Give us your target or disease. We’ll tell you what’s driving it, and will prove it.
No software to learn. No raw data to wrangle. Our scientists analyze your data with the upstream analysis approach, using TRANSFAC, TRANSPATH and HumanPSD to trace the signal from altered genes to transcription factors, upstream pathways, master regulators and druggable control points. We rank the targets that actually matter, and hand you a clear mechanistic answer that can be validated in a lab, with a named expert behind it. Your data and any resulting IP stay yours.
“Here’s the data. Here’s the disease. We don’t know what’s driving it.”
One call, then a defined engagement, priced case by case, with IP and data terms agreed up front.
A ranked, mechanistically justified answer, traceable to the evidence, with a named scientist who stands behind it, and optional wet lab validation.
Pay on success — a low starting fee, the rest only when your targets get validated.
50+
funded R&D projects delivered (EU · BMBF · national grants)
30+
disease mechanisms of action uncovered
3
drugs repurposed to new indications
1
novel anti-cancer drug lead preclinically validated
100%
of results and IP stay with you
Antibiotic repurposed as anti-IBD drug. Trial is planned
geneXplain applied its Upstream Analysis technology to IBD data from patients, organoids, xenografts, and immune cells to reconstruct disease-driving NF-κB regulatory networks, identify master regulators and drug targets, and prioritize compounds for repurposing. This led to the prediction of clarithromycin as a potential anti-IBD agent, later validated in vitro and in vivo.
Sometimes you don’t want another tool to learn. You just want the answer.
You have the question and the data. What you’re missing is the time, the specialist depth, and someone who will put their name on the conclusion. That’s what we do.
“We have a result, now what’s the next experiment?”
A list of differentially expressed genes isn’t a plan. We deliver the mechanism and the next step, not another table to read.
“Too many candidates, no way to rank them.”
We turn a long list into a short, ordered one, built on causal regulatory biology, not statistical association.
“Our pipeline is five disconnected tools.”
Gene → regulation → pathway → disease → target, run as one engagement by the people who built the underlying knowledge.
Every bioinformatics shop runs analyses. Almost none run them on this.
The difference isn’t that we run analyses — everyone does. It’s the hand-curated, mechanistic knowledge underneath, built and maintained for nearly four decades.
TRANSFAC®
Transcription factors and experimentally verified binding sites — the most comprehensive library of DNA motifs anywhere.
TRANSPATH®
Causal, directional signalling reactions, not correlation networks. Each with direction, cellular context, and a primary literature source.
HumanPSD™
Diseases, clinical trials, biomarkers and drug targets with mechanistic annotations — molecular biology connected to clinical context.
Mechanism, not correlation.
A standard CRO runs the same omics pipelines as everyone else and tells you what changed. The harder question — why it changed, and what to do next — is where most projects stop and ours begins.
Because our answer traces through regulation → pathway → disease, every conclusion is anchored to a record you can audit, not a black box you have to trust.
And the biggest cost in R&D is rarely the data itself — it’s moving forward on the wrong biological hypothesis. This is the layer that lowers the budget you put at risk, before the expensive experiments begin.
Bring us the problem a standard pipeline can’t solve.
Anyone can run a standard pipeline and guarantee a reproducible result, for a few hundred dollars. We can do more. Our work is the non-routine, inventive part: the disease no one has mapped, the resistance no one can explain, the target no one else will commit to.
Fifty funded research projects, many at the frontier of science and genuinely inventive, are the track record behind that.
A model can generate a conclusion. It can’t take responsibility for one.
In a regulated pipeline, “the model said so” is not an answer. Someone has to stand behind the science: read the evidence, defend the call, and be reachable when it matters.
“The same DNA sequence is controlled by different transcription factors in different cell types. A model that pattern-matches will miss that. A person who knows the biology won’t.”
Prof. Dr. Alexander Kel
CEO & CSO, co-author of TRANSFAC®
Every done-for-you engagement is built around a named scientist who scopes the question, runs the analysis, and is accountable for what comes back — not an automated report with no author.
For teams that have to defend a conclusion downstream, that’s often the whole point of the engagement.
The results are yours, and we put that in writing.
Your IP stays yours
Any target, biomarker or discovery from the work belongs to you — stated explicitly in the contract, on your terms. Where it helps, we’ll go as far as structuring the work through a separate entity you control (the model large pharma has used for exactly this).
Your data stays protected
Not ready to hand over sensitive data on day one? We can start on abstract or example data to show you how it works, then run on yours once you’re comfortable. An NDA comes first, always.
No open questions before we start
Scope, deliverables, IP ownership and data handling are all agreed before any work begins.
