Multiomics to Mechanisms Symposium – Best Poster Awards

The recent EMBO|EMBL Symposium: Multiomics to Mechanisms – Challenges in Data Integration (11-13 Sep 2019) addressed ways of integrating large-scale biological data across the different omics fields.

258 researchers from various fields gathered in Heidelberg last week to listen to 36 talks and engage with 146 poster presenters. Here we present the posters of 5 scientists who received best poster awards at the conference by popular vote.

Benchmarking of multi-omics joint  dimensionality reduction (DR) approaches for cancer study

Laura Cantini is a CNRS Research Scientist at IBENS in France.

Authors: Laura Cantini (1), Pooya Zakeri (2), Aurelien Naldi (1), Denis Thieffry (1), Elisabeth Remy (3), Anaïs Baudot (2)

Dimensionality Reduction (DR), decomposing data into low-dimensional spaces while preserving most of their information content, is among the most prevalent machine learning techniques in data mining. With the advent of high-throughput technologies, high-dimensional data have become a standard in biology, emphasizing the use of DR. This phenomenon is particularly pronounced in cancer biology, where consortia have profiled thousands of patients for multiple molecular assays (“multi-omics”), including at the emerging single-cell scale. DR approaches have been mainly applied to single omics data leading to cancer subtyping, tumor sub-clones quantification and immune infiltration quantification. Recently, DR approaches designed to jointly analyze multiple omics have been proposed. Integrative DR methods are based on various mathematical assumptions, ranging from extensions of CCA, tensors, or more general data fusion approaches, which makes difficult to chose which method to apply.
In this context, we here in-depth benchmark multi-omics DR approaches using: i) artificial multi-omics cancer data ii) multi-omics bulk data from 10 different cancer types downloaded from TCGA iii) multi-omics single-cell data from cancer cell lines In (i), the capability of the various methods to predict the clustering ground truth was found strongly sensible to the size of the clusters, with intNMF, RGCCA, MCIA and JIVE being the more robust methods. For (ii), MCIA, RGCCA, MOFA and JIVE more consistently identified factors associated to survival, clinical annotations and biological annotations. Finally in (iii), despite never being applied to single-cell data, tICA and MSFA outperformed other methods for their ability to cluster  single cells based on their cell line of origin. Overall, our results show that RGCCA, MCIA and JIVE perform consistently better across the three scenarios. This suggests that a mathematical formulation, based on the search of omic-specific factors whose inter-dependence is maximized, better approximates the nature of multi-omics data.

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(1) Institut de Biologie de l’Ecole Normale Superieure IBENS, France, (2) Aix Marseille University, INSERM, MMG, CNRS, France, (3) Aix Marseille University, CNRS, France


Single-cell transcriptome and chromatin accessibility data integration reveals cell specific signatures

Andrés Felipe is a PhD student at the German Cancer Research Center in Heidelberg, Germany.

Authors: Andres Quintero (1), Anne-Claire Kröger (2), Carl Herrmann (2)

The ability to integrate multiple layers of omics data will play an essential role in understanding the complex interplay of different molecular mechanisms that give rise to cellular diversity. In particular, single-cell multi-omics studies provide an enormously valuable source of information, allowing the characterization of different cell states under different biological contexts. However, the integration of distinct cellular modalities to disentangle the regulatory networks and pathways that explain cell identity is still a challenge.Here we introduce Integrative Iterative Non-negative Matrix Factorization (i2NMF), a computational method to dissect cell type associated signatures from multi-omics data sets. i2NMF takes full advantage of data sets with multiple modalities for the same sample or cell, defining cell type-specific features and discerning the shared and specific contribution of each omics type to the identification of different cell types. We applied i2NMF to an early human embryo single-cell multi-omics data set for which scRNA-seq and scATAC-seq profiles were available for every single cell, identifying master transcription factors at the morula and blastocyst stages. Finally, i2NMF is also able to integrate different modalities across multiple experiments. We used this functionality to extract cell-type specific molecular signatures from two complementary datasets of the mouse visual cortex, comprising scATAC-seq and scRNA-seq data. i2NMF was implemented on TensorFlow, presenting a scalable framework and allowing its efficient execution under multiple systems. Our results demonstrate that i2NMF is a useful tool to identify cell-type specific signatures and dissect their underlying molecular features.

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(1) German Cancer Research Center (DKFZ), Germany, (2) University Hospital Heidelberg, Germany


Linking signalling and metabolomic footprints with causal networks

Aurélien Dugourd is a PhD student in mechanistic modelling at JRC Combine, RWTH Aachen, Germany.

