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Synthetic Biology

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Designer artificial environments for membrane protein synthesis.

Nature communications
Protein synthesis in natural cells involves intricate interactions between chemical environments, protein-protein interactions, and protein machinery. Replicating such interactions in artificial and cell-free environments can control the precision of...

A novel interpretability framework for enzyme turnover number prediction boosted by pre-trained enzyme embeddings and adaptive gate network.

Methods (San Diego, Calif.)
It is a vital step to identify the enzyme turnover number (kcat) in synthetic biology and early-stage drug discovery. Recently, deep learning methods have achieved inspiring process to predict kcat with the development of multi-species enzyme-substra...

Engineering a New Generation of Gene Editors: Integrating Synthetic Biology and AI Innovations.

ACS synthetic biology
CRISPR-Cas technology has revolutionized biology by enabling precise DNA and RNA edits with ease. However, significant challenges remain for translating this technology into clinical applications. Traditional protein engineering methods, such as rati...

[Machine learning-aided design of synthetic biological parts and circuits].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Synthetic biology is an emerging interdisciplinary field at the convergence of biology, engineering, and computer science. It employs a bottom-up approach to progressively design biological parts, devices, and circuits, aiming to create artificial bi...

[Intelligent design of nucleic acid elements in biomanufacturing].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Nucleic acid elements are essential functional sequences that play critical roles in regulating gene expression, optimizing pathways, and enabling gene editing to enhance the production of target products in biomanufacturing. Therefore, the design an...

[Artificial intelligence-assisted design, mining, and modification of CRISPR-Cas systems].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
With the rapid advancement of synthetic biology, CRISPR-Cas systems have emerged as a powerful tool for gene editing, demonstrating significant potential in various fields, including medicine, agriculture, and industrial biotechnology. This review co...

[Databases, knowledge bases, and large models for biomanufacturing].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Biomanufacturing is an advanced manufacturing method that integrates biology, chemistry, and engineering. It utilizes renewable biomass and biological organisms as production media to scale up the production of target products through fermentation. C...

Combining diffusion and transformer models for enhanced promoter synthesis and strength prediction in deep learning.

mSystems
UNLABELLED: In the field of synthetic biology, the engineering of synthetic promoters that outperform their natural counterparts is of paramount importance, which can optimize the expression of exogenous genes, enhance the efficiency of metabolic pat...

Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida.

Communications biology
Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obtain the tit...

Paving the way for bacteria-based drug delivery: biohybrid microrobots emerging from microrobotics and synthetic biology.

Advanced drug delivery reviews
Advances in microrobotics and synthetic biology are paving the way for innovative solutions to long-standing challenges in drug delivery. Both fields have independently worked on engineering bacteria as a therapeutic system, focusing on enhancing pro...