Protein Research

Publication Analysis 1998-2009
by Ralf Neumann, Labtimes 05/2011



Europe... ... and the World Most Cited Authors... ... and Papers

Most Cited Authors - Pictures



Lysozyme with different precipitants (K. Kahn, UC Santa Barbara)

Germany heads European protein research by total number of articles and overall citations. Top topics were proteomics and its bioinformatical data analysis as well as protein 3D structure analysis and protein folding.

“Major building blocks of life”, “chief actors within the cell”, “controllers of virtually all biological processes”, “executive agents that carry out all processes in a cell”,... That’s only a small glimpse into the many quotes trying to describe the outstanding role of proteins in cellular life. Therefore it is no wonder that proteins, for example, make up half the dry weight of an Escherichia coli cell, whereas other macromolecules, such as DNA and RNA, make up only 3% and 20%, respectively. And indeed, there is virtually no cellular structure, process or function without the involvement of a protein: enzymatic reactions, sensing and signalling, ligand binding, molecule transport and translocation, regulation and integration, shaping and structuring cell components, ... and many more.

This fact, however, is the crux of our publication analysis as there are very few life scientists who do not have to deal with any protein(s) at all in their research. However, is this enough to treat all of them as qualified “protein researchers”? Certainly not!

Thus, in order for a given scientist to be included in our publication analysis “protein research”, it doesn’t suffice if he studies the role of one or just a few proteins in a certain, well-defined biological process. If, for example, somebody investigates the mechanism, by which a handful of proteins mediate axon guidance, his main interest is centred on certain aspects of neural development but not so much on understanding how proteins work per se.

Blocks, actors and controllers

So where do we draw the line? Simply put, the respective researchers should represent some sort of protein generalists. That means one should be concerned with general aspects of protein structure and function, methodology of protein analysis, protein synthesis and degradation, whole proteome analysis, or something similar. And which kind of researcher was thus only just accepted? For example, people who, on a broad scale, analyse the special features of one of the bigger protein families, as for instance, Philip Cohen (8th in the “Most Cited Authors”-list, see Table on page 50) does with protein kinases.

High average citation rates

In addition to this demarcation issue regarding research content, our publication analysis also faced some inevitable methodological constraints. In order to compare performance of individual European countries in protein research (as shown in the “blue” Table on p. 49), we had to restrict the study to 103 explicit “protein journals” selected from the categories “Biochemistry & Molecular Biology” and “Biochemical Research Methods” of Thomson Reuter’s database Web of Science used for this analysis. Certainly, many of the “top papers” in protein research are published in multidisciplinary science journals like Nature, Science or Proc. Natl. Acad. Sci. Regrettably, however, we had to omit them, at least from this part of the analysis, because Web of Science doesn’t provide any reliable tools to automatically extract relevant protein research articles from those multidisciplinary journals. And before assigning too many “false positives” to the individual countries, we decided to restrict this analysis to the specialist journals only. Nevertheless, we believe that such a “trimmed” survey still provides sufficiently valid indicators for the countries’ overall productivity in protein research.

However, as for the rankings of the most-cited researchers and papers (see Tables, p. 50) no such limitations existed. They could be analysed from publications in all journals.

What were the most striking results? Germany is Europe’s number one in terms of overall number of articles published in the protein journals between 1998 and 2009. England, the European leader in many other biomedical disciplines, this time only reached second place. Moreover, this order still persists when it comes to the total number of citations of those articles to-date – Germany even outperformed England by almost 100,000 citations.

No surprise in the following position, the third-highest number of citations was achieved by France. Clearly “better than usual”, in comparison to most other biomedical disciplines, performed Switzerland (5th position by total citations), Scotland (9th) and Russia (15th).

Very high mean citation rates catch one’s eye immediately. Most of the European top twenty nations achieved rates between 22 and 31 citations per article on average – which is considerably higher than in all other biomedical fields besides “Molecular Genetics & Genomics” (Lab Times 5-2010: 46-8). European leaders in this respect are Scotland and Switzerland (31.3 and 30.2 citations per article), followed by England (29.2).

