3688ab05270e66e50e26cc63233e522a s13059_024_03369_6.pdf 4c6c4c125e67e0d454a034e14d3b164e3bf48aba s13059_024_03369_6.pdf 48359d31804fead0d0a77bc385addcc4e8ee57a2bcadb73388644f7a16632eee s13059_024_03369_6.pdf Title: Current limitations in predicting mRNA translation with deep learning models Subject: Genome Biology, https://doi.org/10.1186/s13059-024-03369-6 Keywords: Translation control;Deep learning;Explainable AI;Systems biology Author: Niels Schlusser Creator: Adobe InDesign 15.1 (Windows) Producer: Adobe PDF Library 15.0; modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) CreationDate: Tue Aug 20 09:51:38 2024 CEST ModDate: Tue Aug 20 16:45:13 2024 CEST Custom Metadata: yes Metadata Stream: yes Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 25 Encrypted: no Page size: 595.276 x 790.866 pts Page rot: 0 File size: 3151401 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID 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Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 1130 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseOutlines Language: en-US Outlines: Item: Title: Current limitations in predicting mRNA translation with deep learning models Children: Item: Title: Abstract Children: Item: Title: Background: Item: Title: Results: Item: Title: Conclusions: Item: Title: Background Children: Item: Title: Experimental measurements of translation output Item: Title: Models for predicting translation output from the mRNA sequence Item: Title: Results Children: Item: Title: Available DL models do not generalize well across experimental systems Item: Title: Reporter sequences differ in translation-relevant properties from endogenous mRNAs Item: Title: A more accurate and parameter-efficient DL model to predict the impact of 5′UTR sequence variation on translation Item: Title: Discussion Item: Title: Conclusion Item: Title: Methods Children: Item: Title: Experimental methods Children: Item: Title: Cell culture Item: Title: Cell lysis and collection Item: Title: Ribosome footprint sequencing Item: Title: RNA-sequencing Item: Title: Data sets Children: Item: Title: Optimus50 Item: Title: Optimus100 Item: Title: Human genetic variants Item: Title: Yeast50 Item: Title: DART​ Item: Title: Human mRNA sequences Item: Title: Yeast mRNA sequences Item: Title: Yeast TE data Item: Title: HEK 293 TE data Item: Title: HepG2 TE data Item: Title: ClinVar data Item: Title: Model architectures Children: Item: Title: Optimus 5-Prime Item: Title: Framepool Item: Title: MTtrans Item: Title: TranslateLSTM Item: Title: Linear models Item: Title: Acknowledgements Item: Title: References Info: Title: Current limitations in predicting mRNA translation with deep learning models Author: Niels Schlusser Subject: Genome Biology, https://doi.org/10.1186/s13059-024-03369-6 Keywords: Translation control;Deep learning;Explainable AI;Systems biology Creator: Adobe InDesign 15.1 (Windows) Producer: Adobe PDF Library 15.0; modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) CreationDate: Tue Aug 20 09:51:38 CEST 2024 ModDate: Tue Aug 20 16:45:13 CEST 2024 ID: 0x3f6e033c7ee65ab97f6b65c65b8f1b12, 0x35b251a7e551345bab734ec4d43cdf73 Filters: FilterPipeline: FlateDecode FilterPipeline: DCTDecode Images: Image: NisoImageMetadata: FormatName: image/png ImageWidth: 39 ImageHeight: 40 BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Intent: RelativeColorimetric Decode: 0, 255 Name: X Image: NisoImageMetadata: FormatName: image/png ImageWidth: 42 ImageHeight: 77 BitsPerSample: 8 BitsPerSampleUnit: integer 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biology False application/pdf https://doi.org/10.1186/s13059-024-03369-6 BioMed Central Genome Biology, https://doi.org/10.1186/s13059-024-03369-6 Translation control Deep learning Explainable AI Systems biology Current limitations in predicting mRNA translation with deep learning models Niels Schlusser Asier González Muskan Pandey Mihaela Zavolan 10.1186/s13059-024-03369-6 2010-04-23 true springer.com springerlink.com https://doi.org/10.1186/s13059-024-03369-6 10.1186/s13059-024-03369-6 1474-760X journal Genome Biology The Author(s) 2010-04-23 true 10.1186/s13059-024-03369-6 noindex springer.com springerlink.com uuid:38bd3319-4e9d-49f0-a953-a0f79baa15da uuid:528cbada-a9c3-4bea-9bd4-768aa3a46833 default 1 converted uuid:38bd3319-4e9d-49f0-a953-a0f79baa15da converted to PDF/A-2b pdfToolbox 2024-08-20T10:20:05Z 2 B Mihaela Zavolan http://orcid.org/0000-0002-8832-2041 http://ns.adobe.com/pdfx/1.3/ pdfx Adobe Document Info PDF eXtension Schema external Mirrors crossmark:MajorVersionDate CrossmarkMajorVersionDate Text external Mirrors crossmark:CrossmarkDomainExclusive CrossmarkDomainExclusive Text internal Mirrors crossmark:DOI doi Text external Mirrors