{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T11:20:30Z","timestamp":1792408830192,"version":"4.4.0"},"reference-count":53,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100010786","name":"Genome Atlantic","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010786","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007567","name":"City University of Hong Kong","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007567","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Fish &amp; Shellfish Immunology"],"published-print":{"date-parts":[[2024,6]]},"DOI":"10.1016\/j.fsi.2024.109606","type":"journal-article","created":{"date-parts":[[2024,5,4]],"date-time":"2024-05-04T02:06:29Z","timestamp":1714788389000},"page":"109606","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":9,"special_numbering":"C","title":["A comparative analysis of alternative splicing patterns in Atlantic salmon (Salmo salar) in response to Moritella viscosa and sea lice (Lepeophtheirus salmonis) infection"],"prefix":"10.1016","volume":"149","author":[{"given":"Shengnan","family":"Gao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suxu","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara L.","family":"Purcell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shona K.","family":"Whyte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathleen","family":"Parrish","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shucheng","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-9775-976X","authenticated-orcid":false,"given":"Yuxuan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruoxi","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9563-1707","authenticated-orcid":false,"given":"Ladan","family":"Jahangiri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1563-1844","authenticated-orcid":false,"given":"Runsheng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark D.","family":"Fast","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenlong","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.fsi.2024.109606_bib1","series-title":"Brief","article-title":"The state of world fisheries and aquaculture 2020","year":"2020"},{"issue":"2","key":"10.1016\/j.fsi.2024.109606_bib2","doi-asserted-by":"crossref","first-page":"119","DOI":"10.3354\/dao03337","article-title":"Atlantic salmon challenged with extracellular products from Moritella viscosa","volume":"133","author":"MacKinnon","year":"2019","journal-title":"Dis. Aquat. Org."},{"key":"10.1016\/j.fsi.2024.109606_bib3","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.micpath.2014.09.014","article-title":"Host specificity and clade dependent distribution of putative virulence genes in Moritella viscosa","volume":"77","author":"Karlsen","year":"2014","journal-title":"Microb. Pathog."},{"issue":"2","key":"10.1016\/j.fsi.2024.109606_bib4","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/j.dci.2013.08.019","article-title":"Fish immune responses to parasitic copepod (namely sea lice) infection","volume":"43","author":"Fast","year":"2014","journal-title":"Dev. Comp. Immunol."},{"issue":"4","key":"10.1016\/j.fsi.2024.109606_bib5","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1111\/jfd.13144","article-title":"Impact of co-infection with Lepeophtheirus salmonis and Moritella viscosa on inflammatory and immune responses of Atlantic salmon (Salmo salar)","volume":"43","author":"Carvalho","year":"2020","journal-title":"J. Fish. Dis."},{"issue":"2","key":"10.1016\/j.fsi.2024.109606_bib6","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/j.dci.2013.08.019","article-title":"Fish immune responses to parasitic copepod (namely sea lice) infection","volume":"43","author":"Fast","year":"2014","journal-title":"Dev. Comp. Immunol."},{"key":"10.1016\/j.fsi.2024.109606_bib7","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquaculture.2023.739531","article-title":"Moritella viscosa early infection and transcriptional responses of intraperitoneal vaccinated and unvaccinated Atlantic salmon","volume":"572","author":"Karlsen","year":"2023","journal-title":"Aquaculture"},{"issue":"10","key":"10.1016\/j.fsi.2024.109606_bib8","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/j.pt.2006.08.006","article-title":"Ecology of sea lice parasitic on farmed and wild fish","volume":"22","author":"Costello","year":"2006","journal-title":"Trends Parasitol."