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.

Follow us:

Meet the Trainer – Anna Kreshuk

PHOTO: EMBL/Marietta Schupp

Meet Dr. Anna Kreshuk, a group leader in the EMBL Cell Biology and Biophysics unit, whose group uses machine learning to develop automated methods to help biologists speed up image analysis. Anna joined EMBL in 2018 and has since been very active in building up training opportunities in her research field.

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

My research is concerned with developing new machine learning-based methods of the analysis of biological images. I enjoy doing science, both for the thrill of finding new things and the joy of seeing others do that in their domain with the help of our tools.

Where do you see this field heading in the future?

I hope to see most of the routine image analysis automated in the future. This will hopefully raise new research questions in biology which can only be answered by imaging at scale, creating, in its turn, more exciting research questions for us.

How has training influenced your career?

We develop software for end users without computational expertise, who want to solve biological problems we don’t quite understand. Participating in training has provided a lot of insight to the user side of things, brought new collaborations and even new research directions for me and for my group.

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

A one-week course can be a great start, however, it’s important to find out how you can get support with the new technology in your everyday work. Try to stay in contact with your course buddies, but also look for online communities. For image analysis, for example, there is a great forum connecting all the popular tools.

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

My 7-year-old recently asked: “you say I can become anything I want to be, but then why didn’t you become an astronaut?”. Seriously though, I’d probably be a programmer, I love automating things.

You are organising the EMBL Course: Deep Learning for Image Analysis (20 – 24 January 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?

Deep learning has brought an enormous advance in computer vision. We can now analyse microscopy images in ways no one thought possible just 10 years ago. While the technology is getting more accessible every year, it’s still difficult even for computationally savvy biologists to apply state-of-the-art methods to their image analysis problems. This is exactly the gap we intend to close.

Follow us:

Meet the Trainer – Katharina Danielski

Meet Katharina Danielski, Field Application Scientist at 10x Genomics, who is an organiser and trainer at the EMBL Course: Immune Profiling of Single Cells (10 – 13 February 2020).

 

 

 

What is the greatest benefit of the course for the scientific community?

It provides researchers with an overview of what is currently possible when studying the immune system at the single-cell level. There are so many new technologies and methods available these days that scientists are overwhelmed with keeping track of everything new. The 10x Genomics Single-Cell Immune Profiling solution allows you to study a broad range of aspects all derived from the same single cell: sequence information of paired full-length T cell or B cell receptor transcripts; gene expression profile; cell surface protein markers; antigen specificity. Linking all these pieces of information back to the same cell is opening a lot of new ways to study the adaptive immune response that were just not possible before.

Are the methods used in this course unusual or new?

The ability to study single cells to the extent as it is currently possible with various assays on the market is still very recent. We are only beginning to scratch the surface of the biological information that will be uncovered in the coming years thanks to the methods discussed in this course, among others.

In comparison to other training environments, what do you enjoy most about teaching at EMBL?

I enjoy teaching at EMBL because of the high level of organisation that the EMBL team displays. The EMBL Heidelberg Campus is also a particularly beautiful location situated on top of a hill surrounded by forests. But most importantly: the food in the canteen is legen- wait for it -dary.

What is your number one tip related to the course?

Don’t be shy. The trainers are more than happy to answer your questions and discuss your projects and  experiments…but skip breakfast so you can fill up on lunch at the EMBL Canteen. You will thank me later.

What, in your opinion, is the most crucial scientific discovery of the past 100 years?

I don’t think any single discovery on its own could be labeled as “the most crucial”. Science in the past 100 years has made so many giant leaps for mankind.

Where is science heading in your opinion?

Studying gene expression of (single) cells spatially resolved within their morphological context of an intact tissue section.

Follow us:

Meet the Trainer – Anders Ståhlberg

Meet Dr. Anders Ståhlberg, Associate Professor at the University of Gothenburg and  Sahlgrenska University Hospital in Sweden, and organiser of the EMBO Practical Course: Single-Cell Omics (12 – 18 May 2019) and EMBL Course: “Liquid Biopsies” (23 – 28 September 2019).

