Anil Wipat

Bi-level diversity optimisation for representative protein panel selection

Zhen Ou, Katherine L. James, Simon J. Charnock, Anil Wipat

Abstract Selecting representative subsets from large protein sequence datasets is a common challenge in enzyme discovery and related tasks under limited screening capacity. In practice, candidate panels are often constructed using clustering-based redundancy reduction or manual selection guided by phylogenetic or similarity-network …

gb (code pays fourni par la source)

Synergistic Network Pharmacology: Preclinical Validation and Clinical Safety in Acute Ischemic Stroke

Ana Isabel Casas, Cristian Nogales, Fabian Szepanowski, Mahmoud H. Elbatreek et autres

Background Most human disease definitions, except for rare and communicable diseases, are based on symptoms in specific organs, not on causal molecular mechanisms. This limits treatments to imprecise symptomatic approaches with high numbers needed to treat. Systems medicine, instead, has a holistic …

nl, de, Égypte, gb, dk (code pays fourni par la source)

Enhancing multi-omic analyses through a federated microbiome analysis service

Alexander B. Rogers, Famke Bäuerle, Martín Beracochea, Alireza Heidari et autres

Multi-omics datasets are an increasingly prevalent and necessary resource for achieving scientificadvances in microbial ecosystem research. However, they present twin challenges to researchinfrastructures: firstly the utility of multi-omics datasets relies entirely on interoperability ofomics layers, i.e. on formalised data linking. Secondly, microbiome …

gb, de, es (code pays fourni par la source)

NeDRex-Web: An Interactive Web Tool for Drug Repurposing by Exploring Heterogeneous Molecular Networks

Andreas Maier, Mahdie Rafiei, Elisa Anastasi, Olga I. Zolotareva et autres

Finding new indications for approved drugs is a promising alternative to the often very lengthy and expensive process of de novo drug development. Systems medicine has brought forth several different approaches to tackle this important task. We recently published NeDRex, a network …

de, gb, dk, nl (code pays fourni par la source)

Metagenomic mining for cold-adapted phage enzymes

A. G. Wiseman, Ehmke Pohl, Anil Wipat

gb (code pays fourni par la source)

A Numerical Bio-Geotechnical Model of Pressure-Responsive Microbially Induced Calcium Carbonate Precipitation

Jianye Wang, Helen Mitrani, Anil Wipat, Polly Moreland et autres

The employment of Microbially Induced Calcium Carbonate Precipitation (MICP) is of increasing interest as a technique for environmentally sustainable soil stabilisation. Recent advancements in synthetic biology have allowed for the conception of a pressure-responsive MICP process, wherein bacteria are engineered to sense …

cn, gb (code pays fourni par la source)

Multiplex detection of the big five carbapenemase genes using solid-phase recombinase polymerase amplification

Christopher Johnson, Matthew A. Setterfield, Waleed A. Hassanain, Anil Wipat et autres

Five carbapenemase enzymes, coined the 'big five', have been identified as the biggest threat to worldwide antibiotic resistance based on their broad substrate affinity and global prevalence. Here we show the development of a molecular detection method for the gene sequences from …

gb (code pays fourni par la source)

BioRxToolbox: a computational framework to streamline genetic circuit design in molecular data communications

Merve Gorkem Durmaz, Neval Tulluk, Recep Deniz Aksoy, Bill Huajian Yang et autres

Developments in bioengineering and nanotechnology have ignited the research on biological and molecular communication systems. Despite potential benefits, engineering communication systems to carry data signals using biological messenger molecules and engineered cells is challenging. Diffusing molecules may fall behind their schedule to …

tr, gb (code pays fourni par la source)

A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem

Christian Atallah, Katherine L. James, Zhen Ou, James Skelton et autres

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GENETTA: a Network-Based Tool for the Analysis of Complex Genetic Designs

Matthew Crowther, Anil Wipat, Ángel Goñi‐Moreno

GENETTA is a software tool that transforms synthetic biology designs into networks using graph theory for analysis and manipulation. By representing complex data as interconnected points, GENETTA allows dynamic customization of visualizations, including interaction networks and parts hierarchies. It can also merge …

es, gb (code pays fourni par la source)

Transcriptional biomarker discovery toward building a load stress reporting system for engineered Escherichia coli strains

Yiming Huang, Anil Wipat, Jaume Bacardit

Foreign proteins are produced by introducing synthetic constructs into host bacteria for biotechnology applications. This process can cause resource competition between synthetic circuits and host cells, placing a metabolic burden on the host cells which may result in load stress and detrimental …

gb (code pays fourni par la source)

Streamlining and generalizing network-based drug discovery with NeDRex and Drugst.One

Fernando M. Delgado-Chaves, Sepideh Sadegh, James Skelton, Andreas Maier et autres

NeDRex (Network-based Drug Repurposing Explorer) (Sadegh et al. 2021, 2022) is a network-based computational tool used for drug repurposing. The NeDRex database houses a rich collection of data on Protein-Protein and Drug-Protein (target) interactions and integrates diverse data sources. The outcome is …

de, gb, mx (code pays fourni par la source)