EMBL Seminars

At EMBL, experts from institutes throughout the world speak on a wide range of scientific and technical topics

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6 June 2023, 11:00

Dynamics and self-organization of confluent cellular systems: a numerical investigation

6 June 20232023External Faculty SpeakerEMBL Heidelberg, Virtual

AbstractOrganization 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... AbstractOrganization 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 speakerhttps://marcdurand.netMeet the speakerTo meet with the speaker informally after the talks,sign up here...

Speaker(s): Marc Durand, Laboratory of Materials and Complex Systems, Université Paris Cité, CNRS, France
Host: Roman Belousov

Place: Large Operon

External Faculty Speaker

EMBL Heidelberg, Virtual

Additional information

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.


7 June 2023, 15:00

"Introducing Curio Seeker: A Whole-Transcriptome, High-Resolution Spatial Sequencing Platform"

7 June 20232023Company RepresentativeEMBL Heidelberg, Virtual

Connection detailsZoom 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... Connection detailsZoom*: [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.

Speaker(s): Bertrand Young, Curio Bioscience, Palo Alto, CA, USA
Host: Vladimir Benes

Place: Small Operon

Company Representative

EMBL Heidelberg, Virtual

Additional information

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.


9 June 2023, 11:00

Genomics regulation by long non-coding RNAs

9 June 20232023External Faculty SpeakerEMBL Rome

AbstractOur 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... AbstractOur 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....

Speaker(s): Piero Carninci, RIKEN Yokoama Campus, Japan
Host: Cornelius Gross

Place: Conf Room/Building 14

External Faculty Speaker

EMBL Rome

Additional information

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.


14 June 2023, 11:00

Planetary Biology Seminar

14 June 20232023Planetary Biology LecturesEMBL Heidelberg

Meeting ID 964 5185 1676 Password PBseminar... Meeting ID 964 5185 1676 Password: PBseminar

Speaker(s): Mike Dorrity & Flora Vincent, EMBL, NOT SPECIFIED

Place: Large Operon (Join the VC)

Planetary Biology Lectures

EMBL Heidelberg

Additional information Meeting ID 964 5185 1676 Password: PBseminar

15 June 2023, 14:00

To be announced

15 June 20232023External Faculty SpeakerEMBL Heidelberg, Virtual

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Speaker(s): Adam Martin, MIT, Department of Biology, USA, USA

Place: Large Operon

External Faculty Speaker

EMBL Heidelberg, Virtual


16 June 2023, 10:00

Probing principles of genome organisation and function

16 June 20232023EMBL Distinguished Visitor LectureEMBL Rome

AbstractThe 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... AbstractThe 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/   

Speaker(s): Bas Van Steensel, Netherlands Cancer Institute, Amsterdam, Netherlands
Host: Jamie Hackett

Place: Conf Room/Building 14

EMBL Distinguished Visitor Lecture

EMBL Rome

Additional information

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/

 

 

 


16 June 2023, 13:00

Use and abuse of functional amyloid: how to control and direct protein self-assembly

16 June 20232023Hamburg SpeakerEMBL Hamburg

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Speaker(s): Daniel Otzen, Aarhus University, Denmark
Host: Joint Seminar CSSB/EMBL

Place: CSSB Auditorium DESY, Notkestraße 85, Building 15

Hamburg Speaker

EMBL Hamburg


16 June 2023, 14:00

Probabilistic modelling in high-resolution metagenomics -

16 June 20232023Theory@EMBL seminarEMBL Heidelberg, Virtual

AbstractMetagenomic 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... AbstractMetagenomic 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 speakerTommi 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...

Speaker(s): Tommi Mäklin, University of Helsinki, Finland
Host: Virginie Uhlmann EMBL EBI

Place: Virtual seminar

Theory@EMBL seminar

EMBL Heidelberg, Virtual

Additional information

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.


23 June 2023, 12:00

Bytes to Bedside: Insights from whole-genome sequencing and its clinical translation

23 June 20232023Human Ecosystems Virtual, Virtual

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 detailsZoom 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... 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 detailsZoom*: 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.

