Focus on the group's mission
The Environmental Bioinformatics Group, led by Robert Waterhouse, is developing data science solutions to address environmental challenges. It builds on the institute’s capacities in coordinating biodata resources and developing data science tools and services to contribute to planetary preservation and restoration by addressing the global crisis and delivering direct benefits for society.
By meeting key needs in data collection, integration, and analysis, the team delivers tools and services to support data-driven, empirically informed, and model-guided policies and actions. It thereby contributes to strongly position Switzerland on environmental issues at national and international levels.
We recognize the need to coordinate efforts to address environmental challenges in a One Health perspective, from data collection and ingestion into open repositories, through to data analysis and the provision of tools and services that take full advantage of the data ecosystem.
Data science solutions to address environmental challenges
Planetary preservation and restoration is vital for human wellbeing. But to protect and restore the environment that sustains humankind we need to understand it. Improved data integration and interoperability greatly enhance the potential of biodiversity and environmental data to guide and assess efforts to restore and protect vital ecosystems. The Environmental Bioinformatics group builds data science solutions by:
- Developing bioinformatics tools and services that address environmental challenges e.g. biodiversity loss, food security, responses to climate change, etc.
- Supporting the FAIRification of environmental/biodiversity data and building Research Data Management capacity amongst researchers
- Fostering synergies among SIB Groups active in environmental sciences and agriculture
- Diversifying the impacts of the future SwissBioData ecosystem through environmental-data driver projects
These data science solutions will aim to advance three principal axes: the stewardship of data collection, concurrently with metadata, into open repositories; the integration of resources to enhance interoperability across biodiversity platforms; and the provision of tools and services including modelling and artificial intelligence to capitalise on the rich and connected data for enhanced analysis.
Connecting to national and international stakeholders
In Switzerland and internationally, there is growing recognition of the need to connect institutes and agencies to bring researchers and practitioners together and coordinate efforts to address environmental challenges. The Environmental Bioinformatics group builds connections by participating in community initiatives and projects:
- The European Reference Genome Atlas (ERGA) initiative is a community effort to coordinate the production of high-quality reference genome sequences of eukaryotic species in Europe. In September 2023, Robert Waterhouse was elected chair of the initiative.
Read more about the ERGA project
- The Biodiversity Genomics Europe (BGE) project brings together the DNA barcoding and reference genome networks to accelerate the use of genomic science to enhance understanding of biodiversity.
- The ELIXIR Biodiversity Community is building connections across the many infrastructures and services active in biodiversity research within and beyond ELIXIR. Robert Waterhouse is also co-leading ELIXIR’s priority area on "Biodiversity, Food Security, and Pathogens" for the Scientific Programme 2024-2028.
- 2023 Biodiversity: an atlas of European reference genomes https://doi.org/10.1038/d41586-023-02229-w
- 2023 The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity https://doi.org/10.12688/f1000research.133724.1
- 2023 How genomics can help biodiversity conservation https://doi.org/10.1016/j.tig.2023.01.005
- 2022 Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR https://doi.org/10.12688/f1000research.73825.2
- 2022 Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes https://doi.org/10.1093/gigascience/giac006
- 2022 A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus https://doi.org/10.1111/1755-0998.13436
- 2021 RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data https://doi.org/10.1111/1755-0998.13360
- 2021 Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits https://doi.org/10.1093/molbev/msaa240
- 2021 Summary Visualizations of Gene Ontology Terms With GO-Figure! https://doi.org/10.3389/fbinf.2021.638255
Members
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