AI Article Synopsis
- Promoters are essential in biotech, and Generative AI (GenAI) has shown promise in creating improved synthetic promoters, but its current methods have limitations related to programming and specific applications.* -
- GPro is a new, user-friendly toolkit that combines various GenAI methods for promoter design, providing a standardized process for training, optimization, and evaluation, along with demos to help users implement these techniques.* -
- Available as open-source software under the MIT license, GPro's source code can be accessed on GitHub and Zenodo, making it accessible for users across different operating systems.*
Article Abstract
Motivation: Promoters with desirable properties are crucial in biotechnological applications. Generative AI (GenAI) has demonstrated potential in creating novel synthetic promoters with significantly enhanced functionality. However, these methods' reliance on various programming frameworks and specific task-oriented contexts limits their flexibilities. Overcoming these limitations is essential for researchers to fully leverage the power of GenAI to design promoters for their tasks.
Results: Here, we introduce GPro (Generative AI-empowered toolkit for promoter design), a user-friendly toolkit that integrates a collection of cutting-edge GenAI-empowered approaches for promoter design. This toolkit provides a standardized pipeline covering essential promoter design processes, including training, optimization, and evaluation. Several detailed demos are provided to reproduce state-of-the-art promoter design pipelines. GPro's user-friendly interface makes it accessible to a wide range of users including non-AI experts. It also offers a variety of optional algorithms for each design process, and gives users the flexibility to compare methods and create customized pipelines.
Availability And Implementation: GPro is released as an open-source software under the MIT license. The source code for GPro is available on GitHub for Linux, macOS, and Windows: https://github.com/WangLabTHU/GPro, and is available for download via Zenodo repository at https://zenodo.org/doi/10.5281/zenodo.10681733.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10937896 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btae123 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Targeted inactivation of EWSR1 : : FLI1 gene in Ewing sarcoma via CRISPR/Cas9 driven by an Ewing-specific GGAA promoter.
Cancer Gene Ther
March 2025
Unidad de Tumores Sólidos Infantiles. Instituto de Investigación de Enfermedades Raras. Instituto de Salud Carlos III. Majadahonda, Madrid, Spain.
We have recently demonstrated that genetic inactivation of EWSR1 : : FLI1 by CRISPR/Cas9, successfully blocks cell proliferation in a cell model of Ewing sarcoma. However, CRISPR/Cas9-mediated gene editing can exhibit off-target effects, and thus, precise regulation of Cas9 expression in target cells is essential to develop gene-editing strategies to inactivate EWSR1 : : FLI1 in Ewing sarcoma cells. In this study, we demonstrate that Cas9 can be specifically expressed in Ewing sarcoma cells when located downstream a promoter consisting of GGAA repeats and a consensus TATA box (GGAAprom).
View Article and Find Full Text PDFUSP14 inhibits sensitization-mediated degradation of KDM4D to epigenetically regulate dendritic cell tolerogenic capacity and mitigates airway allergy.
Cell Immunol
March 2025
State Key Laboratory of Respiratory Diseases Allergy Division at Shenzhen University and Institute of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China. Electronic address:
Numerous immune disorders are caused by the dysfunction of dendritic cells (DC). The mechanism has not been fully comprehended yet. This research is designed to regulate the epigenetic status of lysine-specific demethylase 4D (KDM4D) to enhance DC's immune tolerogenic capacity.
View Article and Find Full Text PDFHealth care institutions and their physicians are the greatest promoters of COVID-19 vaccine acceptance among health care workers.
Vaccine
March 2025
Centre International de Recherche en Infectiologie, Team GIMAP, Univ Lyon, Université Jean Monnet, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR530, France; CIC INSERM 1408 Vaccinologie, CHU de Saint-Etienne, France; Chaire PREVACCI, Université Jean Monnet, Saint-Etienne, France. Electronic address:
Background: ESPERES, a prospective e-cohort study is designed to assess attitudes and perceptions of the COVID-19 pandemic among French health care workers.
Objectives: We aimed to document (i) their confidence in the information directly transmitted by their health care institutions; (ii) the role of physicians in the development of normative beliefs about vaccines against COVID-19 among them; (iii) their view of issues related to governmental health institution communication; and (iv) the impact of this communication on their posture to promote vaccine adherence among patients.
Methods: We conducted semistructured interviews with health care workers from the ESPERES cohort (n = 50).
Cardiac-Specific Gene Editing via an AAV9-Tnnt2-SaCas9-miR122TS Vector.
Bio Protoc
March 2025
School of Basic Medical Sciences, Institute of Cardiovascular Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing, China.
The adeno-associated virus serotype 9 (AAV9)-delivered gene expression driven by the cardiac troponin T (Tnnt2) promoter is broadly considered to be cardiac-specific. However, in cases where low AAV expression is sufficient to trigger a profound biological effect in CRISPR/Cas9 gene editing, the ectopic AAV9-Tnnt2 expression and gene editing in the liver becomes non-negligible. MicroRNA122 is a microRNA that is specifically expressed in the liver.
View Article and Find Full Text PDFdesign of a mechano-pharmaceutical screening platform against formation of individual beta-amyloid oligomers.
Cell Rep Phys Sci
December 2024
Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA.
Small molecules that can reduce the neurotoxic beta-amyloid (Aβ) aggregates in the brain provide a potential treatment for Alzheimer disease (AD). Most screening methods for small-molecule hits focus on the overall Aβ aggregations without a specific target, such as the very first association step (i.e.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!