},{"issue":"1","key":"10.1016\/j.fsi.2024.109606_bib9","doi-asserted-by":"crossref","first-page":"4622","DOI":"10.1038\/s41598-022-08341-7","article-title":"Global gene expression responses of Atlantic salmon skin to Moritella viscosa","volume":"12","author":"Eslamloo","year":"2022","journal-title":"Sci. Rep."},{"issue":"2","key":"10.1016\/j.fsi.2024.109606_bib10","doi-asserted-by":"crossref","first-page":"470","DOI":"10.3390\/vaccines11020470","article-title":"Bacterial pathogenesis in various fish diseases: recent advances and specific challenges in vaccine development","volume":"11","author":"Irshath","year":"2023","journal-title":"Vaccines"},{"key":"10.1016\/j.fsi.2024.109606_bib11","doi-asserted-by":"crossref","first-page":"287","DOI":"10.3389\/fgene.2018.00287","article-title":"Gene expression response to sea lice in atlantic salmon skin: RNA sequencing comparison between resistant and susceptible animals","volume":"9","author":"Robledo","year":"2018","journal-title":"Front. Genet."},{"issue":"6","key":"10.1016\/j.fsi.2024.109606_bib12","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.micpath.2011.02.001","article-title":"Putative virulence genes in Moritella viscosa: activity during in vitro inoculation and in vivo infection","volume":"50","author":"Tunsjo","year":"2011","journal-title":"Microb. Pathog."},{"issue":"7","key":"10.1016\/j.fsi.2024.109606_bib13","doi-asserted-by":"crossref","DOI":"10.3390\/ijms21072417","article-title":"Transcriptomic profiling in fins of atlantic salmon parasitized with sea lice: evidence for an early imbalance between chalimus-induced immunomodulation and the host's defense response","volume":"21","author":"Umasuthan","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.fsi.2024.109606_bib14","article-title":"Transcriptome analysis of atlantic salmon (Salmo salar) skin in response to sea lice and infectious salmon anemia virus Co-infection under different experimental functional diets","volume":"12","author":"Cai","year":"2021","journal-title":"Front. Immunol."},{"issue":"7","key":"10.1016\/j.fsi.2024.109606_bib15","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/nrm.2017.27","article-title":"Alternative splicing as a regulator of development and tissue identity","volume":"18","author":"Baralle","year":"2017","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.fsi.2024.109606_bib16","series-title":"Cambridge, United Kingdom","article-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews","year":"2010"},{"issue":"15","key":"10.1016\/j.fsi.2024.109606_bib17","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.fsi.2024.109606_bib18","series-title":"BMJ Specialist Journals","article-title":"222-K Integrated immunoprofiling and RNA sequencing (RNA-seq) for anti-PD-1 response prediction in head and neck squamous cell carcinomas (HNSCC)","author":"Nikitina","year":"2023"},{"issue":"49","key":"10.1016\/j.fsi.2024.109606_bib19","doi-asserted-by":"crossref","first-page":"107993","DOI":"10.1007\/s11356-023-29981-w","article-title":"Comparative transcriptome profiling reveals RNA splicing alterations and biological function in patients exposed to occupational noise","volume":"30","author":"Chen","year":"2023","journal-title":"Environ. Sci. Pollut. Control Ser."},{"issue":"1","key":"10.1016\/j.fsi.2024.109606_bib20","article-title":"The landscape of isoform switches in sepsis: a multicenter cohort study","volume":"12","author":"Chen","year":"2022","journal-title":"Sci. Rep."},{"key":"10.1016\/j.fsi.2024.109606_bib21","series-title":"An Improved Heatmap Package","author":"Zhao","year":"2021"},{"key":"10.1016\/j.fsi.2024.109606_bib22","series-title":"Circlize\" Implements and Enhances Circular Visualization in R","author":"Gu","year":"2014"},{"key":"10.1016\/j.fsi.2024.109606_bib23","series-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Villanueva","year":"2019"},{"issue":"3","key":"10.1016\/j.fsi.2024.109606_bib24","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"issue":"16. 1","key":"10.1016\/j.fsi.2024.109606_bib25","article-title":"AnnotationHub: client to access AnnotationHub resources","volume":"2","author":"Morgan","year":"2019","journal-title":"R Package Version"},{"issue":"6","key":"10.1016\/j.fsi.2024.109606_bib53","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1089\/152791600459894","article-title":"Primer premier 5","volume":"1","author":"Lalitha","year":"2000","journal-title":"Biotech Softw. Internet Rep.: Comput. Softw. J. Scient."