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Biology subjects

Leinonen, R.

Publications and source records attributed to Leinonen, R..

4 recordsLinked to original sources

Habitat context alters the pace of climate-driven community warming across terrestrial and freshwater ecosystems

As global temperatures rise, ecological communities are increasingly dominated by warm-affiliated species, a process known as community warming or thermophilisation. Yet, why different taxa exhibit different rates of community warming remains unclear. Habitat composition and structure are likely drivers of this variation, as the ecological consequences of warming are filtered by local environmental conditions. Using over 40 years of monitoring data spanning terrestrial (birds, insects, plants) and freshwater (phytoplankton) communities, we show that habitat structure determines how strongly communities track warming. Forest cover systematically slows thermophilisation by reducing communities sensitivity to temperature change, whereas habitat heterogeneity has weak and variable effects that differ among ecosystems. Together, these results demonstrate that uneven thermophilisation arises from habitat-mediated differences in how communities respond to a shared climatic signal. Incorporating these effects is essential for improving predictions of biodiversity change under ongoing climate warming.

ecology↗

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learned. As a component of the Platform, the SARS-CoV-2 Data Hubs enabled the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.

bioinformatics↗

Refget: standardised access to reference sequences

Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing. We have created refget, a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself. We present four reference implementations across in-house and cloud infrastructure, a compliance suite and a web report used to ensure specification conformity across implementations. https://w3id.org/ga4gh/refget.

bioinformatics↗

The COMPARE Data Hubs

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory, and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats often lead to data not being shared, or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.

bioinformatics↗