Related papers: A Comparison of Microbial Genome Web Portals
The aim of this work is the comparison of the performance of the three popular software platforms JAGS, NIMBLE and Stan. These probabilistic programming languages are able to automatically generate samples from the posterior distribution of…
Characterizing the anchoring properties of smectic liquid crystals (LCs) in contact with bacterial solutions is crucial for developing biosensing platforms. In this study, we investigate the anchoring properties of a smectic LC when exposed…
Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
Cervical (CC) and endometrial cancers (EC) are two common types of gynecological tumors that threaten the health of females worldwide. Since their underlying mechanisms and associations remain unclear, computational bioinformatics analysis…
Cancer Biotherapy (CB), as opposed to cancer chemotherapy, is the use of macromolecular, biological agents instead of organic chemicals or drugs to treat cancer. Biological agents usually have higher selectivity and have less toxic side…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably…
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…
Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various…
In many key applications of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect changes in metabolic processes, usually represented in the form of pathways. As an alternative, a broader point of view…
Integrative network modeling of data arising from multiple genomic platforms provides insight into the holistic picture of the interactive system, as well as the flow of information across many disease domains including cancer. The basic…
Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already…
Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers…
Bacteria pose unique challenges for genome-wide association studies (GWAS) because of strong structuring into distinct strains and substantial linkage disequilibrium across the genome. While methods developed for human studies can correct…
The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network…
The heterogeneous computing paradigm has led to the need for portable and efficient programming solutions that can leverage the capabilities of various hardware devices, such as NVIDIA, Intel, and AMD GPUs. This study evaluates the…