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DTSTART;TZID=Europe/Stockholm:20260325T140000
DTEND;TZID=Europe/Stockholm:20260325T150000
DTSTAMP:20260405T153037
CREATED:20260318T102028Z
LAST-MODIFIED:20260318T102029Z
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SUMMARY:What stories can metabolites tell? Exploring data from cohorts to the individual
DESCRIPTION:Gabi Kastenmüller\,  Computational Health Center / ICB\, Helmholtz Munich \n\n\n\nAbstract\n\n\n\nMetabolites provide a direct readout of biological processes and therefore offer unique opportunities to study metabolism across populations and within individuals. In this talk\, I will give examples on how analysis and integration of metabolomics data from large cohort studies as well as smaller\, more specific challenge studies can help uncover relationships between metabolism\, genetic risk\, environmental exposures\, and health. The presentation will highlight three complementary perspectives on human metabolomics studies\, using examples from our own research. First\, I will show how genetic variation influences metabolite levels and how shared metabolite signatures across diseases can point to common biological pathways\, providing a molecular\, mechanism-oriented view on disease. Next\, I will illustrate how combining metabolite and genetic information may help stratify patients in the context of Alzheimer’s disease and its prevention. Finally\, I will discuss the potential of longitudinal metabolite profiles to monitor health and capture individual metabolic changes over time. Rather than focusing on technical aspects\, the talk aims to inspire thinking about metabolomics data analysis as a helpful tool in exploring metabolism in health and disease. \n\n\n\nBiography\n\n\n\nDr. Gabi Kastenmüller is an expert in the analysis\, integration\, and interpretation of metabolomics data and is heading a research group on Systems Metabolomics at Helmholtz Munich\, Germany. Having a background in chemistry and computer science\, she moved into bioinformatics for her PhD\, which she received from the Technische Universität München\, Germany\, in 2009. During her postdoctoral training at Karsten Suhre’s lab and a four-months stay as a visiting scientist at Metabolon Inc.\, USA\, she found her passion in metabolomics and was involved in the analysis of one of the first mass spectrometry-based metabolomics studies at large scale in two population-based cohorts. Inspired by the substantial metabolic individuality uncovered in these studies\, she started her own lab in 2011 with the goal to understand the role of metabolism and metabolic individuality in the development\, treatment\, and prevention of complex human diseases\, including Alzheimer’s disease. Thereby\, her team is particularly interested in a detailed\, systems-level understanding of which factors\, such as genotype\, lifestyle\, and microbiome composition\, shape and influence one’s personal metabolome and its changes over time. To this end\, her group experienced in computational biology collaborates with epidemiologists\, clinicians\, nutrition and sports scientists. Leveraging and integrating large-scale omics data within these collaborations enabled characterization of the human metabolic individuality in many cohorts and conditions\, including individuality in the response to physiological stimuli such as exercise or intake of specific food. \n\n\n\n \n\n\n\nHost: Elena Dracheva\, NBIS (elena.dracheva@scilifelab.se) \n\n\n\nBroadcast link (live event):  https://umu.zoom.us/j/61077879409 \n\n\n\nThe talk is sponsored by the NBIS course Introduction to Metabolomics Data Analysis. \n\n\n\nA recording  will also be available on the NBIS YouTube channel.
