EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Multi-omic data integration enables discovery of hidden biological regularities

Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi-level analysis of genomic, transcriptomic, ribosomal profiling, proteomic and fluxomic data. First, we show that pairwise integration of primary omics data reveals regularities that tie cellular processes together in Escherichia col...

SeqPlots - Interactive software for exploratory data analyses ,

Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate...

The challenges of integrating multi-omic data sets.

Editorial: Multi-omic data integration

As researchers involved in molecular biology, we are witnessing tremendous paradigm changes in a time frame that becomes shorter and shorter. The epoch-making notion, originally put forward by the central dogma of biology (Crick, 1970), that there is a unidirectional process and a privileged level (genetic) of causality at which biological functions are determined, has already long and strongly...

Complementary Domain Prioritization: A Method to Improve Biologically Relevant Detection in Multi-Omic Data Sets

As the speed and quality of different analytical platforms increase, it is more common to collect data across multiple biological domains in parallel (i.e., genomics, transcriptomics, proteomics, and metabolomics). There is a growing interest in algorithms and tools that leverage heterogeneous data streams in a meaningful way. Since these domains are typically non-linearly related, we evaluated...