{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T05:42:39Z","timestamp":1792215759605,"version":"4.4.0"},"reference-count":103,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:00:00Z","timestamp":1790035200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Institutes of Health National Cancer Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"National Institute of Allergy and Infectious Diseases Division of Intramural Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001201","name":"The Kavli Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001201","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000900","name":"California Institute for Regenerative Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000900","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000154","name":"National Science Foundation Division of Integrative Organismal Systems","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000154","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1016\/j.cell.2026.09.043","type":"journal-article","created":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T14:39:59Z","timestamp":1792075199000},"update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Functional diversification of the cephalopod proteome by RNA editing"],"prefix":"10.1016","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3112-667X","authenticated-orcid":false,"given":"Jack M.","family":"Moen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alicia L.","family":"Richards","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Einar K.","family":"Krogsaeter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin J.","family":"Polacco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Gordon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erica","family":"Stevenson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rhiana","family":"Boyles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximilien","family":"Burq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dejan","family":"Stepec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan","family":"Crampton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathaniel","family":"Sin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8598-7048","authenticated-orcid":false,"given":"Zachary","family":"Gale-Day","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason E.","family":"Gestwicki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Cimermancic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua J.C.","family":"Rosenthal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nevan J.","family":"Krogan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6119-6084","authenticated-orcid":false,"given":"Danielle L.","family":"Swaney","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.cell.2026.09.043_bib1","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/0092-8674(88)90253-X","article-title":"An unwinding activity that covalently modifies its double-stranded RNA substrate","volume":"55","author":"Bass","year":"1988","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.09.043_bib2","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1073\/pnas.48.4.613","article-title":"Synthetic polynucleotides and the amino acid code. V","volume":"48","author":"Basilio","year":"1962","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.09.043_bib3","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/nar\/gky1163","article-title":"Inosine induces context-dependent recoding and translational stalling","volume":"47","author":"Licht","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib4","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1038\/s41576-018-0006-1","article-title":"A-to-I RNA editing - immune protector and transcriptome diversifier","volume":"19","author":"Eisenberg","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.cell.2026.09.043_bib5","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/nrm.2015.4","article-title":"A-to-I editing of coding and non-coding RNAs by ADARs","volume":"17","author":"Nishikura","year":"2016","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib6","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/35017558","article-title":"Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2","volume":"406","author":"Higuchi","year":"2000","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.09.043_bib7","doi-asserted-by":"crossref","first-page":"20715","DOI":"10.1073\/pnas.1009231107","article-title":"RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1","volume":"107","author":"Yeo","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.09.043_bib8","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/0896-6273(93)90336-P","article-title":"Determinants of Ca2+ permeability in both TM1 and TM2 of high affinity kainate receptor channels: diversity by RNA editing","volume":"10","author":"K\u00f6hler","year":"1993","journal-title":"Neuron"},{"key":"10.1016\/j.cell.2026.09.043_bib9","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/0092-8674(91)90568-J","article-title":"RNA editing in brain controls a determinant of ion flow in glutamate-gated channels","volume":"67","author":"Sommer","year":"1991","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.09.043_bib10","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1038\/nsmb825","article-title":"Control of human potassium channel inactivation by editing of a small mRNA hairpin","volume":"11","author":"Bhalla","year":"2004","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib11","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/387303a0","article-title":"Regulation of serotonin-2C receptor G-protein coupling by RNA editing","volume":"387","author":"Burns","year":"1997","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.09.043_bib12","doi-asserted-by":"crossref","first-page":"R887","DOI":"10.1016\/j.cub.2012.09.001","article-title":"An embodied view of octopus neurobiology","volume":"22","author":"Hochner","year":"2012","journal-title":"Curr. Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib13","article-title":"Cuttlefish exert self-control in a delay of gratification task","volume":"288","author":"Schnell","year":"2021","journal-title":"Proc. Biol. Sci."},{"key":"10.1016\/j.cell.2026.09.043_bib14","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.05198","article-title":"The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing","volume":"4","author":"Alon","year":"2015","journal-title":"Elife"},{"key":"10.1016\/j.cell.2026.09.043_bib15","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.cell.2017.03.025","article-title":"Trade-off between transcriptome plasticity and genome evolution in cephalopods","volume":"169","author":"Liscovitch-Brauer","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.09.043_bib16","doi-asserted-by":"crossref","first-page":"3999","DOI":"10.1093\/nar\/gkaa172","article-title":"Spatially regulated editing of genetic information within a neuron","volume":"48","author":"Vallecillo-Viejo","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib17","doi-asserted-by":"crossref","first-page":"2427","DOI":"10.1038\/s41467-022-29748-w","article-title":"Genome and transcriptome mechanisms driving cephalopod evolution","volume":"13","author":"Albertin","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2026.09.043_bib18","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1146\/annurev-animal-060322-114534","article-title":"Extensive recoding of the neural proteome in cephalopods by RNA editing","volume":"11","author":"Rosenthal","year":"2023","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"10.1016\/j.cell.2026.09.043_bib19","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1016\/j.cell.2023.04.032","article-title":"RNA recoding in cephalopods tailors microtubule motor protein function","volume":"186","author":"Rangan","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.09.043_bib20","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1126\/science.1212795","article-title":"RNA editing underlies temperature adaptation in K+ channels from polar octopuses","volume":"335","author":"Garrett","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.09.043_bib21","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1000540","article-title":"Regulation of Na+\/K+ ATPase transport velocity by RNA editing","volume":"8","author":"Colina","year":"2010","journal-title":"PLoS Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib22","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1016\/S0896-6273(02)00701-8","article-title":"Extensive editing of mRNAs for the squid delayed rectifier K+ channel regulates subunit tetramerization","volume":"34","author":"Rosenthal","year":"2002","journal-title":"Neuron"},{"key":"10.1016\/j.cell.2026.09.043_bib23","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/S0896-6273(00)80383-9","article-title":"RNA editing generates a diverse array of transcripts encoding squid Kv2 K+ channels with altered functional properties","volume":"19","author":"Patton","year":"1997","journal-title":"Neuron"},{"key":"10.1016\/j.cell.2026.09.043_bib24","doi-asserted-by":"crossref","first-page":"2544","DOI":"10.1016\/j.cell.2023.05.004","article-title":"Temperature-dependent RNA editing in octopus extensively recodes the neural proteome","volume":"186","author":"Birk","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.09.043_bib25","doi-asserted-by":"crossref","first-page":"4046","DOI":"10.1021\/acs.jproteome.0c00347","article-title":"Proteome-wide analysis of ADAR-mediated messenger RNA editing during fruit fly ontogeny","volume":"19","author":"Kliuchnikova","year":"2020","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.cell.2026.09.043_bib26","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1021\/pr900863u","article-title":"Value of using multiple proteases for large-scale mass spectrometry-based proteomics","volume":"9","author":"Swaney","year":"2010","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.cell.2026.09.043_bib27","doi-asserted-by":"crossref","first-page":"1776","DOI":"10.1038\/s41587-023-01714-x","article-title":"Global detection of human variants and isoforms by deep proteome sequencing","volume":"41","author":"Sinitcyn","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2026.09.043_bib62","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmb.2026.169940","article-title":"Tesorai Search: Cloud-based Database Search Engine Boosts Identifications for Mass Spectrometry Proteomics With a Pretrained Peptide-spectrum Deep-learning Model","volume":"438","author":"Burq","year":"2026","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib29","doi-asserted-by":"crossref","DOI":"10.3389\/fgeed.2023.1181713","article-title":"Squid express conserved ADAR orthologs that possess novel features","volume":"5","author":"Vallecillo-Viejo","year":"2023","journal-title":"Front. Genome Ed."},{"key":"10.1016\/j.cell.2026.09.043_bib30","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1126\/science.ads0018","article-title":"Simulating 500 million years of evolution with a language model","volume":"387","author":"Hayes","year":"2025","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.09.043_bib31","doi-asserted-by":"crossref","DOI":"10.1126\/science.adg7492","article-title":"Accurate proteome-wide missense variant effect prediction with AlphaMissense","volume":"381","author":"Cheng","year":"2023","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.09.043_bib32","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-021-02459-z","article-title":"Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution","volume":"22","author":"Georgakopoulos-Soares","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib33","doi-asserted-by":"crossref","first-page":"3139","DOI":"10.1093\/nar\/gkab139","article-title":"Significant non-existence of sequences in genomes and