Yi‐Xin Huo
YOU?
Author Swipe
View article: Design of strictly orthogonal biosensors for maximizing renewable biofuel overproduction
Design of strictly orthogonal biosensors for maximizing renewable biofuel overproduction Open
By demonstrating the dominant role of the BSH counts in TF-SM interactions and establishing a machine learning-guided framework for TF evolution, this work advances rational design principles for engineering TFs with precise molecular reco…
View article: Design of function-regulating RNA via deep learning and AlphaFold 3
Design of function-regulating RNA via deep learning and AlphaFold 3 Open
RNAs are programmable macromolecules that play diverse regulatory roles in living organisms. However, the intricate structure–function relationships underlying their regulatory activities pose significant challenges for RNA design. Here, w…
View article: A recombineering-based platform for high-throughput genomic editing in <i>Escherichia coli</i>
A recombineering-based platform for high-throughput genomic editing in <i>Escherichia coli</i> Open
Functional analysis of bacterial genes or genomic fragments in vivo primarily relies on the analysis of knockout strains. Although various methods have successfully generated bacterial knockout mutants, the parallel operation of multiple s…
View article: Chromosome-segment scanning for gain- or loss-of-function screening (CHASING)
Chromosome-segment scanning for gain- or loss-of-function screening (CHASING) Open
Identifying beneficial or functional mutations for a specific species is a task always relies on the labor-intensive construction of a library containing thousands of single-gene knockout or interference strains. Here, we systematically de…
View article: Protocol for identification of sgRNA mutants using high-throughput screening technique and multiplex genome editing
Protocol for identification of sgRNA mutants using high-throughput screening technique and multiplex genome editing Open
In the CRISPR-Cas9 system, tandem expression of multiple identical single-guide RNAs (sgRNAs) often triggers homologous sequences loss, which affects multiplex genome editing efficiencies. Here, we present a protocol for high-throughput sc…
View article: Customization of Ethylene Glycol (EG)‐Induced BmoR‐Based Biosensor for the Directed Evolution of PET Degrading Enzymes
Customization of Ethylene Glycol (EG)‐Induced BmoR‐Based Biosensor for the Directed Evolution of PET Degrading Enzymes Open
The immense volume of plastic waste poses continuous threats to the ecosystem and human health. Despite substantial efforts to enhance the catalytic activity, robustness, expression, and tolerance of plastic‐degrading enzymes, the lack of …
View article: Recent advances in biosynthesis of non-canonical amino acids and their potentials in strain engineering
Recent advances in biosynthesis of non-canonical amino acids and their potentials in strain engineering Open
Non-canonical amino acids (ncAAs), as derivatives of canonical amino acids (cAAs), when specifically incorporated into proteins, could enrich protein functions. Currently, ncAAs mostly depend on chemical synthesis; however, biosynthesis of…
View article: Language model generates<i>cis-</i>regulatory elements across prokaryotes
Language model generates<i>cis-</i>regulatory elements across prokaryotes Open
Deep learning had succeeded in designing Cis -regulatory elements (CREs) for certain species, but necessitated training data derived from experiments. Here, we present Promoter-Factory, a protocol that leverages language models (LM) to des…
View article: Chlomito: a novel tool for precise elimination of organelle genome contamination from nuclear genome assembly
Chlomito: a novel tool for precise elimination of organelle genome contamination from nuclear genome assembly Open
Introduction Accurate reference genomes are fundamental to understanding biological evolution, biodiversity, hereditary phenomena and diseases. However, many assembled nuclear chromosomes are often contaminated by organelle genomes, which …
View article: Identification of functional sgRNA mutants lacking canonical secondary structure using high-throughput FACS screening
Identification of functional sgRNA mutants lacking canonical secondary structure using high-throughput FACS screening Open
Coexpressing multiple identical single guide RNAs (sgRNAs) in CRISPR-dependent engineering triggers genetic instability and phenotype loss. To provide sgRNA derivatives for efficient DNA digestion, we design a high-throughput digestion-act…
View article: Design nonrepetitive and diverse activity single-guide RNA by deep learning
Design nonrepetitive and diverse activity single-guide RNA by deep learning Open
Multiplex and precise control of the gene expression based on CRISPR/Cas9 is important to metabolic regulation in synthetic biology. However, employing single guide RNAs (sgRNAs) that possess repetitive DNA sequences and exhibit uniform ac…
View article: Species-specific design of artificial promoters by transfer-learning based generative deep-learning model
Species-specific design of artificial promoters by transfer-learning based generative deep-learning model Open
Native prokaryotic promoters share common sequence patterns, but are species dependent. For understudied species with limited data, it is challenging to predict the strength of existing promoters and generate novel promoters. Here, we deve…
View article: Concentration Recognition‐Based Auto‐Dynamic Regulation System (CRUISE) Enabling Efficient Production of Higher Alcohols
Concentration Recognition‐Based Auto‐Dynamic Regulation System (CRUISE) Enabling Efficient Production of Higher Alcohols Open
Microbial factories lacking the ability of dynamically regulating the pathway enzymes overexpression, according to in situ metabolite concentrations, are suboptimal, especially when the metabolic intermediates are competed by growth and ch…
