The Institute’s most cited papers

Frequently cited papers have a great impact on further development in a field, including the further application of results in practice. Citation rate is therefore one of the basic parameters used to assess the significance of a scientific paper. Good scientists are those who produce frequently cited papers, and top-quality institutions are recognized by their proportion to the most cited papers in a country.

Since the citation rates vary by field, one should compare institutions working in similar fields. This applies to our analysis, in which the institutions of the Academy of Sciences of the Czech Republic belonging to the same section are close with regard to field.

A paper can be produced either by a single team or in cooperation by two or more teams. The parent team, i.e. the team by which a major part of the research paper was produced, is usually distinguished by corresponding author. In the vast majority of cases, the first author is from the same team as the corresponding author. In our analysis, own papers of a particular country, organization or team are those which have a corresponding author from that particular country, organization or team. Own papers are important, as they reflect the ability of our scientists to make a significant discovery and publish the result in a prestigious journal.

An analysis of the most cited own papers is one possible approach that allows us to evaluate the quality of research, but its result may not give a complete picture of the performance of a particular team or institution. Papers produced in cooperation with other scientists (particularly with scientists from abroad) are usually cited more frequently. For example, only 20 out of 100 most-cited papers in which the Czech Republic has participated over the last five years have had a corresponding author from the Czech Republic. Understandably, an author’s contribution to a paper produced in a foreign laboratory can be more significant than a paper produced in the Czech Republic. However, the contribution of a Czech author to such a paper can be very low, being merely part of his/her stay abroad. Although the paper of such an author can be highly cited, this does not reflect the author’s ability to do scientific research and produce high-quality papers in his/her laboratory in the Czech Republic. This is well documented by the author’s own papers.

We have performed an analysis of the most cited own papers of the Czech Republic to see how many papers out of the first 100 papers published each year are from our Institute. Due to the dynamics of the citation rate over time, it is necessary to compare the citation rates of papers produced in the same year. Let’s look at the most cited papers to which Czech authors contributed in individual years. The papers of Czech authors found on the WoS for each year (only “Article” or “Review” type papers were considered) were ranked according to the parameter “Times cited,” and the 500 most cited papers were saved in the “Marked” list. After conversion into Excel, we have identified papers in which the corresponding author was from the Czech Republic (searching for “Czech Republic” in the RP column), and selected the 100 most cited papers. This step may not be correct in some cases since some papers can have more corresponding authors, although the WoS will only indicate one corresponding author (who may be less important). However, our experience shows that such cases are not numerous. By using this approach, 1,000 papers published in the period from 2000 to 2009 were selected and used in further evaluation (citation rates have been relatively low over the last few years, and may show slight changes over time).

Participation of the Academy of Sciences of the Czech Republic in such papers is approximately 50% (524 papers). The list below presents the distribution of individual institutions (see Figure). The upper part of the figure shows the distribution of the most cited papers among the institutes, regardless of the institute’s size, whereas the lower part of Figure presents the numbers of the most cited papers normalized to the number of institute’s employees (based on the Annual Report of the Academy of Sciences). It follows from the Figure that the performance of the Institute of Biophysics is one of the highest compared to other institutes of the Academy of Sciences of the Czech Republic, and significantly exceeds the level of performance in other institutes from the same section (Section 5 – extended segments).

The following table shows the numbers of papers, the mean citation rates for the 100 most cited own papers of the Czech Republic, and the number of papers by the Institute of Biophysics among the 100 most cited own papers of the Czech Republic.

Table 1The number of papers (“article” or “review” types) of the Czech Republic published in the period from 2000 - 2010, mean citation rates for the 100 most cited own papers of the Czech Republic, and the contribution of scientists from the Institute of Biophysics to the 100 most cited own papers.