URL:https://www.scilifelab.se/event/what-stories-can-metabolites-tell-exploring-data-from-cohorts-to-the-individual/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20251110T133000
DTEND;TZID=Europe/Stockholm:20251110T140000
DTSTAMP:20260405T153037
CREATED:20251022T105523Z
LAST-MODIFIED:20251022T111011Z
UID:10001641-1762781400-1762783200@www.scilifelab.se
SUMMARY:BiG Talk – Best practices and common pitfalls in methylome sequencing analysis
DESCRIPTION:Abstract\n\n\n\nWhole-genome methylation sequencing provides single-base resolution of DNA methylation but remains one of the most computationally challenging omics data types to process. Its complexity stems from bisulfite-induced sequence conversion\, protocol-specific artifacts\, and the large number of available software tools\, making reproducible analysis and cross-study integration particularly difficult. To address this we systematically benchmarked ten complete computational workflows across five distinct profiling protocols using an experimental gold-standard reference. The results reveal substantial performance differences in accuracy\, computational efficiency\, and downstream analysis\, particularly for low-input samples. Furthermore\, we introduced a continuous\, “living” benchmarking platform for future software developments. To further facilitate large-scale\, standardized methylome analysis\, we developed complementary R package for efficient storage\, manipulation\, and integration of genome-wide methylation data that also supports applications such as methylation-based clocks\, or reference-based cell-type deconvolution enabling tissue composition inference from whole-genome methylomes. Together\, these resources address the difficulties of processing\, analyzing\, and interpreting DNA methylation data at genomic scale to ease reproducible epigenome research. \n\n\n\nBiography\n\n\n\nReka Toth is a computational biologist and group leader at the Luxembourg Institute of Health (LIH). She heads the Multi-omics Data Analysis Group in the Department of Cancer Research and drives omics initiatives within the Medical Informatics\, Bioinformatics & AI Unit. Trained as a molecular biologist\, she completed a PhD in genetic epidemiology at the University of Debrecen (Hungary) focused on chronic diseases and addiction\, and later added Software Engineering to pivot into computational biology. \n\n\n\nIn 2013\, Dr. Toth joined the National Center for Tumor Diseases in Heidelberg\, where she led the Biostatistics and Bioinformatics Group on colorectal cancer. She then moved to the Epigenomics Division at the German Cancer Research Center (DKFZ)\, expanding her work in computational epigenomics across cancer types\, with a particular emphasis on DNA methylation for prognosis and cell-of-origin. She joined LIH in 2021 and established her own group in 2025. Her research focuses on methylation as a diagnostic and prognostic biomarker and on integrative multi-omics to reveal complex biomarker signatures and mechanisms in cancer. \n\n\n\nHost: Louella Vasquez\, NBIS (louella.vasquez@scilifelab.se) \n\n\n\nBroadcast link (live event):  https://lu-se.zoom.us/j/62767371752 \n\n\n\nThe talk is sponsored by the SciLifeLab Epigenomics Symposium. \n\n\n\nA recording  will also be available on the NBIS YouTube channel.
URL:https://www.scilifelab.se/event/big-talk-best-practices-and-common-pitfalls-in-methylome-sequencing-analysis/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241017T130000
DTEND;TZID=Europe/Stockholm:20241017T141500
DTSTAMP:20260405T153037
CREATED:20240909T141724Z
LAST-MODIFIED:20240913T114033Z
UID:10001352-1729170000-1729174500@www.scilifelab.se
SUMMARY:Generation of context-specific genome-scale metabolic models using single-cell RNA-Seq data
DESCRIPTION:Johan Gustafsson\, Postdoc researcher\, Broad Institute\, USA \n\n\n\nAbstract \n\n\n\nThe metabolic networks in cells vary across tissues and cell types\, and to accurately model the metabolism of cells\, the full generic metabolic network defined in the genome needs to be reduced to a context-specific network representing the network expressed specifically in the cells of interest. Single-cell RNA-Seq promises to provide the information needed for such a reduction\, but noise in the form of data sparsity is a challenge. Here\, we present methods to handle data sparsity and estimate the uncertainty of modeling results. \n\n\n\nBiography \n\n\n\nJohan is an expert in modeling cancer metabolism and analyzing single-cell RNA/DNA sequencing data\, aiming to uncover vulnerabilities in cancer. With a background in both computer science and biochemistry\, Johan has completed a PhD in metabolic modeling at Chalmers University of Technology and now works as a postdoc in the Getz lab at the Broad Institute\, focusing on CLL/Richter’s syndrome and hypoxia in solid tumors. \n\n\n\nHost: Rasool Saghaleyni\, NBIS Chalmers University\, Gothenburg (rasool.saghaleyni@scilifelab.se) \n\n\n\nDate: October 17\, 13:00 – 14:15 CET online on zoom \n\n\n\nBroadcast link (live event): link\, pass:spd996The talk will also be available afterwards on the SciLifeLab YouTube channel.More information about the Oimcs Integration and Systems Biology Workshop here.
URL:https://www.scilifelab.se/event/oimcs-integration-and-systems-biology/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241015T100000
DTEND;TZID=Europe/Stockholm:20241015T111500
DTSTAMP:20260405T153037
CREATED:20240902T120825Z
LAST-MODIFIED:20240902T120852Z
UID:10001345-1728986400-1728990900@www.scilifelab.se
SUMMARY:Deriving actionable insight from omics data – an industry perspective
DESCRIPTION:Speaker: Daniel Muthas\, Head of Data Science & Bioinformatics at AstraZeneca \n\n\n\nAbstract \n\n\n\nThis talk will focus on how advancement in omic analysis is enabling the realisation of precision medicine in chronic complex diseases. Large\, well phenotyped cohorts highlights the heterogeneity of disease and through single cell technologies we are able to study disease processes at unprecedented granularity\, but how do we take these insights into actionable and deployable applications? Here I will focus on how we employ a breadth of bioinformatic techniques of different modalities to bridge between populations\, patients\, and cellular level to identify novel targets\, biomarkers and patient populations. \n\n\n\nBackground \n\n\n\nDaniel’s team is working with applied bioinformatics across the whole drug discovery and development pipeline\, from target identification to indication expansion and exploratory biomarker analysis in clinical trials.   \n\n\n\nHost: Rasool Saghaleyni\, NBIS Chalmers University\, Gothenburg (rasool.saghaleyni@scilifelab.se) \n\n\n\nDate: October 15\, 10:00 – 11:15 CET online on zoom \n\n\n\nBroadcast link (live event): link\, pass: spd996 The talk will also be available afterwards on the SciLifeLab YouTube channel.More information about the Oimcs Integration and Systems Biology Workshop here.
