The Oldest Bioinformatics Publication

Question

[Rajarshi Guha]

Hi, can anybody point me to the oldest (or maybe, seminal?) bioinformatics paper? A search of Pubmed gives me a paper from the early 90's but surely there's stuff older than that. Any pointers would be appreciated.

An update based on some comments below: I realized that the answers to this question depends on agreeing what bioinformatics is. Clearly, there are many ways to define the field; what I was hoping to find are the foundational papers (or regarded as such) that initiated core techniques in bioinformatics. Even then I realize it's an open ended question - so if nothing else, I'm happy to get subjective views of bioinformatics 'lore'

[Pierre Lindenbaum]

Somehow related to What Are The Classic Papers In Bioinformatics?

[Rajarshi Guha]

Indeed, just came across this. I was hoping that there would a (or a few) founding papers that are regarded as the starting point for the field. DB Searls paper provides a nice history

[Egon Willighagen]

If the definition of 'bioinformatics' is subjective, so is this question.

Answer 1

[Casey Bergman]

I think this depends on your definition of "bioinformatics".

Although Dayhoff's paper is arguable the oldest application of computers to sequence analysis, there are older publications in crystalography = structural bioinformatics, e.g.

J. M. Bennett and J. C. Kendrew Acta Cryst. (1952). 5, 109-116 The computation of Fourier synthesis with a digital electronic calculating machine.

This paper closes with a very prescient quote:

Digital machines have the great advantages of accuracy (which is becoming increasingly important in crystallography), and of versatility, which enables the capital cost and running expenses of a general-purpose digital machine to be shared among a number of users with very different problems to solve.

True still today nearly 60 years later.

[Rajarshi Guha]

Case, you're right this certainly depends on what is bioinforatics. In fact, I would regard this paper as a crystallography paper rather than a 'structural bioinformatics' paper. I'm actually not sure what 'structural bioinformatics' is? It sounds essentially like protein structure analysis?

[Casey Bergman]

Structural bioinformatics is the "analysis and prediction of the three-dimensional structure of biological macromolecules" (from wikipedia) and my understanding is that it includes predicting 3D protein structures from experimental data, homology, or primary sequence, as well as the analysis of structures (folds, domains, etc.). I'm no expert in this area, so indeed it may be that the computational aspects of crystallography are considered a distinct sub-discpline from structural bioinformatics by experts in the field.

Answer 2

[Pierre Lindenbaum]

Citing Mary: What Are The Classic Papers In Bioinformatics?

Dayhoff, M. O. and R. S. Ledley. Comprotein: A Computer Program to Aid Primary Protein Structure Determination. In Proceedings of the Fall Joint Computer Conference, 1962, 262-274. Santa Monica, CA: American Federation of Information Processing Societies, 1962.

http://doi.acm.org/10.1145/1461518.1461546

Answer 3

[Simon Cockell]

This fascinating overview of the field from Paulien Hogeweg (who apparently is credited with the origination of the term 'bioinformatics') has just popped into my Google Reader. It's a pretty good history lesson I think.

Hogeweg P, 2011 The Roots of Bioinformatics in Theoretical Biology. PLoS Comput Biol 7(3): e1002021. doi:10.1371/journal.pcbi.1002021

I recall the excitement when, in 1982, the first European Molecular Biology Laboratory sequence tape was delivered...

Answer 4

[Pierre Lindenbaum]

Another one: Alan Turing, 1951.

I've just received the following announcement:

[HTML]Fundamenta Informaticae 2012 : [Alan Turing year 2012] Watching the Daisies Grow: from biology to biomathematics and bioinformatics.[HTML]

In 1951 Alan Turing wrote a paper entitled [HTML]"The Chemical Basis of Morphogenesis"[HTML] in which he developed the reaction‐diffusion theory, which became one of the basic models of theoretical biology and is also considered a foundation of chaos theory.

The story started much earlier, in spring 1923, as documented by his mother in a caricature "Hockey or Watching the Daisies Grow". Crucial motif in the drawing is that, while most players are engaged by the game, Alan is investigating a flower emerging just off the field.

In his "Outline of the Development of a Daisy," Turing writes: "At a certain point in the development of the daisy the anatomical changes begin. From this point, as has been mentioned, it becomes hopelessly impracticable to follow the process mathematically...."

[Mary]

That is cool. What an interesting discussion this is.

Answer 5

[Dave Lunt]

I'm not 100% comfortable with defining this as bioinformatics, though some definitions are very broad, but I thought it might be interesting at least.

Edwards (2009) says "the first use of an electronic computer in biology was to tabulate the solution to a differential equation for Fisher (Fisher 1950)". Apparently Fisher had been using computers for population genetics work soon after the war. I heard Edwards speak about it and it sounded like this 1950 paper was not a one-off, rather he had been accessing this rare EDSAC machine regularly for problem solving duties for his group.

Fisher, R. A., 1950 Gene frequencies in a cline determined by selection and diffusion. Biometrics 6: 353–361.

[Casey Bergman]

Now we wander into the difference between bioinformatics and computational biology, which I do believe are distinct: http://rbaltman.wordpress.com/2009/02/18/bioinformatics-computational-biology-same-no/

[Jarretinha]

This paper is an application of numerical algorithm (maximum likelihood) to diffusion equations fitting, typical of population genetics. This is by no means different from other numerical applications. But, in a very broad sense, maybe . . .

[Dave Lunt]

Yes, I hope there is a difference between computational biology and/or bioinformatics and just using a computer as a big calculator. But here the waters start to get murky deciding what is a new approach and what just much more of the old techniques. Bioinformatics? Maybe not. But its an interesting piece of related historical trivia for your next lab pub trip.

[Egon Willighagen]

Don't think I agree with that... What Is Bioinformatics?