Aurélien Dugourd (1), Christoph Kuppe (1), Rafael Kramann (1), Julio Saez-Rodriguez (2)

Renal clear cell carcinomas (RCCC) are the result of a system-wide dysregulation of signaling and metabolic functions  originating from multiple factors. Characterizing cellular molecular machineries across multiple omic layers is a very powerful strategy to understand the cellular effects of such dysregulations. In this study, we performed metabolomics and phosphoproteomics from RCCC tissue in comparison to the non-cancerous kidney tissue in a cohort of 20 patients. In order to extract mechanistic information from these observations and to integrate both datasets, we developed a novel analysis pipeline. Phosphoproteomic abundance changes are used to estimate kinase activity changes across patients. Kinase activity estimations are then correlated with metabolite abundance changes. This points at possible interactions between signaling pathways and metabolism. We subsequently build a generic network integrating signaling pathways and metabolic reaction networks based on literature knowledge and databases. We use this signaling/metabolic network to identify paths across kinases and metabolic enzymes to link the correlated kinase activities and metabolites.
This provides potential mechanisms to explain the effect of deregulation of signaling on metabolism. Our approach was able to recover the structure canonical signaling pathway topologies and highlight specific connections between kinases and metabolite abundance deregulated in kidney tumor tissues. This pipeline allows to extract and compare mechanistic
information from metabolomic, phosphoproteomic (and potentially transcriptomic) data across many kidney cancer patients. This information can be used to select potential therapeutic targets to disrupt cancer specific cellular mechanisms, such as the SP1 kinase. Furthermore, the pipeline offers the advantage of being easily transferable in many different biological contexts.

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(1) RWTH Uniklinikum Aachen, Germany, (2) Heidelberg University, Germany


A network-based approach for the identification of multi-omics modules associated with complex human diseases

Maria Anna Wörheide is a PhD student at the Helmholtz Zentrum München in Germany.

Authors: Maria Anna Wörheide (1), Jan Krumsiek (2), Gabi Kastenmüller (1), Matthias Arnold (1)

Application of advanced high-throughput omics technologies have provided us with vast amounts of quantitative, highly valuable data. For complex, heterogeneous, and untreatable diseases such as Alzheimer’s disease (AD), the integration of different omics levels and their interconnections is desperately needed to understand the underlying molecular pathomechanisms and identify potential therapeutic targets. However, integrated, multivariable analyses of cross-omics data are not straightforward, and even if successfully applied, often lack a human comprehensible representation. Graph databases provide an intuitive and mathematically well defined framework to store and interconnect diverse biological domains in accessible network structures. Here, we propose a network-based, multi-omics framework
developed with the graph database Neo4j, that allows the large-scale integration and analysis of data on biological entities across omics, as well as results from association analysis with specific (endo) phenotypes. The backbone of this framework comes from known biological relationships and functional/pathway annotations available in public databases. It is augmented with experimental, quantitative data for single omics (e.g. tissue-specific gene expression) and across omics (e.g. eQTLs or mQTLs) derived in population-based studies. To identify modules within this network that are potentially relevant to a disease such as AD, we extend the
framework using large-scale association data for AD (e.g. from case-control GWASs). The resulting network is comprised of over 50 million nodes (entities), representing more than 30 different data types, and more than 80 million edges (relationships). We mined this comprehensive catalogue of biological information using established graph algorithms to
identify potentially disease-related modules of tightly interlinked entities, and were able to obtain several subnetworks significantly enriched for AD-associations.

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(1) Helmholtz Zentrum München, Germany, (2) Weill Cornell Medicine, United States of America


Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions

Ignacio Ibarra is a PhD student in Judith Zaugg’s lab at EMBL Heidelberg, Germany.

Authors: Ignacio Ibarra, Nele Hollmann, Bernd Klaus, Sandra Augsten, Britta Velten, Janosch Hennig, Judith Zaugg (EMBL Heidelberg)

Recent high-throughput transcription factor (TF) binding assays revealed that TF cooperativity
is a widespread phenomenon. However, we still miss global mechanistic and functional understanding of TF cooperativity. To close this gap we introduce a statistical learning framework that provides structural insight into TF cooperativity and its functional consequences based on next generation sequencing data. We identify DNA shape as driver for cooperativity, with a particularly strong effect for Forkhead-Ets pairs. Follow-up experiments revealed a local shape preference at the Ets-DNA-Forkhead interface and a decreased cooperativity once the interaction is lost. Additionally, we discovered many novel functional associations for cooperatively bound TFs. Examining the novel link between FOXO1:ETV6 and lymphomas revealed that their joint expression levels improve patient survival stratification.
Altogether, our results demonstrate that inter-family cooperative TF binding is driven by position-specific DNA readout mechanisms, which provides an additional regulatory layer for downstream biological functions.

