CiteULike: Tag citation

Clustering and identifying temporal trends in document databases

A Popescul — 2006-07-27T23:35:24-00:00

Advances in Digital Libraries, 2000. ADL 2000. Proceedings. IEEE (2000), pp. 173-182.

We introduce a simple and efficient method for clustering and identifying temporal trends in hyper-linked document databases. Our method can scale to large datasets because it exploits the underlying regularity often found in hyper-linked document databases. Because of this scalability, we can use our method to study the temporal trends of individual clusters in a statistically meaningful manner. As an example of our approach, we give a summary of the temporal trends found in a scientific literature database with thousands of documents

Citation Generators: Generating Bibliographies for the Next Generation

Jane Kessler — 2005-08-01T12:24:33-00:00

The Journal of Academic Librarianship, Vol. In Press, Corrected Proof

Librarians are frequently consulted about proper citation formats and support the use of PC-based personal bibliographic citation management programs, such as EndNote, often used by faculty and graduate students. Recently, free or inexpensive Web-based tools have been developed that create citations and format bibliographies. An analysis of citations generated by these programs shows that they are as accurate as EndNote and offer some advantages to undergraduates, but that some knowledge of proper citation formats is necessary to use these programs effectively.

Deciphering citation statistics.

2008-06-02T15:50:30-00:00

Nature neuroscience, Vol. 11, No. 6. (June 2008)

Do open access articles have greater citation impact?: A critical review of the literature

Iain Craig — 2008-05-13T13:23:41-00:00

Journal of Informetrics, Vol. 1, No. 3. (July 2007), pp. 239-248.

The last few years have seen the emergence of several open access options in scholarly communication which can broadly be grouped into two areas referred to as [`]gold' and [`]green' open access (OA). In this article we review the literature examining the relationship between OA status and citation counts of scholarly articles. Early studies showed a correlation between the free online availability or OA status of articles and higher citation counts, and implied causality without due consideration of potential confounding factors. More recent investigations have dissected the nature of the relationship between article OA status and citations. Three non-exclusive postulates have been proposed to account for the observed citation differences between OA and non-OA articles: an open access postulate, a selection bias postulate, and an early view postulate. The most rigorous study to date (in condensed matter physics) showed that, after controlling for the early view postulate, the remaining difference in citation counts between OA and non-OA articles is explained by the selection bias postulate. No evidence was found to support the OA postulate per se; i.e. article OA status alone has little or no effect on citations. Further studies using a similarly rigorous approach are required to determine the generality of this finding.

Neural network ensemble pruning using sensitivity measure in web applications

Patrick Chan — 2008-01-26T09:04:47-00:00

Systems, Man and Cybernetics, 2007. ISIC. IEEE International Conference on (2007), pp. 3051-3056.

Multiple Classifier Systems (MCSs) have been shown theoretically and empirically to outperform a single classifier in many applications. However, many ensemble training algorithms sometimes create a very large MCS which is combined by many individual classifiers. A large MCS not only consumes computational resources but also decreases the effectiveness. One of the solutions is the pruning method. It reduces the number of individual classifiers inside an MCS that maintains the performance well or is just slightly worse than the original one. In this paper, a new pruning method, called NNEPSM, for Neural Network ensemble based on a sensitivity measure is proposed. The classifiers which have less impact to the final output of MCS will be removed. The advantages of this method include efficient performance, low-complexity and independence on training method. NNEPSM has been applied in Web applications and other benchmark dataset. The experimental results showed that our approach performs well using different datasets.

Using Data Mining to Enhance Automated Planning and Scheduling

J Frank — 2007-12-27T21:03:56-00:00

Computational Intelligence and Data Mining, 2007. CIDM 2007. IEEE Symposium on (2007), pp. 251-260.

Automated planning is a combinatorial problem that is important to many NASA endeavors, including ground operations and control applications for unmanned and manned space flight. There is significant value to integrating planning and data mining to create better planners. We describe current work in this area, covering uses of data mining to speed up planners, improve the quality of plans returned by planners, and learn domain models for automated planners. The central contribution of this paper is a snap shot of the state of the art in integrating these technologies and a summary of challenges and open research issues

Formally citing the Web

Paul Wouters — 2005-05-06T13:00:29-00:00

Journal of the American Society for Information Science and Technology, Vol. 55, No. 14. (13 August 2004), pp. 1250-1260.

