{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T08:33:38Z","timestamp":1777710818924,"version":"3.51.4"},"reference-count":51,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100002383","name":"King Saud University","doi-asserted-by":"publisher","award":["RSPD2025R966"],"award-info":[{"award-number":["RSPD2025R966"]}],"id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Brain Research"],"published-print":{"date-parts":[[2025,10]]},"DOI":"10.1016\/j.brainres.2025.149825","type":"journal-article","created":{"date-parts":[[2025,7,8]],"date-time":"2025-07-08T11:47:59Z","timestamp":1751975279000},"page":"149825","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Investigation of molecular patterns present in RIPK1 and systemic approach to determine its differential expression in various brain parts"],"prefix":"10.1016","volume":"1864","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9961-3127","authenticated-orcid":false,"given":"Rekha","family":"Khandia","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pankaj","family":"Gurjar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5955-3783","authenticated-orcid":false,"given":"Azmat Ali","family":"Khan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Trisha","family":"Gaur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabiha","family":"Fatima","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.brainres.2025.149825_b0005","doi-asserted-by":"crossref","first-page":"905","DOI":"10.31083\/j.jin2004092","article-title":"Leucine encoding codon TTG shows an inverse relationship with GC content in genes involved in neurodegeneration with iron accumulation","volume":"20","author":"Alqahtani","year":"2021","journal-title":"J. Integr. Neurosci."},{"key":"10.1016\/j.brainres.2025.149825_b0010","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1038\/mt.2012.29","article-title":"UU\/UA dinucleotide frequency reduction in coding regions results in increased mRNA stability and protein expression","volume":"20","author":"Al-Saif","year":"2012","journal-title":"Mol. Ther."},{"key":"10.1016\/j.brainres.2025.149825_b0015","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1002\/jcb.20726","article-title":"Purification and characterization of a novel mammalian endoribonuclease","volume":"98","author":"Bergstrom","year":"2006","journal-title":"J. Cell. Biochem."},{"key":"10.1016\/j.brainres.2025.149825_b0020","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1073\/pnas.86.1.192","article-title":"Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage","volume":"86","author":"Beutler","year":"1989","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.brainres.2025.149825_b0025","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/S1471-4914(02)02424-3","article-title":"Translational control of gene expression and disease","volume":"8","author":"Calkhoven","year":"2002","journal-title":"Trends Mol. Med."},{"key":"10.1016\/j.brainres.2025.149825_b0030","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1534\/genetics.112.143677","article-title":"The relation of codon bias to tissue-specific gene expression in Arabidopsis thaliana","volume":"192","author":"Camiolo","year":"2012","journal-title":"Genetics"},{"key":"10.1016\/j.brainres.2025.149825_b0035","doi-asserted-by":"crossref","first-page":"2439","DOI":"10.1093\/gbe\/evz146","article-title":"The critical role of codon composition on the translation efficiency robustness of the hepatitis a virus capsid","volume":"11","author":"D\u2019Andrea","year":"2019","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.brainres.2025.149825_b0040","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1007\/s00705-020-04890-2","article-title":"Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae","volume":"166","author":"Deb","year":"2021","journal-title":"Arch. Virol"},{"key":"10.1016\/j.brainres.2025.149825_b0045","doi-asserted-by":"crossref","first-page":"e02381","DOI":"10.1128\/JVI.02381-16","article-title":"Dinucleotide composition in Animal RNA viruses is shaped more by virus family than by host species","volume":"91","author":"Di Giallonardo","year":"2017","journal-title":"J. Virol."},{"key":"10.1016\/j.brainres.2025.149825_b0050","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2018.02948","article-title":"The GC content as a main factor shaping the amino acid usage during bacterial evolution process","volume":"9","author":"Du","year":"2018","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.brainres.2025.149825_b0055","doi-asserted-by":"crossref","first-page":"339","DOI":"10.2174\/0929866526666190228144219","article-title":"Applicability of instability index for in vitro protein stability prediction","volume":"26","author":"Gamage","year":"2019","journal-title":"Protein Pept. Lett."