Meet the Trainers – Raffaele Calogero, Jeroen Krijgsveld, Lennart Martens

This month we have not one but three trainers we would like to introduce you to. Meet Raffaele Calogero, Jeroen Krijgsveld and Lennart Martens, organisers and trainers at the EMBL Course: Analysis and Integration of Transcriptome and Proteome Data (2 – 7 February 2020).

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

RC: I have a background in molecular biology, but since 1999 I have been working in transcriptomics data analysis and tool development. I became a scientist because I loved the idea of investigating new unknown topics every day.

LM: My research focus is bioinformatics, which stems directly from becoming completely taken in by computers at an early age. Like many of my generation, I started out with a Commodore 64 when I was 8, and had written my first (very, very simple :)) program in BASIC after two weeks. But my link with science came about after I stumbled across an episode of Jacob Bronowski’s ‘The Ascent of Man’ a few years later (I think I was 10 or 11) on Saturday morning on television, and this inspired a lifelong interest in anything scientific. All in all, I consider myself extremely lucky to be able to combine my passion for computers with my passion for science, and make a living out of it!

JK: My research focus is on proteomics, where we develop and apply mass spectrometry-based technologies to understand the intricate machineries used by cells to respond to their environment. Curiosity to understand how things work is as an important motivation for our current research as it was for me during my studies. Becoming a scientist has always felt a natural path for me to follow, and I have never seriously considered doing anything else. Although at the same time, when looking back, I realise how fortunate I have been being given the opportunity to follow my interest and move between fields. This is due in no small part to having training opportunities and stimulating environments at the various stages of my career!

Where do you see this field heading in the future?

RC: Data integration is the new upcoming frontier for biological studies, and transcriptomics and proteomics are going to be important players in the game.

JK: Proteomics has come a long way in the last 2 decades, reaching its current ability to characterise thousands of proteins in a single experiment, and do this across multiple experiments. I expect that during the next 5-10 years we will see how these investments will pay off, helping to understand processes at the protein level very similar to the way this has been achieved in genomics. After transitioning from a technology exclusively for physicists to a useful tool used by biologists, the next big step to be made is to implement mass spectrometry in the clinical arena. Integration with genomic methods and data types will be key to drive this forward.

LM: Bioinformatics is slowly taking over much of large-scale biology. Of course, focused biochemical and molecular biology research will remain the staple of the life sciences, but our ability to process and interrogate very large amounts of (potentially even heterogeneous) data is transforming our ability to generate new leads, new ideas, and to shed a much more holistic view on life at the molecular level. And with the advent of extremely powerful parallel computing, the field of machine learning has received an enormous boost, further increasing our ability to spot previously hidden patterns in our data. So it’s an exciting time in bioinformatics, with lots of new areas of research opening up to us for the first time! We’re going to continue having a lot of fun for a long time!

How has training influenced your career?

JK: This has been fundamental, in different ways. One is in a formal way, where classes and courses have been key to shaping a foundation, and helping to fill specific knowledge gaps. The second is less formal, which to me has been at least equally important, where I got trained by working in different research environments together with people of different backgrounds.

RC: In my role as an associate professor, training is part of my everyday life. I am involved in many advanced courses through my university, both in Europe and in Asia, and I think that courses are useful for both participants and instructors. The former grab the knowledge from the latter and the latter get new fresh view points from the former.

LM: Many of the excellent teachers I have studied with have left a deep impression on me, and guided my career path indirectly. As to providing training, it is one of the aspects of my job that I most cherish. For me, the importance of sharing and spreading knowledge resonates very closely to the core principles of science: by sharing and exchanging knowledge, all participants in the teaching experience gain something. In all, the biggest contribution that training has had to my career, is in greatly enhancing my ability to be creative in a productive way.

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

LM: Go for it, and seek out courses taught by those rare experts that both intimately know their field, but can also clearly communicate about the essence of that field. You don’t want to only grasp the current ‘hot’ method at a user level, but rather want to understand how that field works, how it has evolved, and how the current methods fit in with this. Courses that focus on these aspects deliver knowledge that lasts for much longer!