How do authors refer to Web-based information sources in their formal scientific publications? It is not yet well known how scientists and scholars actually include new types of information sources, available through the new media, in their published work. This article reports on a comparative study of the lists of references in 38 scientific journals in five different scientific and social scientific fields. The fields are sociology, library and information science, biochemistry and biotechnology, neuroscience, and the mathematics of computing. As is well known, references, citations, and hyperlinks play different roles in academic publishing and communication. Our study focuses on hyperlinks as attributes of references in formal scholarly publications. The study developed and applied a method to analyze the differential roles of publishing media in the analysis of scientific and scholarly literature references. The present secondary databases that include reference and citation data (the Web of Science) cannot be used for this type of research. By the automated processing and analysis of the full text of scientific and scholarly articles, we were able to extract the references and hyperlinks contained in these references in relation to other features of the scientific and scholarly literature. Our findings show that hyperlinking references are indeed, as expected, abundantly present in the formal literature. They also tend to cite more recent literature than the average reference. The large majority of the references are to Web instances of traditional scientific journals. Other types of Web-based information sources are less well represented in the lists of references, except in the case of pure e-journals. We conclude that this can be explained by taking the role of the publisher into account. Indeed, it seems that the shift from print-based to electronic publishing has created new roles for the publisher. By shaping the way scientific references are hyperlinking to other information sources, the publisher may have a large impact on the availability of scientific and scholarly information.

Instruments of cognition: Use of citations and Web links in online teaching materials

Anita Coleman — 2005-05-06T12:47:13-00:00

Journal of the American Society for Information Science and Technology, Vol. 56, No. 4. (22 December 2004), pp. 382-392.

Use of citations and Web links embedded in online teaching materials was studied for an undergraduate course. The undergraduate students enrolled in Geographic Information Science for Geography and Regional Development used Web links more often than citations, but clearly did not see them as key to enhancing learning. Current conventions for citing and linking tend to make citations and links invisible. There is some evidence that citations and Web links categorized and highlighted in terms of their importance and function to be served may help student learning in interdisciplinary domains.

The excitement of Google Scholar, the worry of Google Print

Marcus Banks — 2006-06-06T10:32:16-00:00

Biomedical Digital Libraries, Vol. 2 (22 March 2005), 2.

The "impact factor" revisited

Peng Dong — 2005-12-12T21:09:54-00:00

Biomedical Digital Libraries, Vol. 2, No. 1. (05 December 2005), 7.

The number of scientific journals has become so large that individuals, institutions and institutional libraries cannot completely store their content physically, and much less so intellectually. In order to prioritize the choice of quality information sources, librarians and scientists are in need of reliable decision aids. The "impact factor" is the most commonly used assessment aid in the decision-making process of which journals to contribute to, or to retrieve knowledge from. It is also an often misunderstood tool. This narrative review explains how the impact factor is calculated, how bias is introduced into the calculation, which questions it can or cannot answer, and how different professional groups can benefit from the information that the impact factor provides.

Three options for citation tracking: Google Scholar, Scopus and Web of Science

Nisa Bakkalbasi — 2006-06-29T21:13:39-00:00

Biomedical Digital Libraries, Vol. 3 (29 June 2006), 7.

Relation between online "hit counts" and subsequent citations: prospective study of research papers in the BMJ

Thomas Perneger — 2005-08-17T12:14:46-00:00

BMJ, Vol. 329, No. 7465. (4 September 2004), pp. 546-547.

The effect of "open access" on citation impact: An analysis of ArXiv's condensed matter section

Henk Moed — 2008-06-26T13:14:32-00:00

Journal of the American Society for Information Science and Technology, Vol. 58, No. 13. (2007), pp. 2047-2054.

This article statistically analyzes how the citation impact of articles deposited in the Condensed Matter section of the preprint server ArXiv (hosted by Cornell University), and subsequently published in a scientific journal, compares to that of articles in the same journal that were not deposited in the archive. Its principal aim is to further illustrate and roughly estimate the effect of two factors, ldquoearly viewrdquo and ldquoquality bias,rdquo on differences in citation impact between these two sets of papers, using citation data from Thomson Scientific's Web of Science. It presents estimates for a number of journals in the field of condensed matter physics. To discriminate between an ldquoopen accessrdquo effect and an early view effect, longitudinal citation data were analyzed covering a time period as long as 7 years. Quality bias was measured by calculating ArXiv citation impact differentials at the level of individual authors publishing in a journal, taking into account coauthorship. The analysis provided evidence of a strong quality bias and early view effect. Correcting for these effects, there is in a sample of six condensed matter physics journals studied in detail no sign of a general ldquoopen access advantagerdquo of papers deposited in ArXiv. The study does provide evidence that ArXiv accelerates citation due to the fact that ArXiv makes papers available earlier rather than makes them freely available.

