101 questions with a bioinformatician #38: Gene Myers

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.

Gene Myers is a Director at the Max-Planck Institute for Molecular Cell Biology
and Genetics (MPI-CBG) and the Klaus-Tschiar Chair of the Center for Systems Biology Dresden (CSBD).

Maybe you've heard of Gene for his pivotal role in developing the Celera genome assembler which led to genome assemblies for mouse, human, and drosophila (the first whole genome shotgun assembly of a multicellular organism). You may also know Gene from his work in helping develop a fairly obscure bioinformatics tool that no-one uses (just the 58,000 citations in Google Scholar).

His current research focuses on developing new methods for microscopy and image analysis; from his research page:

"The overarching goal of our group is to build optical devices, collect molecular reagents, and develop analysis software to monitor in as much detail as possible the concentration and localization of proteins, transcripts, and other entities of interest within a developing cohort of cells for the purpose of [developing] a biophysical understanding of development at the level of cell communication and force generation."

You can find out more about Gene by visiting his research page on the MPI-CBG website or by following him on Twitter (@TheGeneMyers). Finally, if you are interested in genome assembly then you may also want to check out his dazzlerblog ('The Dresden AZZembLER for long read DNA projects'). And now, on to the 101 questions...



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

The underlying technology is always changing and presenting new challenges, and the field is still evolving and becoming more "sophisticated". That is, there are still cool unsolved problems to explore despite the fact that some core aspects of the field, now in its middle-age in my view, are "overworked".



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

I'm really bored with networks and -omics. Stamp collecting large parts lists seems to have become the norm despite the fact that it rarely leads to much mechanistic insight. Without an understanding of spatial organization and soft-matter physics, most important biological phenomenon cannot be explained (e.g. AP axis orientation at the outset of worm embryogenesis).

Additionally, I was disgusted with the short-read DNA sequencers that, while cheap, produce truly miserable reconstructions of novel genomes. Good only for resequencing and digital gene expression/transcriptomics. Thank God for the recent emergence of the long-read machines.



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

At age 18 its not so much about career specifics but one's general approach to education. For myself, I would have said, "go to class knuckle head and learn something from all the great researchers that are your teachers (instead of hanging out in your dorm room reading text books)", and for general advice to all at that stage I would say, learn mathematics and programming now while your mind is young and supple, you can acquire a large corpus of knowledge about biological processes later.



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

I don't use bioinformatics software, I make it :-) My favorite problem, yet fully solved in my opinion, is DNA sequence assembly -- it is a combinatorially very rich string problem.



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

N — as it encompasses all the rest :-)

101 questions with a bioinformatician #37: Keith Robison

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.

Keith Robison is a Senior Bioinformatics Scientist at a small biotechnology company based in Cambridge, Massachusetts. His employer has an interest in the natural products drug discovery space and as Keith puts it, his own work concerns 'Assembling and analyzing actinomycete genomes to reveal their biosynthetic moxie'.

If you didn't already know — and shame on you if that is the case — Keith writes about developments in sequencing technologies (and other topics) on his Omics! Omics! blog. This is required reading for anyone interested in trying to understand the significance of the regular announcements made by various companies that develop sequencing technologies. In particular, his analysis of news coming out from the annual AGBT conference is typically detailed and insightful.

You can find out more about Keith by reading his aforementioned blog or by following him on twitter (@OmicsOmicsBlog). A special thanks to Keith for waiting patiently on me to get this interview posted! And now, on to the 101 questions...



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

All sorts of re-thinking how to do things — productive ways to look at old problems. Look at all the exciting improvements in assembly coming from long reads, or alignment-free RNA-Seq and metagenomics. Cool stuff.



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

Too many papers that report a new program without adequate benchmarking or a clear description of what differentiates the program — is it really different, or just old wine in new bottles?



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

Wow. I didn't dabble into bioinformatics until I was 19. I think my advice would be try out a new programming language every other year — I've gotten a lot of mileage out of a few languages, but even learning a new one (that I subsequently drop) productively influences my programming.