},{"key":"10.1016\/j.fsi.2024.109606_bib26","article-title":"Cellular responses to HSV-1 infection are linked to specific types of alterations in the host transcriptome","volume":"6","author":"Hu","year":"2016","journal-title":"Sci. Rep."},{"issue":"12","key":"10.1016\/j.fsi.2024.109606_bib27","doi-asserted-by":"crossref","DOI":"10.3390\/v13122409","article-title":"Genome-wide analysis of alternative splicing during host-virus interactions in chicken","volume":"13","author":"Liu","year":"2021","journal-title":"Viruses"},{"issue":"6","key":"10.1016\/j.fsi.2024.109606_bib28","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1007\/s10126-018-9844-2","article-title":"Increased alternative splicing as a host response to edwardsiella ictaluri infection in catfish","volume":"20","author":"Tan","year":"2018","journal-title":"Mar. Biotechnol."},{"key":"10.1016\/j.fsi.2024.109606_bib29","article-title":"Roles of alternative splicing in infectious diseases: from hosts, pathogens to their interactions","author":"Lyu","year":"2023","journal-title":"Chin. Med. J."},{"issue":"7","key":"10.1016\/j.fsi.2024.109606_bib30","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1007\/s00424-018-2136-x","article-title":"Alternative splicing isoforms in health and disease","volume":"470","author":"Kim","year":"2018","journal-title":"Pfl\u00fcgers Archiv"},{"issue":"6","key":"10.1016\/j.fsi.2024.109606_bib31","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1007\/s00438-010-0538-3","article-title":"Alternative splicing in teleost fish genomes: same-species and cross-species analysis and comparisons","volume":"283","author":"Lu","year":"2010","journal-title":"Mol. Genet. Genom."},{"key":"10.1016\/j.fsi.2024.109606_bib32","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.ijbiomac.2020.03.178","article-title":"Alternative splicing (AS) mechanism plays important roles in response to different salinity environments in spotted sea bass","volume":"155","author":"Tian","year":"2020","journal-title":"Int. J. Biol. Macromol."},{"issue":"1","key":"10.1016\/j.fsi.2024.109606_bib33","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s10126-021-10082-z","article-title":"RNA-Seq analysis reveals alternative splicing under heat stress in rainbow trout (Oncorhynchus mykiss)","volume":"24","author":"Sun","year":"2022","journal-title":"Mar. Biotechnol."},{"key":"10.1016\/j.fsi.2024.109606_bib34","first-page":"11.16.11","article-title":"Alternative splicing signatures in RNA-seq data: percent spliced in (PSI)","volume":"87","author":"Schafer","year":"2015","journal-title":"Curr Protoc Hum Genet"},{"issue":"25","key":"10.1016\/j.fsi.2024.109606_bib35","doi-asserted-by":"crossref","first-page":"17334","DOI":"10.18632\/oncotarget.24671","article-title":"Full in-frame exon 3 skipping of BRCA2 confers high risk of breast andor ovarian cancer","volume":"9","author":"Caputo","year":"2018","journal-title":"Oncotarget"},{"issue":"4","key":"10.1016\/j.fsi.2024.109606_bib36","article-title":"Abnormal global alternative RNA splicing in COVID-19 patients","volume":"18","author":"Myers","year":"2022","journal-title":"PLoS Genet."},{"issue":"s2","key":"10.1016\/j.fsi.2024.109606_bib37","doi-asserted-by":"crossref","first-page":"S343","DOI":"10.3233\/JND-210682","article-title":"Exon-skipping in Duchenne muscular dystrophy","volume":"8","author":"Takeda","year":"2021","journal-title":"J. Neuromuscul. Dis."},{"issue":"1","key":"10.1016\/j.fsi.2024.109606_bib38","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/S0959-440X(00)00167-6","article-title":"Zinc finger proteins new insights into structural and functional diversity","volume":"11","author":"Laity","year":"2001","journal-title":"Curr. Opin. Struct. Biol."},{"issue":"1","key":"10.1016\/j.fsi.2024.109606_bib39","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a004978","article-title":"The collagen family","volume":"3","author":"Ricard-Blum","year":"2011","journal-title":"Cold Spring Harbor Perspect. Biol."},{"issue":"3","key":"10.1016\/j.fsi.2024.109606_bib40","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1007\/s10126-022-10133-z","article-title":"Tissue-specific analysis of alternative splicing events and differential isoform expression in large yellow croaker (larimichthys crocea) after cryptocaryon irritans infection","volume":"24","author":"Qu","year":"2022","journal-title":"Mar. Biotechnol."