Published in Epigenetics & Chromatin
BackgroundCurrent array-based methods for the measurement of DNA methylation rely on the process of sodium bisulfite conversion to differentiate between methylated and unmethylated cytosine bases in DNA. In the absence of genotype data this process can lead to ambiguity in data interpretation when a sample has polymorphisms at a methylation probe s...
Published in Journal of Hydrodynamics
Almost everything I have done in the last twenty years is based on what I have discovered from studying ocean phenomena. Specifically, the waves on the surface of the ocean and their dynamics. Two items stand out: The first one is from studying the evolution of the waves from ripples to fully developed giant ocean waves. To quantify the changes, I ...
Published in BMC Bioinformatics
BackgroundStudies on multiple modalities of omics data such as transcriptomics, genomics and proteomics are growing in popularity, since they allow us to investigate complex mechanisms across molecular layers. It is widely recognized that integrative omics analysis holds the promise to unlock novel and actionable biological insights into health and...
Published in BMC Bioinformatics
BackgroundFlow cytometry (FCM) is a powerful single-cell based measurement method to ascertain multidimensional optical properties of millions of cells. FCM is widely used in medical diagnostics and health research. There is also a broad range of applications in the analysis of complex microbial communities. The main concern in microbial community ...
Published in Journal of Cheminformatics
Metabolic profiling has been shown to be useful to improve our understanding of complex metabolic processes. Shared data are key to the analysis and validation of metabolic profiling and untargeted spectral analysis and may increase the pace of new discovery. Improving the existing portfolio of open software may increase the fraction of shared data...
Abstract: The biggest challenge facing in sugar-energy plants is to move towards the biorefinery concept, without threatening the environment and health. Energy cane is the state-of-the-art of smart energy crops to provide suitable whole-raw material to produce upgraded biofuels, dehydrated alcohol for transportation, refined sugar, yeast- fermente...
Data from social media offer us multimedia data brimming with multiple layers of meanings. Social media enable rapid-fire digital communications. These communications are incredibly complex in content, form and meaning. This representational complexity is a stumbling block in data analysis that stands in the way of deeper explanations. These unstru...
Published in Community Ecology
The methods for data presentation are important in bioinformatics as data processing algorithms. The article describes the software package for the extensive analysis of tables with estimates of bacterial abundance levels in environmental samples. The package was designed to be executed in a distributed hardware environment, with powerful packages ...
Published in BioData Mining
BackgroundThe sequencing platform BGISEQ-500 is based on DNBSEQ technology and provides high throughput with low costs. This sequencer has been widely used in various areas of scientific and clinical research. A better understanding of the sequencing process and performance of this system is essential for stabilizing the sequencing process, accurat...
Published in BMC Bioinformatics
BackgroundAnalysing large and high-dimensional biological data sets poses significant computational difficulties for bioinformaticians due to lack of accessible tools that scale to hundreds of millions of data points.ResultsWe developed a novel machine learning command line tool called PyBDA for automated, distributed analysis of big biological dat...
