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Bioinformatics and Systems Biology services
We can provide the full cycle of your data analysis needs starting from raw omics data processing and ending with solving your particular biomedical problem.
End-to-End multi-omics services
We can start from raw or pre-processed genomics, transcriptomics, proteomics, epigenomics or metabolomics datasets and enhance your understanding of the biology behind any studied process by reconstructing its molecular mechanism based on the power of the combined dataset analysis.
We will assist you in your multi-omics data analysis starting from any point. You can come to us with raw omics data or with pre-processed datasets – we will step in at the stage needed and will bring your data to the meaningful biology hidden behind it.
Promoter analysis: gene regulation studies
We will perform search for TF binding sites on genomic regions of your choice: either in promoters of selected target genes, or in the peaks calculated from ChIP-seq data, or in any input DNA sequences.
We can assist you in identifying your target genes from the omics data that you have from your experiments: we can identify genes carrying sequence variations; differentially expressed genes; genes corresponding to the differentially expressed proteins; genes with differential methylation status; genes encoding enzymes metabolizing given metabolites – we will construct the target gene set characterizing the process under study based on the provided omics data, and will perform gene regulation studies on the list of selected target genes using the TRANSFACdatabase.
We will identify transcription factors regulating your target genes in the given conditions, e.g. limited to a certain tissue type or GO process.
Pathway analysis: identification of Master regulators
We will perform full reconstruction of the molecular mechanism of the studied process by performing integrated promoter and pathway analysis. Taking the transcription factors (TFs) identified on the step of promoter analysis, will will launch pathway analysis by searching for possible common regulators of the selected TFs upstream in the hierarchy of intracellular regulation using the TRANSPATH database.
Identified Master regulators are prospective drug targets and biomarkers of the pathology under study. You can read more about our approach towards integrated promoter and pathway analysis at the Upstream Analysis page.
Precision Medicine services
We can perform full reconstruction of the molecular mechanism of the studied pathology, either in a personalized mode for a given patient, or within a cohort study identifying molecular subtypes of the studied disease.
Search for prospective biomarkers of the studied disease
Search for prospective drug targets of the studied disease
Search for prospective treatments based on the given/identified drug targets, including treatment selection from the full range of known drugs and drugs undergoing clinical trials, as well as drug-like compounds using the cheminformatics approaches
Correlation analysis of patient clinical and omics data
Disease molecular subtypes identification (patient stratification into respective clusters based on the differences in the molecular mechanisms of the disease subtypes)
Pipeline development services
We can develop practically any software solution meeting your bioinformatics analysis needs. Our experts will help you in specifying your exact needs to fit your research pipeline best – starting from raw omics data generation and handling, and ending with ready reports on the performed bioinformatics analysis and associated output files.
Customized automation of data analysis scenarios
We can automatize your bioinformatics routine by developing a customized pipeline in the geneXplain platform meeting your analysis needs. The fully automatized workflow that we will create based on your technical task will process the input of your choice and will output the results in the format that you need.
Consulting services
Our experts are always ready to assist you in any bioinformatics, systems biology, precision medicine or cheminformatics related questions.
We can help in planning your research protocol or equipping your newly created bioinformatics research unit with all the needed software and databases for an easy start.
We are also always open towards consulting you on any analysis results you have obtained either with our help, or in-house, to assist you in their easy interpretation and in making the most out of your research progress.