View article: Chrom-pro: A User-Friendly Toolkit for De-novo Chromosome Assembly and Genomic Analysis
Chrom-pro: A User-Friendly Toolkit for De-novo Chromosome Assembly and Genomic Analysis Open
Chromosome-level genome assembly is fundamental to current genomic and post-genomic research, however, the process remains complicated and challenging due to the lack of a standardized automatic workflow. The frequently-used method for hig…
View article: Chlomito: a novel tool for precise elimination of organelle genome contamination in nuclear genome assemblies
Chlomito: a novel tool for precise elimination of organelle genome contamination in nuclear genome assemblies Open
Accurate genome assemblies are crucial for understanding biological evolution, mechanisms of disease, and biodiversity. However, contamination from organelle genomes in nuclear genome analyses often leads to inaccuracies and unreliability …
View article: Chromosome segment scanning for gain- or loss-of-function screening (CHASING) and its application in metabolic engineering
Chromosome segment scanning for gain- or loss-of-function screening (CHASING) and its application in metabolic engineering Open
Constructing a library of thousands of single-gene knockout or interference strains is a powerful tool to understand the relation between genotype and phenotype, but it is labor and cost intensive. Powered by the computer-aided gene annota…
View article: Advancements in the Bio-degradation of Plastic Waste into Value-added Chemicals: A Recent Perspective
Advancements in the Bio-degradation of Plastic Waste into Value-added Chemicals: A Recent Perspective Open
Plastics are an essential component of modern life, but the plastic waste has caused significant environmental pollution and economic losses. The effective solution to these problems is the biodegradation and high-value conversion of plast…
View article: Species-specific design of artificial promoters by transfer-learning based generative deep-learning model
Species-specific design of artificial promoters by transfer-learning based generative deep-learning model Open
Native prokaryotic promoters share common sequence patterns, but are species dependent. For understudied species with limited data, it is challenging to predict the strength of existing promoters and generate novel promoters. Here, we deve…
View article: Biofuel and chemical production by recombinant microorganisms via fermentation of proteinaceous biomass
Biofuel and chemical production by recombinant microorganisms via fermentation of proteinaceous biomass Open
Provided herein are metabolically modified microorganisms characterized by having an increased keto-acid flux when compared with the wild-type organism and comprising at least one polynucleotide encoding an enzyme that when expressed resul…
View article: Recent advances in screening amino acid overproducers
Recent advances in screening amino acid overproducers Open
Microbial fermentation has contributed to 80% of global amino acid production. The key to microbial fermentation is to obtain fermentation strains with high performance to produce target amino acids with a high yield. These strains are pri…
View article: Incorporation of Non-Canonical Amino Acids into Antimicrobial Peptides: Advances, Challenges, and Perspectives
Incorporation of Non-Canonical Amino Acids into Antimicrobial Peptides: Advances, Challenges, and Perspectives Open
The emergence of antimicrobial resistance is a global health concern and calls for the development of novel antibiotic agents. Antimicrobial peptides seem to be promising candidates due to their diverse sources, mechanisms of action, and p…
View article: A tRNA Modification-based strategy for Identifying amiNo acid Overproducers (AMINO)
A tRNA Modification-based strategy for Identifying amiNo acid Overproducers (AMINO) Open
Amino acids have a multi-billion-dollar market with rising demand, prompting the development of high-performance microbial factories. However, a general screening strategy applicable to all proteinogenic and non-proteinogenic amino acids i…
View article: A consolidated review of commercial-scale high-value products from lignocellulosic biomass
A consolidated review of commercial-scale high-value products from lignocellulosic biomass Open
For decades, lignocellulosic biomass has been introduced to the public as the most important raw material for the environmentally and economically sustainable production of high-valued bioproducts by microorganisms. However, due to the str…
View article: Toward bioproduction of oxo chemicals from C1 feedstocks using isobutyraldehyde as an example
Toward bioproduction of oxo chemicals from C1 feedstocks using isobutyraldehyde as an example Open
Oxo chemicals are valuable chemicals for synthesizing a wide array of industrial and consumer products. However, producing of oxo chemicals is predominately through the chemical process called hydroformylation, which requires petroleum-sou…
View article: Metabolic Engineering and Regulation of Diol Biosynthesis from Renewable Biomass in Escherichia coli
Metabolic Engineering and Regulation of Diol Biosynthesis from Renewable Biomass in Escherichia coli Open
As bulk chemicals, diols have wide applications in many fields, such as clothing, biofuels, food, surfactant and cosmetics. The traditional chemical synthesis of diols consumes numerous non-renewable energy resources and leads to environme…
View article: Efficient Large-Scale and Scarless Genome Engineering Enables the Construction and Screening of Bacillus subtilis Biofuel Overproducers
Efficient Large-Scale and Scarless Genome Engineering Enables the Construction and Screening of Bacillus subtilis Biofuel Overproducers Open
Bacillus subtilis is a versatile microbial cell factory that can produce valuable proteins and value-added chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirabl…