Rime Bioinformatics
Make high-performance bioinformatics accessible
We turn genomic data into solutions for phage therapy, industrial fermentations, and microbiome research.
Why do we exist?
Research needs rigorous analyses that deliver solutions, beyond raw results.
Behind every biological process lies a genome, carrying the information on how that process works.
This information is rarely exploited. Reading it requires several areas of expertise that are hard to combine: biology, genomics, data analysis, and software development. Research and industrial projects alike are often held back by tools and practices that struggle to process genomic data efficiently and to produce high-quality analyses.
These lower-quality analyses have a cost for society: research is slower and more expensive, and those who benefit from it (patients, the environment) are kept waiting.
As disappointed former clients of bioinformatics providers, and as committed scientists, we believe in a new generation of genomic solutions that can reveal deeper insights, enable better-informed decisions, and drive innovation in academic research, healthcare, and industry.
Our answer
Developing the highest-performing analyses, and supporting our partners in turning the results into value.
Unlike providers who run freely available, one-size-fits-all pipelines for their clients, we develop our own tools. They fill the gaps in currently available software, to deliver state-of-the-art analyses.
The results are then interpreted by PhD scientists, experts in turning them into actionable solutions for our clients. Our deliverables take the form of clear, educational reports, and of a long-term collaboration on solving our clients’ problems.
What this means for you
- Get actionable results for decision-making
- Use our deliverables without being a bioinformatics expert
- De-risk your R&D projects by investing in reliable data
Services
High-Performance Genomic Analyses for Phage Therapy
Bacteriophages are viruses that infect and kill bacteria. They land on a target host, inject their DNA, hijack the cell’s machinery to replicate, and burst it open, which releases their progeny.
We characterise phages and their hosts to identify the right candidates for phage therapy.
Bacteriophages (or phages) were discovered in the early 20th century. They can be used to control bacteria in many fields: human health, food safety, agriculture, livestock farming, and cosmetics. This is phage therapy. They are an effective, environmentally friendly alternative to antibiotics, to prevent the millions of deaths increasingly caused by bacterial resistance to antibiotics.
Bioinformatics analyses play a key role in developing safe phage-based medicines. Regulators such as the EMA and the FDA therefore require in-depth analyses before new treatments reach the market. If these studies are not of satisfactory quality, market access can be delayed or blocked.
However, the development of phage therapy is held back by the lack of bioinformatics tools able to replace slow but reliable manual work and to handle the complexity specific to phages.
Without high-performance tools, low-quality data and slow analyses cause extra costs and delays for phage therapy projects.
rTOOLS
rTOOLS delivers results similar to expert manual annotation. A benchmark against the best-performing manual annotation method showed that it could even find, on average, 7 additional gene functions per phage.
Functional annotation, on 27 phages (Culot, Abriat & Furlong K.P., Viruses 2025).
What we deliver
- Complete, reproducible annotation results
- Support for the next steps of your R&D project or regulatory submission
- An in-depth understanding of a bacteriophage genome
- The market’s most accurate detection and characterisation of the prophages present in a host strain
Working on a therapeutic phage?
Tell us about your project.
Genomics-Driven Fermentation Process De-risk & Innovation
Fermentation is one of the long-established fields of biotechnology. It plays a key role in the production of a wide range of products, from the agri-food sector to biofuels.
We analyse microbial communities and fermentation dynamics at scale, identifying solutions to improve productivity, process stability, and product quality.
Industrial fermentation harnesses the metabolic capabilities of yeasts and bacteria to produce a wide range of products, including foods, beverages, biofuels, and high-value chemicals.
In these production systems, microbial activity is affected by several factors that can compromise both product quality and yield, such as the accumulation of unwanted metabolites or prophage induction.
These events can degrade or wipe out production, but could be prevented through high-performance genomic analysis.
We offer an innovative solution, enabling the full use of genomic data and turning it into practical tools for monitoring, predicting, and optimising fermentation processes, while promoting a preventive rather than reactive approach.
What we deliver
- Diagnosis and resolution of fermentation failures
- Analysis and industrial valorisation of strain banks
- Production optimisation through metagenomic analysis
Something wrong with your fermentation?
Tell us about your project.
Genomics-Driven Microbiome Exploration
No bacterium lives alone. Communities of microbes shape health, agriculture, and industrial processes.
We map these ecosystems with metagenomics, revealing the structure that drives their function.
Microbiomes form complex ecosystems that interact with their hosts: plants, animals, and humans. They thereby influence biochemical cycles, metabolism, immunity, productivity, and susceptibility to stress and disease.
However, despite the vast amount of genomic data available, much of it goes unanalysed for lack of tools. This overlooked part of the microbiome limits our ability to detect imbalances and design effective interventions.
We offer a microbiome analysis that brings the viral fraction to light, revealing metabolic pathways and interactions that slip under the radar of traditional genomic methods.
What we deliver
- Unique integrated bacteria + phage/prophage metagenomics, revealing drivers of dysbiosis, inflammation, and treatment response
- Deep microbiome characterisation for clinical studies, comparative analyses, and product development
- Functional insight via pathway reconstruction and protein function prediction: identification of metabolic pathways leading to molecules of interest, guiding the formulation of new products
This expertise has already been applied to a clinical cohort and published in a peer-reviewed scientific journal.
Want to discover what your data has been hiding?
Tell us about your project.
Tailored Algorithmic Development
As data is produced ever faster, the limiting factor in obtaining a result is often whether a tool exists that can produce it: that is why we develop our own.
We offer you the development method that enabled us to publish the best-performing analysis algorithms in their field.
Designing solutions that are both scientifically robust and reliable enough to be used in an operational context requires a rare combination of expertise in biology, bioinformatics, and software development. This is precisely what Rime Bioinformatics’ experts do.
What we deliver
- Analysis pipelines for new biological phenomena
- Construction of custom curated databases
A problem no existing tool solves?
Tell us about your project.
Our partners