JK: It is two-fold: find a course that gives you the theoretical foundation of an area or topic you would like to venture into. After this, I think it is essential to ‘internalise’ this knowledge, so I would advise you to find a collaborator or colleague to help you along the path to use the acquired knowledge. It is like driving a car: you need to get a driver’s license to be allowed on the road, but you really learn how to do it by practicing afterwards.

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

RC: Definitively a Medical Doctor.

LM: Most likely a software developer or systems architect of some sort. I worked in industry for a few years after my Masters degree, and then chose to pursue a PhD rather than take a very nice position at Microsoft. So if I had made a different choice then, I’d probably still be in IT!

JK: I have never really been in a situation where I had to choose between being a scientist or do something else, but thinking about it now I would like to think I would be a writer, a novelist. The reason is that I like writing, and it is part of my every day job, however writing papers and proposals comes with a lot of constraints and requirements. Making up stories without the boundaries of page limits, allowing fantasy and imagination, in an expanded vocabulary and, above all, in my mother tongue sounds all very appealing to me. Maybe one day. 🙂

You are organising the EMBL Course: Analysis and Integration of Transcriptome and Proteome Data (2 – 7 February 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?

JK: The greatest benefit is that it allows participants to have a look ‘over the fence’: most participants usually have a background either in genomics or proteomics, and being exposed to both aspects – along with the technologies and methods used in these fields – allows them to ask questions they may not have thought about before. What we try to achieve is that they could even go a step further, and integrate the new knowledge in their research to gain a more complete picture of the biological systems they are using.

LM: The course is unique in that it brings together the two key fields of research to understand cellular functional: transcriptomics, which traces the usage of the information in the genome in a given cell, and proteomics, which shows the actual biochemical and signalling capability of a given cell. There is important information at each of these levels, and these are moreover more complementary than many might think.

Of course, gene regulation provides important insights into a cell’s internal processes, but proteins are not only made or broken down, they are also closely regulated at the protein level. A complete picture of a cellular process thus requires insight into (and thus data from) both the gene expression level as well as the protein level. This is where this course provides the right skills for researchers; teaching them how to integrate data from their transcriptomics and proteomics experiments.

The usefulness for the bigger picture is therefore more or less implicit: by combining transcriptomics and proteomics, a much more complete picture of cellular functioning can be obtained. And let’s be honest, isn’t that what all of us really want to obtain, after all? 🙂

RC: I think the phrase of Claudia Manzoni in the abstract of her paper in Briefing in Bioinformatics in 2016 (Volume 19, Issue 2, March 2018, Pages 286–302) “Our work intends to target students and researchers seeking knowledge outside of their field of expertise and fosters a leap from the reductionist to the global-integrative analytical approach in research” is a perfect explanation for our course.


Interested in this course? Apply by 10 November!

Cooking for EMBL Events

Head of the EMBL Canteen and Cafeteria Michael Hansen (front, in grey) with his dedicated team. PHOTO: Marietta Schupp/EMBL

Anyone who has ever set foot in the EMBL Canteen is sure to go away wanting more. It’s no coincidence that the canteen has a reputation for serving some of the best food in the Heidelberg area.

So what is their secret?

Head chef Michael Hansen’s team of 29 (23 people in the canteen and 6 in the cafeteria) work tirelessly to cater for over 800 members of staff daily and over 6000 conference and course participants annually. Besides the great dedication of his staff – which involves regular evening and weekend shifts – he places great emphasis on the quality and freshness of the groceries they use.

“We buy our meat, fruit, vegetables, bread and eggs from local suppliers. For us it is important that the groceries have the shortest route so that they are as fresh as possible when they get to us. Our furthest supplier is 90 km away. For food that is not produced in Germany, such as olive oil, we do have to order from abroad, but we do that directly with the producers without going through a distributor.”

Everything is then freshly prepared and cooked before it is served, with close attention paid to nutritional value. This is especially important for the EMBL kindergarten, which caters for over 100 children of staff.