The market is full of shops that run pipelines. Depth is the difference.
A general bioinformatics CRO
TRANSFAC SERVICES
For teams that want the result delivered, not the tools or the raw data.
Pharma & biotech R&D
You have a target or a disease question and need a defensible mechanistic answer, with provenance and a human accountable for it.
Translational research leads
You want the depth of the platform without the learning curve, scoped to your specific target or disease.
Teams in regulated pipelines
You need conclusions that will stand up to criticism: traceable to evidence, signed by someone who can defend them.
Seven service lines, each narrows an expensive decision before you fund it.
Every engagement is scoped case by case, but the work falls into seven lines. Each takes a large, uncertain search space: targets, resistance mechanisms, promoters, biomarkers, therapy designs, and returns the few candidates that are mechanistically justified, with the deliverables to act on them.
01
Disease Mechanism Reconstruction, Master Regulator Discovery & Drug Target Prioritisation
Supports early translational research, target discovery, disease mechanism clarification, and consortium project design.
Disease control network Transcription factor analysis Upstream pathway reconstruction Master regulator ranking Druggable target shortlist Mechanism report
02
Treatment Response, Resistance Mechanisms & Rational Combination Therapy Intelligence
Supports drug rescue, oncology resistance studies, responder / non-responder analysis, and combination therapy design.
Resistance driver map Pathway rewiring analysis Master regulators of non-response Rational combination hypotheses Resistance biomarker shortlist
03
Drug Mechanism of Action, Toxicity Mechanisms & Safety Risk Intelligence
Supports drug development, drug repurposing, preclinical safety assessment, toxicity interpretation, and comparison of desired versus adverse drug effects.
Mechanism of action reconstruction Toxicity driver map Affected pathway and master regulator analysis On-target / off-target mechanism interpretation Safety biomarker shortlist Risk mitigation hypotheses Mechanistic MoA / toxicity report
04
Intelligent Promoter Design & Synthetic Regulatory Element Engineering
Supports gene therapy vector design, synthetic biology, engineered expression systems, and inducible construct development.
Promoter grammar analysis Tissue-/cell-specific regulatory logic Candidate promoter/enhancer designs Specificity assessment Ranked constructs Validation plan
05
CRISPR, CAR-T & Cell / Gene Therapy Design Intelligence
Supports advanced therapy design, CAR-T / CAR-NK target selection, CRISPR perturbation strategy, and regulatory cassette design.
Target selection report Pathway & tissue risk analysis Promoter / cassette logic CRISPR intervention strategy Safety & biomarker roadmap
06
Multi-Omics Biomarker Panel & Companion Diagnostic Design
Supports diagnostic development, patient stratification, companion diagnostic strategy, and clinical biomarker selection.
Biomarker ranking Regulatory network justification Subtype logic Minimal panel concept Assay translation notes Validation cohort plan
07
AI & Knowledge Graph Intelligence for Biomedical R&D
Supports pharma AI, digital twins, internal R&D copilots, disease knowledge graphs, and explainable AI systems.
Disease-specific knowledge graph Curated regulatory relations TRANSFAC / TRANSPATH / HumanPSD mapping AI-ready exports Reasoning workflows
Start with strategy. Pay the rest when your targets validate.
One path, scoped case by case — and you can stop at any step. This turns your spend from a fixed cost into an outcome-linked one.
Intelligence Package
We analyse your data across TRANSFAC®, TRANSPATH® and HumanPSD™ and hand you a ranked shortlist of the targets or master regulators driving your disease, with an expert report and clear validation recommendations. If nothing convincing comes out, this is where it stops, and it’s the cheapest step.
Validated targets
We validate the top targets ourselves in a defined cell line assay (e.g. siRNA or CRISPR knock-down). You pay the success fee for the targets that hold up. We deliver targets — validated. We deliberately don’t do compound screening: it’s a crowded field and not where our edge is, however we will provide a list of known drugs acting on the identified targets if there would be any reported ones.
Full translational development
For teams that want to go further, we coordinate onward wet lab work with partner CROs and academic labs, carrying the question from mechanism through to a validation-ready, development-ready package, as a joint offering for pharma, biotech, diagnostics companies and research consortia.
Tell us the question. We’ll scope the answer.
Every engagement is built case by case: scope, deliverables, IP, data terms and timeline, all agreed before work begins. The first step is a short discovery call to understand what you’re trying to resolve.
No fixed package · scoped to your question · pay on success · expert-delivered · your IP
Prof. Dr. Alexander Kel
CEO & CSO, co-author of TRANSFAC®