Academic Journal
Navigating the landscape of direct cellular reprogramming with DiReG.
| Τίτλος: | Navigating the landscape of direct cellular reprogramming with DiReG. |
|---|---|
| Συγγραφείς: | Lauber M; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany., List M; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany. markus.list@tum.de.; Munich Data Science Institute (MDSI), Technical University of Munich, Garching, Germany. markus.list@tum.de. |
| Πηγή: | NPJ systems biology and applications [NPJ Syst Biol Appl] 2026 Feb 06; Vol. 12 (1). Date of Electronic Publication: 2026 Feb 06. |
| Τύπος έκδοσης: | Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Nature Publishing Group in partnership with SBI, The Systems Biology Institute Country of Publication: England NLM ID: 101677786 Publication Model: Electronic Cited Medium: Internet ISSN: 2056-7189 (Electronic) Linking ISSN: 20567189 NLM ISO Abbreviation: NPJ Syst Biol Appl Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: [London] : Nature Publishing Group in partnership with SBI, The Systems Biology Institute, [2015]- |
| Ιατρικοί όροι (MeSH): | Cellular Reprogramming*/genetics , Cellular Reprogramming*/physiology , Computational Biology*/methods, Transcription Factors/metabolism ; Transcription Factors/genetics ; Regenerative Medicine/methods ; Humans ; Animals ; Software |
| Περίληψη: | Direct cellular reprogramming, converting one differentiated cell type directly into another, holds immense promise for regenerative medicine, developmental biology, and disease modeling. Identifying optimal transcription factor (TF) combinations to control this process remains complex and labor-intensive. Over the last decade, various computational tools emerged to infer TF sets for reprogramming. However, current methodologies possess critical limitations, and the absence of robust benchmarking standards makes it impossible to precisely validate and compare their performance. To address these challenges, we present a comprehensive analysis of existing computational methods for direct reprogramming and introduce a web application designed to support researchers in identifying and validating optimal TF sets. Our platform integrates predictions from established tools, incorporates a state-of-the-art Retrieval-Augmented Generation (RAG) system for efficient literature querying, and offers tools to further validate predictions. By providing a unified and interactive resource, our web application enhances the accessibility and efficiency of TF discovery for direct reprogramming. Furthermore, we discuss critical limitations shared by current methodologies and highlight the need for computational tools that can account for the complex regulatory dynamics of direct reprogramming. This work not only advances the toolkit available to researchers but also lays the groundwork for future innovations aimed at realizing the full potential of direct reprogramming. (© 2026. The Author(s).) |
| Competing Interests: | Competing interests: The authors declare no competing interests. |