URL:https://www.scilifelab.se/event/deriving-actionable-insight-from-omics-data-an-industry-perspective/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240920T130000
DTEND;TZID=Europe/Stockholm:20240920T140000
DTSTAMP:20260405T153037
CREATED:20240902T120600Z
LAST-MODIFIED:20240902T120933Z
UID:10001344-1726837200-1726840800@www.scilifelab.se
SUMMARY:How does epigenetic mechanism impact Type 2 diabetes?
DESCRIPTION:Speaker: Dr. Charlotte Ling is a Professor at Lund University \n\n\n\nDr. Charlotte Ling is a Professor at Lund University and a principal investigator of the Epigenetics and Diabetes Unit at Lund University Diabetes Centre (LUDC). She obtained her PhD in Endocrinology at University of Gothenburg\, Sweden in 2002. After a postdoc at Lund University\, where she studied genetics of type 2 diabetes\, she dedicated her research to the study of epigenetic mechanisms causing type 2 diabetes and metabolic disease. Her research group has over the last two decades pioneered the field of epigenetics in type 2 diabetes. They have made several groundbreaking discoveries such as genome-wide epigenetic modifications in pancreatic islets\, skeletal muscle\, adipose tissue and the liver from patients with type 2 diabetes compared with non-diabetic control subjects. Dr. Ling’s research group has also shown that genetic and non-genetic factors such as SNPs\, exercise\, diet\, obesity and age alter the genome-wide epigenetic pattern in human primary tissues for type 2 diabetes.  More recently\, her group is trying to translate their epigenetic findings to biomarkers and novel therapies for precision medicine to improve prediction\, prevention and treatments of type 2 diabetes.  \n\n\n\nHost: Louella Vasquez\, NBIS (louella.vasquez@scilifelab.se) \n\n\n\nBroadcast link (live event):  https://lu-se.zoom.us/j/67681656100 \n\n\n\nThe talk will also be available afterwards on the NBIS YouTube channel.
URL:https://www.scilifelab.se/event/how-does-epigenetic-mechanism-impact-type-2-diabetes/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210910T140000
DTEND;TZID=Europe/Stockholm:20210910T150000
DTSTAMP:20260405T153037
CREATED:20210827T111618Z
LAST-MODIFIED:20210909T122507Z
UID:10000418-1631282400-1631286000@www.scilifelab.se
SUMMARY:BiG Talks - Network-based integration and visualization of large-scale data
DESCRIPTION:BiG Talks: Integrative Omics\n\n\n\nArranged by the SciLifeLab platforms for Bioinformatics\, Genomics and Diagnostics Development \n\n\n\nThe 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.  \n\n\n\nIn 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:  \n\n\n\nRegistration\n\n\n\n\n\n\n\n\n\n8th of September\, 15:00 – 16:00 CET \n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biologyDr. Pedro BeltraoGroup Leader\, EMBL-EBI\, United Kingdom \n\n\n\nMore info \n\n\n\n \n\n\n\n\n\n10th of September\, 13:00 – 13:55 CET \n\n\n\nMetabolic Atlas: genome-scale metabolic models for easy browsing and analysisMihail AntonProject Manager for Metabolic Atlas\, NBIS / Chalmers University\, Sweden \n\n\n\nMore info \n\n\n\n\n\n10th of September\, 14:00 – 15:00 CET \n\n\n\nNetwork-based integration and visualization of large-scale dataDr. Lars Juhl JensenGroup Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nMore info: See below \n\n\n\n\n\n\n\n\n\n\nNetwork-based integration and visualization of large-scale data\n\n\n\nDr. Lars Juhl Jensen\, Group Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nAbstract \n\n\n\nNetworks 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. \n\n\n\nBiography  \n\n\n\nDr. 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/ \n\n\n\nHost: Rui Benfeitas\, NBIS Stockholm (rui.benfeitas@scilifelab.se) \n\n\n\nDate: September 10\, 14:00 – 15:00 CET online on Zoom \n\n\n\nBroadcast link (live event): SciLifeLab YouTube channel  \n\n\n\n \n\n\n\n \n\n\n\nRegistration form for zoom link
URL:https://www.scilifelab.se/event/big-talks-3/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210910T130000
DTEND;TZID=Europe/Stockholm:20210910T150000
DTSTAMP:20260405T153037
CREATED:20210910T060532Z
LAST-MODIFIED:20210910T081453Z
UID:10000444-1631278800-1631286000@www.scilifelab.se
SUMMARY:BiG Talks - Integrative Omics