},{"key":"10.1016\/j.brainres.2025.149825_b0060","doi-asserted-by":"crossref","unstructured":"Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., Bairoch, A., 2005. Protein Identification and Analysis Tools on the ExPASy Server, in: Walker, J.M. (Ed.), The Proteomics Protocols Handbook, Springer Protocols Handbooks. Humana Press, Totowa, NJ, pp. 571\u2013607. doi: 10.1385\/1-59259-890-0:571.","DOI":"10.1385\/1-59259-890-0:571"},{"key":"10.1016\/j.brainres.2025.149825_b0065","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/0006-2952(96)00046-9","article-title":"Tissue-specific developmental regulation of protein kinase C isoforms","volume":"51","author":"Goldberg","year":"1996","journal-title":"Biochem. Pharmacol."},{"key":"10.1016\/j.brainres.2025.149825_b0070","doi-asserted-by":"crossref","DOI":"10.1016\/j.meegid.2021.105165","article-title":"The dinucleotide composition of sugarcane mosaic virus is shaped more by protein coding regions than by host species","volume":"97","author":"He","year":"2022","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.brainres.2025.149825_b0075","doi-asserted-by":"crossref","DOI":"10.1099\/mic.0.001404","article-title":"Mutation bias and adaptation in bacteria","volume":"169","author":"Horton","year":"2023","journal-title":"Microbiology (Reading)"},{"key":"10.1016\/j.brainres.2025.149825_b0080","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1126\/science.aaf6803","article-title":"RIPK1 mediates axonal degeneration by promoting inflammation and necroptosis in ALS","volume":"353","author":"Ito","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.brainres.2025.149825_b0085","doi-asserted-by":"crossref","first-page":"3369","DOI":"10.1016\/j.jmb.2020.01.011","article-title":"TissueCoCoPUTs: novel human tissue-specific codon and codon-pair usage tablesbased on differential tissue gene expression","volume":"432","author":"Kames","year":"2020","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.brainres.2025.149825_b0090","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/S0168-9525(00)89076-9","article-title":"Dinucleotide relative abundance extremes: a genomic signature","volume":"11","author":"Karlin","year":"1995","journal-title":"Trends Genet."},{"key":"10.1016\/j.brainres.2025.149825_b0095","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.3390\/biomedicines9081001","article-title":"Genes common in primary immunodeficiencies and cancer display overrepresentation of codon CTG and dominant role of selection pressure in shaping codon usage","volume":"9","author":"Khandia","year":"2021","journal-title":"Biomedicines"},{"key":"10.1016\/j.brainres.2025.149825_b0100","doi-asserted-by":"crossref","first-page":"325","DOI":"10.3390\/pathogens12020325","article-title":"Insights into synonymous codon usage bias in hepatitis C virus and its adaptation to hosts","volume":"12","author":"Khandia","year":"2023","journal-title":"Pathogens"},{"key":"10.1016\/j.brainres.2025.149825_b0105","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1097\/MS9.0000000000001725","article-title":"Molecular insights into codon usage analysis of mitochondrial fission and fusion gene: relevance to neurodegenerative diseases","volume":"86","author":"Khandia","year":"2024","journal-title":"Ann. Med. Surg. (Lond)"},{"key":"10.1016\/j.brainres.2025.149825_b0110","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1074\/jbc.RA118.006433","article-title":"Tissue-specific kinase expression and activity regulate flux through the pyruvate dehydrogenase complex","volume":"294","author":"Klyuyeva","year":"2019","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.brainres.2025.149825_b0115","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1038\/nbt0596-610","article-title":"Retroviral transfer and expression of a humanized, red-shifted green fluorescent protein gene into human tumor cells","volume":"14","author":"Levy","year":"1996","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.brainres.2025.149825_b0120","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/s12863-022-01089-z","article-title":"An investigation of codon usage pattern analysis in pancreatitis associated genes","volume":"23","author":"Li","year":"2022","journal-title":"BMC Genom Data"},{"key":"10.1016\/j.brainres.2025.149825_b0125","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/s41573-020-0071-y","article-title":"Receptor-interacting