In 2018, the EMBL Canteen cooked for 6430 course and conference participants, and for this purpose used:

  • 32 crates of salad
  • 160 kg onions/garlic (imagine how many tears must have been shed!)
  • 225 kg fish
  • 225 kg potatoes
  • 290 kg meat
  • 803 kg fruit
  • 935 kg vegan/vegetarian dishes
  • 1,607 kg vegetables
  • 1,376,020 l coffee was served

“In the EMBL spirit, the canteen team is truly international, employing people from 12 nations who, despite their differences, have one thing in common – their love for cooking!  One of the reasons I became a cook is because of food’s power to unite people. And here I see this every day. Preparing one meal requires real team work. Everybody gets together and takes one step of the process so that all is done in the most efficient way, but still has great taste.”

Here is one of the canteen’s most popular recipes, named after Thomas Graf, EMBL Alumnus (1983 – 1998) and currently Senior Scientist at the Centre for Genomics Regulation in Barcelona, Spain:

Thomas Graf potatoes

1kg potatoes

100 ml oyster sauce

1 clove of garlic (pressed)

1 tsp honey

Pinch of salt

Black pepper

1 tbsp oil

Wash the potatoes and cut them into wedges without peeling them. Add all the ingredients and mix well. Preheat the oven to 180°C, place the potatoes on a baking sheet and bake for 40 min.


PHOTO: Marietta Schupp/EMBL
PHOTO: Marietta Schupp/EMBL
PHOTO: Marietta Schupp/EMBL

Mindfulness in Science? That’s MENTAL!

(Yes it is, indeed: Happy Mental Health Day, everyone!)

Mindfulness and stress management trainer Sonja Noss, PHOTO: Sonja Noss

Can you believe it? What’s mindfulness got to do with a scientific conference? I am here to discuss excellent science, not to sit there cross-legged in front of a scented candle, to chant mantras or hug my colleagues”.

Fair point, because what you are talking about is not mindfulness. And yet, as a professional mindfulness facilitator working in a scientific high-performance environment, I encounter this type of statement fairly frequently. It used to upset me, now I usually respond with a smile: “Oh that’s not all. When you come in we will shave your head, put you in a yellow robe and hang a handmade flower garland around your neck”. (Which usually kicks off a more reasonable discussion).

Mindfulness? What is that exactly?!

Mindfulness, to me and in a nutshell, is shutting out the background noise of everyday life and focusing on what you would like to focus on – and being fully aware of what you are doing. Put bluntly, the practice of mindfulness entails a lot of sitting on your bottom / lying on your back / walking around and simply “shutting up”. Without being distracted. In fact, it’s very simple, and yet, not at all easy – otherwise it would not be called a PRACTICE.

Why is this relevant in a scientific surrounding?

In my opinion it is essential, since being able to pay and hold your attention on a certain matter practically equals having a superpower at work – or at a conference for that matter, for example during the last session at 8pm, in a lecture room with no natural light. Many would argue that time is the most limited resource in our working days, but I would argue that it is attention – which a myriad of beeping devices, colleagues, social media, new publications, methods and technological developments, as well as the publication of the daily lunch menu are constantly competing for.

In addition to that, according to the American Psychological Association and the National Health Services (UK) mindfulness can also have a variety of other positive effects on practitioners’ mental health, as the below figure shows.

Figure by Sonja Noss

 

Mental health has long been a taboo subject in science, with increasingly frequent articles in magazines like Nature and Science slowly starting to deconstruct the stereotype: the myth of the “Demi-God in White” doesn’t leave much room for suffering an anxiety attack before your PhD defence, for fear of speaking in public (hello, conference presenters!), for depression caused by glum career perspectives, or any other mental-health challenge. Mindfulness, and especially programmes like the well-studied MBSR programme, can make an important contribution to keeping sane in the pressure cooker that modern science has become. I see them as one pillar in mental health prevention, alongside other aspects such as physical exercise, getting enough sleep, a balanced diet, nourishing social interactions/feeling connected, a sense of purpose, as well as personal interests and hobbies (i.e. having FUN!).