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

My favorite bioinformatics software was the original WWW interface to FlyBase — first: because I wrote it as a lark, second: FlyBase paid me to support it after I showed it off, and third: because its one of the few programs of mine that ever had an explicit sunset!



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

M — Methionine is good at getting things started (KRB: yes I know, Methionine is not an IUPAC nucleotide character…but that was the given answer to the question).

101 questions with a bioinformatician #36: Alicia Oshlack

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.

Alicia Oshlack is the Head of Bioinformatics at the Murdoch Childrens Research Institute (they don't like apostrophes) in Melbourne, Australia. Her research focuses on four main project areas: methods for analysing RNA-seq data, epigenomics, clinical genomics data analysis, and cancer genomics.

Before moving into the field of genomics, Alicia had a background in astronomy and her Ph.D. work concerned the structure of radio quasars. Not many bioinformaticians can claim to have published papers on the topic of estimating the mass of black holes!

You can find out more about Alicia by reading her Wikipedia page or by following her on twitter (@AliciaOshlack). I also encourage you to check out her must read article for fellow computational biologists: A 10-step guide to party conversation for bioinformaticians. And now, on to the 101 questions...



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

I love the pace at which things are changing in the field. There is always something new to work on and there are so many ways to contribute something useful to the research community. I also really love the balance between collaborative analysis on really interesting biological problems and doing careful methods development.



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

I get frustrated that I need to spend so much of my time convincing people that bioinformatics is a real scientific research discipline where we have deep scientific training and use our brains to solve scientific problems. Hopefully I will have convinced everyone in Australia soon.



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

I did my PhD in astrophysics and I often wonder if I would have been better off doing a more relevant subject but I really appreciate the skills I learnt doing that. Within this I probably would tell myself to put a bit more focus on programming and do statistics instead of applied mathematics.



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

I think limma is amazing. Have you seen the users guide? I think it's 145 pages long and although it was originally developed for microarray analysis more than 12 years ago it has adapted to the sequencing revolution and is used more than ever now. I believe it is the most widely used bioconductor analysis package ever.



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

I think S = G/C because I'm always a little bit biased.

101 questions with a bioinformatician #35: Aaron Darling

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.

Aaron Darling is an Associate Professor at the ithree institute — where capital letters are in short supply? — which is part of UTS (University of Technology Sydney). His research focuses on developing computational and molecular techniques to characterize the hidden world of microbes. He helped develop the Mauve multiple genome alignment tool and continues to work on this and other software tools. Aaron also has a long-standing interest in poop:

Of course this interest is all part of an ongoing research project, one that is seeking to understand the development of the infant gut microbiome.

You can find out more about Aaron by visiting his lab's website, or by following him on twitter (@koadman). And now, on to the 101 questions...



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

The growing interplay between informatics, molecular biology, and experimental design is very exciting. In the past 10 years many problems that could only have been solved through decades of experimental work have been transformed from experimental problems to data analysis problems. I think this trend will only accelerate as our technology to interface digital computational systems with biological systems continues to improve. And data analysis feeds back to inspire new experimental designs in a feedback loop that's getting ever-shorter. As an informatician I find it especially fun to discover new ways of designing the lab work that solves long-standing data analysis problems.



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

Data wrangling and data mangling. This is almost certainly cliche by now but inconsistently implemented file formats are the bane of bioinformatics. This was apparent to me within weeks of starting in the field, as my first assigned task was to write a sequence file format parsing library for the E. coli genome project team. I often wonder why I didn't run as fast as I could in the opposite direction.



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

Early on I benefited from a nugget of wisdom in Dan Gusfield's sequence analysis book which emphasized the importance of solving biological data analysis problems that are core to the biology, not the technology platform used to measure the biology. For example the general sequence alignment problem vs. short read alignment. Those are the contributions that are going to matter over the long term. I wish I had also appreciated early on that the elegance and simplicity of the solution, and especially the code implementing it, matters just as much.



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

Probably BEAST, because I learned so much about phylogenetic models, MCMC, and software design from using it and coding up modules for it.



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

H, because as a teenager I always wanted to be a G but in reality was everything but.