protein kinase 1 (RIPK1) as a therapeutic target","volume":"19","author":"Mifflin","year":"2020","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/j.brainres.2025.149825_b0130","doi-asserted-by":"crossref","DOI":"10.1016\/j.meegid.2020.104399","article-title":"Mycobacterium lepromatosis genome exhibits unusually high CpG dinucleotide content and selection is key force in shaping codon usage","volume":"84","author":"Munjal","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.brainres.2025.149825_b0135","doi-asserted-by":"crossref","first-page":"107","DOI":"10.4103\/0973-7847.120508","article-title":"Natural proteins: sources, isolation, characterization and applications","volume":"7","author":"Nehete","year":"2013","journal-title":"Pharmacogn. Rev."},{"key":"10.1016\/j.brainres.2025.149825_b0140","doi-asserted-by":"crossref","first-page":"8196","DOI":"10.1021\/acs.jpca.1c05604","article-title":"Kinetic study of transition mutations from G-C to A-T base pairs in Watson-Crick DNA base pairs: double proton transfers","volume":"125","author":"Odai","year":"2021","journal-title":"J. Phys. Chem. A"},{"key":"10.1016\/j.brainres.2025.149825_b0145","doi-asserted-by":"crossref","first-page":"E8788","DOI":"10.1073\/pnas.1714175114","article-title":"RIPK1 mediates a disease-associated microglial response in Alzheimer\u2019s disease","volume":"114","author":"Ofengeim","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.brainres.2025.149825_b0150","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1007\/s11033-021-06749-4","article-title":"Codon usage bias","volume":"49","author":"Parvathy","year":"2022","journal-title":"Mol. Biol. Rep."},{"key":"10.1016\/j.brainres.2025.149825_b0155","doi-asserted-by":"crossref","first-page":"12588","DOI":"10.1073\/pnas.0404957101","article-title":"Tissue-specific codon usage and the expression of human genes","volume":"101","author":"Plotkin","year":"2004","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.brainres.2025.149825_b0160","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1745-6150-3-38","article-title":"CAIcal: a combined set of tools to assess codon usage adaptation","volume":"3","author":"Puigb\u00f2","year":"2008","journal-title":"Biol. Direct"},{"key":"10.1016\/j.brainres.2025.149825_b0165","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.molcel.2015.05.035","article-title":"Codon bias as a means to fine-tune gene expression","volume":"59","author":"Quax","year":"2015","journal-title":"Mol. Cell"},{"key":"10.1016\/j.brainres.2025.149825_b0170","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/1471-2105-6-59","article-title":"Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein","volume":"6","author":"Raghava","year":"2005","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.brainres.2025.149825_b0175","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1093\/nar\/15.3.1281","article-title":"The codon Adaptation Index\u2013a measure of directional synonymous codon usage bias, and its potential applications","volume":"15","author":"Sharp","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.brainres.2025.149825_b0180","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1093\/oxfordjournals.molbev.a026257","article-title":"Nucleotide bias causes a genomewide bias in the amino acid composition of proteins","volume":"17","author":"Singer","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.brainres.2025.149825_b0185","doi-asserted-by":"crossref","first-page":"2435","DOI":"10.1111\/j.1558-5646.2008.00449.x","article-title":"Estimating nonlinear selection gradients using quadratic regression coefficients: double or nothing?","volume":"62","author":"Stinchcombe","year":"2008","journal-title":"Evolution"},{"key":"10.1016\/j.brainres.2025.149825_b0190","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1007\/BF00163236","article-title":"Intrastrand parity rules of DNA base composition and usage biases of synonymous codons","volume":"40","author":"Sueoka","year":"1995","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.brainres.2025.149825_b0195","doi-asserted-by":"crossref","first-page":"2964","DOI":"10.1093\/nar\/gkq009","article-title":"Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages","volume":"38","author":"Waldman","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.brainres.2025.149825_b0200","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s12863-023-01104-x","article-title":"Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species","volume":"24","author":"Wang","year":"2023","journal-title":"BMC Genom Data"},{"key":"10.1016\/j.brainres.2025.149825_b0205","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1023\/A:1008952302539","article-title":"Codon optimization, genetic insulation, and an rtTA reporter improve performance of the tetracycline switch","volume":"8","author":"Wells","year":"1999","journal-title":"Transgenic Res."