Opiniomics

bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

From there to here

This is going to be quite a self-indulgent post – in summary, I am now a full Professor at the University of Edinburgh, and this is the story of my early life and career up until now.  Why would you want to read it? Well this is just some stuff I want to say, it’s a personal thing.  You might find it boring, or you may not.  There are some aspects of my career that are non-traditional, so perhaps that will be inspiring to others; to learn that there is another way and that there are multiple routes to academic success.

Anyway, let’s get it over with 😉

Early life

I was born and bred in Newcastle.  I come from a working class background (both of my grandfathers were coal miners) and growing up, most of my extended family lived in council houses.  I went to a fairly average comprehensive (i.e. state) school, which I pretty much hated.  Something to endure rather than enjoy.  Academic ability was not celebrated – I don’t know the exact figures but I’d guess less than 5% of my fellow pupils ended up in higher education.  Being able to fight and play football were what made you popular, and I could do neither 🙂 Choosing to work extra hours so I could learn German didn’t improve my popularity much…

My parents both worked hard – really hard – and I had everything I needed, but not everything I wanted.  Looking back this was a good thing.  My Dad especially is a bit of a hero.  He started off as a “painter and decorator” – going to other peoples’ houses and doing DIY, painting, putting up shelves, wallpaper, laying carpets etc.  As if doing that, having a small family (I have an older brother) and buying a house weren’t enough, he studied part-time for a degree in sociology at Newcastle polytechnic, famously going off to do painting and decorating jobs between lectures, and at the weekends.  After graduating, he went on to have a successful career in adult social care, and finished life as lecturer at a further education college.  My mother also worked in social care, and together they supported me through University (BSc and MSc).  Just amazing, hard working parents.  I attribute my own work ethic to both of them, they set the example and both my brother and I followed.

Education

I did a BSc hons in Biology at the University of York.  Some bits I loved, some bits I didn’t, and I came out with a 2.1.

One practical sticks in my mind – in pairs, we had 3 hours to write a program in BASIC (on a BBC B!) to recreate a graph (yes – we had to recreate an ASCII graph) based on an ecological formula (I don’t remember which).  I finished it in ten minutes and my partner didn’t even touch the keyboard.  Writing this now reminds me of two things – firstly, hours sat with my Mum patiently punching type-in programs into our Vic 20 so I could play space invaders (written in, you guessed it, BASIC); and secondly, hacking one of my favourite ZX Spectrum games, United, so I could have infinite money to spend on players.  Happy days!

At the end of my undergraduate, I didn’t know what else to do, so I took the MSc in Biological Computation, also at the University of York.  This was awesome and I loved every minute (previous graduates include Clive Brown, but more about that later).  The prospectus was so wide-ranging – we covered programming (in C), mathematical modelling, statistics (lots and lots of statistics), GIS and Bioinformatics, among many other courses.  It was hard work but wonderful.  It really taught me independence; that I could start the day knowing nothing, and end the day having completed major tasks, using nothing but books and the internet.

At the end of the course I had three job offers and offers to do a PhD – looking back this was a pivotal decision, but I didn’t realise it at the time.  I chose a job in the pharmaceutical industry.

Early career

My first job was a 12 month contract at GlaxoWellcome in Stevenage.  GW had invested pretty heavily in gene expression arrays.  Now, these were very different to modern microarrays – this was pre-genome, so we didn’t know how many genes were in the human genome, nor what they did.  What we had were cDNA libraries taken from various tissues and normalised in various ways.  These would be spotted on to nylon membranes, naively – we didn’t know what was on each spot.  We then performed experiments using radioactively labelled mRNA, and any differentially expressed spots were identified.  We could then go back to the original plate, pick the clone, sequence it and find out what it was.

It’s now obvious that having a genome is really, really useful 😉

I was in a team responsible for all aspects of the bioinformatics of this process.  We manufactured the arrays, so we wrote and managed the LIMS; and then we handled the resulting data, including statistical analysis.  I worked under Clive Brown (now CTO at Oxford Nanopore).  He asked me in interview whether I could code in Perl and I had never heard of it!  How times have changed…. he was very much into Perl in those days, and Microsoft – we wrote a lot of stuff in Visual Basic.  Yes – bioinformatics in Visual Basic.  It can be done…

I spent about four years there – working under Francesco Falciani for a time – then left to find new challenges.  I spent an uneventful year at Incyte Genomics working for Tim Cutts (now at Sanger) and David Townley (now at Illumina), before we were all unceremoniously made redundant.  With the genome being published, Incyte’s core business disappeared and they were shutting everything down.

Remember this when you discuss the lack of job security in academia – there is no job security in industry either.  The notion of job security disappeared with the baby boomers, I’m afraid.

I managed to get a job at Paradigm Therapeutics, also in Cambridge, a small spin-out focused on mouse knockouts and phenotyping.  I set up and ran a local Ensembl server (I think version 12) including the full genome annotation pipeline.  This was really my first experience of Linux sys/admin and running my own LAMP server.  It was fun and I enjoyed it, but again I stayed less than a year.  Having been made redundant from Incyte, my CV was on a few recruitment websites, and from there an agent spotted me and invited me to apply for my first senior role – Head of Bioinformatics at the Institute for Animal Health (now Pirbright).

Academia

So, my first job in academia.  It’s 2002.  I am 28.  I have never been in academia before.  I have no PhD.  I have never written a paper, nor written a grant (I naively asked if we got the opportunity to present our grant ideas in person in front of the committee).  I am a group leader/PI so I am expected to do both – I need to win money to build up a bioinformatics group.  What the institute needed was bioinformatics support; but they wanted me to win research grants to do it.

