Ackermann M, Verleden SE, Kuehnel M, Haverich A, Welte T, Laenger F, Vanstapel A, Werlein C, Stark H, Tzankov A et al (2020) Pulmonary vascular endothelialitis, thrombosis, and angiogenesis in COVID-19. N Engl J Med 383:120–128
CAS PubMed PubMed Central Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29
CAS PubMed PubMed Central Google Scholar
Bates TA, Leier HC, Lyski ZL, McBride SK, Coulter FJ, Weinstein JB, Goodman JR, Lu Z, Siegel SAR, Sullivan P et al (2021) Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum. Nat Commun 12:5135
CAS PubMed PubMed Central Google Scholar
Bian X-W, Team tC-P (2020) Autopsy of COVID-19 victims in China. Natl Sci Rev 7:1414–1418
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z, Galon J (2009) ClueGO: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091–1093
CAS PubMed PubMed Central Google Scholar
Boehm E, Kronig I, Neher RA, Eckerle I, Vetter P, Kaiser L, Centre G, and Geneva Centre for Emerging Viral D (2021) Novel SARS-CoV-2 variants: the pandemics within the pandemic. Clin Microbiol Infect 27:1109–1117
CAS PubMed PubMed Central Google Scholar
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
CAS PubMed PubMed Central Google Scholar
Cai Y, Zhang J, Xiao T, Lavine CL, Rawson S, Peng H, Zhu H, Anand K, Tong P, Gautam A et al (2021) Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants. Science 373:642–648
Cantuti-Castelvetri L, Ojha R, Pedro LD, Djannatian M, Franz J, Kuivanen S, van der Meer F, Kallio K, Kaya T, Anastasina M et al (2020) Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science 370:856–860
CAS PubMed PubMed Central Google Scholar
Cao X (2021) ISG15 secretion exacerbates inflammation in SARS-CoV-2 infection. Nat Immunol 22:1360–1362
Chapin JC, Hajjar KA (2015) Fibrinolysis and the control of blood coagulation. Blood Rev 29:17–24
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R (2020) TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 13:1194–1202
Chen L, Marishta A, Ellison CE, Verzi MP (2021) Identification of transcription factors regulating SARS-CoV-2 entry genes in the intestine. Cell Mol Gastroenterol Hepatol 11:181–184
Conway JR, Lex A, Gehlenborg N (2017) UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 33:2938–2940
CAS PubMed PubMed Central Google Scholar
da Huang W, Sherman BT, Lempicki RA (2009a) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37:1–13
da Huang W, Sherman BT, Lempicki RA (2009b) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57
Daly JL, Simonetti B, Klein K, Chen KE, Williamson MK, Anton-Plagaro C, Shoemark DK, Simon-Gracia L, Bauer M, Hollandi R et al (2020) Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science 370:861–865
Davies J, Randeva HS, Chatha K, Hall M, Spandidos DA, Karteris E, Kyrou I (2020) Neuropilin1 as a new potential SARS-CoV-2 infection mediator implicated in the neurologic features and central nervous system involvement of COVID19. Mol Med Rep 22:4221–4226
CAS PubMed PubMed Central Google Scholar
Demidenko E (2018) The next-generation K-means algorithm. Stat Anal Data Min 11:153–166
PubMed PubMed Central Google Scholar
Deng W, Bao L, Liu J, Xiao C, Liu J, Xue J, Lv Q, Qi F, Gao H, Yu P et al (2020) Primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques. Science 369:818–823
Dey J, Alam MT, Chandra S, Gupta J, Ray U, Srivastava AK, Tripathi PP (2021) Neuroinvasion of SARS-CoV-2 may play a role in the breakdown of the respiratory center of the brain. J Med Virol 93:1296–1303
Fainardi V, Longo F, Chetta A, Esposito S, Pisi G (2020) SARS-CoV-2 infection in patients with cystic fibrosis. An overview. Acta Biomed 91:e2020035
CAS PubMed PubMed Central Google Scholar