Speaker(s): ** On site in Hinxton: Serena Nik-Zainal , University of Cambridge, United Kingdom
Host: Helen Parkinson, EMBL-EBI, United Kingdom

Place: Virtual

Human Ecosystems

Virtual, Virtual

Additional information

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.


30 June 2023, 11:00

2023 EMBL Careers webinar: Product management

30 June 20232023Career EventEMBL Heidelberg

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Speaker(s): Julia Roberti, Product Manager in Advanced Confocal Imaging at Leica, Germany | Nicola Dynes, Manager – Platform Product Management at Sophia Genetics, Switzerland
Host: EMBL Fellows' Career Service

Place: Virtual seminar (Join the VC)

Career Event

EMBL Heidelberg


14 July 2023, 10:00

The Information Theory of Aging

14 July 20232023EMBL Distinguished Visitor LectureEMBL Rome

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Speaker(s): David Sinclair, Harvard Medical School, Blavatnik Institute, Boston MA, USA
Host: Santiago Rompani

Place: Conf Room/Building 14

EMBL Distinguished Visitor Lecture

EMBL Rome


14 July 2023, 13:00

To be announced

14 July 20232023Hamburg SpeakerEMBL Hamburg

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Speaker(s): Phill Stansfeld, University of Warwick, United Kingdom, United Kingdom
Host: Katherine Beckham ( Wilmanns group), EMBL Hamburg Unit, Germany

Place: Seminar Room 48e

Hamburg Speaker

EMBL Hamburg


1 August 2023, 11:00

To be announced

1 August 20232023External Faculty SpeakerEMBL Heidelberg, Virtual

...

Speaker(s): Antonia Monteiro, National University of Singapore, Singapore

Place: Large Operon

External Faculty Speaker

EMBL Heidelberg, Virtual


7 September 2023, 10:00

To be announced

7 September 20232023Human Ecosystems EMBL Rome, Virtual

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Speaker(s): Nicole Sorenzo, Human Technopole/Sanger Institute, Italy
Host: Cornelius Gross, EMBL Rome, Italy

Place: CNR Seminar Room

Human Ecosystems

EMBL Rome, Virtual


11 September 2023, 14:30

To be announced

11 September 20232023Planetary Biology LecturesEMBL Heidelberg, Virtual

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Speaker(s): Claire Veneault-Fourrey, INRAE Research-Director, France
Host: Detlev Arendt

Place: Large Operon

Planetary Biology Lectures

EMBL Heidelberg, Virtual


15 September 2023, 11:00

"Dynamics of memory T cell responses following infection and vaccination”

15 September 20232023External Faculty SpeakerEMBL Rome

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Speaker(s): Luigia Pace, Italian Institute for Genomic Medicine, Turin, italy, Italy
Host: Mathieu Boulard

Place: Conf Room/Building 14

External Faculty Speaker

EMBL Rome


15 September 2023, 11:00

2023 EMBL Careers webinar: Making the transition to a group leader role

15 September 20232023Career EventEMBL Heidelberg

...

Speaker(s): Sarela García Santamarina, Group Leader, Human Microbiota – Xenobiotics Interaction at the Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Portugal | Velia Siciliano, Principal Investigator, Synthetic and System Biology for Biomedicine at Istituto Italiano di Tecnologia (IIT) | Alejo Rodriguez-Fraticelli, Group Leader, Quantitative Stem Cell Dynamics at Institute for Research in Biomedicine (IRB)
Host: EMBL Fellows' Career Service

Place: Virtual seminar (Join the VC)

Career Event

EMBL Heidelberg


21 September 2023, 11:00

To be announced

21 September 20232023Seminar given by an external postdoc EMBL Heidelberg, Virtual

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Speaker(s): Berta Verd, Oxford University, United Kingdom

Place: Large Operon

Seminar given by an external postdoc

EMBL Heidelberg, Virtual


22 September 2023, 11:00

To be announced

22 September 20232023External Faculty SpeakerEMBL Rome

...

