EMBL Seminars

Abstract
Organization of cells within a tissue is fundamental to its biological functioning and mechanical properties. How a reproducible spatial organization emerges in such a system in spite of the intrinsic stochasticity of cell activity is a question that has attracted the attention of many physicists. During this talk, I will show some numerical investigation of self-organization in cell monolayers, using the Cellular Potts Model, a widely used numerical modelling tool of multicellular systems. I will show in particular how cell activity can drive an order-disorder transition in epithelial tissues, and compare this transition with the standard defect-mediated theories for melting of two-dimensional materials.

About the speaker
https://marcdurand.net

Meet the speaker
To meet with the speaker informally after the talks,sign up here [https://docs.google.com/document/d/1DUO-JcsFC-Uq6PgVIlByZtxNAj8tOxy3FudBom7bpdA/edit?usp=sharing]. We especially encourage predocs and postdocs to take advantage of this opportunity.

Connection details
Zoom*: https://embl-org.zoom.us/j/94618809202?pwd=U1hsZ1MxZFN5M3BocDBhd0wwWVlCUT09 (Meeting ID: 946 1880 9202, Password: 886185)

Please note that the talk will be recorded.
*For the FAQ section, as a zoom participant, please use either the chat function (the host will read out your question) or the “raise your hand” function and turn on your microphone.

Connection details
Zoom*: [https://embl-org.zoom.us/j/3528126808?pwd=WEZuRXlZTG83MzgvV2FId1R3STVBUT09] (Meeting ID: [352 812 6808], Password: [2LCN7s])
*For the FAQ section, as a zoom participant, please use either the chat function (the host will read out your question) or the “raise your hand” function and turn on your microphone.

Abstract
Our mission is to understand genome regulation. We previously developed the Cap Analysis of Gene Expression (CAGE) technology, which identifies the transcription starting sites (TSSs) at single-base resolution and quantitatively measures their activity throughout the genome at high-throughput. Using CAGE, the FANTOM5 project has generated comprehensive maps of regulatory elements, such as promoters and enhancers, and their networks using a comprehensive panel of human and mouse primary cells, cell lines and tissues. We also built a reliable atlas of human lncRNAs based in unambiguous identification of their promoters, predicting possible function for 19,175 of them. To further explore lncRNAs function, the FANTOM6 project established a large lncRNA knockdown data set by systematically knocking down several hundreds of lncRNAs in human primary fibroblasts and ES cells. Recently, in the FANTOM6, we have started to comprehensively map the interactome of RNA with chromatin, with our RADICL-seq (RNA and DNA Ligated and Sequenced) technology, identifying various types of completely new types of RNA interactions with chromatin.  

An important subset of lncRNA is constituted by antisense RNAs. We have identified a new class of non-coding antisense RNAs, named SINEUPs, which counterintuitively up-regulate protein translation of the sense RNA that they overlap. Enhancement of protein translation is mediated by SINE elements and the specificity of action is mediated by the region antisense to the 5’UTRs of the target mRNAs. SINEUPs can be designed to target specifically any targeted mRNAs for therapies, including but not limited to haploinsufficiencies. The map of precise TSSs identified by CAGE in FANTOM5 gives us information to flexibly design the antisense region for effective SINEUPs in each cell type, allowing to correct unbalanced gene expression in disease models.  Expanding these activities, we are working with Human Cell Atlas (HCA) project, aiming at the creation of a comprehensive map of all human cells at single cell level. We have developed single cell CAGE and bioinformatics pipeline for the 10X Genomics platform allowing CAGE at single cell level, which will be broadly used to study transcriptional regulation at single cell level.

Abstract
The lab of Bas van Steensel develops and applies new genomics technologies to elucidate principles of gene regulation in mammalian cells. In this seminar he will discuss an approach to efficiently alter the linear structure of a large genomic locus in a highly multiplexed manner and study the impact of these perturbations on gene regulation and spatial chromatin organisation. 

Please find below the connection details (EMBL Members only)

https://www.embl.org/internal-information/updates/distinguished-visitor-lecture-bas-van-steensel/

Abstract
Metagenomic DNA sequencing enables detailed study of the bacteria found in samples from various microbiomes but determining the composition of such samples beyond the genus or species level is challenging when bacteria with shared recent ancestry are sequenced together. In this talk I will cover how probabilistic modelling of read alignments can aid in deconvoluting metagenomic sequencing data and discuss future prospects and challenges of incorporating metagenomics in genomic epidemiological studies through examples from our ongoing work in modelling carriage and competition dynamics between pathogenic bacteria in the human gut.

About the speaker
Tommi Mäklin received a PhD in Computer Science from the University of Helsinki in 2022 and subsequently joined the local Department of Mathematics and Statistics to work on a postdoctoral project in modelling bacterial evolution and ecology using metagenomic DNA sequencing data. Since February 2023 he has been visiting the EMBL-EBI investigating Enterobacteriaceae dynamics in the human gut during carriage and infection. 

Venue:  Garden Room (EBI Main Building) and via Zoom  

Connection details
Zoom* https://embl-org.zoom.us/j/97138788361?pwd=aDVKSENwZG85ZHpyZFhkRkpUSXJwUT09
Meeting ID: 971 3878 8361
Passcode: 057359

Please note that the talk will not be recorded.
*For the FAQ section, as a zoom participant, please use either the chat function (the host will read out your question) or the “raise your hand” function and turn on your microphone.

The talk will be held in person at the Kendrew Lecture Theatre. A virtual Q&A session will be held after for members of the Human Ecosystems Transversal Theme. 

Connection details
Zoom*: https://embl-org.zoom.us/j/98052355080?pwd=dU5GY3RITEp6ZElCRW13dHJpWFVsZz09 (Meeting ID: 980 5235 5080, Password: 774827)

Please note that the talk will not be recorded.
*For the FAQ section, as a zoom participant, please use either the chat function (the host will read out your question) or the “raise your hand” function and turn on your microphone.

The seminar will be held in person at the EBI in the Kendrew Lecture Theatre. 

Connection details
Zoom*: pending.

*For the FAQ section, as a zoom participant, please use either the chat function (the host will read out your question) or the “raise your hand” function and turn on your microphone.