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Working on your own conference poster? Then check out 10 tips to create a scientific poster people want to stop by .

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How does the environment play a role in biodiversity?

Biodiversity – in all its forms and interactions – is the variety of life on Earth. Climate change is exacerbating biodiversity loss, and vice versa. Ahead of the EMBO | EMBL Symposium ‘The Organism and its Environment’ (1–4 March 2020), we talk to Scientific Organiser and EMBL Director General Edith Heard about the impact the environment has on biodiversity and the role of research in solving global challenges.

Does the environment play a large role in the creation of biological diversity?

Biodiversity is the variety of life on Earth. This life, in all its shapes and sizes, occurs in the context of ecosystems: it relies on and interacts with other organisms and the physical environment. Biodiversity represents the collective ‘knowledge learned’ by evolving species over millions of years, about how to survive the vastly varying environmental conditions Earth has and is experiencing. These varying environmental conditions cause natural variations in biodiversity, as well as genetic and epigenetic changes, within and between species over time. Today, scientists are trying to understand the basis of these natural variations, as they will allow us to understand how life evolves.

Fish populations have declined at an alarming rate, and half the world’s shallow water coral reefs have been lost in just 30 years.

But biodiversity is also a measure of the health of any ecosystem. Recent trends in biodiversity loss show very clearly that humans are destroying ecosystems on a massive scale. According to the Director General of the World Wildlife Fund (WWF), increased pollution, deforestation, climate change and other manmade factors have created a “mind-blowing” crisis. The WWF Living Planet Report 2018 (WWF LPR, 2018) also states that freshwater fish populations have declined by more than 80% on average since 1970 and half of the world’s shallow water coral reefs have been lost in the last 30 years (WWF LPR, 2018). Alongside this, deforestation of tropical rainforests means we are currently losing more than 100 species of plants and animals a day (Holley, 2017). In short, human’s influence on the environment greatly impacts biodiversity and we are currently burning the library of life.

How can you determine the effect of the environment on an organism?

The environment can affect an organism in a multitude of ways. The impact can be transient or longer term; within an individual or across generations. The environment can also lead to molecular, cellular, physiological or behavioural changes. For example, the expression of genes in an organism can be influenced by the external environment, such as where the organism develops or factors associated with where it is located. Gene expression could also be influenced by an organism’s internal environment, including hormones or metabolism. Finally, the genome itself – genetic factors that vary between individuals in natural populations – could also influence gene expression.

Research groups at EMBL look at how variety in organisms comes about

Untangling the impact of genetic and environmental variation can be very challenging and for a long time, scientists have tended to focus on minimising variations in the environment in order to understand how changes in genotype affect phenotype. This, alongside the deeply embedded “one genotype = one phenotype” metaphor, has meant that environmentally induced phenotypic variation has been ignored in favour of ‘‘more useful and precise’’ study of genetic polymorphisms. This is despite the fact that from as far back as the early 1900s, scientists have known that the phenotype of an individual depends on the interaction between its genotype and environmental cues! Today, we finally have the power to consider the impact of the environment on phenotype. We can make precise measurements at the molecular, cellular and organism scales in controlled environments that can be varied and we can sequence genomes at the same time.

We can also take human data paired with environmental data – for example in the context of some of EMBL’s research interests such as infectious disease and microbiomes – to understand the quantitative effects of the environment and its influence on human biology. Pioneering projects such as Tara Oceans have also allowed us to research the interactions between organisms and the environment by generating reference data, discovering emergent ecological principles and developing predictions about how ecosystems will be affected by a changing environment. Understanding how organisms exist together and in changing environments is of fundamental importance for our understanding of biological principles and our knowledge of life.

What challenges are currently being faced in this field?

Studying organisms in their environment will become increasingly important.