Some simple (mindful) examples of what you could start trying to do in the workplace or at conferences if it is all getting a bit much:

  • In general: learn what your personal stress reactions are. How do you even know you are stressed? What are your personal stress symptoms? Do you get easily agitated or frustrated? Do you tend to suffer from headaches more when you are stressed? Do you suffer from insomnia? Attention to these details is the first step – and that’s already mindfulness.
  • As soon as you notice these symptoms – if you can- take a break. This does not have to be a long break. There are fantastic quick focusing and grounding practices such as this one from Prof. Mark Williams (Oxford Mindfulness Center). See if that makes a difference.
  • Move! Get up and take a walk around the block, if only for five minutes! Any wild animal just having sprinted for its life in the jungle will have broken down the stress hormones floating around its body by the physical exercise. As would the creature which has just fought for their lives. What do humans do? We go and sit down at our desks or stand at the bench… Get enough movement, fresh air, light (not in that lecture room, I guess!), and oxygen.
  • Establish a regular mindfulness practice. The easiest way to do this is with the help of an experienced teacher. Maybe you can contact your organisation’s HR Department or the Staff Association and ask for support in having a training on site?
  • If you have been feeling unwell for a long time (weather vs. climate), please seek professional help. Many organisations have options for coaching or therapeutic interventions available. If not, speak to a person you trust and ask them for help in finding a private coach or therapist. Asking for help is often the hardest thing – and you want to be a tough guy/gal/…, right?

I have been teaching mindfulness and stress management at EMBL for over 3 years, and the initiative has been a great success. Once set up and piloted with the support of the Administrative Director and other departments, the 8-week programme quickly made a great entrance into EMBL General Training Programme. It has become one of the organisation’s most popular courses, with sessions running in parallel to meet the demand.

If you are interested in my Coaching services or would like to bring mindfulness to your organisation, get in touch via www.sonjanoss.com.

Best Poster Awards – EMBO|EMBL Symposium: Systems Genetics: From Genomes to Complex Traits

The first EMBO|EMBL Symposium: Systems Genetics: From Genomes to Complex Traits (29 Sep – 2 Oct 2019) brought together over 150 international researchers to discuss how genetic variation alters molecular mechanisms to cause phenotypic changes amongst individuals, including quantitative traits and human disease. 

From the 77 posters that were presented on-site, 3 were selected as the winners after a shortlist round by popular vote, followed by a selection round by the conference organisers.

Resolving noise-control conflict by gene duplication

Michal Chapal is a PhD student in Naama Barkai’s lab at the Weizmann Institute of Science in Israel. PHOTO: Michal Chapal

Authors: Michal Chapal, Sefi Mintzer, Sagie Brodsky, Miri Carmi, Naama Barkai, Weizmann Institute of Science, Israel

Gene duplication promotes adaptive evolution in two principle ways: allowing one duplicate to evolve a new function and resolving adaptive conflicts by splitting ancestral functions between the duplicates. In an apparent departure from both scenarios, low-expressing transcription factor duplicates commonly regulate similar sets of genes and act in overlapping conditions. To examine for possible benefits of such apparently redundant duplicates, we examined the budding yeast duplicated stress regulators Msn2 and Msn4. We show that Msn2,4 indeed function as one unit, inducing the same set of target genes in overlapping conditions, yet this two-factor composition allows its expression to be both  environmental-responsive and with low-noise, thereby resolving an adaptive conflict that inherently limits expression of single genes. Our study exemplified a new model for evolution by gene duplication whereby duplicates provide adaptive benefit through cooperation, rather than functional divergence: attaining two-factor dynamics with beneficial properties that cannot be achieved by a single gene.

