What Centre for Computational and Systems Biology does

Centre for Computational and Systems Biology (COSBI) is an Italian research foundation headquartered in Rovereto, Italy, founded in 2005 by Microsoft Research and the University of Trento. The organization operates as a systems biology research centre that delivers computational platforms and analytical services spanning five functional pillars: knowledge extraction from biomedical literature, multi-layer data integration, biomarker signature identification, pathway/network analysis, and quantitative modeling and simulation. COSBI's proprietary software stack includes SCUDO (rank-based gene-expression signature clustering), NASFinder (omics sub-network activity scoring), QSPcc (a universal compiler achieving reported peak speed-ups of ~22,000x for QSP model simulations), MOUSSE (normalization-free multi-omics integration), VisualSHIELD (federated privacy-preserving analysis GUI on top of DataSHIELD), BeeSL (BERT-based biomedical event extraction), CSpace (compact biomedical concept embeddings), and SymbolicR (symbolic regression for PBPK model extension). The TB Knowledgebase aggregates 37,000+ publications and 360+ clinical trials for tuberculosis drug and vaccine research.

COSBI's commercial model is professional-services based, generating revenue through project-based research collaborations rather than licensed software sales or subscription products. Customers include major pharmaceutical firms (GSK, Sanofi, UCB Pharma, Amgen, Biogen, Axcella, Vydiant), a global health research institute (Bill and Melinda Gates Medical Research Institute), and academic partners (University of Trento/CIBIO, Cornell, UZH, University of Auckland, University of Copenhagen, University College Dublin, IEO, CNR, Fondazione Edmund Mach, TNO, University of Verona, UNIMORE). Several collaborations are long-tenured — Biogen and Vydiant relationships span 10+ years. Pricing is not publicly disclosed and is set per collaboration. The foundation is GDPR-compliant, has 11–50 employees, and currently operates with no disclosed venture funding, no subsidiaries, and no M&A activity. New tools continue to be released open-source (CSpace in 2025, SymbolicR in April 2026), and the organization maintains an active conference presence (ENCALS, PAGE, QSPC, BIOMATH 2026) and a 1,720+ LinkedIn following.

Name

Centre for Computational and Systems Biology

Legal name

Fondazione The Microsoft Research – University of Trento Centre for Computational and Systems Biology

Website

https://cosbi.eu

Company type

Private

Founded year

2005

Operating status

Operating

Headcount range

11–50 employees

Short description

COSBI is an Italian systems biology research foundation that develops computational tools and provides project-based modeling, biomarker, and multi-omics analysis services to pharmaceutical, biotechnology, and academic clients worldwide.

Ownership category

akta.pro rank

Product category

Computational Biology Research Services

NAICS

Research and Development in the Physical, Engineering, and Life Sciences (54171)

SIC

Services-Commercial Physical & Biological Research (8731)

akta.pro primary industry

Clinical Research & Trial Central Laboratories (HLAFAMAL)

akta.pro secondary industry

Data Management, Reporting & Regulatory Submissions for Central Labs (HLAGAEAL)

Keywords

• Systems biology research
• Computational biology services
• Biomarker identification
• Drug repurposing analytics
• Knowledge extraction pipelines

Headquarters

HQ city

Rovereto

HQ country

Italy

HQ region

Europe

Offices1 record

Markets served

GTM type

B2B

Offering type

Services

Cost components

Personnel, Technology or R&D, Operations, Infrastructure

Revenue model

1. Research Collaboration Services: COSBI generates revenue through research collaborations with pharmaceutical, biotechnology, food companies, and academic institutions. These collaborations involve developing computational tools, performing systems pharmacology and systems biology analyses, and providing modeling and simulation services for drug development and personalized medicine.

Go-to-market motion1 record

Distribution channels1 record

Marketing channels5 records

Core offering

COSBI is a systems biology research centre that develops and applies computational platforms and proprietary software tools across the full personalized medicine pipeline, integrating experimental data with knowledge extraction, biomarker signature identification, network/pathway analysis, and quantitative systems pharmacology modeling and simulation. It delivers these capabilities through project-based research collaborations with pharmaceutical, biotechnology, and food companies, as well as academic and research institutions.

Product overview

COSBI operates as a systems biology research centre (Fondazione The Microsoft Research – University of Trento Centre for Computational and Systems Biology) offering computational biology platforms and proprietary software tools for personalized medicine research. The portfolio consists of multiple standalone software prototypes including SCUDO for gene expression analysis, NASFinder for network pathway analysis, VisualSHIELD for federated privacy-preserving analysis, QSPcc for model compilation, CSpace for biomedical concept embeddings, SymbolicR for symbolic regression, BeeSL for biomedical event extraction, and MOUSSE for multi-omics integration. These tools support the full computational biology pipeline from data extraction and integration through biomarker identification, pathway analysis, and mathematical modeling and simulation.