Sharing detailed research data is associated with increased citation rate.

HA Piwowar — 2007-11-26T05:13:21-00:00

PLoS ONE, Vol. 2, No. 3. (2007)

BACKGROUND: Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available. PRINCIPAL FINDINGS: We examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. The 48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with a 69% increase in citations, independently of journal impact factor, date of publication, and author country of origin using linear regression. SIGNIFICANCE: This correlation between publicly available data and increased literature impact may further motivate investigators to share their detailed research data.

Nanocomputing

Jennifer Sager — 2008-03-12T21:16:32-00:00

NanoBioTechnology (2008), pp. 215-265.

Nanocomputing encompasses any submicron devices and technologies applied to any computational or related tasks. A brief survey is given, and emphasis is placed on biomolecular devices that use nucleic acids as their substrate. Computational selfassembly of DNA and DNA-based enzymatic computing are surveyed in greater detail. The foremost implementation challenge for computation, namely, DNA word design, is also surveyed.

Population modeling of the emergence and development of scientific fields

Luís Bettencourt — 2008-06-30T16:59:41-00:00

Scientometrics, Vol. 75, No. 3. (1 June 2008), pp. 495-518.

Abstract We analyze the temporal evolution of emerging fields within several scientific disciplines in terms of numbers of authors and publications. From bibliographic searches we construct databases of authors, papers, and their dates of publication. We show that the temporal development of each field, while different in detail, is well described by population contagion models, suitably adapted from epidemiology to reflect the dynamics of scientific interaction. Dynamical parameters are estimated and discussed to reflect fundamental characteristics of the field, such as time of apprenticeship and recruitment rate. We also show that fields are characterized by simple scaling laws relating numbers of new publications to new authors, with exponents that reflect increasing or decreasing returns in scientific productivity.

On the recommending of citations for research papers

Sean Mcnee — 2006-06-27T00:52:26-00:00

(2002), pp. 116-125.

Citation Statistics From More Than a Century of Physical Review

S Redner — 2004-11-22T00:17:30-00:00

(6 October 2004)

We study the statistics of citations from all Physical Review journals for the 110-year period 1893 until 2003. In addition to characterizing the citation distribution and identifying publications with the highest citation impact, we investigate how citations evolve with time. There is a positive correlation between the number of citations to a paper and the average age of citations. Citations from a publication have an exponentially decaying age distribution; that is, old papers tend to not get cited. In contrast, the citations to a publication are consistent with a power-law age distribution, with an exponent close to -1 over a time range of 2 -- 20 years. We also identify a number of strongly-correlated citation bursts and other dramatic features in the time history of citations to individual publications.

Directed Accelerated Growth: Application in Citation Network

Parongama Sen — 2006-10-25T21:29:35-00:00

(7 Sep 2004)

In many real world networks, the number of links increases nonlinearly with the number of nodes. Models of such accelerated growth have been considered earlier with deterministic and stochastic number of links. Here we consider stochastic accelerated growth in a network where links are directed. With the number of out-going links following a power law distribution, the results are similar to the undirected case. As the accelerated growth is enhanced, the degree distribution becomes independent of the “initial attractiveness”, a parameter which plays a key role in directed networks. As an example of a directed model with accelerated growth, the citation network is considered, in which the distribution of the number of outgoing link has an exponential tail. The role of accelerated growth is examined here with two different growth laws.

Aging in Citation Networks

Kamalika Hajra — 2006-10-25T21:27:11-00:00

(1 Sep 2004)

In many growing networks, the age of the nodes plays an important role in deciding the attachment probability of the incoming nodes. For example, in a citation network, very old papers are seldom cited while recent papers are usually cited with high frequency. We study actual citation networks to find out the distribution $T(t)$ of $t$, the time interval between the published and the cited paper. For different sets of data we find a universal behaviour: $T(t) ∼ t^-0.9$ for $t ≤ t_c$ and $T(t) ∼ t^-2$ for $t>t_c$ where $t_c ∼ O(10)$.

Citation networks in high energy physics

S Lehmann — 2006-10-25T21:15:28-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 68, No. 2. (2003)

The citation network constituted by the SPIRES database is investigated empirically. The probability that a given paper in the SPIRES database has k citations is well described by simple power laws, P(k)k–, with 1.2 for k less than 50 citations and 2.3 for 50 or more citations. A consideration of citation distribution by subfield shows that the citation patterns of high energy physics form a remarkably homogeneous network. Further, we utilize the knowledge of the citation distributions to demonstrate the extreme improbability that the citation records of selected individuals and institutions have been obtained by a random draw on the resulting distribution.