Speaker(s): Marcelo Nollmann, Center for Structural Biochemistry, CNRS/INSERM, Montpellier, France
Host: Mathieu Boulard

Place: Conf Room/Building 14

External Faculty Speaker

EMBL Rome


2 October 2023, 11:30

To be announced

2 October 20232023Human Ecosystems Virtual, Virtual

The seminar will be held in person at the EBI in the Kendrew Lecture Theatre Connection detailsZoom 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... The seminar will be held in person at the EBI in the Kendrew Lecture Theatre. Connection detailsZoom*: 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.

Speaker(s): **On site in Hinxton: Andrea Ganna , FIMM, Finland
Host: Helen Parkinson, EMBL-EBI, United Kingdom

Place: Virtual

Human Ecosystems

Virtual, Virtual

Additional information

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.


6 October 2023, 10:00

Mechanisms for Balancing Sleep Need and Sleep

6 October 20232023EMBL Distinguished Visitor LectureEMBL Rome

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Speaker(s): Gero Miesenböck, University of Oxford, United Kingdom
Host: Hiroki Asari

Place: Conf Room/Building 14

EMBL Distinguished Visitor Lecture

EMBL Rome


9 October 2023, 12:00

To be announced

9 October 20232023External Faculty SpeakerEMBL Heidelberg, Virtual

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Speaker(s): John Colbourne, University of Birmingham, United Kingdom
Host: Oliver Stegle, EMBL Heidelberg

Place: Large Operon

External Faculty Speaker

EMBL Heidelberg, Virtual


13 October 2023, 11:00

Genetic conflicts during meiosis drive the rapid evolution of chromatin proteins

13 October 20232023EMBL - Sapienza LectureEMBL Rome

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Speaker(s): Harmit Singh Malik, Fred Hutchinson Cancer Research Center, Seattle, USA
Host: Irene Bozzoni & Ana Boskovic

Place: Sapienza Università di Roma - Aula Odeion - Museo dell'Arte Classica - P.le Aldo Moro, 5 - Roma

EMBL - Sapienza Lecture

EMBL Rome


19 October 2023, 11:00

To be announced

19 October 20232023External Faculty SpeakerEMBL Heidelberg, Virtual

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Speaker(s): Buzz Baum, MRC-LMB Cambridge, United Kingdom

Place: Large Operon

External Faculty Speaker

EMBL Heidelberg, Virtual


20 October 2023, 11:00

Somatic epigenetic mechanisms of stress allostasis and germ cell delivery of extracellular vesicles

20 October 20232023EMBL - Sapienza LectureEMBL Rome

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Speaker(s): Tracy Bale, University of Colorado, USA
Host: Irene Bozzoni & Ana Boskovic

Place: Sapienza Università di Roma - Aula Odeion - Museo dell'Arte Classica - P.le Aldo Moro, 5 - Roma

EMBL - Sapienza Lecture

EMBL Rome


3 November 2023, 10:00

Symposium for Emerging Scientists in Epigenetics & Neurobiology

3 November 20232023External Faculty SpeakerEMBL Rome

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Speaker(s): Sarah Marzi, Imperial College, London,, United Kingdom

Place: Conf Room/Building 14 (Join the VC)

External Faculty Speaker

EMBL Rome


16 November 2023, 10:00

To be announced

16 November 20232023Planetary Biology LecturesVirtual

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Speaker(s): Francis Martin, INRAE, France
Host: Sarah Dyer

Place: Virtual

Planetary Biology Lectures

Virtual


16 November 2023, 11:00

To be announced

16 November 20232023External Faculty SpeakerEMBL Heidelberg, Virtual

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Speaker(s): Eva Kanso, USC Viterbi, USA

Place: Large Operon

External Faculty Speaker

EMBL Heidelberg, Virtual


17 November 2023, 13:00

To be announced

17 November 20232023Hamburg SpeakerEMBL Hamburg

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Speaker(s): Sonja Lorenz, Max-Planck-Institute, Goettingen, Germany
Host: Christian Loew

Place: Seminar Room 48e

Hamburg Speaker

EMBL Hamburg