View PDF Poster


Deep learning on single-cell ATAC-seq data to decipher enhancer logic

Ibrahim Taskiran is a PhD student in Stein Aerts’ lab at the VIB & KU Leuven Center for Brain & Disease Research. PHOTO: Ibrahim Taskiran

Authors: Ibrahim Ihsan Taskiran, Liesbeth Minnoye, Carmen Bravo Gonzalez-Blas, Sara Aibar Santos, Gert Hulselmans, Valerie Christiaens, Stein Aerts
KU Leuven – VIB, Belgium

Single-cell ATAC-seq provides new opportunities to study gene regulation in heterogeneous cell populations such as complex tissues or dynamic processes. We recently developed a probabilistic topic modeling approach, called cisTopic, to predict regulatory topics and sets of co-accessible enhancers from scATAC-seq data. Here, we apply deep learning approaches to analyze these sets of co-accessible enhancers, with the goal to predict the spatiotemporal pattern of enhancer accessibility directly from the enhancer sequence. We trained different types of Artificial Neural Networks, including a hybrid model that combines Convolutional and Recurrent Neural Networks. By applying this approach to a cohort of melanoma patient samples and Drosophila eye disc, we show that key transcription factors can be identified from the convolutional filters. In addition, we use the trained model to analyze the motif architecture in enhancers, such as motif combinations and relationship to nucleosome preferences. We furthermore exploit network explaining methods to predict the impact of somatic mutations, using publicly available SNP databases and in-house whole genome sequencing of inbred fly lines. Currently, to validate our models we are testing (mutated) synthetic cell state specific enhancers using massively parallel enhancer reporter assays (MPRA). In conclusion, training deep learning models on single-cell epigenomics data sets has multiple applications to understand the underlying enhancer logic and decipher gene expression programs.

View PDF Poster


ROADdt: Regulation network remodeling along disease development trajectories

Celine Sin is a Postdoctoral Fellow in Jörg Menche’s Group at the CeMM Research Center for Molecular Medicine, Austria. PHOTO: Celine Sin

Authors: Celine Sin, Jörg Menche
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Austria

The human body is comprised of over 200 different cell types varying in size, shape, and function. The differentiation and subsequent maintenance of these different phenotypic states are governed by complex gene regulatory networks that dynamically orchestrate the activation and deactivation of genes. Abnormalities in these networks may lead to dysfunctional expression programs, e.g. uncontrolled cell proliferation. In order to understand the conditions resulting in disease, we must understand the underlying gene regulatory networks governing
the gene expression program. As cells move through the differentiation space, the networks that govern gene regulation are remodeled in order to achieve the appropriate gene expression program. While statistical physics and network theory have demonstrated numerous relationships between the structure of networks and the dynamic processes that act on them,
few studies link these mathematically rigorous principles to gene regulatory networks, none at the level of cell-trajectory-states. The overall goal of this project is to understand the fundamental architecture of gene regulatory networks associated with cell differentiation processes in disease. We hypothesize that the gene regulatory networks of different
cell-trajectory-states along the differentiation trajectory – e.g. transitory, branching, or terminal states – are each characterized by distinct structural features. I will present our first steps in this direction, starting from single-cell RNA seq profiles of tumors. Ultimately, we expect that detailed characterization of the gene regulatory networks in these disease processes will reveal basic principles applicable to other diseases and cell  developmental processes.

View PDF Poster


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

How to use Twitter at a scientific event

PHOTO: Massimo del Prete/EMBL

Mariana R. P. Alves, 3rd year PhD Student in the Crocker Lab, Developmental Biology, EMBL Twitter @Mariana_RPAlves

When I was a 19-year old biochemistry undergrad, I had heard of Twitter but it was Facebook and Instagram that dominated my social media usage at the time. When I attended my first international conference, the Lindau Nobel Laureate Meeting in 2014, I noticed everyone was using Twitter and – not wanting to be left out- I created my account. Never would I have imagined that 5 years later it would be the only social media account I still have active, and that I would use it so much for work. This article is about my personal experience on the benefits of being active on Twitter,      particularly during scientific events, as well as some tips on how best to use Twitter to your (scientific) advantage!

