Successful DDLS research area conference
The amount and complexity of life science data generated across the world grows exponentially. Making this vast amount of data publicly available is the key that will unlock more scientific discoveries than ever before and forms the basis of the SciLifeLab and Wallenberg National Program on Data-Driven Life Science (DDLS).
The program is divided into four strategic research areas (RAs), Data-Driven Cell and molecular biology, Data-Driven Epidemiology and Biology of infections, Data-Driven Evolution and biodiversity, and Data-Driven Precision medicine and diagnostics, all paramount for improving the lives of people and animals, as well as nature, by detecting and treating diseases, protecting biodiversity and creating sustainability.
On March 22, the DDLS program held its first full day online Research area conference. The event, meant to bring scientists from all research areas together and inspire discussions, was a success, and more than 350 participants listened to an exciting compilation of keynote speakers and research area experts during the day.
SciLifeLab Director Olli Kallioniemi opened up the conference, and gave a short introduction of the 12-year DDLS program. As an example of future initiatives, the national SciLifeLab DDLS Data platform, a key resource that will be linked to the Berzelius super computer capabilities, was highlighted.
“We look forward to collaborating with not just the Fellows, the PhD’s and the postdocs, but also all the departments and universities that contribute to this program. This is really an exciting joint effort that we hope to bring forward” said Olli.
Professor Ewan Birney (CBE FRS FMedSci), joint Director of EMBL’s European Bioinformatics Institute (EMBL-EBI), in Hinxton, Cambridgeshire and Deputy Director general of the European Molecular Biology Laboratory (EMBL) was the keynote speaker of the day. In his talk, Big data in biology – what the pandemic has taught us, Ewan talked about EMBL’s response to the COVID-19 pandemic and the global importance of the COVID-19 data portal, but also about EMBL’s scientific program Molecules to ecosystems, their role in sharing AlphaFold2 data, the Genomic medicine platform, and the important collaborations with SciLifeLab.
“The key learning about rapid health care innovation is that you should set up a modern scalable trial where you just loop through every single thing you want to try very, very quickly. Because if it’s urgent you will have enough patients coming your way and then you will be able to make a decision based on this” Ewan said about the COVID-19 pandemic.
The DDLS research area leads, Erik Lindahl (SU, Cell and molecular biology), Janne Lehtiö (KI, Precision medicine and diagnostics), Oliver Billker (UmU, Epidemiology and Biology of infections), and Fredrik Ronquist (NRM, Evolution and biodiversity), presented their respective research areas and the invited area specific guest speakers.
First up was Data-Driven Cell and molecular biology, where the participants got to listen to Orane Guillaume-Gentil (ETH), presenting on Live-Seq, a recently developed method capable of profiling transcriptomes from living single cells, Aleksandra Walczak (Ecole Normale Supérieure), describing how unique immune fingerprints can be used to identify preexisting COVID-19 immunity or distinguish between identical twins, and Arne Elofsson (Stockholm University), on how to improve AlphaFold2 protocols to enhance predictions of protein complexes.
The next area was Precision medicine and diagnostics and it began with Søren Brunak (University of Copenhagen), who spoke about disease progression patterns/trajectories obtained from health care data and how they can be analyzed to better understand how different risk factors can act as pre-cursors to e.g. pancreatic cancer, and to improve both the quality and swiftness of diagnosis of this disease. Søren Brunak and colleagues has also used the same approach to analyze a large number of drug prescriptions to identify common drug pairs and their impact. Peter Horvath (Biological Research Centre, Szeged), then presented how various machine learning techniques are used in single cell microscopy and finished with a description of CL2M, a technique that is capable of detecting and isolating specific cells. The last presentation (ELLER talk) before lunch was given by Alberto Santos Delgado (University of Copenhagen/Boehringer Ingelheim), and addressed how data collected from many different omics techniques can be integrated and interpreted using various machine learning approaches to improve the accuracy in Precision medicine, regarding patient stratification, biomarker discovery, target identification and treatment recommendations.
After lunch it was time for the Epidemiology and Biology of infections research area, which began with a talk from Laura Michelle Carroll (EMBL and newly recruited DDLS fellow), on how we can leverage genomics data to identify and track emerging bacterial pathogens. Jay Hinton (University of Liverpool), gave his talk about how we can use functional genomics and transcriptomics to understand Salmonella infection biology, and Jeff Barnett (Wellcome Sanger Institute/Nightingale Health), concluded the session with his talk about tracking the rise and fall of SARS-CoV-2 variants in the UK.
The last session for the day, Evolution and biodiversity, started with a talk from Tobias Andermann (Gothenburg University), who uses machine learning to analyze big data to generate new insights on the biodiversity crisis, such as extinction threat levels for many endangered species. Next up was Nicolas Lartillot (CNRS/University of Lyon) who gave a presentation on how to infer evolution by using genomic data and why probabilistic modeling is important. The final talk was given by Ida Moltke (University of Copenhagen), who discussed how medically relevant insights can be gained by using population genetic inference.
The first DDLS research area conference was wrapped-up in separate breakout-room sessions for the four research areas. Here, the participants met, engaged in in-depth discussions, and discussed potential future collaborations.
The SciLifeLab and Wallenberg national DDLS program is funded by the Alice and Knut Wallenbergs Foundation.
Watch a recording of the entire conference on YouTube (split into four themes).
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