[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-detail-120889-en":3,"doc-seo-120889-105":30,"detail-sidebar-cat-0-en-105":83},{"code":4,"msg":5,"data":6},0,"success",{"doc_id":7,"user_id":8,"nickname":9,"user_avatar":10,"doc_module":4,"category_id":11,"category_name":12,"doc_title":13,"doc_description":14,"doc_content":15,"file_id":16,"file_url":17,"file_type":18,"file_size":19,"view_count":4,"is_deleted":4,"is_public":20,"is_downloadable":20,"audit_status":20,"page_count":21,"language":22,"language_code":23,"site_id":24,"html_lang":23,"table_of_contents":25,"faqs":26,"seo_title":27,"seo_description":14,"update_tm":28,"read_time":29},120889,4810365810221,"Aurora","https://ap-avatar.wpscdn.com/davatar_155a257f0dc6eb9ab79c44ca47cae57d",8,"Research & Report","Revealing the grammar of small RNA secretion using interpretable machine learning","Small non-coding RNAs are secreted via mechanisms such as exosomal sorting, small extracellular vesicles, and lipoprotein complexes, yet the cis-regulatory logic controlling their extracellular sorting and release remains insufficiently defined. The study introduces ExoGRU, an interpretable machine-learning model that predicts small RNA secretion probabilities directly from primary RNA sequences, supported by experimental validation. It further introduces exoCLIP to uncover RNA–RBP interactions in the extracellular space and uses ExoGRU-guided design to create synthetic RNAs with high secretion ability, enabling cis and trans factor discovery for therapeutic and synthetic biology.","UCSF  \nUC San Francisco Previously Published Works  \nTitle  \nRevealing the grammar of small RNA secretion using interpretable machine learning.  \nPermalink  \n[https://escholarship.org/uc/item/3zm0f0b4](https://escholarship.org/uc/item/3zm0f0b4)  \nJournal  \nCell Genomics, 4(4)  \nAuthors  \nZirak, Bahar  \nNaghipourfar, Mohsen Saberi, Ali  \net al.  \nPublication Date  \n2024-04-10  \nDOI  \n10.1016/j.xgen.2024.100522  \nPeer reviewed  \n[eScholarship.org](eScholarship.org) Powered by the California Digital Library  \nUniversity of California  \nArticle  \nRevealing the grammar of small RNA secretion using interpretable machine learning  \nAuthors  \nBahar Zirak, Mohsen Naghipourfar, Ali Saberi, ..., Albertas Navickas, Ali Sharifi-Zarchi, Hani Goodarzi  \nCorrespondence  \n[albertas.navickas@curie.fr](albertas.navickas@curie.fr) (A.N.), asharifi[z@gmail.com](z@gmail.com) (A.S.-Z.), [hani.goodarzi@ucsf.edu](hani.goodarzi@ucsf.edu) (H.G.)  \nIn brief  \nZirak et al. introduce ExoGRU, a machine learning model predicting small RNA secretion from primary RNA sequences. Additionally, the study introduces exoCLIP, unveiling RNA and RNA-binding protein interactions in the extracellular space. These insights hold promise for therapeutic and synthetic biology applications.  \nd ExoGRU utilizes primary sequences of small RNAs to accurately predict their secretion  \nd ExoGRU identifies both known and novel RBPs governing small RNA secretion  \nd Using ExoGRU, we generated synthetic small RNAs with high secretion ability  \nZirak et al., 2024, Cell Genomics 4, 100522 April 10, 2024 ª 2024 The Authors.  \n[https://doi.org/10.1016/j.xgen.2024.100522](https://doi.org/10.1016/j.xgen.2024.100522)  \nll  \nll  \nOPEN ACCESS  \nArticle  \nRevealing the grammar of small RNA secretion using interpretable machine learning  \nBahar Zirak,1,2,3,4,15 Mohsen Naghipourfar,5,15 Ali Saberi,6,7,15 Delaram Pouyabahar,8,9,15 Amirhossein Zarezadeh,10,11,15 Lixi Luo,1,2,3,4,12,15 Lisa Fish,1,2,3,4 Doowon Huh,13 Albertas Navickas,1,2,3,4,14,* Ali Sharifi-Zarchi,5,*  \nand Hani Goodarzi1,2,3,4,16,*  \n1Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA  \n2Department of Urology, University of California, San Francisco, San Francisco, CA, USA  \n3Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA  \n4Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, US  \n5Department of Computer Engineering, Sharif University of Technology, Tehran, Iran  \n6Department of Electrical and Computer Engineering, McGill University, Montreal, QC H3A 0E9, Canada  \n7McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC H3A 0G1, Canada  \n8Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada  \n9The Donnelly Centre, University of Toronto, Toronto, ON, Canada  \n10Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran  \n11Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran  \n12Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China  \n13Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA  \n14Institut Curie, CNRS UMR3348, INSERM U1278, Orsay, France  \n15These authors contributed equally  \n16Lead contact  \n*Correspondence: [albertas.navickas@curie.fr](albertas.navickas@curie.fr) (A.N.), asharifi[z@gmail.com](z@gmail.com) (A.S.