Differentiator

Problem solved

Functional benefit

Products and services

• SCUDO (Signature-based Clustering for Diagnostic Purposes) Rank-based method for analysis of gene expression profiles for diagnostic and classification purposes. Identifies sample-specific gene signatures composed of the most up- and down-regulated genes and builds graphs of similar samples for community clustering or supervised classification. Distributed as the rScudo R package on Bioconductor and via the COSBI prototype portal.
• NASFinder (Network Activity Score Finder) Web service for topological and functional analysis of sub-networks connecting omics-determined modules. Guides identification of active network modules based on predefined bio-molecular roles such as receptors, transcription factors, and transporters, with network visualization via Cytoscape.js.
• VisualSHIELD Open-source extensible web interface providing standardized deployment of DataSHIELD infrastructure with a graphical user interface. Simplifies definition of analysis workflows and visualization of results in privacy-preserving federated analysis environments, integrating with dsSwissKnife R packages for histograms, contour plots, heatmaps, boxplots, correlation matrix, K-nearest neighbors, PCA, and randomForest.
• QSPcc Universal compiler handling a wide range of modeling styles in engineering and life sciences. Compiles MATLAB or R code written by scientists without modification and achieves peak speed-ups of 22000x for computational model simulations, supporting Quantitative Systems Pharmacology workflows.
• CSpace Compact concept embedding space for biomedical domain applications that enables semantic similarity measurement between biomedical concepts, ontological identifiers, and short sentences with minimal computational requirements. Supports cross-ontology concept comparison for gene-disease association and drug repurposing.
• SymbolicR Open-source R framework for discovering non-linear formulas directly from data through incremental, memorized symbolic regression workflow. Supports progressive, human-in-the-loop formula discovery with genetic optimization and explicit formula testing, and is used for extending PBPK models through data-driven formula discovery.
• BeeSL (Biomedical Event Extraction as Sequence Labeling) Joint end-to-end neural information extraction model that recasts event extraction as sequence labeling with a BERT encoder pre-trained on biomedical texts. Achieves state-of-the-art performance on the Genia 2011 benchmark for biomedical event extraction and high-precision relation extraction from biomedical literature.
• MOUSSE (Multi-Omics Using Subject-Specific SignaturEs) Unsupervised and normalization-free tool for multi-omics integration that maintains clustering performance across a wide range of omics data. Uses rank-based subject-specific signatures and similarity networks to enable biomarker extraction across multiple omics types.
• Computational Biology Research Collaboration Services Project-based computational biology research services covering knowledge extraction from biomedical literature, multi-omics data integration, biomarker signature identification, pathway/network analysis, and mathematical modeling and simulation. Delivered directly to pharmaceutical, biotechnology, food, and academic clients through research collaboration agreements.

Quantifiable outcome

• Ibrutinib identified as candidate drug for lowering chronic inflammation in obesity through network-based drug repurposing approach
• +2 more outcomes

Named customers11 records

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration3 records

AI capability8 records

Feature9 records

Partnerships

24 partnerships are on record, tiered founding, core, major and minor.

