We manage, integrate and analyse all kinds of life science data from different technologies to enable discoveries, from biomarkers to drug repurposing. Here are some of our specific areas of expertise:
- molecular imaging analysis;
- de novo assembly of sequencing data;
- genome comparative data analysis;
- targeted, exome and whole genome sequencing analysis;
- metagenomic data analysis;
- pathway and transcriptional regulatory network analysis (functional analysis);
- omics analysis;
- data integration;
- data visualization;
- gene prediction and annotation;
- machine learning.
The analysis service you are looking for is not listed? Please get in touch with us, as we might be able with other specific needs.
Case study: Enabling precision medicine through multi-omics data integration
→ Your challenge: Integrating and translating multi-omics big data into functional insights requires specific expertise.
→ Our solution: Through our innovative multi-omics analysis expertise, we combine powerful data integration to help you improve disease prevention, early detection and prediction, monitor progression, design personalized treatments.
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In practice:
Development of an integrative solution for the phenotypic analysis of tumors powered by automated multiplex staining, image analysis and machine learning. With Lunaphore and the Geneva University Hospitals (HUG), as part of an Innosuisse.
Development of a method for interpreting gene expression data with metabolic models which has helped to identify key genes in obesity-related inflammation in adipose tissue
Integrative analysis of mouse and human lipidomics data which led to the discovery of novel lipid biomarker candidates for Type 2 diabetes. IMIDIA pan-European project.
Transcript assembly and functional characterization of heart specific lncRNAs in collaboration with the University of Lausanne Medical School.
Transcriptomics data analysis from muscle biopsies in a human clinical trial investigating the effect of dietary supplementation with Urolithin A, a pomegranate metabolite, on muscle function. In conjunction with EPFL and its spin-off, Amazentis.
- Development of an integrative solution for the phenotypic analysis of tumors powered by automated multiplex staining, image analysis and machine learning. With Lunaphore and the Geneva University Hospitals (HUG), as part of an Innosuisse. Read the news
- Development of a method for interpreting gene expression data with metabolic models which has helped to identify key genes in obesity-related inflammation in adipose tissue Read the paper
- Integrative analysis of mouse and human lipidomics data which led to the discovery of novel lipid biomarker candidates for Type 2 diabetes. IMIDIA pan-European project. Read the paper
- Transcript assembly and functional characterization of heart specific lncRNAs in collaboration with the University of Lausanne Medical School. Read the paper
- Transcriptomics data analysis from muscle biopsies in a human clinical trial investigating the effect of dietary supplementation with Urolithin A, a pomegranate metabolite, on muscle function. In conjunction with EPFL and its spin-off, Amazentis. Read the paper
We assist you by:
- defining and implementing your Data Management Plans (DMP) for research proposals and funding applications;
- reaching data interoperability targets, from local to international scales, within academic or regulated environments;
- extracting, reformatting and migrating patient-related data between systems in clinical set-ups, to ensure data consistency and query traceability;
- ensuring the long-term management and storage of biological data.
Case study: Making your data FAIR to let you focus on what you do best: research and discovery
→ Your challenge: A lack of reproducibility results in a lack of reliability in results from data analysis, and hinders data reuse and innovation potential. Universities, funders, datasets managers, publishers are increasingly expecting data to be FAIR.
→ Our solution: Whatever biological or biomedical data you have, we are experts in making them FAIR and packaging them in a publication-ready way. We let you focus on what you do best: research and discovery.
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Case study: Harmonizing your datasets to advance healthcare
→ Your challenge: Internal resources are lacking to standardize multiple datasets in order to aggregate them.
→ Our solution: We organize large databases containing routine health information, clinical trial or research datasets to enable you to merge them with public datasets.
In practice:
Acting as a Data Coordination Centre in European public-private partnerships to fight disease :
- Set-up of a federated data analysis system across multiple countries to enable access to large patient cohorts while addressing legal, ethical and FAIR principles (read more and watch the video).
- Set-up of a database of ~100 pooled clinical trials as part of the IMI Hypo-RESOLVE consortium. The work has involved setting up ETL (extract, transform, load) pipeline for feeding trial data into a secure Oracle database and the creation of a virtual analysis environment accessible via remote desktop and secured by 2 factor authentication.
Implementing semantic and technical interoperability within the Swiss Personalized Health Network (SPHN) initiative, aiming to make data from consenting patients available securely to researchers from across Switzerland’s hospitals and universities.
Making the human protein interaction dataset curated by ENYO Pharma easily accessible to all and FAIR, through data integration into the open data resource neXtProt.
Biomedical research, and in particular personalized health research, relies on a critical mass of heterogenous sensitive data from patients or clinical trials spread across institutions and sometimes countries. We draw on our extensive experience in large European public-private consortia and national initiatives to enable the secure sharing of interoperable data.
Case study: Enabling “Sharing without sharing” of sensitive health data in biomedical research
→ Your challenge: Making sensitive patient data accessible for research in accordance with specific regulatory frameworks.