Modeling the literature of superstring theory: A case of fast literature

CD Hurt — 2006-11-02T22:01:07-00:00

Scientometrics, Vol. V24, No. 3. (26 July 1992), pp. 471-480.

Stochastic modeling of citation slips

MV Simkin — 2006-10-25T21:53:24-00:00

(28 Nov 2004)

We present empirical data on frequency and pattern of misprints in citations to twelve high-profile papers. We find that the distribution of misprints, ranked by frequency of their repetition, follows Zipf's law. We propose a stochastic model of citation process, which explains these findings, and leads to the conclusion that 70-90% of scientific citations are copied from the lists of references used in other papers.

Life, Death and Preferential Attachment

S Lehmann — 2006-10-25T21:51:55-00:00

(22 Aug 2004)

Scientific communities are characterized by strong stratification. The highly skewed frequency distribution of citations of published scientific papers suggests a relatively small number of active, cited papers embedded in a sea of inactive and uncited papers. We propose an analytically soluble model which allows for the death of nodes. This model provides an excellent description of the citation distributions for live and dead papers in the SPIRES database. Further, this model suggests a novel and general mechanism for the generation of power law distributions in networks whenever the fraction of active nodes is small.

A mathematical theory of citing

M Simkin — 2005-04-18T12:11:53-00:00

(14 April 2005)

Recently we proposed a model in which when a scientist writes a manuscript, he picks up several random papers, cites them and also copies a fraction of their references (<A HREF="/abs/cond-mat/0305150">cond-mat/0305150</A>). The model was stimulated by our discovery that a majority of scientific citations are copied from the lists of references used in other papers (<A HREF="/abs/cond-mat/0212043">cond-mat/0212043</A>). It accounted quantitatively for several properties of empirically observed distribution of citations. However, important features, such as power-law distribution of citations to papers published during the same year and the fact that the average rate of citing decreases with aging of a paper, were not accounted for by that model. Here we propose a modified model: when a scientist writes a manuscript, he picks up several random recent papers, cites them and also copies some of their references. The difference with the original model is the word recent. We solve the model using methods of the theory of branching processes, and find that it can explain the aforementioned features of citation distribution, which our original model couldn't account for. The model can also explain "sleeping beauties in science", i.e., papers that are little cited for a decade or so, and later "awake" and get a lot of citations. Although much can be understood from purely random models, we find that to obtain a good quantitative agreement with empirical citation data one must introduce Darwinian fitness parameter for the papers.

Live and Dead Nodes

S Lehmann — 2006-10-25T21:47:21-00:00

(6 May 2005)

In this paper, we explore the consequences of a distinction between `live' and `dead' network nodes; `live' nodes are able to acquire new links whereas `dead' nodes are static. We develop an analytically soluble growing network model incorporating this distinction and show that it can provide a quantitative description of the empirical network composed of citations and references (in- and out-links) between papers (nodes) in the SPIRES database of scientific papers in high energy physics. We also demonstrate that the death mechanism alone can result in power law degree distributions for the resulting network.

Modelling Aging Characteristics in Citation Networks

Kamalika Hajra — 2006-10-25T21:46:27-00:00

(4 Aug 2005)

Growing network models with preferential attachment dependent on both age and degree are proposed to simulate certain features of citation network noted in \citered2. In this directed network, a new node gets attached to an older node with the probability $∼ K(k)f(t)$ where the degree and age of the older node are $k$ and $t$ respectively. Several functional forms of $K(k)$ and $f(t)$ have been considered. The desirable features of the citation network can be reproduced with $K(k) ∼ k^-β$ and $f(t) ∼ \exp(α t)$ with $β =2.0$ and $α = -0.2$ and with simple modifications in the growth scheme.

