":"Genome Biol"},{"key":"3499_CR105","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1186\/s13059-021-02451-7","volume":"22","author":"J Lause","year":"2021","unstructured":"Lause J, Berens P, Kobak D. Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data. Genome Biol. 2021;22:258.","journal-title":"Genome Biol"},{"key":"3499_CR106","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.spl.2019.01.009","volume":"148","author":"U Bandara","year":"2019","unstructured":"Bandara U, Gill R, Mitra R. On computing maximum likelihood estimates for the negative binomial distribution. Stat Probab Lett. 2019;148:54\u20138.","journal-title":"Stat Probab Lett"},{"key":"3499_CR107","doi-asserted-by":"publisher","first-page":"e1006042","DOI":"10.1371\/journal.pcbi.1006042","volume":"14","author":"Y Pita-Ju\u00e1rez","year":"2018","unstructured":"Pita-Ju\u00e1rez Y, Altschuler G, Kariotis S, Wei W, Koler K, Green C, et al. The pathway coexpression network: revealing pathway relationships. PLoS Comput Biol. 2018;14:e1006042.","journal-title":"PLoS Comput Biol"},{"key":"3499_CR108","doi-asserted-by":"publisher","unstructured":"Consortium TGO, The gene ontology consortium. gene ontology annotations and resources. Nucleic Acids Res. 2012:D530\u2013D535. https:\/\/doi.org\/10.1093\/nar\/gks1050.","DOI":"10.1093\/nar\/gks1050"},{"key":"3499_CR109","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1186\/gm472","volume":"5","author":"GM Altschuler","year":"2013","unstructured":"Altschuler GM, Hofmann O, Kalatskaya I, Payne R, Sui SJH, Saxena U, et al. Pathprinting: an integrative approach to understand the functional basis of disease. Genome Med. 2013;5:68.","journal-title":"Genome Med"},{"key":"3499_CR110","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","volume":"43","author":"ME Ritchie","year":"2015","unstructured":"Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.","journal-title":"Nucleic Acids Res"},{"key":"3499_CR111","doi-asserted-by":"publisher","first-page":"R29","DOI":"10.1186\/gb-2014-15-2-r29","volume":"15","author":"CW Law","year":"2014","unstructured":"Law CW, Chen Y, Shi W, Smyth GK. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15:R29.","journal-title":"Genome Biol"},{"key":"3499_CR112","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1038\/nmeth.4612","volume":"15","author":"C Soneson","year":"2018","unstructured":"Soneson C, Robinson MD. Bias, robustness and scalability in single-cell differential expression analysis. Nat Methods. 2018;15:255\u201361.","journal-title":"Nat Methods"},{"key":"3499_CR113","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","volume":"11","author":"MD Robinson","year":"2010","unstructured":"Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.","journal-title":"Genome Biol"},{"key":"3499_CR114","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139\u201340.","journal-title":"Bioinformatics"},{"key":"3499_CR115","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1214\/16-AOAS920","volume":"10","author":"B Phipson","year":"2016","unstructured":"Phipson B, Lee S, Majewski IJ, Alexander WS, Smyth GK. Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression. Ann Appl Stat. 2016;10:946\u201363.","journal-title":"Ann Appl Stat"},{"key":"3499_CR116","doi-asserted-by":"publisher","unstructured":"Lun ATL, Marioni JC. Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data. Biostatistics. 2017:451\u2013464. https:\/\/doi.org\/10.1093\/biostatistics\/kxw055.","DOI":"10.1093\/biostatistics\/kxw055"},{"key":"3499_CR117","doi-asserted-by":"publisher","first-page":"17040","DOI":"10.1038\/s41598-018-35365-9","volume":"8","author":"D Lee","year":"2018","unstructured":"Lee D, Cheng A, Lawlor N, Bolisetty M, Ucar D. Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA). Sci Rep. 2018;8:17040.","journal-title":"Sci Rep"},{"key":"3499_CR118","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1016\/j.cell.2020.10.002","volume":"183","author":"D Kotliar","year":"2020","unstructured":"Kotliar D, Lin AE, Logue J, Hughes TK, Khoury NM, Raju SS, et al. Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics. Cell. 2020;183:1383\u20131401.e19.","journal-title":"Cell"},{"key":"3499_CR119","doi-asserted-by":"publisher","unstructured":"Cao Y, Guo Z, Vangala P, Donnard E, Liu P, McDonel P, et al. Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults. bioRxiv. bioRxiv. 2020. https:\/\/doi.org\/10.1101\/2020.04.15.042978.","DOI":"10.1101\/2020.04.15.042978"},{"key":"3499_CR120","doi-asserted-by":"publisher","unstructured":"Bost P, Giladi A, Liu Y, Bendjelal Y, Xu G, David E, et al. Host-viral infection maps reveal signatures of severe COVID-19 patients. Cell. 2020:1475\u20131488.e12. https:\/\/doi.org\/10.1016\/j.cell.2020.05.006.","DOI":"10.1016\/j.cell.2020.05.006"},{"key":"3499_CR121","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1186\/s12864-018-4772-0","volume":"19","author":"K Street","year":"2018","unstructured":"Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics. 2018;19:477.","journal-title":"BMC Genomics"},{"key":"3499_CR122","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","volume":"12","author":"S Jin","year":"2021","unstructured":"Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan C-H, et al. Inference and analysis of cell-cell communication using Cell Chat. Nat Commun. 2021;12:1088.","journal-title":"Nat Commun"},{"key":"3499_CR123","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1613\/jair.953","volume":"16","author":"NV Chawla","year":"2002","unstructured":"Chawla NV, Bowyer KW, Hall LO, Kegelmeyer WP. SMOTE: synthetic minority over-sampling technique. J Artif Intell Res. 2002;16:321\u201357.","journal-title":"J Artif Intell Res"},{"key":"3499_CR124","doi-asserted-by":"publisher","first-page":"1794","DOI":"10.1038\/s41587-022-01483-z","volume":"40","author":"S He","year":"2022","unstructured":"He S, Bhatt R, Brown C, Brown EA, Buhr DL, Chantranuvatana K, et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat Biotechnol. 2022;40:1794\u2013806.","journal-title":"Nat Biotechnol"},{"key":"3499_CR125","doi-asserted-by":"publisher","unstructured":"Danaher P, Zhao E, Yang Z, Ross D, Gregory M, Reitz Z, et al. Insitutype: likelihood-based cell typing for single cell spatial transcriptomics. https:\/\/doi.org\/10.1101\/2022.10.19.512902.","DOI":"10.1101\/2022.10.19.512902"},{"key":"3499_CR126","doi-asserted-by":"crossref","unstructured":"Delorey T, Ziegler CG, Heimberg GS, Normand R, Yang Y, Segerstolpe \u00c5, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh K, Dey K, Sen P, Slyper M, Pita-Ju\u00e1rez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov Y, Raju SS, Niezen S, Tsai LT, Siddle K, Sud M, Tran VM, Vellarikkal S, Wang Y, Amir-Zilberstein L, Atri D, Beechem J, Brook O, Chen JH, Divakar P, Dorceus P, Engreitz J, Essene A, Fitzgerald D, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether TD, Jan\u00e9-Valbuena J, Leney-Greene MA, Ma H, McCabe C, McLoughlin D, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe\u2019er C, Pfiffner-Borges J, Pinto C, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert E, Siciliano M, Sturm AP, Todres E, Waghray A, Warren S, Zhang S, Zollinger D, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide WA, Price A, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor P, Hung DT, Sabeti PC, Nov\u00e1k R, Rogers R, Ingber D, Jiang Z, Juric D, Babadi M, Farhi SL, Izar B, Stone J, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani A, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-COV-2 pathology and cellular targets. Gene Expression Omnibus. 2021. Available: https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE171668.","DOI":"10.1038\/s41586-021-03570-8"},{"key":"3499_CR127","unstructured":"Yered Pita-Juarez, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C Melms, Sebastian Niezen, Toni M Delorey, Adam L Essene, Olga R Brook, Deepti Pant, Disha Skelton-Badlani, Pourya Naderi, Pinzhu Huang, Liuliu Pan, Tyler Hether, Tallulah S Andrews, Carly GK Ziegler, Jason Reeves, Andriy Myloserdnyy, Rachel Chen, Andy Nam, Stefan Phelan, Yan Liang, Amit Dipak Amin, Jana Biermann, Hanina Hibshoosh, Molly Veregge, Zachary Kramer, Christopher Jacobs, Yusuf Yalcin, Devan Phillips, Michal Slyper, Ayshwarya Subramanian, Orr Ashenberg, Zohar Bloom-Ackermann, Victoria M Tran, James Gomez, Alexander Sturm, Shuting Zhang, Stephen J Fleming, Sarah Warren, Joseph Beechem, Deborah Hung, Mehrtash Babadi, Robert F Padera Jr, Sonya A MacParland, Gary D Bader, Nasser Imad, Isaac H Solomon, Eric Miller, Stefan Riedel, Caroline BM Porter, Alexandra-Chlo\u00e9 Villani, Linus TY Tsai, Winston Hide, Gyongyi Szabo, Jonathan Hecht, Orit Rozenblatt-Rosen, Alex K Shalek, Benjamin Izar, Aviv Regev, Yury Popov, Z Gordon Jiang, Ioannis S Vlachos. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. In: Zenodo. 2024. Available: https:\/\/zenodo.org\/records\/14541192."},{"key":"3499_CR128","unstructured":"Toni M Delorey, Carly GK Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Asa Segerstolpe, Domenic Abbondanza, Stephen J Fleming, Ayshwarya Subramanian, Daniel T Montoro, Karthik A Jagadeesh, Kushal K Dey, Pritha Sen, Michal Slyper, Yered H Pita-Ju\u00e1rez, Devan Phillips, Zohar Bloom-Ackerman, Nick Barkas, Andrea Ganna, James Gomez, Erica Normandin, Pourya Naderi, Yury V Popov, Siddharth S Raju, Sebastian Niezen, Linus T-Y Tsai, Katherine J Siddle, Malika Sud, Victoria M Tran, Shamsudheen K Vellarikkal, Liat Amir-Zilberstein, Deepak S Atri, Joseph Beechem, Olga R Brook, Jonathan Chen, Prajan Divakar, Phylicia Dorceus, Jesse M Engreitz, Adam Essene, Donna M Fitzgerald, Robin Fropf, Steven Gazal, Joshua Gould, John Grzyb, Tyler Harvey, Jonathan Hecht, Tyler Hether, Judit Jane-Valbuena, Michael Leney-Greene, Hui Ma, Cristin McCabe, Daniel E McLoughlin, Eric M Miller, Christoph Muus, Mari Niemi, Robert Padera, Liuliu Pan, Deepti Pant, Carmel Pe\u2019er, Jenna Pfiffner-Borges, Christopher J Pinto, Jacob Plaisted, Jason Reeves, Marty Ross, Melissa Rudy, Erroll H Rueckert, Michelle Siciliano, Alexander Sturm, Ellen Todres, Avinash Waghray, Sarah Warren, Shuting Zhang, Daniel R Zollinger, Lisa Cosimi, Rajat M Gupta, Nir Hacohen, Winston Hide, Alkes L Price, Jayaraj Rajagopal, Purushothama Rao Tata, Stefan Riedel, Gyongyi Szabo, Timothy L Tickle, Deborah Hung, Pardis C Sabeti, Richard Novak, Robert Rogers, Donald E Ingber, Z Gordon Jiang, Dejan Juric, Mehrtash Babadi, Samouil L Farhi, James R Stone, Ioannis S Vlachos, Isaac H Solomon, Orr Ashenberg, Caroline BM Porter, Bo Li, Alex K Shalek, Alexandra-Chlo\u00e9 Villani, Orit Rozenblatt-Rosen, Aviv Regev. COVID-19 Autopsy Tissue. In: Broad Data Use Oversight System [Internet]. 2021. Available: https:\/\/duos.broadinstitute.org\/dataset\/DUOS-000126."},{"key":"3499_CR129","unstructured":"Yered Pita-Juarez, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C Melms, Sebastian Niezen, Toni M Delorey, Adam L Essene, Olga R Brook, Deepti Pant, Disha Skelton-Badlani, Pourya Naderi, Pinzhu Huang, Liuliu Pan, Tyler Hether, Tallulah S Andrews, Carly GK Ziegler, Jason Reeves, Andriy Myloserdnyy, Rachel Chen, Andy Nam, Stefan Phelan, Yan Liang, Amit Dipak Amin, Jana Biermann, Hanina Hibshoosh, Molly Veregge, Zachary Kramer, Christopher Jacobs, Yusuf Yalcin, Devan Phillips, Michal Slyper, Ayshwarya Subramanian, Orr Ashenberg, Zohar Bloom-Ackermann, Victoria M Tran, James Gomez, Alexander Sturm, Shuting Zhang, Stephen J Fleming, Sarah Warren, Joseph Beechem, Deborah Hung, Mehrtash Babadi, Robert F Padera Jr, Sonya A MacParland, Gary D Bader, Nasser Imad, Isaac H Solomon, Eric Miller, Stefan Riedel, Caroline BM Porter, Alexandra-Chlo\u00e9 Villani, Linus TY Tsai, Winston Hide, Gyongyi Szabo, Jonathan Hecht, Orit Rozenblatt-Rosen, Alex K Shalek, Benjamin Izar, Aviv Regev, Yury Popov, Z Gordon Jiang, Ioannis S Vlachos. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. In: Github. 2024. Available: https:\/\/github.com\/ivlachos\/COVID19-Liver\/."},{"key":"3499_CR130","unstructured":"Yered Pita-Juarez, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C Melms, Sebastian Niezen, Toni M Delorey, Adam L Essene, Olga R Brook, Deepti Pant, Disha Skelton-Badlani, Pourya Naderi, Pinzhu Huang, Liuliu Pan, Tyler Hether, Tallulah S Andrews, Carly GK Ziegler, Jason Reeves, Andriy Myloserdnyy, Rachel Chen, Andy Nam, Stefan Phelan, Yan Liang, Amit Dipak Amin, Jana Biermann, Hanina Hibshoosh, Molly Veregge, Zachary Kramer, Christopher Jacobs, Yusuf Yalcin, Devan Phillips, Michal Slyper, Ayshwarya Subramanian, Orr Ashenberg, Zohar Bloom-Ackermann, Victoria M Tran, James Gomez, Alexander Sturm, Shuting Zhang, Stephen J Fleming, Sarah Warren, Joseph Beechem, Deborah Hung, Mehrtash Babadi, Robert F Padera Jr, Sonya A MacParland, Gary D Bader, Nasser Imad, Isaac H Solomon, Eric Miller, Stefan Riedel, Caroline BM Porter, Alexandra-Chlo\u00e9 Villani, Linus TY Tsai, Winston Hide, Gyongyi Szabo, Jonathan Hecht, Orit Rozenblatt-Rosen, Alex K Shalek, Benjamin Izar, Aviv Regev, Yury Popov, Z Gordon Jiang, Ioannis S Vlachos. Code for A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. In: Zenodo. 