This job really was really, really tough, and I was hopelessly ill-equipped to do it.

My first grant application (to create and manage pathway genome databases for the major bacterial pathogens we worked on) was absolutely annihilated by one reviewer, who wrote a two page destruction of all of my arguments.  Other reviewers were OK, but this one killed it.  Disaster.  I figured out that no-one knew who I was, I needed a foot-print, a track record and I needed to publish (I’d still like to find out who that reviewer was….)

In 2005 I published my first paper, and in 2006 my second.  You’ll note I am the sole author on both.  Take from that what you will.  Meanwhile I was also supporting other PIs at the institute, carrying out data analyses, building collaborations, and these also led to papers; and so slowly but surely I began building my academic life.  I got involved in European networks such as EADGENE, which eventually funded a post-doc in my lab.  I won a BBSRC grant from the BEP-II initiative to investigate co-expression networks across animal gene expression studies; and I successfully applied for and won a PhD studentship via an internal competition.  With papers and money coming in, the institute agreed to provide me with a post-doc from their core support and hey presto, I was up and running.  I had a research group publishing papers, and providing support to the rest of the institute.  It only took me five or six years of hard work; good luck; and some excellent support from one of my managers, Fiona Tomley.  During my time at IAH I had 7 managers in 8 years; Fiona was the only good one, and she provided excellent support and advice I’ll never forget.

So what are the lessons here?  I think this was an awful job and had I known better I wouldn’t have taken it.  At the beginning there was little or no support, and I was expected to do things I had no chance of achieving.  However, I loved it, every minute of it.  I made some great friends, and we did some excellent work.  I forged collaborations that still exist today.  I worked really, really hard and it was quite stressful – at one point my dentist advised gum shields as I was grinding my teeth – but ultimately, through hard work and good luck, I did it.

It’s worth pointing out here that I believe this was only possible in bioinformatics.  My skills were in such short supply that a place like IAH had no choice but to take on an inexperienced kid with no PhD.   This couldn’t have happened in any other discipline, in my opinion.  It’s sad, because ultimately I showed that if you invest in youth they can and will make a success of it.  Being older, or having a PhD, is no guarantee of success; and being young and inexperienced is no guarantee of failure.

Roslin

And so, in 2010, to Roslin.  There was quite an exodus from IAH to Roslin as the former shrank and the latter grew.  I was lucky enough to be part of that exodus.  My role at Roslin was to build a research group and to help manage their sequencing facility, ARK-Genomics.  I certainly don’t claim all of the credit, but when I arrived ARK-Genomics had a single Illumina GAIIx and when we merged to form Edinburgh Genomics, we had three HiSeq 2000/2500.  We also had significantly better computing infrastructure, and I’m proud that we supported well over 200 academic publications.  My research is also going really well – we have, or have had, grants from TSB, BBSRC, and industry, and we’re publishing plenty of papers too.  The focus is on improved methods for understanding big sequencing datasets and how they can contribute to improved farm animal health and production.  Scientifically, we are tackling questions in gut microbiome and host-pathogen interactions.

Roslin is a great place to work and has been very supportive; the group enjoys a small amount of core support through which we help deliver Roslin’s core strategic programmes; and it is an incredibly rich, dynamic environment with over 70 research groups and over 100 PhD students.  You should come join us!

In 2015, I was awarded a PhD by research publication – “Bioinformatic analysis of genome-scale data reveals insights into host-pathogen interactions in farm animals” (I don’t think it’s online yet) – and in 2016 promoted to Personal chair in bioinformatics and computational biology.  Happy days!

A note on privilege

Clearly being a white male born in the UK has provided me with advantages that, in today’s society, are simply not available to others.  I want readers of this blog to know I am aware of this.  I wish we lived in a more equal society, and if you have suggestions about ways in which I could help make that happen, please do get in contact.

So what next?

More of the same – I love what I do, and am lucky to do it!  More specifically, I want to be a champion of bioinformatics as a science and as an area of research; I want to champion the young and early career researchers; I want to continue to train and mentor scientists entering or surviving in the crazy world of academia; and I want to keep pushing for open science.  Mostly, I want to keep being sarcastic on Twitter and pretending to be grumpy.

Cheers 🙂

 

11 Comments

  1. I enjoyed reading your post indeed! good stuff.

  2. According to my FB you’re Happy not Grumpy!

  3. Congratulations Mick! I did not realise how formative the ‘EADGENE’ years would prove for your career 🙂 It surely helped to establish yourself in a wider community.
    Enjoy!

  4. Well done Mick, so pleased for your success. I also appreciate your comment about privilege. From where I’m sitting you are in no way part of the problem but through your continued advocacy very much part of improving things.

  5. Many congratulations on the well deserved promotion. An interesting and thoughtful post that, in parts, resonates with my own experiences of working in this field.

  6. Many congratulations Mick! Really inspiring story.

  7. Thank you for the great post! What a good read indeed!

  8. congratulations!!! thank you for sharing your story.

    every single thing that you said about ph.d. is true and everyone knows it but is seldom said publicly. i am glad you said what you said.

    may the force be with you.

  9. Great read, love to hear other bioinformatician’s path to their career – I find its almost always a weird path. As someone who has bounced between fields (pharmaceuticals/pharmacy school, clinical trials, MSc in Bioinformatics) this is encouraging. Maybe I’ll get a PhD one day if it limits me (I’m only 26) but I plan to go the industry/business route all the way through and develop scientific research in this sector as much as I can. I think we need to claim our stake in this area as well

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