Thursday, November 6, 2014

Massive citations of bioinformatics in biology papers

For those of you who have missed it, the magazine Nature has recently looked at the 100 most highly cited science papers of all time (across all fields):
van Noorden R, Maher B, Nuzzo R (2014) The top 100 papers: Nature explores the most-cited research of all time. Nature 514: 550-553.
The list is dominated by biology papers, with biochemical laboratory techniques taking all of the top spots. However, it also worth noting that bioinformatics papers produce a very good showing, and so I have extracted 10 of them here.

If you have ever wondered what phylogenetic tree-building method is most used then it is at #20, while the most-used tree-building program is at #45 (having got there in only 7 years). You may also wonder why sequence alignment programs (#10 & #28 for Clustal; #12 & #14 for BLAST) do much better than tree-building programs (#45 for MEGA; #75 for GCG; #100 for MrBayes).

As for journals, the papers appeared in Nucleic Acids Research (4), Molecular Biology & Evolution (2), Bioinformatics (2), Journal of Molecular Biology (1) and Evolution (1). This list only partially matches their Journal Citation Reports current 5-Year Impact Factors: 8.378, 10.494, 6.968, 3.795 and 5.469, respectively.

Rank: 10 Citations: 40,289
Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson, J. D., Higgins, D. G. & Gibson, T. J
Nucleic Acids Res. 22, 4673–4680 (1994).

Rank: 12 Citations: 38,380
Basic local alignment search tool.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J.
J. Mol. Biol. 215, 403–410 (1990).

Rank: 14 Citations: 36,410
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs.
Altschul, S. F. et al.
Nucleic Acids Res. 25, 3389–3402 (1997).

Rank: 20 Citations: 30,176
The neighbor-joining method: A new method for reconstructing phylogenetic trees.
Saitou, N. & Nei, M.
Mol. Biol. Evol. 4, 406–425 (1987).

Rank: 28 Citations: 24,098
The CLUSTAL_X Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G.
Nucleic Acids Res. 25, 4876–4882 (1997).

Rank: 41 Citations: 21,373
Confidence limits on phylogenies: an approach using the bootstrap.
Felsenstein, J.
Evolution 39, 783–791 (1985).

Rank: 45 Citations: 18,286
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura, K., Dudley, J., Nei, M. & Kumar, S.
Mol. Biol. Evol. 24, 1596–1599 (2007).

Rank: 75 Citations: 14,226
A comprehensive set of sequence analysis programs for the VAX.
Devereux, J., Haeberli, P. & Smithies, O.
Nucleic Acids Res. 12, 387–395 (1984).

Rank: 76 Citations: 14,099
MODELTEST: Testing the model of DNA substitution.
Posada, D. & Crandall, K. A.
Bioinformatics 14, 817–818 (1998).

Rank: 100 Citations: 12,209
MrBayes 3: Bayesian phylogenetic inference under mixed models.
Ronquist, F. & Huelsenbeck, J. P.
Bioinformatics 19, 1572–1574 (2003).

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