Photo:

Paul Flicek

Favourite Thing: My favourite thing about science is that it rarely seems like work. I really like spending time with clever people and coming up with ways to solve problems. Sometimes this means going over something many times before the answer makes sense. Other times the best approach to solve a problem is to try something, no matter how stupid or crazy, and plan to make the second version better. It’s especially fun when something that I initially thought was crazy turns out to be right.

My CV

School:

Cretin High School, 1985-1989. (Yes that is the real name of the school.)

University:

Drake University (Des Moines, Iowa, USA), BS in Physics, 1989-1993. Washington University (St. Louis, USA), MSc in Computer Science and DSc in Biomedical Engineering, 1998-2004.

Work History:

After university I worked at the Hanford Nuclear Site in Washington State, USA, and than spend 4 years as an officer in the US Army managing the radiation safety program at Walter Reed Hospital in Washington, DC. I’ve been at the European Bioinformatics Institute since 2005 and formally affiliated with the Sanger since 2008.

Department:

Vertebrate Genomics

Area of Research:

Computational genomics

Find out more:

The best place to start is http://www.ensembl.org

Me and my work

I manage a big team of people that are trying to understand how the genomes of vertebrate species work and create tools that other scientists can use to do their work.

My group creates resources that other scientists can use in their work.  The biggest and most well known resource is called Ensembl (http://www.ensembl.org) and provides annotation and other information for vertebrate genomes.  In this case annotation means the location of genes, variation and information about how the genome controls and regulates other processes.  All of the information that we provide through Ensembl is completely free for other people to use. We also provide much of the data management infrastrcture for the 1000 Genomes Project meaning that my group is one of the biggest users of disk space and internet bandwidth at the EBI.

Besides Ensembl, my group runs large databases that store human variation data and connections between this data and disease.  Storing this type of data require special data security because each person’s genome sequence is unique. 

Finally, my research group is trying to understand how the genome evolves into the functions that it has.  For example, human liver and mouse liver do very much the same thing and use genes that are very closely related to perform these functions.  Because of this, most people expected that the way that these genes were controlled would be almost identical between human and mouse.  However, this is now seems not to be the case and we have shown that there are more differences in the gene regulation than was initially thought.  We are working to understand these differences more fully.

My Typical Day

Email, meetings, phone calls, writing and other work designed to keep our various projects running.

When I am not travelling, I normally come into work about an hour before most of the other people do so that I can have a relaxing cup of coffee, plan out my day and get caught up on email or other issues.  In a typical day I will meet with at least one student or post doc regarding his or her research and two or more of the teams working on Ensembl or one of the other big projects.  There will often be at least one conference call in the afternoon timed so that scientists in the US and Europe can all attend.  I will also normally work on writing either a paper, a grant or some other information and often I will be working on reviewing papers or grants that other scientists have written.

I do travel a lot for work and am normally away about 10-12 days per month.  Those days actually have less variety than normal work days at the institute because travel is mostly to all day meetings or to larger conferences.  I often give talks at the meetings or conferences describing the most recent work from the group.

Genome sequencing and my research

Everything I do starts either with a full genome sequence such as the human genome or with the analysis of new DNA sequence generated for a specific purpose.

Genome sequencing and especially the recent advances in sequencing technology are fundamental to my work.  The resources that we create in Ensembl start with whole genome sequences from about 60 different species with human and mouse being the most popular.  But it is more that just the whole genome sequence: genome sequencing is creating maps of human variation in the 1000 Genomes project and is being used to map the sites of genome regulation as part of my research group.  These are just two examples of the many ways we use genome sequencing.

My Interview

How would you describe yourself in 3 words?

Calm, determined, busy

What music do you have on your iPod?

Michael Franti, Ladyhawke, the Trashcan Sinatras and a whole selection of alt country

What is the most fun thing you've done?

Spending the night on a beach in northern Trinidad with nesting leatherback turtles.

What do you like to do away from work?

I enjoy food and cooking, traveling and sports (now watching more than playing). When I can combine these things it is even better.

What did you want to be after you left school?

A scientist

Were you ever in trouble in at school?

Yes. (Do I have to give more details?)

What's the best thing you've done as a scientist?

Created resources that are useful for others (and for me!) to do better science.

Tell us a joke.

How do you kill a circus? Go for the juggler.