Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Designing Molecular RNA Switches with Restricted Boltzmann Machines

ABSTRACT: Designing Molecular RNA Switches with Restricted Boltzmann Machines

PROVIDER: PRJNA1106466 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28856500_1.fastq.gz	Fastqsanger.gz
	SRR28856500_2.fastq.gz	Fastqsanger.gz
	SRR28856600_1.fastq.gz	Fastqsanger.gz
	SRR28856600_2.fastq.gz	Fastqsanger.gz
	SRR28856501_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 344

Similar Datasets

Designing Molecular RNA Switches with Restricted Boltzmann Machines

Project description:Riboswitches are structured allosteric RNA molecules that change conformation in response to a metabolite binding event, eventually triggering a regulatory response. Computational modelling of the structure of these molecules is complicated by a complex network of tertiary contacts, stabilized by the presence of their cognate metabolite. In this work, we focus on the aptamer domain of SAM-I riboswitches and show that Restricted Boltzmann machines (RBM), an unsupervised machine learning architecture, can capture intricate sequence dependencies induced by secondary and tertiary structure, as well as a switching mechanism between open and closed conformations. The RBM model is then used for the design of artificial allosteric SAM-I aptamers. To experimentally validate the functionality of the designed sequences, we resort to chemical probing (SHAPE-MaP), and develop a tailored analysis pipeline adequate for high-throughput tests of diverse homologous sequences. We probed a total of 476 RBM designed sequences in two experiments, showing between 20% and 40% divergence from any natural sequence, obtaining ≈ 30% success rate of correctly structured aptamers that undergo a structural switch in response to SAM.

2024-05-06 | GSE266263 | GEO

Light-activated molecular machines are new mode-of-action, fast-acting broad-spectrum antibacterials that target the membrane

Project description:Light-activated molecular machines (MNM) are synthetic molecular structures that, following light activation, undergo successive unidirectional rotation that results in a drilling-like rapid motion that can thrust the motor through biological membranes.Visible light (405 nm) activated MM were investigated for their antibacterial potential and their mechanism of action was investigated by RNAseq.

2022-01-27 | GSE194286 | GEO

Bacteria in Washing machines

Project description:Washing machines Raw sequence reads

| PRJNA971391 | ENA

Cell Fate Determining Molecular Switches and Signaling Pathway in Pax7-expressing Somitic Mesoderm

Project description:Cell Fate Determining Molecular Switches and Signaling Pathway in Pax7-expressing Somitic Mesoderm

| PRJNA666903 | ENA

Assessing antibiotic-resistant genes in University Dormitory Washing Machines

Project description:antibiotic-resistant genes in Washing Machines

| PRJEB75912 | ENA

Biofilm clogging water pumps in ice machines.

Project description:Biofilm clogging water pumps in ice machines. Raw sequence reads

| PRJNA782825 | ENA

Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study

Project description:Allergen-specific immunotherapy (AIT) induces immune tolerance, showing the highest success rate (>95%) for insect venom while a much lower chance for pollen allergy. However, the molecular switches leading to successful durable tolerance restoration remain elusive. Here we applied a multilayer-omics approach to reveal dynamic peripheral immune landscapes during AIT-initiation phase in venom allergy patients (VAP) versus pollen-allergic and healthy controls. Already at baseline, VAP exhibited altered abundances of several cell types, including classical monocytes (cMono) and CD4/CD8 type 1-type 17 hybrids. At 8-24h following AIT launch in VAP, we identified a uniform AIT-elicited pulse of late-transitional/IL-10-producing B cells, IL-6 signaling within Th2 cells and non-inflammatory serum-IL-6 levels. Sequential induction of activation and survival protein markers also immediately occurred. A disequilibrium between serum IL-6 and cMono in VAP baseline was restored at day seven following AIT launch. Our longitudinal analysis discovers molecular switches during initiation-phase insect-venom AIT that secure long-term outcomes. Trial number: NCT02931955.

2024-10-30 | GSE240503 | GEO

Temperature based Restricted Boltzmann Machines.

Project description:Restricted Boltzmann machines (RBMs), which apply graphical models to learning probability distribution over a set of inputs, have attracted much attention recently since being proposed as building blocks of multi-layer learning systems called deep belief networks (DBNs). Note that temperature is a key factor of the Boltzmann distribution that RBMs originate from. However, none of existing schemes have considered the impact of temperature in the graphical model of DBNs. In this work, we propose temperature based restricted Boltzmann machines (TRBMs) which reveals that temperature is an essential parameter controlling the selectivity of the firing neurons in the hidden layers. We theoretically prove that the effect of temperature can be adjusted by setting the parameter of the sharpness of the logistic function in the proposed TRBMs. The performance of RBMs can be improved by adjusting the temperature parameter of TRBMs. This work provides a comprehensive insights into the deep belief networks and deep learning architectures from a physical point of view.

| S-EPMC4725829 | biostudies-other

A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs.

Project description:The programmability of RNA-RNA interactions through intermolecular base-pairing has been successfully exploited to design a variety of RNA devices that artificially regulate gene expression. An in silico design for interacting structured RNA sequences that satisfies multiple design criteria becomes a complex multi-objective problem. Although multi-objective optimization is a powerful technique that explores a vast solution space without empirical weights between design objectives, to date, no web service for multi-objective design of RNA switches that utilizes RNA-RNA interaction has been proposed. We developed a web server, which is based on a multi-objective design algorithm called MODENA, to design two interacting RNAs that form a complex in silico. By predicting the secondary structures with RactIP during the design process, we can design RNAs that form a joint secondary structure with an external pseudoknot. The energy barrier upon the complex formation is modeled by an interaction seed that is optimized in the design algorithm. We benchmarked the RNA switch design approaches (MODENA+RactIP and MODENA+RNAcofold) for the target structures based on natural RNA-RNA interactions. As a result, MODENA+RactIP showed high design performance for the benchmark datasets.

| S-EPMC7962656 | biostudies-literature

Light-activated molecular machines are new mode-of-action, fast-acting broad-spectrum antibacterials that target the membrane

Project description:Light-activated molecular machines are new mode-of-action, fast-acting broad-spectrum antibacterials that target the membrane

| PRJNA800066 | ENA