101 questions with a bioinformatician #16: Melissa Wilson Sayres

This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

Melissa Wilson Sayres is Assistant Professor of Genomics, Evolution, and Bioinformatics in the School of Life Sciences and The Biodesign Institute at Arizona State University. Her lab is interested in the evolution of sex chromosomes among other topics that relate to genome evolution and comparative genomics.

I applaud Melissa for clearly setting out both her expectations of people that join her lab in addition to listing her responsibilities to her lab members. I wish more PIs were as communicative about this, though I would add an expectation for grad students: 'I will not leave food — especially cheese — on, in, or near my computer'.

You can find out more about Melissa by visiting her (well documented) lab page, checking out her mathbionerd blog, or by following her on twitter (@mwilsonsayres). And now, on to the 101 questions...

 

 

001. What's something that you enjoy about current bioinformatics research?

That we can use computers to collect, analyze, and learn new things about our biology and evolutionary history.

 

010. What's something that you *don't* enjoy about current  bioinformatics research?

That there isn't a straightforward way to get into it. Some people come from computer science and may feel intimidated about learning the biology. Some come from biology and are intimidated by learning to program. Some (like myself) come from some other background, and learn both! Although there are a few collegiate bioinformatics programs, it is my impression that many schools do not have the kinds of background courses that students need in order to break into bioinformatics. Many of us are self-taught. 

 

011. If you could go back in time and visit yourself as an 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

Learn a programming language. 

 

100. What's your all-time favorite piece of bioinformatics software, and why?

I really like Galaxy, because it has the GUI-based format for newbies, as well as the command-line option for those who prefer it, and it makes computational biology easier to reproduce.

 

101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality?

Y! Because the sex chromosomes are the most interesting (and there is no 'X' nucleotide ambiguity code).

Why I twitter →

I cannot sit on the fence. I like twitter and what it offers. I have learned things I never would, built genuine relationships with international people who I would have perhaps have only met over a quick coffee at a conference. And I have changed the way I speak about science.

This post by Mark Brandon sets out nine great reasons as to why he finds Twitter so useful, many of which relate to science communication.

I believe twitter is a strong positive for science, and it is a worthwhile investment of your time.

I completely agree with just about everything he has to say. It's a good list.

101 questions with a bioinformatician #15: Karyn Meltz Steinberg


This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

Karyn Meltz Steinberg is a staff scientist at The Genome Institute at Washington University ('TGI' to those in the know, but it will forever be the GSC to some of us). Prior to joining, Karyn was a postdoc in Evan Eichler's lab at the University of Washington (perhaps she is destined to head here, here, or here when time comes to move on?).

Her current position sees her work as part of the Genome Reference Consortium to improve the human reference assembly. In particular, she is involved with characteHrizing and resolving the particularly 'messy' regions of the genome that have complex genomic architecture.

You can find out more about Karyn by following her on twitter (@KMS_Meltzy). And now, on to the 101 questions...

 

 

001. What's something that you enjoy about current bioinformatics research?

I enjoy the collaborative community of bioinformatics. Although we are all working on our own research questions, the basic issues of how to process sequence data and report and annotate variants are the same. I've attended some workshops recently and have been impressed with how much people want to work together to solve these problems particularly with respect to the new reference assembly and dealing with the alternative loci.

 

010. What's something that you *don't* enjoy about current  bioinformatics research?

File formats. Can we please agree on something, friends? (KB: see Law's First Law!)

 

011. If you could go back in time and visit yourself as an 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

I actually love the fact that I was not a bio major and that I did tons of non-sciencey activities as an undergrad. My non-traditional journey has definitely shaped who I am as a researcher. I would advise my 18 year old self to not be afraid of the command line and to learn a programming language earlier.

 

100. What's your all-time favorite piece of bioinformatics software, and why?

BEDTools. Full stop.

 

101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality?

I was going to say '.' because I work on filling gaps in the human genome, but Deanna Church already took that. So, I will go with 'S' as I like a GC-rich challenge and the flexibility of being either a purine or pyrimidine.