YEAR	2000	2001	2002	2003	2004	2005	2006	2007	2008	2009
The number of papers of the Czech Republic	3585	3835	3946	4129	4522	4659	5464	6334	7155	7694
The mean citation rate for the 100 most cited own papers of the Czech Republic	84	67	80	75	61	54	55	34	26	9.8
The contribution of the Institute of Biophysics to the 100 most cited own papers of the Czech Republic	3/100	3/100	8/100	8/100	6/100	6/100	5/100	3/100	5/100	5/100

Note: Citation rates in 2009 are still quite low and consequently the contribution of the Institute of Biophysics to the 100 most cited papers may change over time.

It follows from the Table that the number of papers to which the Czech Republic has contributed shows an increasing trend. A decline in the citation rate is due to a shorter period of time since the paper was published. In spite of double competition, the number of papers by the Institute of Biophysics among the most cited papers has remained approximately the same over the last years, being still markedly high with regard to the size of the Institute of Biophysics.

According to the Report on Research and Development of the Czech Statistical Office, the annual costs for basic research in the Czech Republic amount to 16 billion Czech crowns. The budget of the Institute of Biophysics is approximately 120 million Czech crowns per year (50% subsidies/50% grants). On the assumption that the performance of all research teams in the Czech Republic is the same, the probability that a paper produced by the Institute of Biophysics will rank among the 100 best papers would be 0.75%. Therefore, it follows from the Table that the performance of the Institute of Biophysics in terms of producing top-quality results is seven times higher than the average in the Czech Republic.

Initially, only some of the Institute’s departments were involved in such papers. Now, all departments have improved and published their own papers, among the best over the last five years since the Institute started to evaluate the performance of its teams on a regular basis.

The most cited, original papers by the Institute of Biophysics of the Academy of Sciences of the Czech Republic (Biofyzikální ústav AV ČR, v.v.i.) in individual years (the status as per 6 August 2010):

2009

• Kejnovsky, E., Hobza, R., Cermak, T., Kubat, Z., Vyskot, B. (2009), The role of repetitive DNA in structure and evolution of sex chromosomes in plants, HEREDITY 102, 533-541 [AIS=1.586, IF=4.122 V]
• Kypr, J., Kejnovska, I., Renciuk, D., Vorlickova, M. (2009), Circular dichroism and conformational polymorphism of DNA, NUCLEIC ACIDS RESEARCH 37, 1713-1725 [AIS=3, IF=7.48 V]
• Fadrna, E., Spackova, N., Sarzynska, J., Koca, J., Orozco, M., Cheatham, TE., Kulinski, T., Sponer, J. (2009), Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 5, 2514-2530 [AIS=1.731, IF=4.804 V]
• Novakova, O., Nazarov, AA., Hartinger, CG., Keppler, BK., Brabec, V. (2009), DNA interactions of dinuclear Ru-II arene antitumor complexes in cell-free media, BIOCHEMICAL PHARMACOLOGY 77, 364-374 [AIS=1.166, IF=4.254 V]

2008

• Cahova, H., Havran, L., Brazdilova, P., Pivonkova, H., Pohl, R., Fojta, M., Hocek, M. (2008), Aminophenyl- and nitrophenyl-labeled nucleoside triphosphates: Synthesis, enzymatic incorporation, and electrochemical detection, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 47, 2059-2062 [AIS=3.296, IF=11.829 V]
• Bartova, E., Krejci, J., Harnicarova, A., Kozubek, S. (2008), Differentiation of human embryonic stem cells induces condensation of chromosome territories and formation of heterochromatin protein 1 foci, DIFFERENTIATION 76, 24-32 [AIS=1.248, IF=3.311 V]
• Palecek, E., Ostatna, V., Masarik, M., Bertoncini, CW., Jovin, TM. (2008), Changes in interfacial properties of alpha-synuclein preceding its aggregation, ANALYST 133, 76-84 [AIS=0.93, IF=3.272 V]
• Bartova, E., Krejci, J., Harnicarova, A., Galiova, G., Kozubek, S. (2008), Histone modifications and nuclear architecture: A review, JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY 56, 711-721 [AIS=0.909, IF=2.372 V]
• Ciz, M., Pavelkova, M., Gallova, L., Kralova, J., Kubala, L., Lojek, A. (2008), The influence of wine polyphenols on reactive oxygen and nitrogen species production by murine macrophages RAW 264.7, PHYSIOLOGICAL RESEARCH 57, 393-402 [AIS=0.41, IF=1.43 V]