DESCRIPTION:Arranged by the SciLifeLab platforms for Bioinformatics\, Genomics and Diagnostics Development.\n\n\n\nHost: Rui Benfeitas\, NBIS Stockholm (rui.benfeitas@scilifelab.se) \n\n\n\nThe 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.  \n\n\n\nIn 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. \n\n\n\nRegistration\n\n\n\n\n\n\n\n\n\n8th of September\, 15:00 – 16:00 CET \n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biologyDr. Pedro BeltraoGroup Leader\, EMBL-EBI\, United Kingdom \n\n\n\nMore info \n\n\n\n \n\n\n\n\n\n10th of September\, 13:00 – 13:55 CET \n\n\n\nThe Metabolic Atlas: genome-scale metabolic models for easy browsing and analysisMihail AntonProject Manager for Metabolic Atlas\, NBIS / Chalmers University\, Sweden \n\n\n\nMore info\, see below \n\n\n\n\n\n10th of September\, 14:00 – 15:00 CET \n\n\n\nNetwork-based integration and visualization of large-scale dataDr. Lars Juhl JensenGroup Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nMore info\, see below \n\n\n\n\n\n\nMetabolic Atlas: Genome-scale metabolic models for easy browsing and analysis\n\n\n\nMihail Anton\, Project Manager for Metabolic Atlas\, NBIS / Chalmers University of Technology\, Sweden \n\n\n\nAbstract \n\n\n\nAs 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. \n\n\n\nMetabolic 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. \n\n\n\nThe 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. \n\n\n\nBiography: 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/ \n\n\n\nDate: September 10\, 13:00 – 14:00 CET online on Zoom \n\n\n\nregistration for both talks\n\n\n\n\n\n\n\nNetwork-based integration and visualization of large-scale data\n\n\n\nDr. Lars Juhl Jensen\, Group Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nAbstract \n\n\n\nNetworks 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. \n\n\n\nBiography \n\n\n\nDr. 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/ \n\n\n\nDate: September 10\, 14:00 – 15:00 CET online on Zoom \n\n\n\nregistration for both talks
URL:https://www.scilifelab.se/event/big-talks/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210910T130000
DTEND;TZID=Europe/Stockholm:20210910T135500
DTSTAMP:20260405T153037
CREATED:20210827T111000Z
LAST-MODIFIED:20210909T122434Z
UID:10000417-1631278800-1631282100@www.scilifelab.se
SUMMARY:BiG Talks - Metabolic Atlas: genome-scale metabolic models for easy browsing and analysis
DESCRIPTION:BiG Talks: Integrative Omics\n\n\n\nArranged by the SciLifeLab platforms for Bioinformatics\, Genomics and Diagnostics Development \n\n\n\nThe 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.  \n\n\n\nIn 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:  \n\n\n\nRegistration\n\n\n\n\n\n\n\n\n\n8th of September\, 15:00 – 16:00 CET \n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biologyDr. Pedro BeltraoGroup Leader\, EMBL-EBI\, United Kingdom \n\n\n\nMore info \n\n\n\n \n\n\n\n\n\n10th of September\, 13:00 – 13:55 CET \n\n\n\nThe Metabolic Atlas: genome-scale metabolic models for easy browsing and analysisMihail AntonProject Manager for Metabolic Atlas\, NBIS / Chalmers University\, Sweden \n\n\n\nMore info\, see below \n\n\n\n\n\n10th of September\, 14:00 – 15:00 CET \n\n\n\nNetwork-based integration and visualization of large-scale dataDr. Lars Juhl JensenGroup Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nMore info \n\n\n\n\n\n\n\n\n\n\nMetabolic Atlas: Genome-scale metabolic models for easy browsing and analysis\n\n\n\nMihail Anton\, Project Manager for Metabolic Atlas\, NBIS / Chalmers University of Technology\, Sweden \n\n\n\nAbstract \n\n\n\nAs 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. \n\n\n\nMetabolic 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. \n\n\n\nThe 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. \n\n\n\nBiography: 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/ \n\n\n\nHost: Rui Benfeitas\, NBIS Stockholm (rui.benfeitas@scilifelab.se) \n\n\n\nDate: September 10\, 13:00 – 13:55 CET online on Zoom \n\n\n\nBroadcast link (live event): SciLifeLab YouTube channel \n\n\n\n \n\n\n\nRegistration form for zoom link
URL:https://www.scilifelab.se/event/big-talks-2/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210908T150000
DTEND;TZID=Europe/Stockholm:20210908T160000
DTSTAMP:20260405T153037
CREATED:20210827T090406Z
LAST-MODIFIED:20210902T144342Z