},{"key":"10.1016\/j.brainres.2025.149825_b0210","doi-asserted-by":"crossref","first-page":"R13","DOI":"10.1186\/gb-2005-6-2-r13","article-title":"Variation in tissue-specific gene expression among natural populations","volume":"6","author":"Whitehead","year":"2005","journal-title":"Genome Biol."},{"key":"10.1016\/j.brainres.2025.149825_b0215","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1038\/s41419-021-04333-z","article-title":"Genetic inhibition of RIPK3 ameliorates functional outcome in controlled cortical impact independent of necroptosis","volume":"12","author":"Wu","year":"2021","journal-title":"Cell Death Dis."},{"key":"10.1016\/j.brainres.2025.149825_b0220","doi-asserted-by":"crossref","first-page":"1477","DOI":"10.1016\/j.cell.2018.07.041","article-title":"TBK1 suppresses RIPK1-driven apoptosis and inflammation during development and in aging","volume":"174","author":"Xu","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.brainres.2025.149825_b0225","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1186\/s12864-020-6674-1","article-title":"The genome-wide landscape of C:G > T:A polymorphism at the CpG contexts in the human population","volume":"21","author":"Youk","year":"2020","journal-title":"BMC Genomics"},{"key":"10.1016\/j.brainres.2025.149825_b0230","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1007\/s00705-020-04857-3","article-title":"Comprehensive analysis of synonymous codon usage patterns and influencing factors of porcine epidemic diarrhea virus","volume":"166","author":"Yu","year":"2021","journal-title":"Arch. Virol"},{"key":"10.1016\/j.brainres.2025.149825_b0235","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/s41583-018-0093-1","article-title":"Necroptosis and RIPK1-mediated neuroinflammation in CNS diseases","volume":"20","author":"Yuan","year":"2019","journal-title":"Nat. Rev. Neurosci."},{"key":"10.1016\/j.brainres.2025.149825_b0240","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109112","article-title":"RIPK1 activation mediates neuroinflammation and disease progression in multiple sclerosis","volume":"35","author":"Zelic","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.brainres.2025.149825_b0245","doi-asserted-by":"crossref","first-page":"3142","DOI":"10.3390\/ijms19103142","article-title":"Differences in codon usage bias between photosynthesis-related genes and genetic system-related genes of chloroplast genomes in cultivated and wild solanum species","volume":"19","author":"Zhang","year":"2018","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.brainres.2025.149825_b0250","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/s12870-022-03450-x","article-title":"Codon usage patterns across seven Rosales species","volume":"22","author":"Zhang","year":"2022","journal-title":"BMC Plant Biol."},{"key":"10.1016\/j.brainres.2025.149825_b0255","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1038\/s41420-024-01957-w","article-title":"RIPK3 signaling and its role in regulated cell death and diseases","volume":"10","author":"Zhou","year":"2024","journal-title":"Cell Death Discov"}],"container-title":["Brain Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0006899325003865?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0006899325003865?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T09:59:23Z","timestamp":1777456763000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0006899325003865"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10]]},"references-count":51,"alternative-id":["S0006899325003865"],"URL":"https:\/\/doi.org\/10.1016\/j.brainres.2025.149825","relation":{},"ISSN":["0006-8993"],"issn-type":[{"value":"0006-8993","type":"print"}],"subject":[],"published":{"date-parts":[[2025,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Investigation of molecular patterns present in RIPK1 and systemic approach to determine its differential expression in various brain parts","name":"articletitle","label":"Article Title"},{"value":"Brain Research","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.brainres.2025.149825","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier B.V. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"149825"}}