Effect of aging on network structure

Han Zhu — 2005-06-29T19:19:02-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 68, No. 5. (2003)

In network evolution, the effect of aging is universal: in scientific collaboration network, scientists have a finite time span of being active; in movie actors network, once popular stars are retiring from stage; devices on the Internet may become outmoded with techniques developing so rapidly. Here we find in citation networks that this effect can be represented by an exponential decay factor, e–, where is the node age, while other evolving networks (the Internet, for instance) may have different types of aging, for example, a power-law decay factor, which is also studied and compared. It has been found that as soon as such a factor is introduced to the Barabasi-Albert scale-free model, the network will be significantly transformed. The network will be clustered even with infinitely large size, and the clustering coefficient varies greatly with the intensity of the aging effect, i.e., it increases linearly with for small values of and decays exponentially for large values of . At the same time, the aging effect may also result in a hierarchical structure and a disassortative degree-degree correlation. Generally the aging effect will increase the average distance between nodes, but the result depends on the type of the decay factor. The network appears like a one-dimensional chain when exponential decay is chosen, but with power-law decay, a transformation process is observed, i.e., from a small-world network to a hypercubic lattice, and to a one-dimensional chain finally. The disparities observed for different choices of the decay factor, in clustering, average node distance, and probably other aspects not yet identified, are believed to bear significant meaning on empirical data acquisition.

Evolution of networks with aging of sites

SN Dorogovtsev — 2006-10-25T21:35:47-00:00

Physical Review E, Vol. 62, No. 2. (2000), 1842.

We study the growth of a network with aging of sites. Each new site of the network is connected to some old site with probability proportional (i) to the connectivity of the old site as in the BarabÃ¡si-Albertâs model and (ii) to Ï -Î± ; where Ï is the age of the old site. We find both from simulation and analytically that the network shows scaling behavior only in the region Î± < 1. When Î± increases from -â to 0; the exponent Î³ of the distribution of connectivities [ P ( k )â k -Î³ for large k ] grows from 2 to the value for the network without aging. The ensuing increase of Î± to 1 causes Î³ to grow to â. For Î± > 1; the distribution P ( k ) is exponentional.

Statistics of citation networks

Alexei Vazquez — 2005-09-29T10:50:56-00:00

(2 May 2001)

The out-degree distribution of citation networks is investigated. Statistical data of the number of papers cited within a paper (out-degree) for different journals in the period 1991-1999 is reported. The out-degree distribution is characterized by a maximum at intermediate out-degrees. At the left of the maximum there are strong fluctuations from journal to journal while is quite universal at the right, with two classes of journals. These two classes are associated with the existence or not of a restriction in the maximum number of pages per paper. The shape of the out-degree distribution does not change appreciable from period to period, but the average out-degree is observed to increase logarithmically with the number of published papers. These features are modeled using a recursive search model.

The effect of 'Open Access' upon citation impact: An analysis of ArXiv's Condensed Matter Section

Henk Moed — 2006-11-15T16:45:55-00:00

(14 Nov 2006)

This article statistically analyses how the citation impact of articles deposited in the Condensed Matter section of the preprint server ArXiv (hosted by Cornell University), and subsequently published in a scientific journal, compares to that of articles in the same journal that were not deposited in that archive. Its principal aim is to further illustrate and roughly estimate the effect of two factors, 'early view' and 'quality bias', upon differences in citation impact between these two sets of papers, using citation data from Thomson Scientific's Web of Science. It presents estimates for a number of journals in the field of condensed matter physics. In order to discriminate between an 'open access' effect and an early view effect, longitudinal citation data was analysed covering a time period as long as 7 years. Quality bias was measured by calculating ArXiv citation impact differentials at the level of individual authors publishing in a journal, taking into account co-authorship. The analysis provided evidence of a strong quality bias and early view effect. Correcting for these effects, there is in a sample of 6 condensed matter physics journals studied in detail, no sign of a general 'open access advantage' of papers deposited in ArXiv. The study does provide evidence that ArXiv accelerates citation, due to the fact that that ArXiv makes papers earlier available rather than that it makes papers freely available.

The evolution of the Science Citation Index.

E Garfield — 2007-05-13T14:15:14-00:00

Int Microbiol, Vol. 10, No. 1. (March 2007), pp. 65-69.

Gene expression responses of European flounder (Platichthys flesus) to 17-[beta] estradiol

Tim Williams — 2007-09-10T13:40:01-00:00

Toxicology Letters, Vol. 168, No. 3. (5 February 2007), pp. 236-248.

Male European flounder (Platichthys flesus) were intraperitoneally injected with 10 mg/kg 17-beta estradiol and tissues taken from individuals over a timecourse of 16 days. The GENIPOL P. flesus cDNA microarray was employed to detect hepatic gene expression differences between fish treated with estradiol and saline controls. Known biomarkers of estrogen exposure, choriogenin L and vitellogenins, showed sustained induction over the time-course. Among 175 identified clones showing sustained statistically significant induction or repression, those associated with the Gene Ontology terms mitochondria, amino acid synthesis, ubiquitination and apoptosis were included amongst those induced while those associated with immune function, electron transport, cell signalling and protein phosphorylation were repressed. Thus, we show the gene expression response of an environmentally relevant fish species to a high dose of an estrogenic endocrine disruptor and also report the sequencing of a further 2121 flounder ESTs.

