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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Improving the understanding and management of late-effects in adolescents and young adults (AYA) with cancer


Programme: Horizon Europe Framework Programme (HORIZON)
Type of action: HORIZON-RIA HORIZON Research and Innovation Actions


Expected Outcome:

Proposals under this topic should aim to deliver results that are directed and tailored towards and contribute to the following expected outcomes:

  • Increased awareness and improved understanding of the incidence, severity, and impact of late effects in AYA cancer survivors among healthcare providers, patients, caregivers and the general public;
  • Researchers, innovators, and professionals from different disciplines and sectors ensure accessibility and re-usability of their data, models, tools and technology to support the [1] platform, which is currently in preparation;
  • Identification of effective interventions and best practices to support AYA patients and survivors in preventing, reducing and better managing late-effects, promoting optimal health outcomes and overcoming disparities between regions;
  • Improved quality of life and long-term outcomes for AYA cancer survivors, including improved physical, emotional, and social well-being.


This topic will contribute to the achievement of the Mission’s objective to improve the quality of life of cancer patients, survivors and their families. The focus should be exclusively on adolescent and young adult (AYA, age range 15-39)[2] cancer patients and survivors.

Each year, more than 150,000 AYA cancers are diagnosed in the EU, and over 1.2 million worldwide. About 300,000 AYA patients live with or beyond cancer in the EU; the majority experience late-effects due to their cancer treatment, including chronic pain, cardiovascular disease, organ and skin alterations, cosmetic sequelae, fertility problems, cognitive and functional impairment, and mental health issues such as depression and anxiety. Survivors may also be at increased risk of second cancers due to the long-term effects of radiation and chemotherapy. The negative impact on education and employment of AYA survivors and in general the financial burden borne by them is also commonly observed.

Late effects are particularly challenging for AYA cancer survivors, who often experience them during a critical phase of their lives. Late effects are also challenging for caregivers. The considerable progress made in treating AYA cancers has further exposed gaps in the understanding, prevention and management of late-effects, which warrant more targeted pan-European research on AYA cancer survivorship.

Proposals should focus on one or more cancer types and address only one of the following interventions:

  • Building on data from existing or newly established AYA patient cohorts, ensuring comparability of data across participating countries as appropriate, obtain a thorough assessment by cancer type of the prevalence, specific effect(s), severity, time of onset, relative risk, and risk factors associated to late effects in AYA cancer patients. Attention should be paid also to social and health determinants, including sex, gender, age and other relevant variables, including socio-economic status, living in rural or remote areas and education;
  • Develop, test and scale-up evidence-based screening methods for the early detection of late-effects in AYA cancer patients;
  • Develop, test and scale up in real-life settings, innovative, holistic approaches and tools (including digital tools), optimising cancer treatment and follow-up regimens to prevent, reduce and/or effectively manage late-effects, including psycho-social aspects. Approaches could focus on education, sports, nutrition, medical follow-up and counselling, for example on mental and physical health, pain management, and wellbeing in general, as well as reproductive matters, including infertility, onco-fertility and fertility options in general and development of effective methods for fertility preservation and guidelines on related counselling.

This topic requires direct involvement of cancer patients and survivors, survivor representative organisations, caregivers, and the effective contribution of SSH disciplines and the involvement of SSH experts, institutions as well as the inclusion of relevant SSH expertise, in order to produce meaningful and significant results, enhancing the impact of the related research activities.

The use of participative research models, such as oncology-centred living labs or other approaches to deliver (social) innovation should be considered.



  • Admissibility conditions: described in Annex A and Annex E of the Horizon Europe Work Programme General Annexes
  • For details please refer to information on this page.


Key dates:

  • Open Date – 18 April 2024
    • Expiration Date – 18 September 2024 17:00:00 Brussels time


    Further info >>