2024. Available: https:\/\/zenodo.org\/records\/14547678."}],"container-title":["Genome Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13059-025-03499-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13059-025-03499-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13059-025-03499-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,14]],"date-time":"2025-03-14T07:13:15Z","timestamp":1741936395000},"score":1,"resource":{"primary":{"URL":"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-025-03499-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,14]]},"references-count":130,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["3499"],"URL":"https:\/\/doi.org\/10.1186\/s13059-025-03499-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.10.27.514070","asserted-by":"object"}]},"ISSN":["1474-760X"],"issn-type":[{"value":"1474-760X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,14]]},"assertion":[{"value":"4 July 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 February 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 March 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All sample collection procedures were reviewed by the IRB of the relevant hospital. The related protocols were as follows: Beth Israel Deaconess Medical Center (IRB 2020P000406, 2020P000418), Brigham and Women\u2019s Hospital and Massachusetts General Hospital (2020P000804, 2020P000849, 2015P002215), New York Presbyterian Hospital\/Columbia University Medical Center (IRB-AAAT0785, IRB-AAAB2667, IRB-AAAS7370). All patients had confirmed COVID-19 by PCR testing. Consent for autopsy and research was obtained from the healthcare proxy or the next of kin. Massachusetts Institute of Technology (MIT) IRB protocols 1603505962 and 1612793224, and\/or the not-involving-human-subjects research protocol ORSP-3635, cover all secondary analyses performed at the Broad Institute of MIT and Harvard. No subject recruitment or ascertainment was performed as part of the Broad protocol. Donor identities and accompanying information were encoded at the relevant hospital site prior to shipping to or sharing with the Broad Institute for sample processing or data analysis.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"A.K.S. reports compensation for consulting and\/or SAB membership from Merck, Honeycomb Biotechnologies, Cellarity, Repertoire Immune Medicines, Ochre Bio, Third Rock Ventures, Hovione, Relation Therapeutics, FL82, Senda Biosciences, Empress Therapeutics, IntrECate Biotherapeutics, and Dahlia Biosciences unrelated to this work. A.R. is a founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics and until August 31, 2020 was an SAB member of Syros Pharmaceuticals, Neogene Therapeutics, Asimov and Thermo Fisher Scientific. From August 1, 2020, A.R. is an employee of Genentech, a member of the Roche Group, with equity in Roche. I.S.V. consults for Guidepoint Global, Mosaic, and Chronicle Medical Software. G.S. consults in Alnylam Pharmaceuticals, Merck, Generon, Glympse Bio, Inc., Mayday Foundation, Novartis Pharmaceuticals, Quest Diagnostics, Surrozen, Terra Firma, Zomagen Bioscience, Pandion Therapeutics, Inc., Durect Corporation; royalty from UpToDate Inc. and Editor service for Hepatology Communications. Y.V.P. receives grant support from Enanta Pharmaceuticals, CymaBay Therapeutics, Morphic Therapeutic; consulting and\/or SAB in Ambys Medicines, Morphic Therapeutics, Enveda Therapeutics, BridgeBio Pharma, as well as being an Editor of American Journal of Physiology-Gastrointestinal and Liver Physiology. Z.G.J. receives grant support from Gilead Science, Pfizer and compensation for consulting from Olix Pharmaceuticals. L.P, T.H., S.W, J.B, E.M, and J.R. are employees and\/or stockholders of NanoString Technologies. B.I. has received honoraria from consulting with Merck, Janssen Pharmaceuticals, AstraZeneca, and Volastra Therapeutics. A.R. and O.R.R. are inventors on multiple patents from the Broad Institute related to single-cell and spatial genomics.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"56"}}