},{"key":"10.1016\/j.fsi.2024.109606_bib41","article-title":"STAT5b: a master regulator of key biological pathways","volume":"13","author":"Smith","year":"2022","journal-title":"Front. Immunol."},{"issue":"10","key":"10.1016\/j.fsi.2024.109606_bib42","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.2217\/fon.09.125","article-title":"Muc4\/MUC4 functions and regulation in cancer","volume":"5","author":"Carraway","year":"2009","journal-title":"Future Oncol."},{"issue":"2","key":"10.1016\/j.fsi.2024.109606_bib43","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1084\/jem.20150435","article-title":"Btn2a2, a T cell immunomodulatory molecule coregulated with MHC class II genes","volume":"213","author":"Sarter","year":"2016","journal-title":"J. Exp. Med."},{"issue":"39","key":"10.1016\/j.fsi.2024.109606_bib44","doi-asserted-by":"crossref","first-page":"63215","DOI":"10.18632\/oncotarget.11438","article-title":"FAM65B controls the proliferation of transformed and primary T cells","volume":"7","author":"Froehlich","year":"2016","journal-title":"Oncotarget"},{"issue":"5","key":"10.1016\/j.fsi.2024.109606_bib45","first-page":"992","article-title":"Front-signal-dependent accumulation of the RHOA inhibitor FAM65B at leading edges polarizes neutrophils","volume":"128","author":"Gao","year":"2015","journal-title":"J. Cell Sci."},{"key":"10.1016\/j.fsi.2024.109606_bib46","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.clim.2018.10.017","article-title":"CD84 cell surface signaling molecule: an emerging biomarker and target for cancer and autoimmune disorders","volume":"204","author":"Cuenca","year":"2019","journal-title":"Clin Immunol"},{"key":"10.1016\/j.fsi.2024.109606_bib47","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.654960","article-title":"Roles of BTLA in immunity and immune disorders","volume":"12","author":"Ning","year":"2021","journal-title":"Front. Immunol."},{"issue":"4","key":"10.1016\/j.fsi.2024.109606_bib48","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1042\/BST20160077","article-title":"The role of Trim25 in development, disease and RNA metabolism","volume":"44","author":"Heikel","year":"2016","journal-title":"Biochem. Soc. Trans."},{"issue":"2","key":"10.1016\/j.fsi.2024.109606_bib49","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1016\/j.cyto.2014.11.018","article-title":"IL12Rbeta1: the cytokine receptor that we used to know","volume":"71","author":"Robinson","year":"2015","journal-title":"Cytokine"},{"key":"10.1016\/j.fsi.2024.109606_bib50","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.3389\/fimmu.2020.01464","article-title":"An unusual MHC molecule generates protective CD8+ T cell responses to chronic infection","volume":"11","author":"Tsitsiklis","year":"2020","journal-title":"Front. Immunol."},{"key":"10.1016\/j.fsi.2024.109606_bib51","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1111\/j.1600-065X.2008.00624.x","article-title":"IL-1, IL-18, and IL-33 families of cytokines","volume":"223","author":"Arend","year":"2008","journal-title":"Immunol. Rev."},{"issue":"5","key":"10.1016\/j.fsi.2024.109606_bib52","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1016\/j.immuni.2016.04.019","article-title":"The TNF receptor superfamily in Co-stimulating and Co-inhibitory responses","volume":"44","author":"Ward-Kavanagh","year":"2016","journal-title":"Immunity"}],"container-title":["Fish &amp; Shellfish Immunology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1050464824002511?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1050464824002511?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,6,2]],"date-time":"2024-06-02T05:22:56Z","timestamp":1717305776000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1050464824002511"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6]]},"references-count":53,"alternative-id":["S1050464824002511"],"URL":"https:\/\/doi.org\/10.1016\/j.fsi.2024.109606","relation":{},"ISSN":["1050-4648"],"issn-type":[{"value":"1050-4648","type":"print"}],"subject":[],"published":{"date-parts":[[2024,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A comparative analysis of alternative splicing patterns in Atlantic salmon (Salmo salar) in response to Moritella viscosa and sea lice (Lepeophtheirus salmonis) infection","name":"articletitle","label":"Article Title"},{"value":"Fish & Shellfish Immunology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.fsi.2024.109606","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"109606"}}