{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T04:20:17Z","timestamp":1790914817281,"version":"4.1.0"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T00:00:00Z","timestamp":1770854400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Biotechnology and Biological \u00adSciences Research Council","award":["BB\/G009953\/1"],"award-info":[{"award-number":["BB\/G009953\/1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Alternative splicing (AS) involves production of several different RNA molecules from a single pre-mRNA. Calorie restriction (CR) is a sustained calorie deficit without malnutrition, which extends health and lifespan. AS is dysregulated in aging but less so following CR, suggesting a role for AS in the beneficial effects of CR. To test the hypothesis that AS is involved in the CR response and explore its tissue specificity, male C57BL\/6 mice were exposed to 3 months of graded CR (0\u201340% at 10% increments) and RNA sequencing data from six tissues (epididymal white adipose tissue [eWAT], liver, hypothalamus, gastrocnemius muscle, testes, and stomach) were analyzed to provide a multi-tissue characterization of differential AS (DAS). The number of differentially expressed splicing regulators increased with CR levels in all tissues but primarily the muscle, eWAT, and liver. The total number of DAS genes also increased with increasing CR levels and was largely tissue-specific. Most DAS genes were not differentially expressed. DAS was functionally integrated across tissues with the same processes being overrepresented: namely, mitochondria and oxidative phosphorylation, transcription and translation, and quality checking and degradation of RNA and especially proteins. This study demonstrates that short-term CR evokes a functionally integrated cross-tissue AS response in mice that is largely independent of expression changes.<\/jats:p>","DOI":"10.1093\/lifemeta\/loaf046","type":"journal-article","created":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T12:44:10Z","timestamp":1770813850000},"source":"Crossref","is-referenced-by-count":1,"title":["A functionally integrated cross-tissue alternative splicing program during short-term calorie restriction"],"prefix":"10.1093","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7242-0598","authenticated-orcid":false,"given":"Daniel P","family":"Phillips","sequence":"first","affiliation":[{"name":"School of Biological Sciences, University of Aberdeen , Aberdeen AB24 2TZ, Scotland,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3941-0309","authenticated-orcid":false,"given":"Sharon E","family":"Mitchell","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Aberdeen , Aberdeen AB24 2TZ, Scotland,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9041-4607","authenticated-orcid":false,"given":"Davina","family":"Derous","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Aberdeen , Aberdeen AB24 2TZ, Scotland,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John R","family":"Speakman","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Aberdeen , Aberdeen AB24 2TZ, Scotland,","place":["United Kingdom"]},{"name":"Shenzhen Key Laboratory of Metabolic Health, Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences and Shenzhen University of Advanced Technology , Shenzhen, Guangdong 518055,","place":["China"]},{"name":"State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences , Beijing 100101,","place":["China"]},{"name":"Institute of Health Sciences, China Medical University , Shenyang, Liaoning 110122,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,2,12]]},"reference":[{"key":"2026042520014686100_loaf046-B1","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.2337\/diacare.27.5.1047","article-title":"Global prevalence of diabetes: estimates for the year 2000 and projections for 2030","volume":"27","author":"Wild","year":"2004","journal-title":"Diabetes Care"},{"key":"2026042520014686100_loaf046-B2","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/nature20411","article-title":"Ageing, neurodegeneration and brain rejuvenation","volume":"539","author":"Wyss-Coray","year":"2016","journal-title":"Nature"},{"key":"2026042520014686100_loaf046-B3","doi-asserted-by":"crossref","first-page":"2061","DOI":"10.1113\/JP270538","article-title":"Ageing, metabolism and cardiovascular disease","volume":"594","author":"Costantino","year":"2016","journal-title":"J Physiol"},{"key":"2026042520014686100_loaf046-B4","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1038\/s41416-019-0721-1","article-title":"Cancer as a disease of old age: changing mutational and microenvironmental landscapes","volume":"122","author":"Laconi","year":"2020","journal-title":"Br J Cancer"},{"key":"2026042520014686100_loaf046-B5","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1016\/j.cell.2014.10.039","article-title":"Geroscience: linking aging to chronic