DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis.
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| Titel: | DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis. |
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| Autoren: | Liu W; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Li J; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Tang Y; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, USA., Zhao Y; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Liu C; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA., Song M; Brown University, Providence, RI, USA., Ju Z; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Kumar SV; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Lu Y; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Akbani R; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA., Mills GB; Knight Cancer Institute and Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA., Liang H; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. hliang1@mdanderson.org.; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, USA. hliang1@mdanderson.org.; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. hliang1@mdanderson.org.; Institute for Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. hliang1@mdanderson.org. |
| Quelle: | Nature communications [Nat Commun] 2025 Mar 06; Vol. 16 (1), pp. 2256. Date of Electronic Publication: 2025 Mar 06. |
| Publikationsart: | Journal Article |
| Sprache: | English |
| Info zur Zeitschrift: | Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: [London] : Nature Pub. Group |
| MeSH-Schlagworte: | Proteomics*/methods , Neoplasms*/metabolism , Neoplasms*/genetics , Computational Biology*/methods , Software*, Humans ; Biomarkers, Tumor/metabolism ; Cell Line, Tumor ; Protein Array Analysis ; Generative Artificial Intelligence |
| Abstract: | Functional proteomics provides critical insights into cancer mechanisms, facilitating the discovery of novel biomarkers and therapeutic targets. We have developed a comprehensive cancer functional proteomics resource using reverse phase protein arrays, incorporating data from nearly 8000 patient samples from The Cancer Genome Atlas and approximately 900 samples from the Cancer Cell Line Encyclopedia. Our dataset includes a curated panel of nearly 500 high-quality antibodies, covering all major cancer hallmark pathways. To enhance the accessibility and analytic power of this resource, we introduce DrBioRight 2.0 ( https://drbioright.org ), an intuitive bioinformatic platform powered by state-of-the-art large language models. DrBioRight enables researchers to explore protein-centric cancer omics data, perform advanced analyses, visualize results, and engage in interactive discussions using natural language. By streamlining complex proteogenomic analyses, this tool accelerates the translation of large-scale functional proteomics data into meaningful biomedical insights. (© 2025. The Author(s).) |
| Competing Interests: | Competing interests: R.A. is a bioinformatics consultant for the University of Houston. G.B.M. is on the scientific advisory board and/or a consultant for Amphista, Astex, AstraZeneca, BlueDot, Chrysallis Biotechnology, Ellipses Pharma, GSK, ImmunoMET, Infinity, Ionis, Leapfrog Bio, Lilly, Medacorp, Nanostring, Nuvectis, PDX Pharmaceuticals, Qureator, Roche, Signalchem Lifesciences, Tarveda, Turbine, and Zentalis Pharmaceuticals. G.B.M. has stock or receives income from BlueDot, Catena Pharmaceuticals, ImmunoMet, Nuvectis, SignalChem, Tarveda, and Turbine. G.B.M. has licensed HRD assay to Myriad Genetics. G.B.M. is an inventor on a patent (U.S. Patent No. 10501777) titled “Simultaneous quantification of a plurality of proteins in a user-defined region or a cross-sectioned tissue,” licensed to NanoString Technologies, Inc., which is unrelated to this study. G.B.M. also receives income for sponsored research from AstraZeneca. H.L. is a shareholder and advisor for Precision Scientific. The remaining authors declare no competing interests. |
| References: | Cancer Res. 2017 Nov 1;77(21):e23-e26. (PMID: 29092932) Cancer Cell. 2017 Feb 13;31(2):225-239. (PMID: 28196595) Oncogene. 2001 Apr 12;20(16):1981-9. (PMID: 11360182) F1000Res. 2019 Oct 18;8:1774. (PMID: 31819800) Nat Cancer. 2024 Oct;5(10):1579-1595. (PMID: 39227745) Nucleic Acids Res. 2013 Jan;41(Database issue):D955-61. (PMID: 23180760) Clin Proteomics. 2010 Dec;6(4):129-51. (PMID: 21691416) Nat Genet. 2013 Oct;45(10):1113-20. (PMID: 24071849) Nat Commun. 2014 May 29;5:3887. (PMID: 24871328) Nature. 2020 Dec;588(7837):331-336. (PMID: 33299191) Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S15-S25. (PMID: 31201206) Cell. 2016 Jul 28;166(3):740-754. (PMID: 27397505) Nature. 2012 Mar 28;483(7391):603-7. (PMID: 22460905) Genome Biol. 2021 Dec 20;22(1):343. (PMID: 34930405) Cell. 2013 Aug 29;154(5):1151-1161. (PMID: 23993102) Nat Cancer. 2020 Feb;1(2):235-248. (PMID: 32613204) Cell Syst. 2015 Dec 23;1(6):417-425. (PMID: 26771021) Adv Exp Med Biol. 2019;1188:113-147. (PMID: 31820386) Nature. 2012 Mar 28;483(7391):570-5. (PMID: 22460902) Cancer Discov. 2015 Nov;5(11):1210-23. (PMID: 26482930) Bioinformatics. 2007 Aug 1;23(15):1986-94. (PMID: 17599930) Nat Methods. 2013 Nov;10(11):1046-7. (PMID: 24037243) Mol Cell Proteomics. 2014 Jul;13(7):1625-43. (PMID: 24777629) |
| Grant Information: | P30 CA016672 United States CA NCI NIH HHS; U24 CA264128 United States CA NCI NIH HHS; U01 CA253472 United States CA NCI NIH HHS; P50 CA281701 United States CA NCI NIH HHS; U24264128 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI); U24 CA210950 United States CA NCI NIH HHS; U24 CA264006 United States CA NCI NIH HHS; R01 CA251150 United States CA NCI NIH HHS; P50 CA221703 United States CA NCI NIH HHS; P50 CA070907 United States CA NCI NIH HHS; U24 CA210949 United States CA NCI NIH HHS; U01 CA281902 United States CA NCI NIH HHS; R50 CA221675 United States CA NCI NIH HHS |
| Substance Nomenclature: | 0 (Biomarkers, Tumor) |
| Entry Date(s): | Date Created: 20250306 Date Completed: 20250511 Latest Revision: 20250721 |
| Update Code: | 20250721 |
| PubMed Central ID: | PMC11885830 |
| DOI: | 10.1038/s41467-025-57430-4 |
| PMID: | 40050282 |
| Datenbank: | MEDLINE |
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Nájsť tento článok vo Web of Science | Abstract: | Functional proteomics provides critical insights into cancer mechanisms, facilitating the discovery of novel biomarkers and therapeutic targets. We have developed a comprehensive cancer functional proteomics resource using reverse phase protein arrays, incorporating data from nearly 8000 patient samples from The Cancer Genome Atlas and approximately 900 samples from the Cancer Cell Line Encyclopedia. Our dataset includes a curated panel of nearly 500 high-quality antibodies, covering all major cancer hallmark pathways. To enhance the accessibility and analytic power of this resource, we introduce DrBioRight 2.0 ( https://drbioright.org ), an intuitive bioinformatic platform powered by state-of-the-art large language models. DrBioRight enables researchers to explore protein-centric cancer omics data, perform advanced analyses, visualize results, and engage in interactive discussions using natural language. By streamlining complex proteogenomic analyses, this tool accelerates the translation of large-scale functional proteomics data into meaningful biomedical insights.<br /> (© 2025. The Author(s).) |
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| ISSN: | 2041-1723 |
| DOI: | 10.1038/s41467-025-57430-4 |