proteomes","volume":"49","author":"Koulouras","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib34","doi-asserted-by":"crossref","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: The universal protein knowledgebase in 2025","volume":"53","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib35","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.70784","article-title":"Assessing target engagement using proteome-wide solvent shift assays","volume":"10","author":"Van Vranken","year":"2021","journal-title":"Elife"},{"key":"10.1016\/j.cell.2026.09.043_bib36","doi-asserted-by":"crossref","DOI":"10.1126\/science.1255784","article-title":"Tracking cancer drugs in living cells by thermal profiling of the proteome","volume":"346","author":"Savitski","year":"2014","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.09.043_bib37","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2314853121","article-title":"Transfer learning to leverage larger datasets for improved prediction of protein stability changes","volume":"121","author":"Dieckhaus","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cell.2026.09.043_bib38","doi-asserted-by":"crossref","first-page":"3158","DOI":"10.1111\/ejn.12681","article-title":"Downregulation of Centaurin gamma1A increases synaptic transmission at Drosophila larval neuromuscular junctions","volume":"40","author":"Homma","year":"2014","journal-title":"Eur. J. Neurosci."},{"key":"10.1016\/j.cell.2026.09.043_bib39","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib40","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-018-08191-w","article-title":"Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics","volume":"10","author":"Geladaki","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2026.09.043_bib41","doi-asserted-by":"crossref","DOI":"10.1186\/s12964-021-00741-y","article-title":"Types of nuclear localization signals and mechanisms of protein import into the nucleus","volume":"19","author":"Lu","year":"2021","journal-title":"Cell Commun. Signal."},{"key":"10.1016\/j.cell.2026.09.043_bib42","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1038\/nmeth.2646","article-title":"pLogo: a probabilistic approach to visualizing sequence motifs","volume":"10","author":"O\u2019Shea","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.09.043_bib43","doi-asserted-by":"crossref","first-page":"23884","DOI":"10.1074\/jbc.M002926200","article-title":"Arginine kinase from Nautilus pompilius, a living fossil. Site-directed mutagenesis studies on the role of amino acid residues in the Guanidino specificity region","volume":"275","author":"Suzuki","year":"2000","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cell.2026.09.043_bib44","doi-asserted-by":"crossref","DOI":"10.15252\/msb.202110591","article-title":"System-wide optimization of an orthogonal translation system with enhanced biological tolerance","volume":"19","author":"Mohler","year":"2023","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib45","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1038\/nchembio.2474","article-title":"Continuous directed evolution of aminoacyl-tRNA synthetases","volume":"13","author":"Bryson","year":"2017","journal-title":"Nat. Chem. Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib46","doi-asserted-by":"crossref","first-page":"3489","DOI":"10.1093\/bioinformatics\/btx415","article-title":"The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics","volume":"33","author":"Wiredja","year":"2017","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.09.043_bib47","doi-asserted-by":"crossref","first-page":"3618","DOI":"10.1038\/sj.emboj.7601249","article-title":"A novel mitochondrial ubiquitin ligase plays a critical role in mitochondrial dynamics","volume":"25","author":"Yonashiro","year":"2006","journal-title":"EMBO J."},{"key":"10.1016\/j.cell.2026.09.043_bib48","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1083\/jcb.200611064","article-title":"The mitochondrial E3 ubiquitin ligase March5 is required for Drp1 dependent mitochondrial division","volume":"178","author":"Karbowski","year":"2007","journal-title":"J. Cell Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib49","doi-asserted-by":"crossref","DOI":"10.1038\/s41597-024-03327-8","article-title":"Analysis of AlphaMissense data in different protein groups and structural context","volume":"11","author":"Tordai","year":"2024","journal-title":"Sci. Data"},{"key":"10.1016\/j.cell.2026.09.043_bib50","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.devcel.2024.09.010","article-title":"Outer mitochondrial membrane E3 Ub ligase MARCH5 controls de novo peroxisome biogenesis","volume":"60","author":"Verhoeven","year":"2025","journal-title":"Dev. Cell"},{"key":"10.1016\/j.cell.2026.09.043_bib51","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1038\/sj.embor.7400790","article-title":"MARCH-V is a novel mitofusin 2- and Drp1-binding protein able to change mitochondrial morphology","volume":"7","author":"Nakamura","year":"2006","journal-title":"EMBO Rep."},{"key":"10.1016\/j.cell.2026.09.043_bib52","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1038\/nprot.2017.060","article-title":"A fluorescence-based imaging method to measure in vitro and in vivo mitophagy using mt-Keima","volume":"12","author":"Sun","year":"2017","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.cell.2026.09.043_bib53","doi-asserted-by":"crossref","DOI":"10.1016\/j.xpro.2020.100245","article-title":"Measurement of mitochondrial respiration in adherent cells by Seahorse XF96 Cell Mito Stress Test","volume":"2","author":"Gu","year":"2021","journal-title":"STAR Protoc."},{"key":"10.1016\/j.cell.2026.09.043_bib54","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.cell.2015.08.056","article-title":"Kinome-wide decoding of network-attacking mutations rewiring cancer signaling","volume":"163","author":"Creixell","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.09.043_bib55","doi-asserted-by":"crossref","first-page":"2774","DOI":"10.1016\/j.cub.2023.05.066","article-title":"Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity","volume":"33","author":"Ahuja","year":"2023","journal-title":"Curr. Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib56","doi-asserted-by":"crossref","first-page":"D543","DOI":"10.1093\/nar\/gkae1011","article-title":"The PRIDE database at 20 years: 2025 update","volume":"53","author":"Perez-Riverol","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib57","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib59","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1126\/science.1241459","article-title":"Genomically recoded organisms expand biological functions","volume":"342","author":"Lajoie","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.09.043_bib58","doi-asserted-by":"crossref","first-page":"4597","DOI":"10.1016\/j.cell.2023.08.026","article-title":"SARS-CoV-2 variants evolve convergent strategies to remodel the host response","volume":"186","author":"Bouhaddou","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.09.043_bib60","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1002\/biot.201400821","article-title":"Optimized Sleeping Beauty transposons rapidly generate stable transgenic cell lines","volume":"10","author":"Kowarz","year":"2015","journal-title":"Biotechnol. J."},{"key":"10.1016\/j.cell.2026.09.043_bib61","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0018762","article-title":"A flow cytometry-based screen of nuclear envelope transmembrane proteins identifies NET4\/Tmem53 as involved in stress-dependent cell cycle withdrawal","volume":"6","author":"Korfali","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.cell.2026.09.043_bib63","article-title":"Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform","volume":"14","author":"Yu","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2026.09.043_bib64","doi-asserted-by":"crossref","first-page":"W344","DOI":"10.1093\/nar\/gkw408","article-title":"ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules","volume":"44","author":"Ashkenazy","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/nprot.2015.123","article-title":"SIFT missense predictions for genomes","volume":"11","author":"Vaser","year":"2016","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.cell.2026.09.043_bib66","doi-asserted-by":"crossref","first-page":"D652","DOI":"10.1093\/nar\/gkaf1126","article-title":"OmniPath: integrated knowledgebase for multi-omics analysis","volume":"54","author":"T\u00fcrei","year":"2026","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib67","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib68","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: A cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.cell.2026.09.043_bib69","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.09.043_bib70","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2026.09.043_bib71","doi-asserted-by":"crossref","first-page":"2289","DOI":"10.1016\/j.csbj.2024.05.025","article-title":"A survey of k-mer methods and applications in bioinformatics","volume":"23","author":"Moeckel","year":"2024","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.cell.2026.09.043_bib72","doi-asserted-by":"crossref","DOI":"10.12688\/wellcomeopenres.21000.1","article-title":"Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control","volume":"9","author":"Iosub","year":"2024","journal-title":"Wellcome Open Res."},{"key":"10.1016\/j.cell.2026.09.043_bib73","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2026.09.043_bib74","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0177459","article-title":"Singularity: Scientific containers for mobility of compute","volume":"12","author":"Kurtzer","year":"2017","journal-title":"PLoS One"},{"key":"10.1016\/j.cell.2026.09.043_bib75","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.09.043_bib76","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":"10.1016\/j.cell.2026.09.043_bib77","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1038\/s41596-019-0279-7","article-title":"Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal","volume":"15","author":"Lo Giudice","year":"2020","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.cell.2026.09.043_bib78","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1006169","article-title":"riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data","volume":"14","author":"Lauria","year":"2018","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib79","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkz223","article-title":"Generally applicable transcriptome-wide analysis of translation using anota2seq","volume":"47","author":"Oertlin","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib80","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/nmeth.1541","article-title":"SAINT: probabilistic scoring of affinity purification-mass spectrometry data","volume":"8","author":"Choi","year":"2011","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.09.043_bib81","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.09.043_bib82","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-018-2367-z","article-title":"Biotite: a unifying open source computational biology framework in Python","volume":"19","author":"Kunzmann","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.cell.2026.09.043_bib83","doi-asserted-by":"crossref","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":"10.1016\/j.cell.2026.09.043_bib84","doi-asserted-by":"crossref","first-page":"2524","DOI":"10.1093\/bioinformatics\/btu305","article-title":"MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments","volume":"30","author":"Choi","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.09.043_bib85","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-12-77","article-title":"pROC: an open-source package for R and S+ to analyze and compare ROC curves","volume":"12","author":"Robin","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.cell.2026.09.043_bib86","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0146021","article-title":"Dose-response