Comparative analysis of whole-genome sequences of Streptococcus suis

Wu Wei — 2007-09-10T13:38:17-00:00

Chinese Science Bulletin, Vol. 51, No. 10. (16 May 2006), pp. 1199-1209.

Abstract The outbreak of Streptococcus suis recently in some districts of Sichuan Province in China has caused over 30 deaths and over 200 infections in human beings. In order to study the pathogenicity mechanism and to prevent the bacteria from spreading and infecting human beings and swine, we have annotated and analyzed the genomes of two strains, Streptococcus suis P1/7 and 89-1591 respectively. The whole length of P1/7 is 2.007 Mb, and has 1969 ORFs. In contrast, the partial genome sequence of 89-1591 is 1.98 Mb in length and exists in 177 contigs with 1918 ORFs. Analysis shows that the average lengths of CDSs in two genomes are very close, and the numbers of the homolog ORFs are 1306 between those two strains. Most of the toxicity factors of the two strains are homologeous, but there are still some significant differences between those two strains. For example, among the 11 genes (cps2A-cps2K) encoding for the capsules in P1/7, 4 (cps2A, 2B, 2I, 2J) are not detected in strain 89-1591. At the same time, the genes encoding EF and Haemolysin in P1/7 are also not found in strain 89-1591. Besides, the genes related to DNA replication, repair and recombination differ from each other significantly and there also exist certain differences among the surface proteins. Those characteristics indicate that those two strains have evolved their own specific functions to adapt to the different environments and that the pathogenesis of the two strains is different. We have accumulated comprehensive genomics information for future systematic studies of S. sui. Our results are helpful for disease prevention, vaccine development, as well as drug design for S. suis.

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform.

SH Nagaraj — 2007-09-06T10:51:51-00:00

Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)

The analysis of expressed sequence tag (EST) datasets offers a rapid and cost-effective approach to elucidate the transcriptome of an organism, but requiring several computational methods for assembly and annotation. ESTExplorer is a comprehensive workflow system for EST data management and analysis. The pipeline uses a 'distributed control approach' in which the most appropriate bioinformatics tools are implemented over different dedicated processors. Species-specific repeat masking and conceptual translation are in-built. ESTExplorer accepts a set of ESTs in FASTA format which can be analysed using programs selected by the user. After pre-processing and assembly, the dataset is annotated at the nucleotide and protein levels, following conceptual translation. Users may optionally provide ESTExplorer with assembled contigs for annotation purposes. Functionally annotated contigs/ESTs can be analysed individually. The overall outputs are gene ontologies, protein functional identifications in terms of mapping to protein domains and metabolic pathways. ESTExplorer has been applied successfully to annotate large EST datasets from parasitic nematodes and to identify novel genes as potential targets for parasite intervention. ESTExplorer runs on a Linux cluster and is freely available for the academic community at http://estexplorer.biolinfo.org.

Generation, annotation and analysis of ESTs from Trichoderma harzianumCECT 2413

Juan Vizcaino — 2006-07-28T01:47:09-00:00

BMC Genomics, Vol. 7 (27 July 2006), 193.

Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance

Javier Terol — 2007-01-26T18:40:17-00:00

BMC Genomics, Vol. 8 (25 January 2007), 31.

Transcriptional response of Citrus aurantifolia to infection by Citrus tristeza virus

Monica Gandia — 2007-09-06T10:27:13-00:00

Virology, Vol. In Press, Corrected Proof

Changes in gene expression of Mexican lime plants in response to infection with a severe (T305) or a mild (T385) isolate of Citrus tristeza virus (CTV) were analyzed using a cDNA microarray containing 12,672 probes to 6875 different citrus genes. Statistically significant (P < 0.01) expression changes of 334 genes were detected in response to infection with isolate T305, whereas infection with T385 induced no significant change. Induced genes included 145 without significant similarity with known sequences and 189 that were classified in seven functional categories. Genes related with response to stress and defense were the main category and included 28% of the genes induced. Selected transcription changes detected by microarray analysis were confirmed by quantitative real-time RT-PCR. Changes detected in the transcriptome upon infecting lime with T305 may be associated either with symptom expression, with a strain-specific defense mechanism, or with a general response to stress.