One of the consequences is that the all-European average citation rate in protein research outnumbered that of their US colleagues (22.4 vs. 20.6). Nevertheless, the USA collected a higher number of total citations due to producing more articles in the protein journals between 1998 and 2009 (204,000 vs. 168,000). In addition, Canada performed markedly strong by producing more “protein articles” than any European country and almost matching the German result in terms of overall citations.

Why not all at once?

When turning to the lists of the most-cited heads and papers of the years 1998-2009, one thing immediately becomes apparent: Both lists strongly mirror the recent trend of “Why do only some proteins, if you can have all of them at once?” No doubt, the advent of proteomics has changed protein research profoundly as, like in genomics, one of the most crucial factors has become the development of methods and tools to generate, organise and analyse huge datasets. Accordingly, the four most-cited “protein papers” describe bioinformatical tools to graphically model structural protein data or to specifically analyse protein sequence databases.

This trend is also apparent in the list of the 30 most-cited European protein researchers headed by the two proteomics pioneers Matthias Mann, Martinsried, and Ruedi Aebersold, Zurich, followed by computational biologist Peer Bork, EMBL Heidelberg. In total, half of the top 30 can be attributed to the field of proteomics and computational protein biology.

What are the remaining topics represented by the other authors in the list? Apart from some “loners”, such as Philip Cohen (8th, protein phosphorylation), Aaron Ciechanover (20th, protein degradation) or Michel Lazdunski (21st, channel and receptor proteins), two further big topics emerge: the elucidation of three-dimensional protein structures, as represented by Dino Moras (5th), Martin Karplus (6th) and others, and the dynamics and regulation of protein folding including protagonists like Christopher Dobson (4th), Vladimir Uversky (19th) and Alan Fersht (23rd).

So it seems that those are the topics you should, as a young protein researcher, aim to work on if you want to be maximally cited. However, as we all know, this isn’t automatically a synonym for good or even brilliant research.




Method

Articles appearing between 1998 and 2009 in ‘protein journals’ as listed by Thomson Reuters’ Web of Science under ‘Biochemistry & Molecular Biology’ and ‘Biochemical Research Methods’. The citation numbers are accurate as of July 2011. A country’s figures are derived from articles, where at least one author working in the respective European nation is included in the authors’ list. Israel is included because it is a member of many European research organisations and programmes (EMBO, FP7 of the EU...).

Citations of articles published between 1998 and 2009 were recorded up until July 2011 using the Web of Science database from Thomson Reuters. The “most-cited papers” had correspondence addresses in Europe or Israel.





Europe...

Country Citations Articles Cit./Art.
1.Germany878.33034.38225,5
2.England784.39526.82029,2
3.France573.27423.99323,9
4.Italy323.35616.52419,6
5.Switzerland263.8388.73430,2
6.Sweden250.4389.56226,2
7.Spain244.00112.04320,3
8.Netherlands226.9138.29527,4
9.Scotland141.1154.50531,3
10.Israel130.4544.80227,2
11.Belgium130.2535.35624,3
12.Denmark129.3054.82626,8
13.Austria95.3294.21022,6
14.Russia79.6257.36610,8
15.Finland71.2892.96024,1
16.Poland61.8795.42811,4
17.Hungary44.4633.14214,2
18.Ireland42.1081.82723,1
19.Norway41.6151.87322,2
20.Czech Rep.39.8052.99613,3



... and the World

Citations Articles Cit./Art.
Europe3.770.526168.06622,4
USA4.213.969204.17120,6
Canada876.27440.81321,5
Japan420.01421.02620,0
Australia227.99822.15610,3
China191.6738.30223,1
New Zealand131.66510.08913,1



Most Cited Authors...