Spread the knowledge

Sharing is caring! And scientists should share. Being at a conference is truly a privilege for scientific exchange. Some scientists might not be able to attend the event you are in because of personal commitments, lack of funding, or even to reduce their carbon footprint. I’m sure almost everyone has taken notes of talks to share with their lab colleagues – now you can share what you learn with a bigger scientific community! If you share the highlights of the event you are attending, you are making the new exciting information available to those who would otherwise not have access to it. Isn’t this a good enough reason to start your Twitter account?

Minimise missed opportunities

Conferences can be overwhelming and you want to maximise your networking and scientific exchange. If you tweet about the scientific event and use its hashtag, other people in the conference can find you and you might find people with common interests that you wouldn’t have bumped into in the crowd. It was on Twitter also that I found people inside and outside my institute who wrote interesting things – you can always DM them for a coffee, and you might find a new friend!

Exposure

This is again about networking. Not only do you minimise the missed matches you could have with scientific minds at an event, but you also maximise your exposure and that can bring you unexpected opportunities. Opportunities could be someone advertising a job directly to you, a journal editor becoming interested in your paper, or someone from the press at that event wanting to feature you.

Fun

It can be super fun to act as a reporter of a conference. In 2018, the Social Media Manager of the time at EMBL gave me the challenge of taking over EMBL’s official Twitter account to post about the Lindau Nobel Laureate Meeting. It was a wild ride, I was super scared at the beginning but it was a lot of fun, and definitely fulfilled the 3 previous benefits I wrote. It also caught the eye of the conference organisers, who thought it was really cool of EMBL to do this.

-> Check out the social media report from my Lindau EMBL Twitter Takeover!

Win prizes

If the sensible reasons above are not enough to convince you, maybe you will be interested to know that some scientific conferences and courses have competitions over Twitter where you can win prizes. I once won a brand-new multi-dispenser pipette in a CamBioScience Course in Cambridge, because I had the most likes on my Twitter posts. Moreover, I did not even have that many likes, but there was not much competition around. Now I am very proud of my pipette and brought it with me from the UK to Germany. With EMBL Events, you can also win prizes – see more in the how-to bullet points below.

10 Tips on how to use Twitter

These are just some tips I have written down from the top of my head, but you can find a lot of useful info online, and on Twitter itself. In addition, several institutes have guidelines on their intranets about how to use social media for work. Finally, get advice from your institute’s Social Media Manager or Communications Department – they are the experts!

  1. Check the hashtag and handle of the scientific event you are attending and use it to check other people’s posts and always include it in your tweets.
  2. Follow the scientists and institutes you are interested in and admire.
  3. Don’t know what to tweet about? You can start by the highlights of your favourite talks.
  4. Make sure you follow a diverse group of tweeters, this way your timeline will definitely be richer.
  5. You do not need to tweet just about data and new scientific findings, you can share interesting anecdotes from the conference, highlight some conference features that should be replicated such as accessibility logistics, diversity or environmentally friendly upgrades.
  6. Debates and discussions are also very good content for live-tweeting.
  7. You can group several tweets about the same subject in what is called a “thread”. You just need to make your first tweet and write the others as comments below it. Frequently people indicate how many tweets will be in the thread by adding something like “1/5” at the end of the tweet.
  8. If your institute is open to it, you can propose to them that you take over their Twitter account for that conference – it could be a very interesting experience for all!
  9. Do not start a tweet with a handle because it will not show on your timeline. You can add a dot before it. For example, instead of “@emblevents I had an amazing time” you can write “. @emblevents…”.
  10. Have you attended an @emblevents conference or course? Don’t forget to post a picture of the EMBL or EMBO bag in any location around the world using the hashtag #EMBLbag and @emblevents to enter the competition

Furthermore, Twitter can be a great tool to find new papers, share your new paper, ask questions (it would be interesting to compare the effectiveness of asking on Twitter vs ResearchGate), learn about other conferences and about scientific community topics – from struggles to healthy changes (great hashtag for that is #eLifeAmbassador) – support other scientists, find job ads, and more…

So, what are you waiting for?!