Discovery of knowledge flow in science

Hai Zhuge — 2006-05-08T15:25:26-00:00

Commun. ACM, Vol. 49, No. 5. (May 2006), pp. 101-107.

Citances: Citation Sentences for Semantic Analysis of

Bioscience Preslav — 2006-07-03T13:13:53-00:00

We propose the use of the text of the sentences surrounding citations as an important tool for semantic interpretation of bioscience text. We hypothesize several di#erent uses of citation sentences (which we call citances), including the creation of training and testing data for semantic analysis (especially for entity and relation recognition), synonym set creation, database curation, document summarization, and information retrieval generally. We illustrate some of these ideas, showing that...

Prestige is factored into journal ratings

Philip Ball — 2006-02-18T12:38:32-00:00

Nature, Vol. 439, No. 7078. (15 February 2006), pp. 770-771.

Citation analysis as a tool in journal evaluation.

E Garfield — 2006-04-12T17:59:32-00:00

Science, Vol. 178, No. 60. (3 November 1972), pp. 471-479.

Open access increases citation rate.

CJ Maccallum — 2006-05-16T02:26:55-00:00

PLoS Biol, Vol. 4, No. 5. (May 2006)

Citation Analysis in Research Evaluation

Henk Moed — 2006-01-23T15:36:47-00:00

(31 December 2005)

This book deals with the evaluation of scholarly research performance, and focuses on the contribution of scholarly work to the advancement of scholarly knowledge. Its principal question is: how can citation analysis be used properly as a tool in the assessment of such a contribution? Citation analysis involves the construction and application of a series of indicators of the ‘impact’, ‘influence’ or ‘quality’ of scholarly work, derived from references cited in footnotes or bibliographies of scholarly research publications. It describes primarily the use of data extracted from the Science Citation Index and the Web of Science, published by the Institute for Scientific Information (ISI)/Thomson Scientific. But many aspects to which this book dedicates attention relate to citation analysis in general, It provides a wide range of important facts, and corrects a number of common misunderstandings about citation analysis. It introduces basic notions and distinctions, and deals both with theoretical and technical aspects, and with its applicability in various policy contexts, at the level of individual scholars, research groups, departments, institutions, national scholarly systems, disciplines or subfields, and scholarly journals. Although the major part of the analysis relates to the basic science – a domain in which citation analysis is used most frequently – this book also addresses its uses and limits in the applied and technical sciences, social sciences and humanities. It reveals the enormous potential of quantitative, bibliometric analyses of the scholarly literature for a deeper understanding of scholarly activity and performance, and highlights their policy relevance. But this book is also critical, underlines the limits of citation analysis in research evaluation, and issues warnings for potential misuse. It proposes criteria for proper use of citation analysis as a research evaluation tool. In order to be used properly as a research evaluation tool, it is essential that all participants have insight into the nature of citation analysis, how its indicators are constructed and calculated, what the various theoretical positions state about what they measure, and what are their potentialities and limitations, particularly in relation to peer review. This book aims at providing such insight.

Toward alternative metrics of journal impact: A comparison of download and citation data

Johan Bollen — 2005-08-01T12:26:07-00:00

Information Processing & Management, Vol. 41, No. 6. (December 2005), pp. 1419-1440.

We generated networks of journal relationships from citation and download data, and determined journal impact rankings from these networks using a set of social network centrality metrics. The resulting journal impact rankings were compared to the ISI IF. Results indicate that, although social network metrics and ISI IF rankings deviate moderately for citation-based journal networks, they differ considerably for journal networks derived from download data. We believe the results represent a unique aspect of general journal impact that is not captured by the ISI IF. These results furthermore raise questions regarding the validity of the ISI IF as the sole assessment of journal impact, and suggest the possibility of devising impact metrics based on usage information in general.

Statistical relationships between downloads and citations at the level of individual documents within a single journal

Henk Moed — 2005-11-20T20:17:55-00:00

Journal of the American Society for Information Science and Technology, Vol. 56, No. 10. (31 May 2005), pp. 1088-1097.