Anders’ research focuses on basic tumour biology and cancer diagnostics.

What is the greatest benefit of the Liquid Biopsies course for the scientific community?

Liquid biopsy analysis is an emerging tool in biological/medical research as well as in clinical diagnostics. However, most analyses require ultrasensitive methods. In this course we cover both theoretical aspects and practical consideration that need to be addressed to utilise the potential of liquid biopsy analysis, and use both state-of-art techniques and novel approaches.

What could the techniques in this course be used for in the bigger picture?

The applied techniques include ultrasensitive analysis of DNA, proteins and single-cells. These techniques can be applied to a wide range of applications in any type of liquid biopsy. In addition, these techniques can be used on any type of challenging sample types. Application areas include cancer, immunology, prenatal testing, forensics, evolution studies, drug screening, pathogen detection and beyond.

In comparison to other training environments, what do you enjoy most about teaching at EMBL?

The superb facilities, including everything from course arrangement to the research lab. However, the best part of EMBL courses is the dynamic interactions between teachers, tutors, staff and all students. It is a perfect environment to network and discuss science.

What is the strangest or funniest thing that has ever happened in a course?

The course dinners are very enjoyable and may end in unexpected but fun ways.

What challenges is your research field facing?

Translating basic research into clinical use.

Where is science heading in your opinion?

The amount of generated data will increase dramatically with all available high-throughput methods. One major challenge is to translate this data into useful information.

What was your first ever job?

I got my first job when I was 15 years old in basic industry, making valves.

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

A teacher or farmer.

What is the greatest risk you’ve ever taken?

In science, saying no to academically rewarding positions and instead following my research interest with an unsure future.

What is your favourite book?

I cannot resist a good fantasy book.

Follow us:

Meet the Trainer – Estefanía Lozano-Andrés

Meet Estefanía Lozano-Andrés, a Marie Sklodowska-Curie PhD Candidate at the University of Utrecht in the Netherlands. We first met Estefanía in 2016 when she was a participant at the EMBL Course “Extracellular Vesicles: from Biology to Biomedical Applications” and she is back as a trainer at this year’s course.

What is your research focus, and what challenges is the field facing?

My main research interest is the study of Extracellular Vesicles (EVs), which are nano-sized membrane-enclosed particles released by cells. EVs contain selected proteins, lipids and nucleic acids that reflect the status and origin of cells, making them very attractive for biomarker profiling. However, their small size hampers robust detection of single EVs, so more sensitive technology needs to be developed to truly exploit the potential of EVs. Particularly, I am interested in the use of flow cytometry to analyse EVs in a high-throughput and multiparametric manner, but there are quite some challenges to overcome like the optimisation of EV-labelling strategies, the development of reference materials and the standardisation of measurements.

You attended the EMBL Course on Extracellular Vesicles 3 years ago and now you are one of the trainers in this year’s course. How has the course influenced your career?

The course had a great impact on my scientific career. When I was selected to attend the course, I was at an early stage of my PhD and it helped me to develop as a scientist and to have a more critical eye. Thanks to the course I met many leading researchers in the field and it’s probably one of the reasons why I am currently a Marie Skłodowska-Curie Early Stage Researcher within the TRAIN-EV Consortium, which brings together leading European scientists working on EVs (grant agreement No 722148). I was thrilled to know that this year I could attend the course as a trainer to help all the participants during the practical sessions and to shed some light on the use of flow cytometry for EV analysis.

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

Don’t be afraid to engage with people, it can really help you to find out about great training opportunities that could further improve your career. And always try to make the most out of any given moment.

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

A multifaceted artist, I love creating things. Painting, writing and photography make me very happy. Fun fact: when I was a child I wanted to be a professional gift wrapper.

If you were a superhero what power would you have?

Teleportation, I would really enjoy to travel across space (and time).

Follow us: