Forum:Who are the Greatest Bioinformaticians Of All Time (GBOAT)

Question

[Istvan Albert]

I am planning to write a chapter on bioinformatics personalities - an acronym popped into my mind:

GBOAT - The Greatest Bioinformaticians Of All Time

So who is on your list? Who are the most influential bioinformaticians as they affect your career (keep it to 5-10 people). I am looking to find people whose work directly benefits you and make your achievements possible. I am not looking for the traditional sciency measures of "Nobel prize" candidates that "discovered" something.

For example, take BLAST, the authors are important - but they are not the ones that made BLAST so special. The true potential of BLAST is reached because there is a global repository to search. If we had the global repository and no blast we would be better off than vice versa.

PS: For those that missed them here are some posts in the "Uses this" series: https://www.biostars.org/t/uses-this/

[grant.hovhannisyan]

I'd suggest to classify by disciplines. For many people here Bioinformatics is usually related to NGS, but there are also phylogenetics, population genetics, structural biology, etc which were "Bioinformatics" long before NGS.

[zizigolu]

I will nominate Rahul Satija for Seurat

Answer 1

[Pierre Lindenbaum]

According to biostars ( https://www.biostars.org/user/list/?sort=reputation&limit=all%20time&q= ) me, Devon, Istvan, genomax, Neil, Michael... :-D

[Devon Ryan]

Obviously biostars tells the truth :)

[Kevin Blighe]

You need to go to the second row on that listing, too... ;)

[5heikki]

TIL I'm in the Top 50 of the Greatest Bioinformaticians of All Time

Edit. but truly Heng Li is the Messi of Bioinformatics. No question about it..

Answer 2

[Istvan Albert]

1. Heng Li
2. Steven Salzberg
3. Lior Pachter
4. Aaron Quinlan
5. James Kent
6. Ewan Birney
7. Benjamin Langmead
8. Cole Trapnell
9. Lincoln Stein

Each person on this list produced algorithms, software that was revolutionary for its time, used by millions - and with that changed the world of bioinformatics.

Each should be a billionaire based on the value they produced for mankind.

[jean.elbers]

Here's another vote for James (Jim) Kent (https://en.wikipedia.org/wiki/Jim_Kent)

[MutationalMeltdown]

Nice list, also surprised no-one mentioned Johannes Köster for Snakemake, Bioconda, and Rust-Bio

[GenoMax]

Possibly because while important they are utilities/tools that facilitate bioinformatics analysis.

[MutationalMeltdown]

maybe, but Rust-Bio is like Biopython (Peter Cock already rightly mentioned) and people already mentioned Hadley Wickham, who is far more removed from bioinformatics

[5heikki]

Good list. Maybe also Altschul because of the Blast paper?

[Istvan Albert]

I would want to list NCBI blast and its integration with Entrez - it is a complete reimplementation with unique improvements to work at the scale it does work now - but I am not sure who to credit for that.

Answer 3

[GenoMax]

In no particular order:
Gene Myers - Genome assembly
Bill Pearson - FASTA aligner and format both, Participates on Biostars!
Margaret Dayhoff - She has been called "mother and father of bioinformatics"
Michael Waterman/Temple Smith - Smith-Waterman
Webb Miller - Genome scale alignments
Sean Eddy - HMM's
Janet Thornton - Structural biology
Joseph Felsenstein - Evolutionary inference
David Baker - Protein structure prediction
Craig Venter - EST/Microbiomes
Eric Lander

[h.mon]

Good someone doesn't forget the very early bioinformaticians. I would include Paulien Hogeweg, who coined the word bioinformatics.

[Istvan Albert]

did not know that, excellent definition - one that still eludes most biologists:

she defined the term bioinformatics as "the study of informatic processes in biotic systems".

https://en.wikipedia.org/wiki/Paulien_Hogeweg

Most biologists think that bioinformatics is about data analysis, Dr. Hogeweg already knew in 1970 that it is about information

[gaberoo]

Argh! I was just about to post her :)

[i.sudbery]

Came here to add Margaret Dayhoff, glad someone beat me to it! Not only created the first way of measuring relationships between DNA and protein sequences, but also started the first catelouge of sequences and structures.

[Joe]

+1 for Gene Myers/Bill Pearson

[gjacobs]

No one person, and of course there's always more you could add, e.g.