Statistical relationships between downloads from ScienceDirect of documents in Elsevier's electronic journal Tetrahedron Letters and citations to these documents recorded in journals processed by the Institute for Scientific Information/Thomson Scientific for the Science Citation Index (SCI) are examined. A synchronous approach revealed that downloads and citations show different patterns of obsolescence of the used materials. The former can be adequately described by a model consisting of the sum of two negative exponential functions, representing an ephemeral and a residual factor, whereas the decline phase of the latter conforms to a simple exponential function with a decay constant statistically similar to that of the downloads residual factor. A diachronous approach showed that, as a cohort of documents grows older, its download distribution becomes more and more skewed, and more statistically similar to its citation distribution. A method is proposed to estimate the effect of citations upon downloads using obsolescence patterns. It was found that during the first 3 months after an article is cited, its number of downloads increased 25% compared to what one would expect this number to be if the article had not been cited. Moreover, more downloads of citing documents led to more downloads of the cited article through the citation. An analysis of 1,190 papers in the journal during a time interval of 2 years after publication date revealed that there is about one citation for every 100 downloads. A Spearman rank correlation coefficient of 0.22 was found between the number of times an article was downloaded and its citation rate recorded in the SCI. When initial downloads - defined as downloads made during the first 3 months after publication - were discarded, the correlation raised to 0.35. However, both outcomes measure the joint effect of downloads upon citation and that of citation upon downloads. Correlating initial downloads to later citation counts, the correlation coefficient drops to 0.11. Findings suggest that initial downloads and citations relate to distinct phases in the process of collecting and processing relevant scientific information that eventually leads to the publication of a journal article.

Free online availability substantially increases a paper's impact.

S Lawrence — 2005-04-18T07:26:48-00:00

Nature, Vol. 411, No. 6837. (31 May 2001)

Journal Status

Johan Bollen — 2006-02-23T08:51:20-00:00

(9 Jan 2006)

[Web, digital library, computers and society, citation, impact factor, page rank, popular vs. prestige] The status of an actor in a social context is commonly defined in terms of two factors: the total number of endorsements the actor receives from other actors and the prestige of the endorsing actors. These two factors indicate the distinction between popularity and expert appreciation of the actor, respectively. We refer to the former as popularity and to the latter as prestige. These notions of popularity and prestige also apply to the domain of scholarly assessment. The ISI Impact Factor (ISI IF) is defined as the mean number of citations a journal receives over a 2 year period. By merely counting the amount of citations and disregarding the prestige of the citing journals, the ISI IF is a metric of popularity, not of prestige. We demonstrate how a weighted version of the popular PageRank algorithm can be used to obtain a metric that reflects prestige. We contrast the rankings of journals according to their ISI IF and their weighted PageRank, and we provide an analysis that reveals both significant overlaps and differences. Furthermore, we introduce the Y-factor which is a simple combination of both the ISI IF and the weighted PageRank, and find that the resulting journal rankings correspond well to a general understanding of journal status.

Ten-Year Cross-Disciplinary Comparison of the Growth of Open Access and How it Increases Research Citation Impact

C Hajjem — 2006-06-20T08:19:08-00:00

IEEE Data Engineering Bulletin, Vol. 28, No. 4. (18 Jun 2005), pp. 39-47.

Lawrence (2001)found computer science articles that were openly accessible (OA) on the Web were cited more. We replicated this in physics. We tested 1,307,038 articles published across 12 years (1992-2003) in 10 disciplines (Biology, Psychology, Sociology, Health, Political Science, Economics, Education, Law, Business, Management). A robot trawls the Web for full-texts using reference metadata ISI citation data (signal detectability d'=2.45; bias = 0.52). Percentage OA (relative to total OA + NOA) articles varies from 5%-16% (depending on discipline, year and country) and is slowly climbing annually (correlation r=.76, sample size N=12, probability p < 0.005). Comparing OA and NOA articles in the same journal/year, OA articles have consistently more citations, the advantage varying from 25%-250% by discipline and year. Comparing articles within six citation ranges (0, 1, 2-3, 4-7, 8-15, 16+ citations), the annual percentage of OA articles is growing significantly faster than NOA within every citation range (r > .90, N=12, p < .0005) and the effect is greater with the more highly cited articles (r = .98, N=6, p < .005). Causality cannot be determined from these data, but our prior finding of a similar pattern in physics, where percent OA is much higher (and even approaches 100% in some subfields), makes it unlikely that the OA citation advantage is merely or mostly a self-selection bias (for making only one's better articles OA). Further research will analyze the effect's timing, causal components and relation to other variables.

Self-citation corrections for the Hirsch index

Michael Schreiber — 2007-01-22T06:10:19-00:00

(19 Jan 2007)

I propose to sharpen the index h, proposed by Hirsch as a useful index to characterize the scientific output of a researcher, by excluding the self-citations. Performing a self-experiment and also analyzing two anonymous data sets, it is shown that self-citations can significantly reduce the $h$ index in contrast to Hirsch's expectations.