UID:10000416-1631113200-1631116800@www.scilifelab.se
SUMMARY:BiG Talks - Network based analysis of 1002 GWAS study defines a pleiotropy map of human cell biology
DESCRIPTION:BiG Talks: Integrative Omics\n\n\n\nArranged by the SciLifeLab platforms for Bioinformatics\, Genomics and Diagnostics Development \n\n\n\nThe 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.  \n\n\n\nIn 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:  \n\n\n\nRegistration\n\n\n\n\n\n\n\n\n\n8th of September\, 15:00 – 16:00 CET \n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biologyDr. Pedro BeltraoGroup Leader\, EMBL-EBI\, United Kingdom \n\n\n\nMore info\, see below \n\n\n\n \n\n\n\n\n\n10th of September\, 13:00 – 13:55 CET \n\n\n\nMetabolic Atlas: genome-scale metabolic models for easy browsing and analysisMihail AntonProject Manager for Metabolic Atlas\, NBIS / Chalmers University\, Sweden \n\n\n\nMore info \n\n\n\n\n\n10th of September\, 14:00 – 15:00 CET \n\n\n\nNetwork-based integration and visualization of large-scale dataDr. Lars Juhl JensenGroup Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nMore info \n\n\n\n\n\n\n\n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biology\n\n\n\nDr. Pedro Beltrao\, Group Leader\, EMBL – EBI\, United Kingdom \n\n\n\nAbstract \n\n\n\nUnderstanding how genetic variation contributes to phenotypic differences is a central question in biology. This requires models that can describe how rare and common genetic variability impacts on different cellular components and traits. To study the impact of rare variants we develop and combine variant effect predictors for protein stability\, interaction affinity\, and gene expression regulation. We have applied these to study the impact of rare variants on trait variation in strains of micro-organisms\, including panels of 1000 strains of E. coli and S. cerevisiae.  For human we have used a network-based approach to study 1002 traits analysed by genome wide association studies (GWAS). Based on the principle that genes associated with the same phenotype tend to be involved in the same cellular processes\, we performed a network expansion and prioritization of trait associated genes. The network based gene-trait association scores allows for the identification of related traits and the biological processes that they share. Based on this we can identify pleiotropic biological processes that can influence a large number of human traits and identify opportunities for drug repurposing. Finally\, I will illustrate how this analysis can be combined with patient specific mRNA/protein data for further prioritization. I will focus on neurodegeneration diseases to illustrate the identification of shared aetiology and further integrate ALS SOD1 mutant patient mRNA/protein data to identify novel astrocyte candidate ALS linked genes. As a future perspective I will briefly discuss the need for approaches that can jointly integrate common and rare genetic variation to improve our understanding of trait variation. \n\n\n\nBiography \n\n\n\nDr. Pedro Beltrao is a group leader at EMBL – EBI where his research group seeks to understand how cellular functions have diverged during evolution as well as how they are altered in disease. He employs systems biology techniques to analyse GWAS\, post-translational modifications (PTMs) data from mass-spectrometry experiments\, among other omics\, to study the molecular sources of phenotypic novelties\, exploring how DNA changes are propagated through molecular structures and interaction networks to give rise to phenotypic variability. Dr. Beltrao has a PhD in Biology from the University of Aveiro (research conducted at EMBL-Heidelberg)\, after which he conducted his postdoctoral research at the University of California San Francisco. Dr. Beltrao is a group leader at EMBL-EBI since 2013\, and will join ETH Zurich in 2022.  Homepage: https://www.ebi.ac.uk/research-beta/beltrao/ \n\n\n\nHost: Rui Benfeitas\, NBIS Stockholm (rui.benfeitas@scilifelab.se) \n\n\n\nDate: September 8\, 15:00 – 16:00 CET online on Zoom \n\n\n\nBroadcast link (live event): SciLifeLab YouTube channel  \n\n\n\nRegistration form for zoom link
URL:https://www.scilifelab.se/event/big-talks-1/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
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END:VCALENDAR