As a highly active biomedical research contributor, geneXplain GmbH is proud to offer you its excellent competences in bioinformatics and systems biology, and precision medicine

With over 10 years of experience behind, we guarantee you the best result of your contract study, supported by continuous consultations of our experts to assist you in results interpretation and their integration into your research pipeline.

We can step in at any stage of your research project, starting from the study protocol planning and ending with the obtained results tuning and interpretation – simply contact us using the form below to provide some details on your tasks and timing, and we will get in touch shortly with a reasonable offer.

We can also assist you in bioinformatics unit launch and facility resources planning – trust the renowned bioinformatics software and databases provider in setting up your very own bioinformatics research center.

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What we can do for you



Bioinformatics service

Precision medicine service

Pipeline development services

Consulting service


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.

Analysis pipeline example

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.

Raw omics data processing

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Genes functional annotation


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.

Promoter analysisWe 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 TRANSFAC database.

We will identify transcription factors regulating your target genes in the given conditions, e.g. limited to a certain tissue type or GO process.

View demo reports on promoter analysis

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Pathway analysis: identification of Master regulators

Upstream analysis - integrated promoter and pathway analysisWe 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.


View demo reports on pathway analysis

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Examples of bioinformatics services you can request from us

Our bioinformatics services cover a wide range of biological and biomedical applications. Here are some examples of what you can request from us:

  • Causal analysis of genes in focus by performing integrated promoter and pathway analysis allowing to reconstruct the molecular mechanism of the studied process and identify its master regulators

Example reports:

for differentially expressed genes

for genes carrying sequence variations


View further details on our bioinformatics services


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. We will identify key master-regulators responsible for the pathology development and will point out to promising biomarkers and drug targets using the Upstream Analysis approach.

Precision medicineAnalysis highlights:

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)

View demo reports on precision medicine

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Pipeline development services

Customized workflow developmentWe 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.

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Consulting services

Consulting servicesOur 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.


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Why to select us as your CRO partner

GeneXplain GmbH is a highly active biomedical research company. Our 10+ years of experience in partnering and leading of some big international research projects have made our name a recognisable brand in the global scientific community.

Currently geneXplain is a project partner (or coordinator) in the following projects: COPreDict, OxidoResist, GlioResolveE-REDALERT, FindingMS, .

And recently we were project partners (or coordinators) in such projects as COLOSSUS, GlioTrain, PD-MitoQUANT, ExITox-II, OxidoCurin, miRCol, MyPathSem, miRNA-DisEASYOptogenerapy, SysmedIBD, MIMOmics, Mediomics, ExITox, SYSCOL, EPIMETAB, RESOLVE, GERONTOSHIELD, TEMPUS.

As a project partner or coordinator we offer our excellence in gene regulation studies, as well as our unique approaches towards reconstruction of molecular mechanisms of the studied pathologies. Our experts hold superior expertise in bioinformatics, systems biology, artificial intelligence and machine learning.

We can overtake the whole bioinformatics part of the project and perform multi-omics data analysis of any complexity, starting from basic raw data preprocessing and quality control operations, and ending with identified molecular mechanism of the studied pathological process, coupled with in silico prediction of prospective drugs and chemical substances acting on its key regulators. Our in-house Upstream Analysis approach integrates promoter and pathway analysis and serves as a unique and powerful basis for the performed studies.

We work with genomics, transcriptomics, proteomics, epigenomics, and metabolomics data, that we can further integrate with available clinical data. Our approaches allow identification of hidden correlations, leading to deeper understanding of disease molecular mechanisms, associated patient stratification, and novel treatment strategies.

In addition to our unique scientific expertise, we also accommodate great experience in management and data handling issues, including complex procedures of secure data storing and transmission. Our in-house software provides a reliable collaboration research environment to all project partners and serves as a unified solution for storing, sharing and processing of project biomedical data.

Have any questions? Contact us via for any details on our products and services.