-Z.), [hani.goodarzi@ucsf.edu](hani.goodarzi@ucsf.edu) (H.G.) [https://doi.org/10.1016/j.xgen.2024.100522](https://doi.org/10.1016/j.xgen.2024.100522)  \nSUMMARY  \nSmall non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellula","cbCaioefMhK17AA9","https://ap.wps.com/l/cbCaioefMhK17AA9","pdf",4401213,1,21,"English","en",105,"# Summary\n## ExoGRU model and prediction framework\n## ExoCLIP and extracellular RNA–RBP interactions\n## Experimental validation and synthetic RNA design\n# Introduction\n## Background on extracellular small non-coding RNAs\n## Knowledge gaps in sorting and secretion mechanisms\n## Development of ExoGRU for cis-regulatory grammar discovery","[{\"question\":\"How was the model validated experimentally?\",\"answer\":\"The study validates ExoGRU performance using ExoGRU-guided mutagenesis and synthetic RNA sequence analysis. It also uses the model to identify cis and trans factors, including known and novel RBPs.\"}]","Revealing the grammar of small RNA secretion using interpretable machine learning | PDF",1785732507,53,{"code":4,"msg":31,"data":32},"ok",{"site_id":24,"language":23,"slug":33,"title":13,"keywords":34,"description":14,"schema_data":35,"social_meta":78,"head_meta":80,"extra_data":82,"updated_unix":28},"revealing-the-grammar-of-small-rna-secretion-using-interpretable-machine-learning","",{"@graph":36,"@context":77},[37,54,68],{"@type":38,"itemListElement":39},"BreadcrumbList",[40,44,48,51],{"item":41,"name":42,"@type":43,"position":20},"https://docshare.wps.com","Home","ListItem",{"item":45,"name":46,"@type":43,"position":47},"https://docshare.wps.com/document/","Document",2,{"item":49,"name":12,"@type":43,"position":50},"https://docshare.wps.com/document/research-report/",3,{"item":52,"name":13,"@type":43,"position":53},"https://docshare.wps.com/document/revealing-the-grammar-of-small-rna-secretion-using-interpretable-machine-learning/120889/",4,{"url":52,"name":13,"@type":55,"author":56,"headline":13,"publisher":58,"fileFormat":61,"inLanguage":23,"description":14,"dateModified":62,"datePublished":62,"encodingFormat":61,"isAccessibleForFree":63,"interactionStatistic":64},"DigitalDocument",{"name":9,"@type":57},"Person",{"url":41,"name":59,"@type":60},"DocShare","Organization","application/pdf","2026-08-03",true,{"@type":65,"interactionType":66,"userInteractionCount":4},"InteractionCounter",{"@type":67},"ViewAction",{"@type":69,"mainEntity":70},"FAQPage",[71],{"name":72,"@type":73,"acceptedAnswer":74},"How was the model validated experimentally?","Question",{"text":75,"@type":76},"The study validates ExoGRU performance using ExoGRU-guided mutagenesis and synthetic RNA sequence analysis. It also uses the model to identify cis and trans factors, including known and novel RBPs.","Answer","https://schema.org",{"og:url":52,"og:type":79,"og:title":13,"og:site_name":59,"og:description":14},"article",{"robots":81,"canonical":52},"index,follow",{"doc_id":7,"site_id":24},{"code":4,"msg":5,"data":84},[85,89,93,97,102,107,112,115,120,123,127],{"id":20,"doc_module":4,"doc_module_name":46,"category_name":86,"show_sort_weight":87,"slug":88},"Story & Novel",90,"story-novel",{"id":47,"doc_module":4,"doc_module_name":46,"category_name":90,"show_sort_weight":91,"slug":92},"Literature",80,"literature",{"id":53,"doc_module":4,"doc_module_name":46,"category_name":94,"show_sort_weight":95,"slug":96},"Exam",70,"exam",{"id":98,"doc_module":4,"doc_module_name":46,"category_name":99,"show_sort_weight":100,"slug":101},5,"Comic",60,"comic",{"id":103,"doc_module":4,"doc_module_name":46,"category_name":104,"show_sort_weight":105,"slug":106},6,"Technology",50,"technology",{"id":108,"doc_module":4,"doc_module_name":46,"category_name":109,"show_sort_weight":110,"slug":111},7,"Healthcare",40,"healthcare",{"id":11,"doc_module":4,"doc_module_name":46,"category_name":12,"show_sort_weight":113,"slug":114},30,"research-report",{"id":116,"doc_module":4,"doc_module_name":46,"category_name":117,"show_sort_weight":118,"slug":119},9,"Religion & Spirituality",20,"religion-spirituality",{"id":118,"doc_module":4,"doc_module_name":46,"category_name":121,"show_sort_weight":118,"slug":122},"World Cup","world-cup",{"id":124,"doc_module":4,"doc_module_name":46,"category_name":125,"show_sort_weight":124,"slug":126},10,"Lifestyle","lifestyle",{"id":128,"doc_module":4,"doc_module_name":46,"category_name":129,"show_sort_weight":98,"slug":130},19,"General","general"]