Russell Doolittle (lots of stuff, esp. evolutionary aspects of bioinformatics) + David Penny (have to add a fellow New Zealander!) Needleman, Wunsch, Sellers (early sequence alignment) Walter Fitch (early RNA structure prediction work) Roger Staden (Staden package), also the UWGCG package crowd David & Jane Richardson, VI Lim, George Rose (protein structure) Chou, Fasman and Robson (secondary structure prediction; widely used in it's day)

These just from the 60s and 70s; many more if I added more recent names. Free easter egg (just one I love to share!): in 1986 R Lewin wrote a paper entitled “The DNA databases are swamped” :-)

Answer 4

[i.sudbery]

Difficult question, but my personal list would definitely include:

Margaret Dayhoff (created the field)
Janet Thornton (head of the EBI at the time of the human genome project),
Richard Durbin,
Heng Li (Was a postdoc across the hall when I was doing my first NGS project, had just written MAQ and samtools),
James Bonfield (no staden package, no human genome)
Philip Green (ditto for phred, phrap and consed),
Wolfgang Huber (one of the earliest of the new breed of functional genomics bioinformaticians?),
Mike Eisen (hello? Biclustered heatmaps anyone?)
Gorden Smyth (of course),
Mike Love,

I'm sure there are loads more that I'm missing. The list above is probably revealing my career history...

[h.mon]

Great mentions to James Bonfield and Philip Green!

Answer 5

[Devon Ryan]

There are a lot of great suggestions, so I'll add "The bioconductor core team", because we'd mostly be lost without them. Among the core team members Martin Morgan really stands out as having facilitated huge amounts of what we now take for granted.

Answer 6

[Michael]

I think we really, really have to nominate Stephen Altschul for that list. He has co-authored one of the most influential (by citation) Bioinformatics tool, BLAST. In addition, he has popularized bioinformatics in general and through his work at NCBI helped to shape web-blast and make it the popular tool we have now. Indeed, the natural way in which we take blast and web-blast, and other applications and databases for granted justifies these honors. Certainly, the coupling of Genbank and other large databases with an efficient algorithm to search through them is what has made these tools so popular and indispensable for biological research. He, and of course the NCBI team, have thereby shaped the way we view web-applications in bioinformatics today and that long before any web 2.0,3,0,4.0 gimmicks. Simply, think about how much research this resource has enabled.

A lot of current achievements are actually team achievements, and this needs to certainly be pointed out in the context of this question. But there always have been some inspiring minds that are specifically influential.

Answer 7

[Friederike]

I very quickly run into the usual problem of "what's a bioinformatician?"

The first persons that came to mind were Hadley Wickham, Gordon Smyth, Rafa Irizarry, Wolfgang Huber, Timothy Bailey, Heng Li and then I ran into the next problem that was: most of their packages, that I use so much, are surely team efforts (think Aaron Lun, Mike Love, Simon Anders, Alicia Oshlack, Stephanie Hicks), and then the whole bioconductor infrastructure is so valuable....

[A. Domingues]

Alicia Oshlack in particular has been doing a lot of good stuff under the radar: bpipe, diffvar, missMethyl,and clustree.

Answer 8

[Joe]

I dunno if "Of all time" is OTT or not, but in terms of big, direct impact on how I work/what I do/have done:

• Peter Cock (among others) for BioPython. For I would be truly lost without it.
• Torsten Seeman for Prokka and just a generally solid, pragmatic approach for writing very usable bioinformatics software.
• Heng Li (duh).
• Elaine Meng/Tom Goddard/Eric Pettersen/Greg Couch (and others no doubt) - Slightly less conventionally perhaps, but no less invaluably to me these guys dilligently answer literally hundreds of queries on the UCSF Chimera user message boards, all the while actively developing the software and documentation etc.
• Sean Eddy et al.

I'll add more as they come to me.

Answer 9

[gaberoo]

Joe Felsenstein, without him there would be no "modern" likelihood-based phylogenetics.

[gaberoo]

Oh, and also Peter Schuster for pretty much developing energy landscape calculations for RNA folding. Maybe also add Manfred Eigen to this.

Answer 10

[jared.andrews07]

I'll throw Gary Stormo on the list, as he was largely responsible for bringing position weight matrices into play.

Peter Cock, for biopython, and generally just being a very helpful person.

Hadley Wickham.

Fernando Pérez and Brian Granger for coming up iPython (now better known as Jupyter, with support for a heck of a lot more than interactive Python analyses). Did a ton to make the field more accessible.

Bo Peng for taking it to the next level and creating a backend that allows for multiple kernels in the same notebook.

[gjacobs]

Thanks for adding Gary - should have nominated himself. I wanted to work with him in the late 80s, but couldn't find the money and ended up doing my PhD elsewhere.

Answer 11

[jean.elbers]

I would also like to nominate Brian Bushnell for the unbelievely useful BBTools/BBMap Suite.

[GenoMax]

@Brian is no doubt one of the best (if not the best) java programmers out there.

Answer 12

[Alex Reynolds]

Jim Kent and Shane Neph, for developing tools and algorithms that are either used directly or indirectly in their toolkits for whole-genome scale work, or reused by others in other toolkits.

Answer 13

[zx8754]

More subjective choice: Stephen Turner, his Getting Genetics Done blogs helped me to step into bio world.

This post is great, and lists most of the GBOATs:

• Getting Genetics Done: Staying Current in Bioinformatics & Genomics: 2017 Edition