Citations Articles
1.Matthias Mann, Max Planck-Inst. (MPI) Biochem. Martinsried37.178287
2.Ruedi Aebersold, Mol. Syst. Biol. ETH Zurich33.497288
3.Peer Bork, Europ. Mol. Biol. Lab. Heidelberg / MDC Berlin33.080242
4.Christopher M. Dobson, Chem. Univ. Cambridge21.553271
5.Dino Moras, Struct. Biol. Inst. Genet. and Cell. & Mol. Biol. Illkirch/F19.515313
6.Martin Karplus, Biophys. Chem. Univ. Strasbourg (& Harvard Univ.) 17.263218
7.Rolf Apweiler, EMBL-Europ. Bioinform. Inst. (EBI) Hinxton16.341142
8.Philip Cohen, MRC Protein Phosphoryl. Unit Univ. Dundee16.244134
9.Michael Nilges, Struct. Biol. & Chem. Pasteur Inst. Paris16.01880
10.Piet Gros, Bijvoet Ctr. Biomol. Res. Univ. Utrecht15.58259
11.Gunnar von Heijne, Ctr. Biomembrane Res. Stockholm Univ.15.398126
12.Thomas Simonson, Biochem. Ecole Polytech.CNRSPalaiseau/F14.90946
13.Dario R. Alessi, MRC Protein Phosphoryl. Unit Univ. Dundee14.431125
14.Robert Huber, MPI Biochem. Martinsried (& Univ. Duisb.-Essen)14.037310
15.Søren Brunak, Integr. Syst. Biol. Tech. Univ. Denmark Lyngby12.939106
16.Amos Bairoch, Swiss Inst. Bioinformatics Geneva12.66074
17.Alex Bateman, Wellcome Trust Sanger Inst. Hinxton12.32956
18.Eric L.L. Sonnhammer, Stockholm Bioinformat. Ctr. Stockholm Univ.11.44764
19.Vladimir N. Uversky, Russ. Acad. Sci. Pushchino (& USA)11.049221
20.Aaron Ciechanover, Biochem. Technion-Israel Inst. Technol. Haifa10.98080
21.Michel Lazdunski, Mol. & Cell. Pharmacol. Univ. Nice Valbonne9.705147
22.Andreas Engel, Struct. Biol. Biozentrum Univ. Basel9.431177
23.Alan R. Fersht, MRC Lab. Mol. Biol.Cambridge9.366189
24.Peter Roepstorff, Biochem. & Mol. Biol. Univ. S. Denmark Odense9.310213
25.Janet M. Thornton, EMBL-Europ. Bioinform. Inst. (EBI) Hinxton8.986176
26.F. Ulrich Hartl, Max Planck-Inst. Biochem. Martinsried8.86385
27.Andrej Shevchenko, MPI Mol. Cell. Biol. & Gen. Dresden8.846118
28.Toby J. Gibson, European Mol. Biol. Lab. Heidelberg8.74441
29.Ruth Nussinov, Human Genet. Sackler Inst. Mol. Med.Tel Aviv Univ.8.729246
30.Bernd Bukau, Ctr. Mol. Biol. Univ. Heidelberg8.597100



... and Papers

Citations
1.Emsley, P; Cowtan, K
Coot: model-building tools for molecular graphics.
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 60: 2126-2132 Part 12 Sp. Iss. 1 DEC 2004
6.376
2.Perkins, DN; Pappin, DJC; Creasy, DM; Cottrell, JS
Probability-based protein identification by searching sequence databases using mass spectrometry data.
ELECTROPHORESIS, 20 (18): 3551-3567 DEC 1999
3.022
3.Bendtsen, JD; Nielsen, H; von Heijne, G; Brunak, S
Improved prediction of signal peptides: SignalP 3.0.
JOURNAL OF MOLECULAR BIOLOGY, 340 (4): 783-795 JUL 16 2004
2.861
4.Larkin, MA; Blackshields, G; [...]; Thompson, JD; Gibson, TJ; Higgins, DG
Clustal W and clustal X version 2.0.
BIOINFORMATICS, 23 (21): 2947-2948 NOV 1 2007
2.697
5.Davies, SP; Reddy, H; Caivano, M; Cohen, P
Specificity and mechanism of action of some commonly used protein kinase inhibitors.
BIOCHEMICAL JOURNAL, 351: 95-105 Part 1 OCT 1 2000
2.605




Last Changed: 31.03.2012




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