2007

• Fojta, M., Kostecka, P., Trefulka, MR., Havran, L., Palecek, E. (2007), Multicolor electrochemical labeling of DNA hybridization probes with osmium tetroxide complexes, ANALYTICAL CHEMISTRY 79, 1022-1029 [AIS=1.49, IF=5.214 V]
• Palecek, E., Fojta, M. (2007), Magnetic beads as versatile tools for electrochemical DNA and protein biosensing, TALANTA 74, 276-290 [AIS=0.74, IF=3.29 V]
• Palecek, E., Ostatna, V. (2007), Electroactivity of nonconjugated proteins and peptides. Towards electroanalysis of all proteins, ELECTROANALYSIS 19, 2383-2403 [AIS=0.615, IF=2.63 V]

2006

• Brabec, V., Novakova, O. (2006), DNA binding mode of ruthenium complexes and relationship to tumor cell toxicity, DRUG RESISTANCE UPDATES 9, 111-122 [AIS=2.48, IF=12.581 V]
• Spackova, N., Sponer, J. (2006), Molecular dynamics simulations of sarcin-ricin rRNA motif, NUCLEIC ACIDS RESEARCH 34, 697-708 [AIS=3, IF=7.48 V]
• Sponer, J., Jurecka, P., Marchan, I., Luque, FJ., Orozco, M., Hobza, P. (2006), Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps, CHEMISTRY-A EUROPEAN JOURNAL 12, 2854-2865 [AIS=1.593, IF=5.382 V]
• Krasovska, MV., Sefcikova, J., Reblova, K., Schneider, B., Walter, NG., Sponer, J. (2006), Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme, BIOPHYSICAL JOURNAL 91, 626-638 [AIS=1.917, IF=4.39 V]
• Bartova, E., Kozubek, S. (2006), Nuclear architecture in the light of gene expression and cell differentiation studies, BIOLOGY OF THE CELL 98, 323-336 [AIS=1.657, IF=3.974 V]

2005

• Brabec, V., Kasparkova, J. (2005), Modifications of DNA by platinum complexes - Relation to resistance of tumors to platinum antitumor drugs, DRUG RESISTANCE UPDATES 8, 131-146 [AIS=2.48, IF=12.581 V]
• Vorlickova, M., Chladkova, J., Kejnovska, I., Fialova, M., Kypr, J. (2005), Guanine tetraplex topology of human telomere DNA is governed by the number of (TTAGGG) repeats, NUCLEIC ACIDS RESEARCH 33, 5851-5860 [AIS=3, IF=7.48 V]
• Bartova, E., Pachernik, J., Harnicarova, A., Kovarik, A., Kovarikova, M., Hofmanova, J., Skalnikova, M., Kozubek, M., Kozubek, S. (2005), Nuclear levels and patterns of histone H3 modification and HP1 proteins after inhibition of histone deacetylases, JOURNAL OF CELL SCIENCE 118, 5035-5046 [AIS=3.251, IF=6.144 V]
• Skalicka, K., Lim, KY., Matyasek, R., Matzke, M., Leitch, AR., Kovarik, A. (2005), Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco, NEW PHYTOLOGIST 166, 291-303 [AIS=2.07, IF=6.03 V]
• Razga, F., Koca, J., Sponer, J., Leontis, NB. (2005), Hinge-like motions in RNA kink-turns: The role of the second A-minor motif and nominally unpaired bases, BIOPHYSICAL JOURNAL 88, 3466-3485 [AIS=1.917, IF=4.39 V]
• Kovarik, A., Pires, JC., Leitch, AR., Lim, KY., Sherwood, AM., Matyasek, R., Rocca, J., Soltis, DE., Soltis, PS. (2005), Rapid concerted evolution of nuclear ribosomal DNA in two tragopogon allopolyploids of recent and recurrent origin, GENETICS 169, 931-944 [AIS=0.973, IF=2.416 V]