crossmark:CrosMarkDomains CrossMarkDomains seq Text internal A name object indicating whether the document has been modified to include trapping information robots Text internal ID of PDF/X standard GTS_PDFXVersion Text internal Conformance level of PDF/X standard GTS_PDFXConformance Text internal Company creating the PDF Company Text internal Date when document was last modified SourceModified Text http://crossref.org/crossmark/1.0/ crossmark Crossmark Schema internal Usual same as prism:doi DOI Text external The date when a publication was publishe. MajorVersionDate Text internal CrossmarkDomainExclusive CrossmarkDomainExclusive Text internal CrossMarkDomains CrossMarkDomains seq Text http://prismstandard.org/namespaces/basic/2.0/ prism Prism Schema external This element provides the url for an article or unit of content. The attribute platform is optionally allowed for situations in which multiple URLs must be specified. PRISM recommends that a subset of the PCV platform values, namely “mobile” and “web”, be used in conjunction with this element. NOTE: PRISM recommends against the use of the #other value allowed in the PRISM Platform controlled vocabulary. In lieu of using #other please reach out to the PRISM group at prism-wg@yahoogroups.com to request addition of your term to the Platform Controlled Vocabulary. url URI external The Digital Object Identifier for the article. The DOI may also be used as the dc:identifier. If used as a dc:identifier, the URI form should be captured, and the bare identifier should also be captured using prism:doi. If an alternate unique identifier is used as the required dc:identifier, then the DOI should be specified as a bare identifier within prism:doi only. If the URL associated with a DOI is to be specified, then prism:url may be used in conjunction with prism:doi in order to provide the service endpoint (i.e. the URL). doi Text external ISSN for an electronic version of the issue in which the resource occurs. Permits publishers to include a second ISSN, identifying an electronic version of the issue in which the resource occurs (therefore e(lectronic)Issn. If used, prism:eIssn MUST contain the ISSN of the electronic version. issn Text internal Volume number volume Text internal Issue number number Text internal Starting page startingPage Text internal Ending page endingPage Text external The aggregation type specifies the unit of aggregation for a content collection. Comment PRISM recommends that the PRISM Aggregation Type Controlled Vocabulary be used to provide values for this element. Note: PRISM recommends against the use of the #other value currently allowed in this controlled vocabulary. In lieu of using #other please reach out to the PRISM group at info@prismstandard.org to request addition of your term to the Aggregation Type Controlled Vocabulary. aggregationType Text external Title of the magazine, or other publication, in which a resource was/will be published. Typically this will be used to provide the name of the magazine an article appeared in as metadata for the article, along with information such as the article title, the publisher, volume, number, and cover date. Note: Publication name can be used to differentiate between a print magazine and the online version if the names are different such as “magazine” and “magazine.com.” publicationName Text external Copyright copyright Text http://ns.adobe.com/pdf/1.3/ pdf Adobe PDF Schema internal A name object indicating whether the document has been modified to include trapping information Trapped Text http://ns.adobe.com/xap/1.0/mm/ xmpMM XMP Media Management Schema internal UUID based identifier for specific incarnation of a document InstanceID URI internal The common identifier for all versions and renditions of a document. DocumentID URI internal The common identifier for all versions and renditions of a document. OriginalDocumentID URI http://www.aiim.org/pdfa/ns/id/ pdfaid PDF/A ID Schema internal Part of PDF/A standard part Integer internal Amendment of PDF/A standard amd Text internal Conformance level of PDF/A standard conformance Text Springer Nature ORCID Schema http://springernature.com/ns/xmpExtensions/2.0/ sn authorInfo Bag AuthorInformation external Author information: contains the name of each author and his/her ORCiD (ORCiD: Open Researcher and Contributor ID). An ORCiD is a persistent identifier (a non-proprietary alphanumeric code) to uniquely identify scientific and other academic authors. AuthorInformation http://springernature.com/ns/xmpExtensions/2.0/authorInfo/ author Specifies the types of author information: name and ORCID of an author. name Text Gives the name of an author. orcid URI Gives the ORCID of an author. 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