Gao Q, Bao L, Mao H, Wang L, Xu K, Yang M, Li Y, Zhu L, Wang N, Lv Z et al (2020) Development of an inactivated vaccine candidate for SARS-CoV-2. Science 369:77–81
Garcia-Beltran WF, Lam EC, St Denis K, Nitido AD, Garcia ZH, Hauser BM, Feldman J, Pavlovic MN, Gregory DJ, Poznansky MC et al (2021) Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 184:2372–2383
CAS PubMed PubMed Central Google Scholar
Giordo R, Paliogiannis P, Mangoni AA, Pintus G (2021) SARS-CoV-2 and endothelial cell interaction in COVID-19: molecular perspectives. Vasc Biol 3:R15–R23
CAS PubMed PubMed Central Google Scholar
Gudowska-Sawczuk M, Mroczko B (2021) The role of Neuropilin-1 (NRP-1) in SARS-CoV-2 infection: review. J Clin Med 10:2772
CAS PubMed PubMed Central Google Scholar
Gupta A, Madhavan MV, Sehgal K, Nair N, Mahajan S, Sehrawat TS, Bikdeli B, Ahluwalia N, Ausiello JC, Wan EY et al (2020) Extrapulmonary manifestations of COVID-19. Nat Med 26:1017–1032
Han H, Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E et al (2018) TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic Acids Res 46:D380–D386
Han H, Yang L, Liu R, Liu F, Wu KL, Li J, Liu XH, Zhu CL (2020a) Prominent changes in blood coagulation of patients with SARS-CoV-2 infection. Clin Chem Lab Med 58:1116–1120
Han X, Zhou Z, Fei L, Sun H, Wang R, Chen Y, Chen H, Wang J, Tang H, Ge W et al (2020b) Construction of a human cell landscape at single-cell level. Nature 581:303–309
Harrison AG, Lin T, Wang P (2020) Mechanisms of SARS-CoV-2 transmission and pathogenesis. Trends Immunol 41:1100–1115
CAS PubMed PubMed Central Google Scholar
Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A, Consortium C-GU et al (2021) SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol 19:409–424
CAS PubMed PubMed Central Google Scholar
Karim SSA, Karim QA (2021) Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic. Lancet 398:2126–2128
CAS PubMed PubMed Central Google Scholar
Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S et al (2014) A draft map of the human proteome. Nature 509:575–581
CAS PubMed PubMed Central Google Scholar
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360
CAS PubMed PubMed Central Google Scholar
Koyuncu OO, Hogue IB, Enquist LW (2013) Virus infections in the nervous system. Cell Host Microbe 13:379–393
CAS PubMed PubMed Central Google Scholar
Kudose S, Batal I, Santoriello D, Xu K, Barasch J, Peleg Y, Canetta P, Ratner LE, Marasa M, Gharavi AG et al (2020) Kidney biopsy findings in patients with COVID-19. J Am Soc Nephrol 31:1959–1968
CAS PubMed PubMed Central Google Scholar
Lamers MM, Beumer J, van der Vaart J, Knoops K, Puschhof J, Breugem TI, Ravelli RBG, Paul van Schayck J, Mykytyn AZ, Duimel HQ et al (2020) SARS-CoV-2 productively infects human gut enterocytes. Science 369:50–54
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079
Li MY, Li L, Zhang Y, Wang XS (2020) Expression of the SARS-CoV-2 cell receptor gene ACE2 in a wide variety of human tissues. Infect Dis Poverty 9:45
PubMed PubMed Central Google Scholar
Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet J 17:10–12
Mistry P, Barmania F, Mellet J, Peta K, Strydom A, Viljoen IM, James W, Gordon S, Pepper MS (2021) SARS-CoV-2 variants, vaccines, and host immunity. Front Immunol 12:809244
Mostafavi S, Yoshida H, Moodley D, LeBoite H, Rothamel K, Raj T, Ye CJ, Chevrier N, Zhang SY, Feng T et al (2016) Parsing the interferon transcriptional network and its disease associations. Cell 164:564–578
CAS PubMed PubMed Central Google Scholar
Muszbek L, Bereczky Z, Bagoly Z, Komaromi I, Katona E (2011) Factor XIII: a coagulation factor with multiple plasmatic and cellular functions. Physiol Rev 91:931–972
留言 (0)