2004

• Vyskot, B., Hobza, R. (2004), Gender in plants: sex chromosomes are emerging from the fog, TRENDS IN GENETICS 20, 432-438 [AIS=4.41, IF=8.69 V]
• Sponer, J., Jurecka, P., Hobza, P. (2004), Accurate interaction energies of hydrogen-bonded nucleic acid base pairs, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 126, 10142-10151 [AIS=2.701, IF=8.58 V]
• Fojta, M., Havran, L., Vojtiskova, M., Palecek, E. (2004), Electrochemical detection of DNA triplet repeat expansion, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 126, 6532-6533 [AIS=2.701, IF=8.58 V]
• Palecek, E., Masarik, M., Kizek, R., Kuhlmeier, D., Hassmann, J., Schulein, J. (2004), Sensitive electrochemical determination of unlabeled MutS protein and detection of point mutations in DNA, ANALYTICAL CHEMISTRY 76, 5930-5936 [AIS=1.49, IF=5.214 V]
• Fadrna, E., Spackova, N., Stefl, R., Koca, J., Cheatham, TE., Sponer, J. (2004), Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations, BIOPHYSICAL JOURNAL 87, 227-242 [AIS=1.917, IF=4.39 V]
• Kovarik A, Matyasek R, Lim KY, Skalicka K, Koukalova B, Knapp S, Chase M, Leitch AR (2004), Concerted evolution of 18-5.8-26S rDNA repeats in Nicotiana allotetraploids, BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY [AIS=2.04, IF=0.991 V]

2003

• Novakova, O., Kasparkova, J., Malina, J., Natile, G., Brabec, V. (2003), DNA-protein cross-linking by trans-[PtCl2(E-iminoether)(2)]. A concept for activation of the trans geometry in platinum antitumor complexes, NUCLEIC ACIDS RESEARCH 31, 6450-6460 [AIS=3, IF=7.48 V]
• Kasparkova, J., Novakova, O., Marini, V., Najajreh, Y., Gibson, D., Perez, JM., Brabec, V. (2003), Activation of trans geometry in bifunctional mononuclear platinum complexes by a piperidine ligand - Mechanistic studies on antitumor action, JOURNAL OF BIOLOGICAL CHEMISTRY 278, 47516-47525 [AIS=2.223, IF=5.328 V]
• Reblova, K., Spackova, N., Stefl, R., Csaszar, K., Koca, J., Leontis, NB., Sponer, J. (2003), Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E, BIOPHYSICAL JOURNAL 84, 3564-3582 [AIS=1.917, IF=4.39 V]
• Kasparkova, J., Marini, V., Najajreh, Y., Gibson, D., Brabec, V. (2003), DNA binding mode of the cis and trans geometries of new antitumor nonclassical platinum complexes containing piperidine, piperazine, or 4-picoline ligand in cell-free media. Relations to their activity in cancer cell lines, BIOCHEMISTRY 42, 6321-6332 [AIS=1.315, IF=3.226 V]
• Skalicka, K., Lim, KY., Matyasek, R., Koukalova, B., Leitch, AR., Kovarik, A. (2003), Rapid evolution of parental rDNA in a synthetic tobacco allotetraploid line, AMERICAN JOURNAL OF BOTANY 90, 988-996 [AIS=1.339, IF=2.684 V]
• Sponer, J., Hobza, P. (2003), Molecular interactions of nucleic acid bases. A review of quantum-chemical studies, COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS 68, 2231-2282 [AIS=0.208, IF=0.856 V]