| References: | Genes Dev. 2011 Sep 15;25(18):1915-27. (PMID: 21890647) Cell. 2006 Aug 25;126(4):663-76. (PMID: 16904174) Nat Genet. 2016 Mar;48(3):331-5. (PMID: 26780608) Nat Rev Mol Cell Biol. 2021 Jun;22(6):410-424. (PMID: 33619373) Science. 2017 May 26;356(6340):. (PMID: 28495876) BMC Syst Biol. 2017 Nov 21;11(1):105. (PMID: 29157246) Nat Genet. 2006 Jun;38 Suppl:S20-4. (PMID: 16736020) Stem Cell Reports. 2013 Aug 22;1(3):235-47. (PMID: 24319660) Neuropsychopharmacology. 2013 Jan;38(1):23-38. (PMID: 22781841) Nature. 2018 Oct;562(7727):367-372. (PMID: 30283141) iScience. 2022 Jun 24;25(7):104651. (PMID: 35811849) Bioessays. 2023 Apr;45(4):e2200208. (PMID: 36871150) Nat Biotechnol. 2025 Feb;43(2):247-257. (PMID: 38609714) Nature. 2011 Jul 13;476(7359):228-31. (PMID: 21753754) Bioinform Adv. 2022 Mar 08;2(1):vbac016. (PMID: 36699385) Nat Methods. 2020 Oct;17(10):991-1001. (PMID: 32868927) Cell. 2014 Aug 14;158(4):889-902. (PMID: 25126792) Nucleic Acids Res. 2017 Jan 4;45(D1):D145-D150. (PMID: 27789689) Genome Res. 2021 Jul;31(7):1216-1229. (PMID: 33975875) Mol Cell. 2020 Aug 20;79(4):660-676.e8. (PMID: 32755593) Science. 2017 May 5;356(6337):. (PMID: 28473536) BMC Bioinformatics. 2010 Apr 01;11:165. (PMID: 20356413) Sci Adv. 2019 Mar 27;5(3):eaav3262. (PMID: 30944857) Histol Histopathol. 2022 Aug;37(8):723-737. (PMID: 35417038) Brief Funct Genomics. 2022 Jul 27;21(4):270-279. (PMID: 35411370) PLoS Comput Biol. 2023 Mar 27;19(3):e1010962. (PMID: 36972296) Cell. 1987 Dec 24;51(6):987-1000. (PMID: 3690668) PLoS One. 2013 May 21;8(5):e63577. (PMID: 23704920) Nature. 2020 Jul;583(7817):590-595. (PMID: 32669714) Proc Natl Acad Sci U S A. 2007 May 1;104(18):7327-31. (PMID: 17452639) Cell. 2014 Aug 14;158(4):903-915. (PMID: 25126793) Genome Biol. 2015 Aug 14;16:161. (PMID: 26268681) Cell. 2019 Feb 7;176(4):928-943.e22. (PMID: 30712874) Mol Syst Biol. 2016 Oct 20;12(10):883. (PMID: 27951527) Front Mol Biosci. 2022 Dec 02;9:1067406. (PMID: 36533073) Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. (PMID: 16199517) Cell Mol Life Sci. 2017 Oct;74(19):3553-3575. (PMID: 28698932) Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275. (PMID: 29126285) Int J Mol Sci. 2022 Dec 13;23(24):. (PMID: 36555471) PLoS Biol. 2007 Jan;5(1):e8. (PMID: 17214507) NAR Genom Bioinform. 2021 Nov 08;3(4):lqab100. (PMID: 34761218) Nat Genet. 2024 Jun;56(6):1181-1192. (PMID: 38769457) Nat Commun. 2021 Mar 12;12(1):1659. (PMID: 33712564) Nat Genet. 1999 Jul;22(3):281-5. (PMID: 10391217) Cell. 2023 Jan 5;186(1):209-229.e26. (PMID: 36608654) Trends Pharmacol Sci. 2014 Feb;35(2):76-85. (PMID: 24388790) Bioessays. 2011 Nov;33(11):830-9. (PMID: 21915889) Proteomics. 2023 Dec;23(23-24):e2200462. (PMID: 37706624) Nat Methods. 2022 Jul;19(7):812-822. (PMID: 35710610) Clin Epigenetics. 2021 Jul 23;13(1):144. (PMID: 34301318) Cell Death Differ. 2011 Dec;18(12):1815-24. (PMID: 21941372) Nucleic Acids Res. 2021 Aug 20;49(14):7966-7985. (PMID: 34244796) Nature. 2008 Oct 2;455(7213):627-32. (PMID: 18754011) iScience. 2022 Jul 14;25(8):104743. (PMID: 35942105) Adv Cancer Res. 2007;97:275-94. (PMID: 17419950) Nucleic Acids Res. 2023 Nov 10;51(20):10934-10949. (PMID: 37843125) Nat Commun. 2021 Sep 23;12(1):5609. (PMID: 34556644) Nucleic Acids Res. 2016 Jul 08;44(12):5615-28. (PMID: 26969735) Nature. 2010 Feb 25;463(7284):1035-41. (PMID: 20107439) Cell. 2018 Feb 8;172(4):650-665. (PMID: 29425488) Stem Cell Reports. 2015 Nov 10;5(5):763-775. (PMID: 26603904) In Silico Biol. 2020;14(3-4):89-113. (PMID: 34897081) |
| Substance Nomenclature: | 0 (Transcription Factors) |
| Entry Date(s): | Date Created: 20260206 Date Completed: 20260707 Latest Revision: 20260813 |
| Update Code: | 20260813 |
| PubMed Central ID: | PMC12988218 |
| DOI: | 10.1038/s41540-026-00652-z |
| PMID: | 41651868 |
| Βάση Δεδομένων: | MEDLINE |
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