AIMC Topic: Synthetic Biology
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Cell-type-directed design of synthetic enhancers.
Nature
Dec 12, 2023
Transcriptional enhancers act as docking stations for combinations of transcription factors and thereby regulate spatiotemporal activation of their target genes. It has been a long-standing goal in the field to decode the regulatory logic of an enhan...
Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.
Nature
Dec 12, 2023
Enhancers control gene expression and have crucial roles in development and homeostasis. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning t...
Enabling AI in synthetic biology through Construction File specification.
PloS one
Nov 13, 2023
The Construction File (CF) specification establishes a standardized interface for molecular biology operations, laying a foundation for automation and enhanced efficiency in experiment design. It is implemented across three distinct software projects...
Generative Artificial Intelligence GPT-4 Accelerates Knowledge Mining and Machine Learning for Synthetic Biology.
ACS synthetic biology
Sep 8, 2023
Knowledge mining from synthetic biology journal articles for machine learning (ML) applications is a labor-intensive process. The development of natural language processing (NLP) tools, such as GPT-4, can accelerate the extraction of published inform...
Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes.
ACS synthetic biology
Jul 19, 2023
Engineering biology relies on the accurate prediction of cell responses. However, making these predictions is challenging for a variety of reasons, including the stochasticity of biochemical reactions, variability between cells, and incomplete inform...
De novo design of protein interactions with learned surface fingerprints.
Nature
Apr 26, 2023
Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. ...
Synthetic biology, genetic circuits and machine learning: a new age of cancer therapy.
Molecular oncology
Apr 1, 2023
Synthetic biology has made it possible to rewire natural cellular responses to treat disease, notably demonstrated by chimeric antigen receptor (CAR) T cells as cancer immunotherapy. Building on the success of T-cell activation using synthetic recept...
Precision engineering of biological function with large-scale measurements and machine learning.
PloS one
Mar 29, 2023
As synthetic biology expands and accelerates into real-world applications, methods for quantitatively and precisely engineering biological function become increasingly relevant. This is particularly true for applications that require programmed sensi...
Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.
Plant communications
Feb 9, 2023
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of...
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