Understanding the behaviour of individual molecules, cells or whole organisms is already challenging. Understanding how the environment influences an organism – or populations of organisms – represents a whole new scale in complexity. This is an area that I think EMBL could uniquely contribute to in the future. It will be necessary to shift from researching organisms mainly in the laboratory to studying them in their environment. We will also need to ensure the rapid development of technologies and tools to meet these scientific needs. Alongside this, we need new approaches to integrate large, complex data sets and make sense of them. To rise up to this challenge, we need theory. We are now in a unique position to address the dynamics and complexity of living matter across multiple scales and in the context of changing environment. But we need theory to address societal and planetary issues too. We must aim for a rate of scientific discovery that outpaces the rate of calamity such as biodiversity loss, ecosystem degradation, epidemics and climate change.

What can be done to prepare for the future with regard to biological diversity, the organism and its environment?

Research, research and more research! Environmental problems such as the hole in the ozone layer or acid rain were solved by sound scientific approaches. We need to learn from these past scientific and societal successes. Today the ever-increasing numbers of new technologies are allowing us to collect, measure and store data at unprecedented scales. We also need to bring ecologists, zoologists, population geneticists and environmental experts together to address these research questions. Together we can apply cutting-edge technology with rigour, attract new scientific talent and disseminate knowledge to global communities.

What inspired you to organise this symposium?

As a geneticist and epigeneticist, I have explored the intersection between genotype and the environment and how that produces a phenotype. From observing many areas of research – ranging from social insects such as bees and ants, to plant vernalisation and variations between identical twins – I felt that the time is ripe to bring together scientists from many different areas. I also wanted this to be a symposium that would attract scientists from different areas to EMBL.

At EMBL, we want to understand the molecular basis of life. Until now, EMBL has been known for exploring genomic, molecular, structural and cell biology at the level of individual organisms. Looking ahead, we want to study organisms in the context of their physical and biological environments not just in isolation. In order to truly understand life on Earth, we need to study organisms in nature, not just in the lab. One way to understand life at the molecular level will be to try to bring relevant ecosystems back to the lab, to measure and perturb them under controlled conditions. The speakers we’ve invited are experts from many different areas of biology or ecology, and will bring exciting new perspectives to our research.

The EMBO|EMBL Symposium: The Organism and its Environment will take place at EMBL Heidelberg, Germany, from 1-4 March 2020

What is the greatest benefit of this symposium for the scientific community?

The symposium is an opportunity to address how organisms are influenced by a changing environment. It will bring together different research disciplines and go beyond pure genetic or ecological perspectives of phenotypic variation. Geneticists, molecular biologists, evolutionary biologists and ecologists do not necessarily meet under ordinary circumstances. This meeting will enable such interactions and cross-fertilisation.

What will be the main highlight of the symposium?

Today we are in a unique position to address the complexity and dynamics of life at multiple scales, from molecules to ecosystems. We also need to consider the idea that change including in the environment is not necessarily a bad thing. After all, without change, evolution could not occur and none of the amazing biodiversity of life on our planet would exist! I hope that a highlight of this symposium will be some wonderful new insights into evolutionary processes.

 

References

Holley D., (2017). General Biology II, Organisms and Ecology. Indianapolis: Dog Ear Publishing, 898.

World Wildlife Fund, (2018). Living Planet Report: Aiming higher [PDF] https://wwf.panda.org/knowledge_hub/all_publications/living_planet_report_2018/ [Accessed 25 July 2019].

https://wwf.panda.org/knowledge_hub/all_publications/living_planet_report_2018/

However the WWF DG is quoted by several articles as describing the crisis as mind-blowing, for example: “https://www.voanews.com/science-health/report-earth-has-lost-60-percent-its-wildlife-1970

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We’ve proved it, biologists can also program

“Like punning, programming is a play on words.” Alan J. Perlis.

You don’t have to be a programmer to have programming skills. Writing code is an essential part of being a programmer (duh!), but is also a vital component of being a scientific developer, software developer or computer scientist. You can utilise computer programs to automate tedious and repetitive tasks, extract results from experimental data, apply models to solve your research questions or purely have fun with your own projects.

Today is Programmers’ Day (yay!🥳) and we want to recognise all those who submerge themselves in the deepest mysteries of code (especially their own) and aim to automate the future.

If you’re looking to start venturing into the programming world or embark on your next project, get some inspiration from some scientists who are helping out at our EMBL Events’ courses.

Florian Huber PHOTO: Marietta Schupp/EMBL

“What do I love about programming? It allows me to go from zero to one: gaining new biological insights from data.” Florian Huber (Postdoctoral Fellow, at the Typas Group in EMBL Heidelberg and the Beltrao Group at EMBL–EBI in Hinxton).