analysis using R","volume":"10","author":"Ritz","year":"2015","journal-title":"PLoS One"},{"key":"10.1016\/j.cell.2026.09.043_bib87","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1128\/AEM.06516-11","article-title":"DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences","volume":"78","author":"Wright","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.cell.2026.09.043_bib88","doi-asserted-by":"crossref","first-page":"3812","DOI":"10.1093\/nar\/gkg509","article-title":"SIFT: Predicting amino acid changes that affect protein function","volume":"31","author":"Ng","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.09.043_bib89","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1093\/genetics\/49.1.49","article-title":"The interaction of selection and linkage. I. general considerations; Heterotic models","volume":"49","author":"Lewontin","year":"1964","journal-title":"Genetics"},{"key":"10.1016\/j.cell.2026.09.043_bib90","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1007\/BF01245622","article-title":"Linkage disequilibrium in finite populations","volume":"38","author":"Hill","year":"1968","journal-title":"Theor. Appl. Genet."},{"key":"10.1016\/j.cell.2026.09.043_bib91","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.RA120.002411","article-title":"Carboxylate-modified magnetic bead (CMMB)-based isopropanol gradient peptide fractionation (CIF) enables rapid and robust off-line peptide mixture fractionation in bottom-up proteomics","volume":"20","author":"Deng","year":"2021","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.cell.2026.09.043_bib92","doi-asserted-by":"crossref","first-page":"3510","DOI":"10.1021\/pr401032q","article-title":"Phosphoproteomic approach to characterize protein mono- and poly(ADP-ribosyl)ation sites from cells","volume":"13","author":"Daniels","year":"2014","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.cell.2026.09.043_bib93","doi-asserted-by":"crossref","first-page":"2010","DOI":"10.1021\/acs.jproteome.0c00853","article-title":"QCloud2: An improved cloud-based quality-control system for mass-spectrometry-based proteomics laboratories","volume":"20","author":"Olivella","year":"2021","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.cell.2026.09.043_bib94","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nmeth1019","article-title":"Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry","volume":"4","author":"Elias","year":"2007","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.09.043_bib96","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1038\/nmeth.4256","article-title":"MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics","volume":"14","author":"Kong","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.09.043_bib97","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1074\/mcp.M114.044305","article-title":"Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues","volume":"14","author":"Bruderer","year":"2015","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.cell.2026.09.043_bib98","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1021\/acs.jproteome.2c00834","article-title":"MSstats version 4.0: Statistical analyses of quantitative mass spectrometry-based proteomic experiments with chromatography-based quantification at scale","volume":"22","author":"Kohler","year":"2023","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.cell.2026.09.043_bib99","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.ymeth.2017.05.028","article-title":"Transcriptome-wide measurement of translation by ribosome profiling","volume":"126","author":"McGlincy","year":"2017","journal-title":"Methods"},{"key":"10.1016\/j.cell.2026.09.043_bib100","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2026.09.043_bib101","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2020.00194","article-title":"Quantifying RNA editing in deep transcriptome datasets","volume":"11","author":"Lo Giudice","year":"2020","journal-title":"Front. Genet."},{"key":"10.1016\/j.cell.2026.09.043_bib102","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3002409","article-title":"Biological factors and statistical limitations prevent detection of most noncanonical proteins by mass spectrometry","volume":"21","author":"Wacholder","year":"2023","journal-title":"PLoS Biol."},{"key":"10.1016\/j.cell.2026.09.043_bib103","doi-asserted-by":"crossref","DOI":"10.1002\/pro.5022","article-title":"DSFworld: A flexible and precise tool to analyze differential scanning fluorimetry data","volume":"33","author":"Wu","year":"2024","journal-title":"Protein Sci."},{"key":"10.1016\/j.cell.2026.09.043_bib104","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/j.molcel.2015.10.009","article-title":"Measuring in vivo mitophagy","volume":"60","author":"Sun","year":"2015","journal-title":"Mol. Cell"},{"key":"10.1016\/j.cell.2026.09.043_bib105","article-title":"Longitudinal tracking of neuronal mitochondria delineates PINK1\/Parkin-dependent mechanisms of mitochondrial recycling and degradation","volume":"7","author":"Li","year":"2021","journal-title":"Sci. Adv."}],"container-title":["Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0092867426011840?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0092867426011840?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T05:12:04Z","timestamp":1792213924000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0092867426011840"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":103,"alternative-id":["S0092867426011840"],"URL":"https:\/\/doi.org\/10.1016\/j.cell.2026.09.043","relation":{},"ISSN":["0092-8674"],"issn-type":[{"value":"0092-8674","type":"print"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Functional diversification of the cephalopod proteome by RNA editing","name":"articletitle","label":"Article Title"},{"value":"Cell","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cell.2026.09.043","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}