Ningfeng Wu
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View article: DLFea4AMPGen de novo design of antimicrobial peptides by integrating features learned from deep learning models
DLFea4AMPGen de novo design of antimicrobial peptides by integrating features learned from deep learning models Open
Deep learning models show promise in accelerating the design and optimization of antimicrobial peptides (AMPs), but current methods face challenges, such as low success rates, or large virtual library scales. In this study, we introduce DL…
View article: <scp>MediaMatch</scp> : Prediction of Bacterial Growth on Different Culture Media Using the <scp>XGBoost</scp> Algorithm
<span>MediaMatch</span> : Prediction of Bacterial Growth on Different Culture Media Using the <span>XGBoost</span> Algorithm Open
Microorganism culturing is essential in microbiological research, with the selection of suitable culture media being critical for successful microbial growth. Traditionally, this selection has relied on empirical knowledge or trial and err…
View article: Rational protein engineering using an omni-directional multipoint mutagenesis generation pipeline
Rational protein engineering using an omni-directional multipoint mutagenesis generation pipeline Open
Generative models have transformed protein design by enabling the generation of extensive datasets. However, accurate identification of biologically active sequences with specific functions within such data remains a significant challenge.…
View article: Effective Gene Expression Prediction and Optimization from Protein Sequences
Effective Gene Expression Prediction and Optimization from Protein Sequences Open
High soluble protein expression in heterologous hosts is crucial for various research and applications. Despite considerable research on the impact of codon usage on expression levels, the relationship between protein sequence and expressi…
View article: Protein–protein interaction and site prediction using transfer learning
Protein–protein interaction and site prediction using transfer learning Open
The advanced language models have enabled us to recognize protein–protein interactions (PPIs) and interaction sites using protein sequences or structures. Here, we trained the MindSpore ProteinBERT (MP-BERT) model, a Bidirectional Encoder …
View article: MECE: a method for enhancing the catalytic efficiency of glycoside hydrolase based on deep neural networks and molecular evolution
MECE: a method for enhancing the catalytic efficiency of glycoside hydrolase based on deep neural networks and molecular evolution Open
High efficiency glycoside hydrolases (GH) are in high demand for numerous industrial applications. This study demonstrates the use of a deep neural network and molecular evolution (MECE) platform for predicting catalysis-enhancing mutation…
View article: Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome
Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome Open
Background Advances in DNA sequencing technologies have transformed our capacity to perform life science research, decipher the dynamics of complex soil microbial communities and exploit them for plant disease management. However, soil is …
View article: Additional file 1 of A novel thermophilic chitinase directly mined from the marine metagenome using the deep learning tool Preoptem
Additional file 1 of A novel thermophilic chitinase directly mined from the marine metagenome using the deep learning tool Preoptem Open
Additional file 1: Table S1. Genome information. Table S2. Chitinase_prediction.
View article: Cadmium Pollution Impact on the Bacterial Community Structure of Arable Soil and the Isolation of the Cadmium Resistant Bacteria
Cadmium Pollution Impact on the Bacterial Community Structure of Arable Soil and the Isolation of the Cadmium Resistant Bacteria Open
Microorganisms play an important role in the remediation of cadmium pollution in the soil and their diversity can be affected by cadmium. In this study, the bacterial community in arable soil samples collected from two near geographical si…
View article: An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25
An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25 Open
Background: Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd 2+ resistance. Results: In this study, we isolated two different Cd 2+ resistance Bacillus sp . strains, Bacillus vietamensis …
View article: An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25
An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25 Open
Background: Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd 2+ resistance. Results: In this study, we isolated two different Cd 2+ resistance Bacillus sp . strains, Bacillus vietamensis …
View article: An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25
An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25 Open
Background: Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd 2+ resistance. Results: In this study, we isolated two different Cd 2+ resistance Bacillus sp . strains, Bacillus vietamensis …
View article: An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25
An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25 Open
Background: Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd 2+ resistance. Results: In this study, we isolated two different Cd 2+ resistance Bacillus sp . strains, Bacillus vietamensis …
View article: An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25
An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25 Open
Background: Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd 2+ resistance. Results: In this study, we isolated two different Cd 2+ resistance Bacillus sp . strains, Bacillus vietamensis …
View article: Identification and characterization of sequence signatures in the Bacillus subtilis promoter Pylb for tuning promoter strength
Identification and characterization of sequence signatures in the Bacillus subtilis promoter Pylb for tuning promoter strength Open
Objective To thoroughly characterize the P ylb promoter and identify the elements that affect the promoter activity. Result The sequences flanking the − 35 and − 10 box of the P ylb promoter were divided into six segments, and six random-s…
View article: An operon consisting of a P-type ATPase gene and a transcriptional regular gene given the different cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25
An operon consisting of a P-type ATPase gene and a transcriptional regular gene given the different cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25 Open
Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd2+ resistance. In this study, we isolated two different Cd2+ resistance Bacillus sp. strains, Bacillus vietamensis 151-6 and Bacillus maris…
View article: Improving Cadmium Resistance in Escherichia coli Through Continuous Genome Evolution
Improving Cadmium Resistance in Escherichia coli Through Continuous Genome Evolution Open
Cadmium (Cd) is a heavy metal that is extremely toxic to many organisms; however, microbes are highly adaptable to extreme conditions, including heavy metal contamination. Bacteria can evolve in the natural environment, generating resistan…
View article: Presyncodon, a Web Server for Gene Design with the Evolutionary Information of the Expression Hosts
Presyncodon, a Web Server for Gene Design with the Evolutionary Information of the Expression Hosts Open
In the natural host, most of the synonymous codons of a gene have been evolutionarily selected and related to protein expression and function. However, for the design of a new gene, most of the existing codon optimization tools select the …