disease","volume":"159","author":"Kennedy","year":"2014","journal-title":"Cell"},{"key":"2026042520014686100_loaf046-B6","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.cell.2013.05.039","article-title":"The hallmarks of aging","volume":"153","author":"L\u00f3pez-Ot\u00edn","year":"2013","journal-title":"Cell"},{"key":"2026042520014686100_loaf046-B7","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1007\/s00439-019-02094-6","article-title":"Alternative splicing in aging and longevity","volume":"139","author":"Bhadra","year":"2020","journal-title":"Hum Genet"},{"key":"2026042520014686100_loaf046-B8","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.molcel.2019.09.017","article-title":"Alternative splicing regulatory networks: functions, mechanisms, and evolution","volume":"76","author":"Ule","year":"2019","journal-title":"Mol Cell"},{"key":"2026042520014686100_loaf046-B9","first-page":"21","article-title":"Epigenetic regulation of alternative splicing: how lncRNAs tailor the message","volume":"7","author":"Pisignano","year":"2021","journal-title":"Noncoding RNA"},{"key":"2026042520014686100_loaf046-B10","doi-asserted-by":"crossref","first-page":"e56","DOI":"10.1371\/journal.pgen.0030056","article-title":"Lifespan regulation by evolutionarily conserved genes essential for viability","volume":"3","author":"Curran","year":"2007","journal-title":"PLoS Genet"},{"key":"2026042520014686100_loaf046-B11","doi-asserted-by":"crossref","first-page":"e1000639","DOI":"10.1371\/journal.pgen.1000639","article-title":"A transcription elongation factor that links signals from the reproductive system to lifespan extension in","volume":"5","author":"Ghazi","year":"2009","journal-title":"PLoS Genet"},{"key":"2026042520014686100_loaf046-B12","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1111\/j.1474-9726.2011.00726.x","article-title":"Human aging is characterized by focused changes in gene expression and deregulation of alternative splicing","volume":"10","author":"Harries","year":"2011","journal-title":"Aging Cell"},{"key":"2026042520014686100_loaf046-B13","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1111\/acel.12499","article-title":"Changes in the expression of splicing factor transcripts and variations in alternative splicing are associated with lifespan in mice and humans","volume":"15","author":"Lee","year":"2016","journal-title":"Aging Cell"},{"key":"2026042520014686100_loaf046-B14","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1261\/rna.052795.115","article-title":"The in vivo dynamics of TCERG1, a factor that couples transcriptional elongation with splicing","volume":"22","author":"S\u00e1nchez-Hern\u00e1ndez","year":"2016","journal-title":"RNA"},{"key":"2026042520014686100_loaf046-B15","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/nature20789","article-title":"Splicing factor 1 modulates dietary restriction and TORC1 pathway longevity in","volume":"541","author":"Heintz","year":"2017","journal-title":"Nature"},{"key":"2026042520014686100_loaf046-B16","doi-asserted-by":"crossref","first-page":"e12817","DOI":"10.1111\/acel.12817","article-title":"Proper splicing contributes to visual function in the aging Drosophila eye","volume":"17","author":"Stegeman","year":"2018","journal-title":"Aging Cell"},{"key":"2026042520014686100_loaf046-B17","doi-asserted-by":"crossref","first-page":"e13963","DOI":"10.1111\/acel.13963","article-title":"Calorie restriction modulates the transcription of genes related to stress response and longevity in human muscle: the CALERIE study","volume":"22","author":"Das","year":"2023","journal-title":"Aging Cell"},{"key":"2026042520014686100_loaf046-B18","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/s41392-022-01251-0","article-title":"Aging and aging-related diseases: from molecular mechanisms to interventions and treatments","volume":"7","author":"Guo","year":"2022","journal-title":"Signal Transduct Target Ther"},{"key":"2026042520014686100_loaf046-B19","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.mam.2011.07.001","article-title":"Caloric restriction","volume":"32","author":"Speakman","year":"2011","journal-title":"Mol Aspects Med"},{"key":"2026042520014686100_loaf046-B20","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/s41580-021-00411-4","article-title":"Molecular mechanisms of dietary restriction promoting health and longevity","volume":"23","author":"Green","year":"2022","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2026042520014686100_loaf046-B21","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/s41467-017-00370-5","article-title":"Differential alternative splicing coupled to nonsense-mediated decay of mRNA ensures dietary restriction-induced longevity","volume":"8","author":"Tabrez","year":"2017","journal-title":"Nat Commun"},{"key":"2026042520014686100_loaf046-B22","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.cels.2019.12.002","article-title":"Molecular and functional networks linked to sarcopenia prevention by caloric restriction in rhesus monkeys","volume":"10","author":"Rhoads","year":"2020","journal-title":"Cell Syst"},{"key":"2026042520014686100_loaf046-B23","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1093\/gerona\/glx101","article-title":"The effects of graded levels of calorie restriction: X. Transcriptomic responses of epididymal adipose tissue","volume":"73","author":"Derous","year":"2018","journal-title":"J Gerontol A Biol Sci Med Sci"},{"key":"2026042520014686100_loaf046-B24","doi-asserted-by":"crossref","first-page":"1770","DOI":"10.18632\/aging.101269","article-title":"The effects of graded levels of calorie restriction: XI. Evaluation of the main hypotheses underpinning the life extension effects of CR using the hepatic transcriptome","volume":"9","author":"Derous","year":"2017","journal-title":"Aging (Albany NY)"},{"key":"2026042520014686100_loaf046-B25","doi-asserted-by":"crossref","first-page":"642","DOI":"10.18632\/aging.100895","article-title":"The effects of graded levels of calorie restriction: VI. Impact of short-term graded calorie restriction on transcriptomic responses of the hypothalamic hunger and circadian signaling pathways","volume":"8","author":"Derous","year":"2016","journal-title":"Aging (Albany NY)"},{"key":"2026042520014686100_loaf046-B26","doi-asserted-by":"crossref","first-page":"glae299","DOI":"10.1093\/gerona\/glae299","article-title":"Effects of graded levels of calorie \u00adrestriction XXI: impact of short-term graded restriction on gene expression profiles of stomach and skeletal muscle","volume":"80","author":"Xia","year":"2025","journal-title":"J Gerontol A Biol Sci Med Sci"},{"key":"2026042520014686100_loaf046-B27","doi-asserted-by":"crossref","first-page":"15902","DOI":"10.18632\/oncotarget.4142","article-title":"The effects of graded levels of calorie restriction: I. Impact of short term calorie and \u00adprotein\u00a0restriction on body composition in the C57BL\/6 mouse","volume":"6","author":"Mitchell","year":"2015","journal-title":"Oncotarget"},{"key":"2026042520014686100_loaf046-B28","doi-asserted-by":"crossref","first-page":"14063","DOI":"10.1038\/ncomms14063","article-title":"Caloric restriction improves health and survival of rhesus monkeys","volume":"8","author":"Mattison","year":"2017","journal-title":"Nat Commun"},{"key":"2026042520014686100_loaf046-B29","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1007\/s00394-020-02361-7","article-title":"Effect of 2 years of calorie restriction on liver biomarkers: results from the CALERIE phase 2 randomized controlled trial","volume":"60","author":"Dorling","year":"2021","journal-title":"Eur J Nutr"},{"key":"2026042520014686100_loaf046-B30","doi-asserted-by":"crossref","first-page":"e1643","DOI":"10.1002\/wrna.1643","article-title":"Splicing alterations in healthy aging and disease","volume":"12","author":"Angarola","year":"2021","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2026042520014686100_loaf046-B31","doi-asserted-by":"crossref","first-page":"e13701","DOI":"10.1111\/acel.13701","article-title":"Production of MHCII-\u00adexpressing classical monocytes increases during aging in mice and humans","volume":"21","author":"Barman","year":"2022","journal-title":"Aging Cell"},{"key":"2026042520014686100_loaf046-B32","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1186\/1471-2164-10-585","article-title":"Genes and gene expression modules associated with caloric restriction and aging in the laboratory mouse","volume":"10","author":"Swindell","year":"2009","journal-title":"BMC Genomics"},{"key":"2026042520014686100_loaf046-B33","doi-asserted-by":"crossref","first-page":"3788","DOI":"10.1002\/jcp.30852","article-title":"RBM3 is an outstanding cold shock protein with multiple physiological functions beyond hypothermia","volume":"237","author":"Hu","year":"2022","journal-title":"J Cell Physiol"},{"key":"2026042520014686100_loaf046-B34","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/S0047-6374(96)01803-9","article-title":"A tumor preventive effect of dietary restriction is antagonized by a high housing temperature through deprivation of torpor","volume":"92","author":"Koizumi","year":"1996","journal-title":"Mech Ageing Dev"},{"key":"2026042520014686100_loaf046-B35","doi-asserted-by":"crossref","first-page":"eabb2490","DOI":"10.1126\/scisignal.abb2490","article-title":"Metabolic adaptation to calorie restriction","volume":"13","author":"Guijas","year":"2020","journal-title":"Sci Signal"},{"key":"2026042520014686100_loaf046-B36","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/j.nbd.2011.04.010","article-title":"The RNA-binding protein RBM3 is involved in hypothermia induced neuroprotection","volume":"43","author":"Chip","year":"2011","journal-title":"Neurobiol Dis"},{"key":"2026042520014686100_loaf046-B37","doi-asserted-by":"crossref","first-page":"fcaa078","DOI":"10.1093\/braincomms\/fcaa078","article-title":"Cold stress protein RBM3 