• Microsoft ResearchfoundingStrategic or Co-development Partner · 1 January 2005COSBI was founded in 2005 by Microsoft Research and The University of Trento, representing a unique research center that exploits a comprehensive systems biology pipeline.
• University of TrentofoundingStrategic or Co-development Partner · 1 January 2005COSBI was founded in 2005 by Microsoft Research and The University of Trento. The center is based in Rovereto and maintains deep research partnership with the university's CIBIO department.
• GSKcoreStrategic or Co-development PartnerMajor pharmaceutical collaboration including predicting efficacy of trivalent influenza vaccines, developing QSP approach for mRNA vaccine platforms, and multiple case studies.
• SanoficoreStrategic or Co-development PartnerCollaborative development of robust computational pipeline for model-based and data-driven phenotype clustering in clinical applications.
• BiogencoreStrategic or Co-development PartnerLong-standing collaboration spanning 10+ years focused on modeling neurofilament trafficking in neurodegenerative disorders including ALS, SMA, and MS. Includes scientific guidance from former Head of Pharmacometrics Ivan Nestorov.
• AmgencoreStrategic or Co-development PartnerCollaboration on computational analysis of cytokine release following bispecific T-cell engager therapy for cancer treatment.
• AxcellacoreStrategic or Co-development PartnerCollaboration in systems biology and drug discovery including work on hepatocellular energy metabolism.
• UCB PharmacoreStrategic or Co-development PartnerResearch partnership including infant gut bacteria and immune system studies as part of New Zealand National Science Challenge.
• Bill and Melinda Gates Medical Research InstitutecoreStrategic or Co-development PartnerCollaboration on tuberculosis drug and vaccine development research.
• VydiantcoreStrategic or Co-development PartnerMulti-dimensional dataset analysis collaboration with FDA and Nestle Research spanning 10+ years.
• Cornell UniversitycoreStrategic or Co-development PartnerAcademic research partnership including collaborative work on folate-mediated one-carbon metabolism modeling with Professor Patrick Stover.
• UZH - University of ZurichmajorStrategic or Co-development PartnerAcademic research partnership in computational and systems biology.
• University of AucklandmajorStrategic or Co-development PartnerAcademic partnership contributing to infant gut bacteria research in New Zealand National Science Challenge.
• University of CopenhagenmajorStrategic or Co-development PartnerAcademic research partnership in computational biology.
• University College DublinmajorStrategic or Co-development PartnerAcademic research partnership in computational biology.
• IEO - Istituto Europeo di OncologiamajorStrategic or Co-development PartnerHospital and research centre partnership for cancer research.
• CNR - Consiglio Nazionale RicercamajorStrategic or Co-development PartnerItalian National Research Council partnership for advancing research.
• Fondazione Edmund MachmajorStrategic or Co-development PartnerResearch foundation partnership in Trentino region.
• TNOmajorStrategic or Co-development PartnerNetherlands-based research organization partnership for life sciences innovation.
• Autifony TherapeuticsminorStrategic or Co-development PartnerMedical research partnership in therapeutic development.
• CRNH - Centre de Recherche en NutritionmajorStrategic or Co-development PartnerFrench nutrition research center partnership.
• University of VeronamajorStrategic or Co-development PartnerAcademic partnership including COVID-19 logical modeling collaboration.
• University of Modena and Reggio Emilia (UNIMORE)majorStrategic or Co-development PartnerMultidisciplinary collaboration in ALS research combining clinical expertise with computational biology approaches.
• Azienda Ospedaliero-Universitaria di ModenamajorStrategic or Co-development PartnerHospital-university partnership contributing to ALS research collaboration.

Scale indicators6 records

Expansion highlights6 records

Direct peers

• Certara: Largest independent provider of model-informed drug development, biosimulation and quantitative systems pharmacology services to pharma and biotech. Closest direct comparable to COSBI given overlapping QSP, PBPK and model-based drug development capabilities and similar pharma customer base.
• Genedata: Provides enterprise scientific informatics platforms (Genedata Screener, Expressionist, Biologics) for biopharma R&D, with comparable multi-omics integration and biomarker workflows used by large pharma computational biology groups.
• Optibrium: Provider of software and services for drug discovery, including StarDrop and related computational chemistry/ADMET platforms; comparable to COSBI's combination of proprietary modeling software with collaborative research services for pharma.

Emerging players

• Insilico Medicine: AI-focused drug discovery company with proprietary target identification and generative chemistry platforms; comparable to COSBI in applying computational biology to drug discovery, though operating end-to-end with substantially more capital.
• CytoReason: Computational biology company building cell-level disease models from multi-omics data for pharma R&D; directly comparable to COSBI's systems-biology pipeline and multi-omics integration use cases (PFE, Sanofi collaborations).
• Recursion Pharmaceuticals: AI-driven drug discovery company combining high-throughput biology with computational models; overlaps with COSBI's systems-biology and biomarker-discovery use cases but pursues an asset-owning rather than services model.
• Exscientia: AI-native pharma combining patient-derived biology with computational design; competes with COSBI for pharma partnerships in translational and systems biology, with a stronger emphasis on generative chemistry and asset development.

Broad incumbents

• Dotmatics: Scientific R&D informatics platform serving drug discovery workflows, including data integration and biomarker analytics; competes for the same pharma informatics budgets as COSBI's pipeline tools, though as a broader platform rather than specialist CRO.
• Evidera (PPD/Pharmaceutical Product Development): Large evidence-based solutions provider offering modeling, health economics and real-world evidence services to pharma; overlaps with COSBI's model-based drug development work though across a broader services portfolio.
• Schrödinger: Public computational chemistry and biology platform company with its own drug discovery programs and enterprise software; overlaps with COSBI in physics- and biology-based modeling for pharma partners but operates at significantly larger scale.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks7 records

Key highlights6 records

Customer concentration

• YouTubeyoutube.com/@COSBIResearchCentre
• LinkedInlinkedin.com/company/cosbi

Compliance1 record

Revenue estimate

Valuation estimate

Number of profiles

Profiles1 record

Funding overview

Funding rounds

Investors

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M&A

Investments

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Frequently asked questions about Centre for Computational and Systems Biology