2002

• Brabec, V., Kasparkova, J. (2002), Molecular aspects of resistance to antitumor platinum drugs, DRUG RESISTANCE UPDATES 5, 147-161 [AIS=2.48, IF=12.581 V]
• Jelen, F., Yosypchuk, B., Kourilova, A., Novotny, L., Palecek, E. (2002), Label-free determination of picogram quantities of DNA by stripping voltammetry with solid copper amalgam or mercury electrodes in the presence of copper, ANALYTICAL CHEMISTRY 74, 4788-4793 [AIS=1.49, IF=5.214 V]
• Kozubek, S., Lukasova, E., Jirsova, P., Koutna, I., Kozubek, M., Ganova, A., Bartova, E., Falk, M., Pasekova, R. (2002), 3D Structure of the human genome: order in randomness, CHROMOSOMA 111, 321-331 [AIS=2.272, IF=4.979 V]
• Palecek, E., Kizek, R., Havran, L., Billova, S., Fojta, M. (2002), Electrochemical enzyme-linked immunoassay in a DNA hybridization sensor, ANALYTICA CHIMICA ACTA 469, 73-83 [AIS=0.855, IF=3.757 V]
• Marini, V., Kasparkova, J., Novakova, O., Scolaro, LM., Romeo, R., Brabec, V. (2002), Biophysical analysis of natural, double-helical DNA modified by a dinuclear platinum(II) organometallic compound in a cell-free medium, JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY 7, 725-734 [AIS=1.195, IF=3.415 V]
• Palecek, E., Billova, S., Havran, L., Kizek, R., Miculkova, A., Jelen, F. (2002), DNA hybridization at microbeads with cathodic stripping voltammetric detection, TALANTA 56, 919-930 [AIS=0.74, IF=3.29 V]
• Palecek, E. (2002), Past, present and future of nucleic acids electrochemistry, TALANTA 56, 809-819 [AIS=0.74, IF=3.29 V]
• Fojta, M. (2002), Electrochemical sensors for DNA interactions and damage, ELECTROANALYSIS 14, 1449-1463 [AIS=0.615, IF=2.63 V]
• Palecek, E., Jelen, F. (2002), Electrochemistry of nucleic acids and development of DNA sensors, CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY 32, 261-270 [AIS=0.922, IF=2.621 V]
• Brabec, V. (2002), DNA modifications by antitumor platinum and ruthenium compounds: Their recognition and repair, PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY, VOL 71 71, 1-68 [AIS=2.69, IF=2.29 V]

2001

• Palecek, E., Fojta, M. (2001), Detecting DNA hybridization and damage, ANALYTICAL CHEMISTRY 73, 74A-83A [AIS=1.49, IF=5.214 V]
• Kizek, R., Trnkova, L., Palecek, E. (2001), Determination of metallothionein at the femtomole level by constant current stripping chronopotentiometry, ANALYTICAL CHEMISTRY 73, 4801-4807 [AIS=1.49, IF=5.214 V]

2000

• Kasparkova, J., Farrell, N., Brabec, V. (2000), Sequence specificity, conformation, and recognition by HMG1 protein of major DNA interstrand cross-links of antitumor dinuclear platinum complexes, JOURNAL OF BIOLOGICAL CHEMISTRY 275, 15789-15798 [AIS=2.223, IF=5.328 V]
• Trantirek, L., Stefl, R., Vorlickova, M., Koca, J., Sklenar, V., Kypr, J. (2000), An A-type double helix of DNA having B-type puckering of the deoxyribose rings, JOURNAL OF MOLECULAR BIOLOGY 297, 907-922 [AIS=2.051, IF=3.871 V]
• Brabec, V., Neplechova, K., Kasparkova, J., Farrell, N. (2000), Steric control of DNA interstrand cross-link sites of trans platinum complexes: specificity can be dictated by planar nonleaving groups, JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY 5, 364-368 [AIS=1.195, IF=3.415 V]