responds to hypothermia and is associated with good stroke outcome","volume":"2","author":"\u00c1vila-G\u00f3mez","year":"2020","journal-title":"Brain Commun"},{"key":"2026042520014686100_loaf046-B38","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1080\/15384101.2021.1889187","article-title":"Splicing regulation in brain and testis: common themes for highly specialized organs","volume":"20","author":"Naro","year":"2021","journal-title":"Cell Cycle"},{"key":"2026042520014686100_loaf046-B39","doi-asserted-by":"crossref","first-page":"4873","DOI":"10.1093\/nar\/gkp471","article-title":"Stochastic noise in splicing machinery","volume":"37","author":"Melamud","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2026042520014686100_loaf046-B40","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.1016\/j.cell.2021.04.012","article-title":"Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection","volume":"184","author":"Wan","year":"2021","journal-title":"Cell"},{"key":"2026042520014686100_loaf046-B41","doi-asserted-by":"crossref","first-page":"e201800281","DOI":"10.26508\/lsa.201800281","article-title":"Dietary restriction induces posttranscriptional regulation of longevity genes","volume":"2","author":"Rollins","year":"2019","journal-title":"Life Sci Alliance"},{"key":"2026042520014686100_loaf046-B42","first-page":"182","article-title":"The energy\u2013splicing resilience axis hypothesis of aging","volume":"2","year":"2022","journal-title":"Nat\u00a0Aging"},{"key":"2026042520014686100_loaf046-B43","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/s41388-021-02069-w","article-title":"The emerging roles of G\u03b112\/13 proteins on the hallmarks of cancer in solid tumors","volume":"41","author":"Rasheed","year":"2022","journal-title":"Oncogene"},{"key":"2026042520014686100_loaf046-B44","doi-asserted-by":"crossref","first-page":"169","DOI":"10.3233\/JAD-210068","article-title":"Construction of long noncoding RNA-associated ceRNA networks reveals potential biomarkers in Alzheimer\u2019s disease","volume":"82","author":"Ou","year":"2021","journal-title":"J Alzheimers Dis"},{"key":"2026042520014686100_loaf046-B45","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/s41419-020-03311-1","article-title":"GNA13 regulates BCL2 expression and the sensitivity of GCB-DLBCL cells to BCL2 inhibitors in a palmitoylation-dependent manner","volume":"12","author":"Xia","year":"2021","journal-title":"Cell Death Dis"},{"key":"2026042520014686100_loaf046-B46","doi-asserted-by":"crossref","first-page":"5195","DOI":"10.1113\/JP271957","article-title":"Nuclear factor erythroid-derived 2-like 2 (NFE2L2, Nrf2) mediates exercise-induced mitochondrial biogenesis and the anti-oxidant response in mice","volume":"594","author":"Merry","year":"2016","journal-title":"J Physiol"},{"key":"2026042520014686100_loaf046-B47","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1208\/s12248-022-00679-0","article-title":"Nfe2l2 regulates metabolic rewiring and epigenetic reprogramming in mediating cancer protective effect by fucoxanthin","volume":"24","author":"Wang","year":"2022","journal-title":"AAPS J"},{"key":"2026042520014686100_loaf046-B48","doi-asserted-by":"crossref","first-page":"15197","DOI":"10.3390\/ijms232315197","article-title":"Age-related decline in Nrf2\/ARE signaling is associated with the mitochondrial DNA damage and cognitive impairments","volume":"23","author":"Gureev","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2026042520014686100_loaf046-B49","doi-asserted-by":"crossref","first-page":"4236","DOI":"10.1038\/s41598-019-40974-z","article-title":"G-protein G\u03b113 functions as a cytoskeletal and mitochondrial regulator to restrain osteoclast function","volume":"9","author":"Nakano","year":"2019","journal-title":"Sci Rep"},{"key":"2026042520014686100_loaf046-B50","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.taap.2018.09.014","article-title":"Regulatory crosstalk between the oxidative stress-related transcription factor Nfe2l2\/Nrf2 and mitochondria","volume":"359","author":"Ryoo","year":"2018","journal-title":"Toxicol Appl Pharmacol"},{"key":"2026042520014686100_loaf046-B51","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1111\/cge.13756","article-title":"PDCD6IP, encoding a regulator of the ESCRT complex, is mutated in microcephaly","volume":"98","author":"Khan","year":"2020","journal-title":"Clin Genet"},{"key":"2026042520014686100_loaf046-B52","doi-asserted-by":"crossref","first-page":"e12188","DOI":"10.1002\/jev2.12188","article-title":"29 Linked ubiquitination of Arrdc4 regulates its function in extracellular vesicle biogenesis","volume":"11","author":"Farooq","year":"2022","journal-title":"J Extracell Vesicles"},{"key":"2026042520014686100_loaf046-B53","doi-asserted-by":"crossref","first-page":"e12154","DOI":"10.1002\/jev2.12154","article-title":"Roles of extracellular vesicles in the aging microenvironment and age-related