→ Our solution: We help you achieve greater value in your health research projects by analyzing sensitive data collaboratively and safely using our innovative federated database for remote analysis. This approach enables researchers to access data for analysis but without physically sharing it.
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In practice:
Set up of a federated database for biomarker discovery in type 2 diabetes (T2D) as part of the pan-European RHAPSODY consortium. In this database, 10 observational clinical cohorts with a combined total of 50K patients were standardized, harmonized and made available for statistical analysis. We developed data mining and statistical tools in an analysis package for researchers to use within the consortium.
Secure data management platform for tumour exome sequencing and imaging data as part of the pan-European IMMUcan consortium which we co-lead.
Swiss Pathogen Surveillance Platform: we have developed the Swiss Pathogen Surveillance Platform to enable national near real-time sharing of pathogen whole genome sequences and their associated clinical/epidemiological metadata for surveillance of outbreaks. In particular, standardization, curation and sharing of national SARS-CoV-2 genomic data for surveillance and Open Science databases access
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Hundreds of clinical trials transferred and hosted onto a secure central server, in the context of the Hypo-RESOLVE pan-European project – supported by the Innovative Medicines Initiative (IMI) and including 23 leading academic experts, pharmaceutical and device manufacturers, as well as patients’ organizations – to find better solutions to alleviate the burden and consequences of hypoglycaemia, a common and serious complication of diabetes.
Secure Data Processing Platform: set-up by SIB as part of the nationwide secure infrastructure enabling the exchange of biomedical data between health institutions across Switzerland and researchers. This infrastructure has been set up as part of our BioMedIT Project in the context of the national initiative for personalized health, SPHN.
Our experts harmonize and optimize internal data handling processes through the customization and development of analysis pipelines or software tools. This includes multi-site data processing tracking pipeline, diagnostic tools and more. Our teams also contribute to some of the world-leading Open Science databases and tools for life sciences which can be adapted to your in-house needs.
Case study: Clinical software development
→ Your challenge: Robust and user-friendly software is required for data collection in routine laboratory activities. Over the years, your analytical processes may be relying on a range of disconnected tools which slow down your research, and developing a complete software solution for collecting, processing, analysing and visualising your data may not be your core business.
→ Our solution: With our agile, iterative and collaborative approach, we can help you to build a proof of concept with a powerful prototype (database, interface, scientific processing, …), before embarking on a full-scale development project.
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In practice:
Oncobench ®: together with the Geneva University Hospitals, we launched a user-friendly platform that streamlines and automates the analysis of patient tumour DNA for cancer diagnosis, while ensuring the privacy of the patient’s data. Read about the latest key development of the platform.
Melanie: our commercial off-the-shelf software for the analysis of 2D electrophoresis gel and blot images, supporting the discovery of protein biomarkers, monitoring the adaptation of organisms to their environment, development of diagnostic tests, quality control of food samples, development of HCP ELISA tests (choice and validation of immunoassay reagents), etc.
Our biocuration experts excel in the art of generating and representing knowledge from a growing body of publications and on various data types including proteomics, lipidomics and transcriptomics. This includes help with setting up expert-¬annotated resources for a wide range of applications, such as understanding protein function, facilitating clinical interpretation of cancer variants or enabling biomarker discovery. Read more
In practice:
Our Swiss-Prot team provides the manually annotated section of UniProt, the world-leading protein information resource (together with EMBL-EBI and PIR) accessed by thousands of users every day.
The Swiss Variant Interpretation Platform aims to harmonize the interpretation of genetic variants across Swiss hospitals, and will combine clinical data from hospital partners with publicly available information from international projects (e.g. ClinVar, CIViC) and published literature, sourced by expert biocurators.
The SwissLipids knowledgebase is a comprehensive library of over 500,000 lipid structures enriched with expert-curated information on lipid metabolism, protein interactions and occurrence in organelles, cells, tissues and organs.
Our comprehensive – and constantly evolving – course portfolio provides hands-on experience of the most up-to-date bioinformatics techniques and resources, including clinical applications for researchers or healthcare professionals. We offer about 100 course-days per year. Gain high-quality introductory and advanced data science expertise in specific area. Discover our specific offer for companies
Case study: Develop programming and data analysis skills in your team
→ Your challenge: Onboarding a group of employees with mixed skills levels in R programming language and RNA-seq data analysis, and who are running on a very tight schedule.
→ Our solution: We adapt our regular and successful courses to create a training path adjusted to your schedule constraints and team-specific needs.
In practice:
Certificate of Advanced Studies (CAS) in Personalized Molecular Oncology: First of its kind in Switzerland the CAS aims to establish a common language between the wide range of professionals involved in the personalized oncology process, from biologists and bioinformaticians to pathologists and clinicians. It is co-organized by SIB and the University Hospitals of Basel and Lausanne.
SIB was commissioned by the Food and Agriculture Organization of the United Nations (FAO) and the International Atomic Energy Agency (IAEA) joint programme to produce two e-learning modules, accessible via the dedicated website Viral Zone