Today's PhDetails is with Vivian Link, a PhD student at the University of Fribourg here in Switzerland. I met Vivian when she came to Eawag to give a talk as part of our weekly seminar series and was really impressed with her talk and the work that she was doing as part of her PhD. Vivian is much more involved in the computing side of genomics and has developed a program to call genotypes from samples with damaged DNA, which I think is pretty amazing for a third year PhD student! So if you want to understand more about the techy side of evolution and what it's like to publish your own program as a student here are Vivian's PhDetails
Well let’s start off by
talking about completely unscientific stuff. What's your favourite band/musical artist pre
1980?
Joni Mitchel maybe? And Led Zeppelin. It’s so
hard to choose only one!
Favourite band/musical
artist post 1980?
Again, this is like choosing your favorite
child! I always come back to System of a Down and Amy Winehouse. Or Calle 13.
Ah and someone just showed me Esperanza Spalding! I’m sorry I can’t just pick
one.
Favourite movie?
Napoleon Dynamite
Where do you study and
who is/are your supervisor(s)?
I’m at the University of Fribourg under the
supervision of Daniel Wegmann.
What year of your PhD
are you in?
I’m in my 3rd year.
My supervisor has different grants and
sometimes I’m paid from one of these and sometimes he pays me with the money he
gets from the university. I will be
funded for 4 years.
Do you have any
publications – if so where?
I have a publication about my master’s work,
published in Genome Biology and Evolution. From my PhD I have several
publications where I’m not the first author. They’re in the journals Genetics,
PNAS and Science. But I’m still working on publishing my paper about the
program I’m working on called ATLAS. For now it’s only online on BioRxiv and I
guess it will be the paper I am most proud of so far even though it is only two
pages long!
Did you do a masters -
was it about?
I did my masters at the University of Lausanne.
It was called Molecular Life Sciences and I chose to take some specialized courses
in bioinformatics. I did my master project in Henrik Kaessmann’s lab under the
supervision of Diego Cortez and it was about male mutation bias in monotremes.
Male mutation bias is characterized by a higher substitution rate in the male
sex chromosomes than in the other chromosomes, caused by a higher number of
cell divisions in spermatogenesis than oogenesis. This phenomenon had been
observed in all mammals besides in the most basal clade of the monotremes, i.e.
the platypus and echidna, and it was my goal to see if it exists also in these
animals with very weird sex chromosomes. It does!
How many PhDs did you
apply for – what were you looking for?
I think it was around 4. I was looking for a
lab in which I could learn a lot, especially about informatics and statistics,
and a lab consisting of nice people of course!
Since my first project was already in the field
of bioinformatics I have never done any fieldwork.
What is the most bodged
piece of equipment you have had to use during fieldwork – did it work?
I got 99 problems, but this ain’t one!
What one piece of
advice would you give to a masters student applying to PhDs now?
Don’t settle! Apply to as many positions you
can. Talk to the people in the lab about what it’s like to work there and if
they’re happy. It’s more important to be in a lab that’s stimulating and where
people are happy than in a lab that’s famous.
What supervisor traits
are important to you?
My supervisor always tries to make sure we have
fun and I think that’s very important. He also always has time to listen to our
problems and find solutions. And he has cool ideas.
I guess a supervisor who would cheat scientifically?
Or one who would be racist or sexist. Or maybe less extreme someone who expects
a specific type of result without having any idea about the project.
In one sentence what
is your PhD about?
I’m developing methods to analyze high
throughput sequencing data that is suboptimal by avoiding to have to call
genotypes but instead taking into account their uncertainty.
What has been your
academic highlight of the last year?
The fact that more and more people are using
ATLAS
Which academic
idol/scientist have you met?
I don’t really have any academic idol.
Which academic
idol/scientist would you most like to meet?
Anyone who could fundamentally change the way I
see the world.
Do you have a
favourite paper?
Can I say one of ours :)? No seriously speaking
I can’t say I do. I have a favorite book though, Coalescent Theory by John
Wakeley.
What has been your
favourite conference so far – why?
Last year I went to a summer school at UCLA. It
was not really a conference but there were many talks about very diverse
statistical and computational methods in biology. It was very nice to learn
about so many things I had never heard of before and also to meet the other
students, of which many had very different projects from mine, and who came
from different backgrounds. It broadened my horizon and I also had a very good
time.
What hours do you
typically work?
9:30 – 6:30
What do you do when
you’re not working – how do you balance it with your phd?
On week-ends I sometimes go see to my family
and friends close to Zürich. I like spending time with my flatmates, read, play
badminton, play guitar... I recently got into hiking and that’s what I plan to
do during my next vacation.
If a genie could grant
you one wish to help with your phd what would you wish for?
A magic keyboard that writes code without bugs
What would be your
dream job?
Honestly, right now my PhD is my dream job. I
guess any job where I can continue learning and see other people using my work
would fit that category.
Where do you see
yourself in 5 years?
I hope I will have a job for which I like to
get up in the morning, in a country that’s definitely not colder than
Switzerland
One word to sum up
your future in academia:
Exciting
What do you want to
achieve outside of academia in the coming year?
This summer I want to take more trips on
the week-ends, biking or hiking!
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