BiG Talks – Integrative Omics
September 10 @ 13:00 – 15:00 CEST
Arranged by the SciLifeLab platforms for Bioinformatics, Genomics and Diagnostics Development.
Host: Rui Benfeitas, NBIS Stockholm (rui.benfeitas@scilifelab.se)
The Bioinformatics and Genomics seminar series (“BiG Talks”) is an initiative arranged by the SciLifeLab platforms for Bioinformatics (NBIS), Genomics (NGI) and Clinical Genomics platform. The seminar series aims to give inspiration to the SciLifeLab community and to create new networking possibilities. Each event will be broadcasted over Zoom where you will be able to interact with the speakers, and live broadcasted at the SciLifeLab YouTube channel.
In this seminar series, run in parallel with the ELIXIR-SE / NBIS workshop in Omics Integration and Systems Biology, we will be broadcasting three seminars about research and tools for integration of omics data through systems biology approaches, in humans and model organisms. Please use the following link to register and access the Zoom link.
8th of September, 15:00 – 16:00 CET
Network based analysis of 1002 GWAS study defines a pleiotropy map of human cell biology
Dr. Pedro Beltrao
Group Leader, EMBL-EBI, United Kingdom
10th of September, 13:00 – 13:55 CET
The Metabolic Atlas: genome-scale metabolic models for easy browsing and analysis
Mihail Anton
Project Manager for Metabolic Atlas, NBIS / Chalmers University, Sweden
More info, see below
10th of September, 14:00 – 15:00 CET
Network-based integration and visualization of large-scale data
Dr. Lars Juhl Jensen
Group Leader, Novo Nordisk Foundation Center for Protein Research, Denmark
More info, see below
Metabolic Atlas: Genome-scale metabolic models for easy browsing and analysis
Mihail Anton, Project Manager for Metabolic Atlas, NBIS / Chalmers University of Technology, Sweden
Abstract
As science is advancing towards full reproducibility, the ecosystem of tools and resources for genome-scale metabolic modelling is increasingly open-source. The talk will be centred on showcasing how Metabolic Atlas is aiding discovery of disease-related alterations of metabolism by contributing to this ecosystem.
Metabolic Atlas integrates open-source GEMs of several model organisms, and provides visualisations for these, such as the Map Viewer via the manually curated 2D maps and the automatically generated 3D maps, and the gene- and metabolite-centric Interaction Partners. In concert with other supporting features, Metabolic Atlas is making open source genome-scale metabolic models easy to browse and analyse.
The talk will also promote a way to organise a model in a git repository, the model test suite Memote, and how this and other automations can be deployed on GitHub, with the ultimate purpose of facilitating transparent community curation.
Biography: In his role as project manager for Metabolic Atlas, Mihail has been watching and contributing to the infrastructure supporting the development and community curation of genome scale metabolic models. Homepage: https://nbis.se/about/staff/mihail-anton/
Date: September 10, 13:00 – 14:00 CET online on Zoom
Network-based integration and visualization of large-scale data
Dr. Lars Juhl Jensen, Group Leader, Novo Nordisk Foundation Center for Protein Research, Denmark
Abstract
Networks are a powerful abstraction for modeling and visualizing the interplay between the many proteins within a cell. In this lecture, I will first introduce the STRING database, which uses the network abstraction to integrate a wide range of evidence types for physical protein interactions and functional association. This includes predicted interactions, interactions from other public databases, and automatic text mining of the biomedical literature. I will show a common use case of STRING, namely network-based visualization of omics data via the Cytoscape stringApp.
Biography
Dr. Lars Juhl Jensen started his research career in Søren Brunak’s group at the Technical University of Denmark (DTU), from where he in 2002 received the Ph.D. degree in bioinformatics for his work on non-homology-based protein function prediction. During this time, he also developed methods for visualization of microbial genomes, pattern recognition in promoter regions, and microarray analysis. From 2003 to 2008, he was at the European Molecular Biology Laboratory (EMBL) where he worked on literature mining, integration of large-scale experimental datasets, and analysis of biological interaction networks. Since 2009, he has continued this line of research as a professor at the Novo Nordisk Foundation Center for Protein Research at the Panum Institute in Copenhagen and as a founder, owner and scientific advisor of Intomics A/S. He is a co-author of more than 200 scientific publications that have in total received more than 40,000 citations. He was awarded the Lundbeck Foundation Talent Prize in 2003, his work on cell-cycle research was named “Break-through of the Year” in 2006 by the magazine Ingeniøren, his work on text mining won the first prize in the “Elsevier Grand Challenge: Knowledge Enhancement in the Life Sciences” in 2009, and he was awarded the Lundbeck Foundation Prize for Young Scientists in 2010. Homepage: https://jensenlab.org/
Date: September 10, 14:00 – 15:00 CET online on Zoom
info@nbis.se
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