On big data in biology

by Nicolas Descostes

In recent years, big data is a term that invaded the media and that the public has been exposed to. From finance to social networks, data are collected to infer trends and sometimes to manipulate opinions as it has been observed during recent elections. However, the public is less aware of the big data revolution that is occurring in biology. In this post, I would like to begin by explaining how big data is used in biology, and more specifically in genomics, and end by sharing some thoughts on how big data is currently shaping research.

In the early 2000’s, a battle opposed J. Craig Venter and the International Human Genome Sequencing Consortium to publish the first sequencing data of the human genome. The race produced two articles published in Science and Nature but more importantly, opened an intellectual revolution giving new possibilities to explore the 3 billion base-pair DNA sequence of the human genome in its entirety. Even if sequencing was used a long time before, sequencing the human genome opened the door to sequencing the genome of many other species.

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Staying up to date and organised with scientific literature

By Santiago Rompani

Biological research has never been more vibrant and interesting, but the flipside is an ever-increasing number of studies to keep track of. Gone are the days when the ponderous intellectual could leaf through the latest journals while twirling a goblet of brandy or smouldering pipe. Therefore, I had to come up with other ways to keep up with the scientific literature.

The first is to spend a few minutes to learn how pubmed searches work, watch a tutorial here. Then register for “My NCBI”, which is free and allows you to setup automated pubmed searches and have the website output any new results every day via email. I have searches setup for specific scientists I wish follow, like “gross cornelius[Author]” (use without the quotation marks). I also have more complex searches for keywords in particular journals such as “(Lateral Geniculate) AND (“Nature”[Journal] OR “Science (New York, N.Y.)”[Journal] OR “elife”[Journal])” (the list of journals in my actual search is very long, again, don’t include the quotation marks, but keep the square brackets).

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Taste is King

Jim Sawitzke running Beer 101

We recently had out first Beer 101 course for staff members. International beer judge and Head of our Genetic and Viral Engineering Facility, Jim Sawitzke, first challenged us to a blind tasting and then a tour of major beer varieties. Take home messages were: “if you like it, it’s a good beer” and “if it doesn’t come in a brown bottle, it’s skunked!” – which left me wondering why I kind of like Heineken. Apparently Heineken tried to change their green bottle color at some point, but were forced to relent by popular demand. Find a scientific explanation for the skunk effect here. The tour ended with us sipping beers with names like ‘Arrogant Bastard Ale’ and ‘Rauchbier’ (trans. Smoke Beer) – both dreadful! Unless of course you’re at the higher levels of beer appreciation. Can’t wait for the advanced course.

Here’s why I became a neuroscientist

Brains come in all colours (Timm staining of mouse hippocampus with Warhol colouring; T. Ferreira, E. Audero, EMBL)

An intern in my lab recently asked me why I became a neuroscientist – he had read this piece about how it’s all just luck. I’m not so sure. I am convinced there are explicit and hidden environmental (and a few genetic) influences that restrict and channel our behaviours during our lifetime. It’s only the fiercely independent that escape these influences – and then that is usually itself a reaction to them.

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Why is Epigenetics so sexy? And other related questions.

Giuseppe Testa

By Sara Formichetti

When I was asked to write a post about the last Science & Society talk we had at our EMBL site in Rome I was particularly excited. Science & Society lectures are all about the impact of science on society and the speakers work in fields that are of utmost relevance to the public – but often misunderstood.

Most recently, Giuseppe Testa spoke at EMBL Rome. Testa works on epigenetic regulation, cell reprogramming and disease models. His talk dealt with the impact of epigenetics on society, which is a concern for all of us working at EMBL Rome, considering that we recently chose to rename our unit “Epigenetics and Neurobiology” to focus the interests of new group leaders in these two fields.

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Lab Olympics anyone?

