AIMC Topic: Bacillus subtilis
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QSSR Modeling of Bacillus Subtilis Lipase A Peptide Collision Cross-Sections in Ion Mobility Spectrometry: Local Descriptor Versus Global Descriptor.
The protein journal
Jan 16, 2021
To investigate the structure-dependent peptide mobility behavior in ion mobility spectrometry (IMS), quantitative structure-spectrum relationship (QSSR) is systematically modeled and predicted for the collision cross section Ω values of totally 162 s...
Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome.
Nature communications
Dec 11, 2020
The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcrip...
Automated classification of bacterial cell sub-populations with convolutional neural networks.
PloS one
Oct 26, 2020
Quantification of phenotypic heterogeneity present amongst bacterial cells can be a challenging task. Conventionally, classification and counting of bacteria sub-populations is achieved with manual microscopy, due to the lack of alternative, high-thr...
Prediction and analysis of prokaryotic promoters based on sequence features.
Bio Systems
Aug 2, 2020
Promoter recognition is an important part of functional genomic annotation but a difficult problem. Many studies have been carried out to address this issue. However, they still cannot meet application needs. Most of the methods exhibit specificity, ...
Signal Peptides Generated by Attention-Based Neural Networks.
ACS synthetic biology
Jul 27, 2020
Short (15-30 residue) chains of amino acids at the amino termini of expressed proteins known as signal peptides (SPs) specify secretion in living cells. We trained an attention-based neural network, the Transformer model, on data from all available o...
A neural network model predicts community-level signaling states in a diverse microbial community.
PLoS computational biology
Jun 24, 2019
Signal crosstalk within biological communication networks is common, and such crosstalk can have unexpected consequences for decision making in heterogeneous communities of cells. Here we examined crosstalk within a bacterial community composed of fi...
A computational method for prediction of xylanase enzymes activity in strains of Bacillus subtilis based on pseudo amino acid composition features.
PloS one
Oct 22, 2018
Xylanases are hydrolytic enzymes which based on physicochemical properties, structure, mode of action and substrate specificities are classified into various glycoside hydrolase (GH) families. The purpose of this study is to show that the activity of...
Construction of an enzymatic route using a food-grade recombinant Bacillus subtilis for the production and purification of epilactose from lactose.
Journal of dairy science
Dec 28, 2017
Lactose is a main by-product in the cheese industry. Many attempts have been made to convert the lactose to high value-added products, including epilactose. Epilactose is a valuable prebiotic and can be epimerized from lactose with cellobiose 2-epime...
Antimicrobial Furoquinoline Alkaloids from Vepris lecomteana (Pierre) Cheek & T. Heller (Rutaceae).
Molecules (Basel, Switzerland)
Dec 21, 2017
Three new prenylated furoquinoline alkaloids named lecomtequinoline A (), B (), and C (), together with the known compounds anhydroevoxine (), evoxine (), dictamnine (), methylflindersine (), evoxanthine (), hesperidin, lupeol, -sitosterol, stigmaste...
Exploiting non-linear relationships between retention time and molecular structure of peptides originating from proteomes and comparing three multivariate approaches.
Journal of pharmaceutical and biomedical analysis
Jan 27, 2016
Peptides' retention time prediction is gaining increasing popularity in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics. This is a promising approach for improving successful proteome mapping, useful both in identification ...
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