 

 

 

 

Ullrich Köthe PHOTO: Ullrich Köthe

“Automated image analysis has always been an interesting and fun field of research, but thanks to the deep learning revolution and the wide availability of wonderful neural network libraries, we can now actually solve hard practical problems.” Ullrich Köthe (Group Leader in the Visual Learning Lab Heidelberg).

 

 

Valentyna Zinchenko PHOTO: Carolina Cuadras/EMBL

“Programming skills allow you to automate the routineparts of your job and focus more on the exciting ones. At some moment you just have so much data, that you would not want to process it manually. You would not wash your clothes by hand if you have a washing machine, would you? Then why analyzing your data manually, when you can have it done by a machine as well?” Valentyna Zinchenko (Predoctoral Fellow in the Kreshuk Group).

 

Adrian Wolny PHOTO: Carolina Cuadras/EMBL

“Whenever I build something, be it a new machine learning model or my pet project, I always try to make it easy to understand and generic enough so that other people could use it in their work. I try to open source my projects whenever I can and contribute back to the community. There is nothing more rewarding than seeing your little piece of software used by others to find answers to their own research questions.” Adrian Wolny (Visiting Researcher at EMBL and PhD candidate at Heidelberg University).

 

Pavel Baranov PHOTO: Pavel Baranov

“The relationship between computer science and modern biology is akin to that between mathematics and physics.” Pavel Baranov (Professor of Biomolecular Informatics, University College Cork, Ireland)

 

 

 

 

It’s no secret that managing biological data efficiently can be overwhelming and feel impossible. If you’re a biologist who’s interested in learning how to process, analyse, organise and interpret your almost innumerable data sets – preferably with the most suitable and state-of-the-art techniques and tools out there – EMBL Events has got you covered.

EMBL Course: Deep Learning for Image Analysis, Apply by 20 September 2019

EMBL Course: Exploratory Analysis of Biological Data: Data Carpentry, Apply by 5 November 2019

EMBL Course: Analysis and Integration of Transcriptome and Proteome Data, Apply by 10 November 2019

EMBL Course: Immune Profiling of Single Cells, Apply by 10 November 2019

EMBO Practical Course: Microbial Metagenomics: A 360º Approach, Apply by 27 January 2020

EMBO Practical Course: Measuring Translational Dynamics by Ribosome Profiling, Apply by 9 February 2020

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14 tips for a smooth conference experience

The date of your first EMBL conference in Heidelberg is fast approaching. You are excited, have already bookmarked interesting abstracts in the conference app and are ready to make your travel arrangements. Here are 14 tips that will help you stay out of trouble and focus on the science.

1. Don’t try to book a flight to Heidelberg

Although it is one of the most popular tourist destinations in Germany, Heidelberg does not have an airport. The closest airports are Frankfurt International Airport, Stuttgart Airport and Airport Karlsruhe/Baden-Baden. More information on how to reach Heidelberg is available here.

2. Make sure you read the final logistical email (FLE) we send you

The information provided in this email is vital for your travel plans and conference schedule and will be your bible for the days you spend at the conference. It provides important attachments such as the programme, the onsite handout and the poster listing.

3. Try not to miss the shuttle bus

The EMBL campus is located on a hill outside of Heidelberg which makes it a beautiful and inspiring place to visit, away from the hustle and bustle of downtown Heidelberg. However, it also makes it more difficult to reach by public transport. Although efforts have been made to improve the public transport connection to the campus, there is still the need of conference shuttle busses that operate on a strict schedule (included in the FLE). So if you miss the shuttle bus, your only way up the hill may be by taxi. Please note that there are no UBER services in Heidelberg.

Our team has prepared an onsite handout with pictures of all bus stops so that you don’t miss the bus because you don’t know where the correct stop is. This information is provided in the FLE.

4. Get the app instead of the abstract book

When you register online, you will be asked if you would like to receive a printed copy of the abstract book. If you click yes, you will get your copy onsite, but make sure that you don’t lose it as this is the only copy you will get. Many participants diligently take notes in the abstract book during the sessions, only to go home one day realising they have lost their copy.

One way to avoid that is by using the app instead. It includes everything contained in the printed abstract book and more, and it also allows you to review the abstracts ahead of the conference and offers the option to export your notes directly to your email.

