Meet the Trainers – Tobias Rausch and Alexey Larionov

On the occasion of World Cancer Day (4 February), we meet two of the trainers of the virtual EMBL Course: Cancer Genomics  (17 – 21 May 2021) – Tobias Rausch and Alexey Larionov.

PHOTO: EMBL Photolab

Tobias Rausch (TR) received his PhD in “Computational Biology and Scientific Computing” at the International Max Planck Research School in 2009. He then started to work at the European Molecular Biology Laboratory (EMBL) as a bioinformatician. His primary research interests are population and cancer genomics, structural variant discovery and omics computational methods development. (https://github.com/tobiasrausch).

 

PHOTO: Alexey Larionov

Initially educated as a clinical oncologist in Russia, Alexey Larionov (AL) switched to  experimental oncology upon completion of his PhD. Initially he worked as a postdoctoral researcher in Edinburgh University studying transcriptomics of breast cancer, with a focus on markers and mechanisms of endocrine response and resistance.  Working with data-rich methods (qPCR, micro-arrays, NGS) he became interested in data analysis and switched to bioinformatics. Since completing his MSc in Applied Bioinformatics, Alexey has worked as a bioinformatician at Cambridge University, focusing on NGS data analysis and heritable predisposition to cancer. See http://larionov.co.uk for more details.

What is your research focus?

TR: Computational genomics.

ALHeritable predisposition to cancer

Why did you choose to become a scientist?

TR: When I started at EMBL I saw myself as a software engineer who loves to design, develop and implement algorithms to solve data analysis problems. With the advent of high-throughput sequencing, this engineering background gave me a competitive edge as a data scientist, and that’s how it happened!

ALIt was interesting…

Where do you see this field heading in the future?

TR: Nowadays cancer genomics is a data-driven team science, but it is a long way from obtaining data to obtaining insight. In the age of analytics we all have to wrap our heads around multi-domain data with spatio-temporal resolution, ideally in real-time.

AL: I assume that the question is about translational cancer research in general.  I expect that in the near future the field needs better integration of different types of biological data and better collection of relevant clinical data. 

How has training influenced your career?

TR: I think training is essential to get you started. Training is like a kind person who takes your hand and guides you through unknown territory. It goes along with mentorship and I was lucky enough to have good training and good mentorship already as a student.

ALSince my initial clinical and bioinformatics degrees, cancer research has changed so much that I would not be able to even understand current papers if I hadn’t taken regular in-depth training in different aspects of computing and bioinformatics. 

How has cancer research changed over the years?

TR: I hope I am still too young to answer that :-). I leave that question for Bert Vogelstein or Robert A. Weinberg.

ALCancer research has become much more complex and powerful because of the development of new methods; specifically significant progress in bioinformatics, sequencing and human genomics.

Which methods and new technologies will be addressed in the course?

TR: We try to give an overview of how high-throughput sequencing can be applied in cancer genomics. We cover a range of technologies (short-read and long-read sequencing), data types (RNA-Seq, DNA-Seq and ATAC-Seq) and data modalities (bulk and single-cell sequencing), and last but not least – we take a deep dive into cancer genomics data analysis.

ALIn my sections of the course, I will discuss established methods for the analysis of bulk RNA sequencing, focusing on differential gene expression.  Then I will touch on the new methods being developed for the analysis of long-read RNA sequencing.  

What learning outcomes should participants expect to take home after the course?

TR: To come back to my previous answer: I hope after the course, cancer genomics won’t be an unknown territory anymore for the participants. I hope we pave the way and then it’s up to the students to make something out of it.

ALIn my section of the course, participants will learn:

1) Bioinformatics algorithms and tools for QC, alignment, and gene expression measurement in bulk short-read RNA-sequencing data

2) Current approaches to analysis of long-read RNA-seq data, comparing the Oxford Nanopore and PacBio sequencing technologies.


Interested in this course? Apply by 26 February.

For more upcoming events on cancer research take a look at our event listing.

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Meet the Trainer – María del Mar Vivanco

PHOTO: María del Mar Vivanco

Meet María del Mar Vivanco, Team Leader at CIC bioGUNE in Bilbao, Spain. Maria is one of the organisers of the EMBO Practical Course: Techniques for Mammary Gland Research (1 – 6 March 2020).

What is your research focus?

I am interested in cancer heterogeneity, why some cells respond to therapy while others do not, thus contributing to development of resistance and metastasis. In particular, I am intrigued about the complex effects of transcription factors, which are required for normal physiology of the mammary gland and are also implicated in tumorigenesis and development of resistance to therapy in breast cancer.

Why did you choose to become a scientist?

When I was young I had a variety of interests – psychology, physics, art, biology… However, I was intrigued by science and anything related to DNA and its regulation. Then I did my PhD at EMBL Heidelberg (Gene Expression Programme) and discovered the opportunities in research for identifying problems, looking for solutions and the thrill of finding some of the answers…and I was hooked!

Where do you see this field heading in the future?

Despite significant progress in cancer research and clinical advances, breast cancer still is the most commonly diagnosed cancer – one in eight women will develop this disease during their lifetime – and it claims the lives of more women than any other cancer, plus men can also get breast cancer. This highlights the unmet clinical need for improved strategies for prevention, early detection and more efficient and specific treatments in order to accelerate progress and help more patients survive the disease.

One of the features that characterises breast cancer is its heterogeneity, both among patients and within each patient tumor. This heterogeneity is found at molecular, phenotypic and functional levels, complicating diagnosis and challenging approaches to therapy. Currently, huge efforts are dedicated to understanding this heterogeneity at all levels, including at single-cell resolution, which is anticipated to open new possibilities for more efficient and specific anti-cancer therapies.

How has training influenced your career? 

Doing my PhD at EMBL marked the way I envision science, and this vision was reinforced and developed further at UCSF. Science can – and SHOULD – be fun. Later on, funding struggles and the current publishing madness have somehow taken a toll on the fun element, so I just have to remind myself sometimes that science is still exciting!

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

An artist.

You are one of the organisers of the EMBO Practical Course: Techniques for Mammary Gland Research (1 – 6 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?

Some of the techniques practiced at this course are specific for the mammary gland and thus it provides a solid base for researchers starting in this field. In addition, there is a significant emphasis on imaging and comparison of mouse and human studies, the two major systems for looking at normal physiology and cancer research that, when combined, offer great insights into this heterogeneous disease. In addition, having the opportunity to work alongside other trainees contributes to the establishment of a network that may be helpful in the future. Cancer is a very complex problem, and having collaborators with different views and expertise will be very useful in your career.

Interested in this course? Submit your application by 8 December!

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