Research collaboration

Research in geneXplain


Research collaboration


As a highly active biomedical research company, geneXplain is proud to offer its expertise and products to all interested partners. You are welcome to invite us for collaboration in any of the applicable grant programs (we would act as a German SME partner) or include our software and databases in your grant applications for covering the license costs with the received funding.



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geneXplain as a software and databases provider for your research project

Being responsible for development, maintenance, and distribution of a number of best-in-class bioinformatics and cheminformatics tools and biological databases, geneXplain GmbH is always open for supporting your research, either ongoing or planned, with the needed resources.

Whenever you have to deal with gene regulation studies or perform (multi)-omics data analysis of any complexity, our tools will allow you to achieve the best result possible granting your project a reliable basis for the conducted research. Our flexible licensing models will allow individual project partners, as well as the whole consortia, receive access to the collaborative research solutions with full automation and due security protocols for handling, storing and processing of the project data.

We are proud to offer you the licenses for the following products, which you can include into your grant application budget in advance, or obtain them from us immediately on your request at any time:

TRANSFAC – the gold standard in the area of transcriptional regulation. TRANSFAC® is the database of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. TRANSFAC® can be used as an encyclopedia of transcriptional regulation, or as a tool for identification of potential transcription factor binding sites in the regulatory regions of the genes(s) of your interest.

HumanPSD + TRANSPATH – a unified resource, granting you access to TRANSPATH® database of mammalian signal transduction and metabolic pathways, and HumanPSDTM (Human Proteome Survey Database) containing information on diseases, their biomarkers, associated drugs and clinical trials.

geneXplain platform – an online toolbox and workflow management system for a broad range of bioinformatics and systems biology applications.

Genome Enhancer – a fully automatized pipeline for patient omics data analysis that identifies prospective drug targets and corresponding treatments by reconstructing the molecular mechanism of the studied pathology.

BRENDA – the most comprehensive information repository on enzymes and enzyme ligand data.

PASS – a tool for prediction of potential biological activities of the given compound based on its structural formula.

GUSAR – a tool for creation of quantitative structure-activity relationship models. It outputs the reliable quantitative SAR/SPR (Structure Activity and Property Relationship) model based on the provided training set of chemical structures and quantitative data on their biological activities.

PharmaExpert – a tool to analyze the relationship between biological activities, drug-drug interactions, and multiple targeting of chemical compounds to select compounds that have a pre-defined biological activity.


To receive a quote for the license of your interest, please fill in the following form:



geneXplain as a biomedical research project 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.

It is a common practice that all our project partners receive shared access to our software and databases resources in the scope of the respective project throughout its whole duration. We are pleased to provide our best-in-class tools and databases to our colleagues for achieving the best result possible in each of the projects where geneXplain is affiliated.

If you want to invite us for collaboration in any of your grant applications, or you need an experienced subcontractor for taking care of the bioinformatics part of your project, please contact us via with all respective info, and our R&D department representative will contact you back shortly. We are always open for collaboration in any interesting biomedical research projects that aim to improve the current level of disease mechanism knowledge and prospective treatment options.


Open grant application calls

Below you will find the information on some of the open grant application calls that we found interesting. If you have a suggestion for extension of this list, please send us the info about the respective calls via We are always glad to do everything in our power for expanding the coverage of biomedical research funding possibilities info worldwide.


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Eureka Germany and Israel call for projects

Germany and Israel are announcing a call for proposals for joint R&D projects, focusing on developing innovative products and applications in all technological and application areas.

Israel Innovation Authority and the German Federal Ministry for Economic Affairs and Climate Action (BMWK) will provide access to public funding for joint projects provided by The Innovation Authority and by BMWK’s ZIM program (Central Innovation Program for SMEs), respectively.



  • The project idea must represent international cooperation in the form of a specific project.
  • The project must be directed at researching or developing an innovative product, process or service with the goal of commercialisation.
  • The project must have a civilian purpose.
  • The consortium must include at least two independent legal entities from a minimum of two Eureka countries.
  • No single organisation or country can be responsible for more than 70% of the project budget.
  • Germany and Israel have additional criteria for organisations to be eligible to receive funding. For details please see section funding details.


Key dates:

  • Open Date – September 19, 2022
    • Expiration Date – February 20, 2023


    Further info >>