diseases","volume":"10","author":"Yin","year":"2021","journal-title":"J Extracell Vesicles"},{"key":"2026042520014686100_loaf046-B54","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1186\/s12864-017-4002-1","article-title":"Evaluation and comparison of computational tools for RNA-seq isoform quantification","volume":"18","author":"Zhang","year":"2017","journal-title":"BMC Genomics"},{"key":"2026042520014686100_loaf046-B55","doi-asserted-by":"crossref","first-page":"B379","DOI":"10.1093\/gerona\/57.11.B379","article-title":"Survival characteristics and age-adjusted disease incidences in C57BL\/6 mice fed a commonly used cereal-based diet modulated by dietary restriction","volume":"57","author":"Turturro","year":"2002","journal-title":"J Gerontol A Biol Sci Med Sci"},{"key":"2026042520014686100_loaf046-B56","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1007\/s00223-003-0101-x","article-title":"Growth of C57BL\/6 mice and the material and mechanical properties of cortical bone from the tibia","volume":"74","author":"Somerville","year":"2004","journal-title":"Calcif Tissue Int"},{"key":"2026042520014686100_loaf046-B57","doi-asserted-by":"crossref","first-page":"e1091","DOI":"10.7717\/peerj.1091","article-title":"Mice that gorged during dietary restriction increased foraging related behaviors and differed in their macronutrient preference when released from restriction","volume":"3","author":"Hambly","year":"2015","journal-title":"PeerJ"},{"key":"2026042520014686100_loaf046-B58","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.12688\/f1000research.15931.1","article-title":"FastQ screen: a tool for multi-genome mapping and quality control","volume":"7","author":"Wingett","year":"2018","journal-title":"F1000Res"},{"key":"2026042520014686100_loaf046-B59","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize ana\u00adlysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2026042520014686100_loaf046-B60","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J"},{"key":"2026042520014686100_loaf046-B61","article-title":"TrimGalore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files","author":"Krueger","year":"2015","journal-title":"Babraham Bioinformatics"},{"key":"2026042520014686100_loaf046-B62","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat Methods"},{"key":"2026042520014686100_loaf046-B63","doi-asserted-by":"crossref","first-page":"1574","DOI":"10.1080\/15476286.2020.1858253","article-title":"3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists","volume":"18","author":"Guo","year":"2021","journal-title":"RNA Biol"},{"key":"2026042520014686100_loaf046-B64","doi-asserted-by":"crossref","first-page":"1424","DOI":"10.1105\/tpc.18.00177","article-title":"Rapid and dynamic alternative splicing impacts the arabidopsis cold response transcriptome","volume":"30","author":"Calixto","year":"2018","journal-title":"Plant Cell"},{"key":"2026042520014686100_loaf046-B65","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.12688\/f1000research.7563.1","article-title":"Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences","volume":"4","author":"Soneson","year":"2015","journal-title":"F1000Res"},{"key":"2026042520014686100_loaf046-B66","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2014-15-2-r29","article-title":"voom: precision weights unlock linear model analysis tools for RNA-seq read counts","volume":"15","author":"Law","year":"2014","journal-title":"Genome Biology."},{"key":"2026042520014686100_loaf046-B67","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"Limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2026042520014686100_loaf046-B68","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat Commun"},{"key":"2026042520014686100_loaf046-B69","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new \u00adfeatures for data integration and network visualization","volume":"27","author":"Smoot","year":"2011","journal-title":"Bioinformatics"}],"container-title":["Life Metabolism"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/lifemeta\/advance-article-pdf\/doi\/10.1093\/lifemeta\/loaf046\/66865435\/loaf046.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/lifemeta\/article-pdf\/5\/2\/loaf046\/66865435\/loaf046.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/lifemeta\/article-pdf\/5\/2\/loaf046\/66865435\/loaf046.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,26]],"date-time":"2026-04-26T00:02:05Z","timestamp":1777161725000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/lifemeta\/article\/doi\/10.1093\/lifemeta\/loaf046\/8475404"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,12]]},"references-count":69,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,4,24]]}},"URL":"https:\/\/doi.org\/10.1093\/lifemeta\/loaf046","relation":{},"ISSN":["2755-0230"],"issn-type":[{"value":"2755-0230","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,4]]},"published":{"date-parts":[[2026,2,12]]},"article-number":"loaf046"}}