Here at EMBL Rome we aspire to scientific excellence. This means insightful ideas, hard work, state-of-the-art facilities and perhaps a touch of luck. Occasionally, we like to blow off steam too, and the recent ‘Lab Olympics’ was a light-hearted excuse for the EMBL Rome groups to test their labcraft against one another. Including such classics as the Lab-bench race, Pasteur blow football, and of course the mind-boggling Chocolate-balls and a tape measure game, the evening fanfare was fun, a chance to interact, and fuelled by a freshly brewed batch of IPA from EMBL Rome brewmeister Jim Sawitzke.

The now annual Lab Olympics is spun out of an event organised last year by our lab to celebrate our arrival at EMBL Rome. Each lab enters a team of four people (preferably including a group leader) and then rotate around a series of loosely scientific-based games. Outstanding performances this year included the Asari lab in the Neuroepigenetics speed pictionary, the Hackett lab in the Lab-benchrelay, and finally a spectacular score by the Heppanstall lab/FACS facility in the Chocolate-balls and a tape measure game.

The Asari Lab with the 2018 Lab Olympics Trophy

Naturally, the evening had a theme, this year being the World Cup, with EMBL Rome bedecked in flags and international football colours. Of course, any respectable EMBL social has a best dressed and the Lab Olympics was no exception, with costumes reflecting an international culture/figure. There were some remarkable efforts including a full Mexican mariachi band, full Viking, and Napoleon complete with inflatable horse. The winning effort however was King Louis XIV (well done Violetta!). Which leads to the final question, who took the Lab Olympics crown this year. Well, once the scores were totted up and the dust had settled, and after an impressive performance, the victors were… the Asari Lab. Congratulations!

Fortunately, on hand was Sean Sawitzke, who made a great film about the evening, which you can find below.


Bitter about Brexit?


The author about to do the hard work of taste testing his latest creation – “Still bitter about Brexit”.

As the “official” beer producer for EMBL Rome, I have a demanding job, one that I take nearly as seriously as my real job as Head of Genetic and Viral Engineering. I started producing homemade beer over 25 years ago. I have won many competitions and brewed my recipes in multiple brewpubs to be sold. Along the way, I have become an international beer judge and educator and am always happy to discuss beer with anyone. In fact, it is one of my favorite things to do! Hopefully, in the near future, I will hold some of my beer appreciation courses here at EMBL Rome. Believe it or not, you are all beer judges and I can prove it to you in my course! Continue reading “Bitter about Brexit?”

Remembering the snow

The days are so balmy now that I can’t help thinking back to our recent freak snowstorm. Do you remember this – February 26, 2018?!

Rare snowstorm at EMBL Rome

Daniel won kudos as the only staff member to ski to work that day. Here he is getting ready to ski home – skins strapped to his touring skis in what ended up turning into a night-time hike under headlamp illumination back up the hill to Monterotondo. You learn useful things growing up in Switzerland.

EMBL postdoc Daniel Rossier skiing home from the lab




“Why did you want to become a scientist?”

It was an innocent question – I had an innocent answer. It feels almost painful to think about it.

A few weeks ago, I had the privilege to visit St. Stephen’s School in Rome to teach 9th grade biology classes about CRISPR.

I don’t know much about CRISPR, or teaching. So I recruited the lab CRISPR guru Angelo, who was also very excited about this. Together we came up with a lesson plan, hoping to introduce the latest, coolest CRISPR applications and pique the interest of 15-year-olds. We decided on case studies to make sure that everyone was engaged; we chose cases that covered a broader spectrum of applications, from cancer immunotherapy to gene drives…

– Impact. I wanted to cure cancer.

Adhering to Asian stereotypes, my parents “asked” if I would apply to medical school. Short-sighted, I thought- doctors can save maybe a hundred lives, but if I find the cure for some deadly disease, I would be saving millions.

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Sex sells & immigrants steal

The embarrassing fact: sex sells

The brain is hard wired to respond in predictable ways to important environmental stimuli. This was certainly an advantage to our ancestors living off the land, but it can lead to some awkward situations in our modern lives. The large letters plastered over the explicit magazine section that we’ve all seen at airports – SEX SELLS – ring true to us in an embarrassing way. Yes, when it comes to sex our rational thought system has been hijacked and our instincts rule.

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