AIMC Topic: Gene Library

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Forty years of directed evolution and its continuously evolving technology toolbox: A review of the patent landscape.

Biotechnology and bioengineering Jan 7, 2022
Generating functional protein variants with novel or improved characteristics has been a goal of the biotechnology industry and life sciences, for decades. Rational design and directed evolution are two major pathways to achieve the desired ends. Whi...
Biotechnology Directed Molecular Evolution Gene Library Artificial Intelligence Mutagenesis
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Precise Prediction of Promoter Strength Based on a De Novo Synthetic Promoter Library Coupled with Machine Learning.

ACS synthetic biology Dec 19, 2021
Promoters are one of the most critical regulatory elements controlling metabolic pathways. However, the fast and accurate prediction of promoter strength remains challenging, leading to time- and labor-consuming promoter construction and characteriza...
Gene Library Metabolic Networks and Pathways Artificial Intelligence Promoter Regions, Genetic Machine Learning
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Sequence motifs and prediction model of GBE editing outcomes based on target library analysis and machine learning.

Journal of genetics and genomics = Yi chuan xue bao Dec 2, 2021
Machine Learning Gene Editing Gene Library
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Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens.

Nature communications Aug 25, 2021
Base editors are chimeric ribonucleoprotein complexes consisting of a DNA-targeting CRISPR-Cas module and a single-stranded DNA deaminase. They enable transition of C•G into T•A base pairs and vice versa on genomic DNA. While base editors have great ...
Humans Genome Gene Library Algorithms Gene Editing High-Throughput Nucleotide Sequencing Deep Learning Base Pairing
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Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods.

Nature communications Aug 12, 2021
Efficient and precise base editors (BEs) for C-to-G transversion are highly desirable. However, the sequence context affecting editing outcome largely remains unclear. Here we report engineered C-to-G BEs of high efficiency and fidelity, with the seq...
Cytidine Deaminase Gene Library Caenorhabditis elegans Uracil-DNA Glycosidase Base Sequence Humans Escherichia coli Binding Sites Female CRISPR-Cas Systems Codon Reproducibility of Results HEK293 Cells Gene Editing Animals Machine Learning Mice
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A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers.

PLoS computational biology Aug 3, 2021
The selection of a DNA aptamer through the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method involves multiple binding steps, in which a target and a library of randomized DNA sequences are mixed for selection of a single, nucl...
Humans Artificial Intelligence Aptamers, Nucleotide Protein Binding Computational Biology Machine Learning Algorithms Ligands Gene Library Decision Trees Logistic Models SELEX Aptamer Technique Support Vector Machine Natural Language Processing Bayes Theorem
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Machine learning guided aptamer refinement and discovery.

Nature communications Apr 22, 2021
Aptamers are single-stranded nucleic acid ligands that bind to target molecules with high affinity and specificity. They are typically discovered by searching large libraries for sequences with desirable binding properties. These libraries, however, ...
Models, Chemical Lipocalin-2 Gene Library Ligands Drug Discovery Aptamers, Nucleotide Protein Binding Machine Learning Computer Simulation
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Machine learning based CRISPR gRNA design for therapeutic exon skipping.

PLoS computational biology Jan 8, 2021
Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders. However, many of the clinically successful therapies for exon skipping are transient oligonucleotide-based treatments ...
Mice Humans Exons CRISPR-Cas Systems Genetic Therapy Embryonic Stem Cells Cells, Cultured Machine Learning Gene Editing Gene Library RNA, Guide, CRISPR-Cas Systems Animals
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OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods.

Journal of chemical information and modeling Nov 19, 2020
Side-chain modeling is critical for protein structure prediction since the uniqueness of the protein structure is largely determined by its side-chain packing conformation. In this paper, differing from most approaches that rely on rotamer library sa...
Proteins Neural Networks, Computer Gene Library Protein Conformation Software
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Denoising DNA Encoded Library Screens with Sparse Learning.

ACS combinatorial science Jun 26, 2020
DNA-encoded libraries (DELs) are large, pooled collections of compounds in which every library member is attached to a stretch of DNA encoding its complete synthetic history. DEL-based hit discovery involves affinity selection of the library against ...
Gene Library Machine Learning DNA
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