5. Share your dietary requirements

The EMBL canteen makes a special effort to cater to everyone’s needs by providing fresh food every day and appropriate substitutes for participants on vegetarian, vegan, lactose-free or gluten-free diets. In our registration system you have the option to indicate your preferences, but should you have special requirements based on food allergies or intolerances, please do not hesitate to reach out to us, so we can ensure you are well fed.

6. Send your flash talk slides well in advance

If you are presenting a flash talk, make sure to send us your slides well in advance to make sure they are looped on the screen in time. You will have only 2 minutes to present your poster in the flash talk, so you don’t want to waste any second with technical difficulties.

For some more tips on how to give a flash talk, watch this video.

7. Avoid asking for a certificate of participation during the registration

As much as we’d like to help you out, registration is not the best time to ask for a certificate of participation. These are normally sent out after the end of the event via email.

8. Hold on to your badge

Your badge is your access card to the conference venue and your coupon for the lunch and dinner buffets, so make sure you don’t lose it or leave it in your hotel room.

9. No cash policy on the EMBL Campus

If you arrive on campus outside of the conference times and you would like to get something to eat or drink, it might not be possible. EMBL has a no cash policy on its campus and the only way to purchase something from the cafeteria or canteen is via a special guest credit card. Therefore, it would be a good idea to grab something to eat on your way to the campus, especially for breakfast as we normally only have coffee available in the mornings.

10. Do not ask us for medicine

As much as we would like to help you with your headache or cold symptoms, we are not authorised to hand out any medicine. However, we have a list of pharmacies that are close to the conference venue which we are happy to share with you.

11. When you sign up for a social event, show up!

Most conference social events like dinners, lunches, parties take place in the EMBL Advanced Training Centre (ATC) and are open to all conference participants without prior registration. In the case that there are organised social events taking place outside of the conference venue such as tours or downtown dinners, these are usually restricted to a limited number of participants, and prior registration is necessary.

All the logistics are meticulously coordinated with the service providers and very often there are waiting lists for these events, so if you are unable to attend, please inform us, so that we can give your spot to someone who can.

12. Stay on the paths in the woods

The EMBL Heidelberg Campus is surrounded by a beautiful forest which offers a great opportunity for lunch-time walks or runs. However, before you set on exploring the woods, please familiarise yourself with the paths so that you easily find your way back. In the app you will find 4 different walking routes of various lengths.

13. Take down your poster on the last day

You have put in so much work in your poster that it is a shame to leave it with us. Make sure you take it down on the last day of the event as you may end up needing it for another conference.

14. Stay away from red push buttons on the emergency exit doors

Not all exit doors in the ATC Foyer may be opened. Look out for a silver button with a key on it to open the door without activating the emergency exit alarm.

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Meet the Trainer – Imre Gaspar

Meet Dr. Imre Gaspar, Senior Research Assistant in the Kikuë Tachibana Group at the Institute of Molecular Biotechnology in Vienna, Austria, which focuses on understanding how chromatin is spatially reorganised in totipotent cells.

What is your research focus and why did you choose to become a scientist?

I’m interested in the central dogma, that is how gene expression is regulated on the transcriptional and post-transcriptional levels and how these regulations allow development of an organism.

I became a scientist because I always fancied solving riddles – and as a scientist you get to work on solving the ultimate riddle that interests us, humans.

Where do you see this field heading in the future?

Right now, there is a boom of high-throughput and omics techniques in studying gene expression allowing us to create predictive quantitative models of regulatory networks, which will allow us to get mechanistic understanding of the processes underlying development, homeostasis and pathogenesis. Microscopy analysis is already essential for the latter and is also gaining importance also in the omics studies with the advent of high-throughput hybridisation techniques.

What is your number one tip for people looking for scientific training?

Being a microscopist, it was absolutely essential for my career to receive training in state-of-the-art imaging and image analysis technologies. Courses are important, of course, but I find that the best source of training a scientist can receive is core facilities, internal trainings, and of course close colleagues in the lab.

If you weren’t a scientist, what would you be?

I have a degree in medicine, so I probably would have become a medical software developer – that profession is closest to the work of a scientist and having a background in medicine would allow me to contribute to the development of medical instrumentation.

You are organising the EMBO Practical Course ”FISHing for RNAs: Classical to Single Molecule Approaches” (15 – 20 March 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

We are at the onset of quantitative analysis in biology: many labs have already implemented corresponding work-flows, but this principle should be spread widely, especially in the fields working on the understanding of gene expression. I expect that the single molecule techniques we will cover during the course will serve as mind-changers to help people embrace the concept of quantitative biology.

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