Temporal Patterns of Genes in Scientific Publications

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2007 Jul 11

PMID 17620606

Citations 32

Authors

Thomas Pfeiffer

Robert Hoffmann

Affiliations

Soon will be listed here.

Abstract

Publications in scientific journals contain a considerable fraction of our scientific knowledge. Analyzing data from publication databases helps us understand how this knowledge is obtained and how it changes over time. In this study, we present a mathematical model for the temporal dynamics of data on the scientific content of publications. Our data set consists of references to thousands of genes in the >15 million publications listed in PubMed. We show that the observed dynamics may result from a simple process: Researchers predominantly publish on genes that already appear in many publications. This might be a rewarding strategy for researchers, because there is a positive correlation between the frequency of a gene in scientific publications and the journal impact of the publications. By comparing the empirical data with model predictions, we are able to detect unusual publication patterns that often correspond to major achievements in the field. We identify interactions between yeast genes from PubMed and show that the frequency differences of genes in publications lead to a biased picture of the resulting interaction network.

Citing Articles

Underexplored Molecular Mechanisms of Toxicity.

Arowolo O, Suvorov A J Xenobiot. 2024; 14(3):939-949.

PMID: 39051348 PMC: 11270369. DOI: 10.3390/jox14030052.

Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results.

Richardson R, Tejedor Navarro H, Nunes Amaral L, Stoeger T Elife. 2024; 12.

PMID: 38546716 PMC: 10977968. DOI: 10.7554/eLife.93429.

Broad functional profiling of fission yeast proteins using phenomics and machine learning.

Rodriguez-Lopez M, Bordin N, Lees J, Scholes H, Hassan S, Saintain Q Elife. 2023; 12.

PMID: 37787768 PMC: 10547477. DOI: 10.7554/eLife.88229.

Functional unknomics: Systematic screening of conserved genes of unknown function.

Rocha J, Jayaram S, Stevens T, Muschalik N, Shah R, Emran S PLoS Biol. 2023; 21(8):e3002222.

PMID: 37552676 PMC: 10409296. DOI: 10.1371/journal.pbio.3002222.

Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results.

Richardson R, Tejedor Navarro H, Nunes Amaral L, Stoeger T bioRxiv. 2023; .

PMID: 36909550 PMC: 10002660. DOI: 10.1101/2023.02.28.530483.

References

von Mering C, Krause R, Snel B, Cornell M, Oliver S, Fields S . Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002; 417(6887):399-403. DOI: 10.1038/nature750. View

Borner K, Maru J, Goldstone R . The simultaneous evolution of author and paper networks. Proc Natl Acad Sci U S A. 2004; 101 Suppl 1:5266-73. PMC: 387306. DOI: 10.1073/pnas.0307625100. View

Blackmore S . The power of memes. Sci Am. 2000; 283(4):64-6, 68-71, 73. DOI: 10.1038/scientificamerican1000-64. View

Plotkin H . People do more than imitate. Sci Am. 2000; 283(4):72. View

Uetz P, Giot L, Cagney G, Mansfield T, Judson R, Knight J . A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000; 403(6770):623-7. DOI: 10.1038/35001009. View

Newman M . The structure of scientific collaboration networks. Proc Natl Acad Sci U S A. 2001; 98(2):404-9. PMC: 14598. DOI: 10.1073/pnas.98.2.404. View

Gavin A, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A . Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002; 415(6868):141-7. DOI: 10.1038/415141a. View

Barabasi , ALBERT . Emergence of scaling in random networks. Science. 1999; 286(5439):509-12. DOI: 10.1126/science.286.5439.509. View

Chen C . Searching for intellectual turning points: progressive knowledge domain visualization. Proc Natl Acad Sci U S A. 2004; 101 Suppl 1:5303-10. PMC: 387312. DOI: 10.1073/pnas.0307513100. View

10.

Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y . A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A. 2001; 98(8):4569-74. PMC: 31875. DOI: 10.1073/pnas.061034498. View

11.

Price D . NETWORKS OF SCIENTIFIC PAPERS. Science. 1965; 149(3683):510-5. DOI: 10.1126/science.149.3683.510. View

12.

Garfield E . Citation analysis as a tool in journal evaluation. Science. 1972; 178(4060):471-9. DOI: 10.1126/science.178.4060.471. View

13.

Ioannidis J . Why most published research findings are false. PLoS Med. 2005; 2(8):e124. PMC: 1182327. DOI: 10.1371/journal.pmed.0020124. View

14.

Hoffmann R, Valencia A . Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics. 2005; 21 Suppl 2:ii252-8. DOI: 10.1093/bioinformatics/bti1142. View

15.

Boyd R, Richerson P . Meme theory oversimplifies how culture changes. Sci Am. 2000; 283(4):70-1. View

16.

Ho Y, Gruhler A, Heilbut A, Bader G, Moore L, Adams S . Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002; 415(6868):180-3. DOI: 10.1038/415180a. View

17.

Dugatkin L . Animals imitate, too. Sci Am. 2000; 283(4):67. View

18.

Hoffmann R, Valencia A . Protein interaction: same network, different hubs. Trends Genet. 2003; 19(12):681-3. DOI: 10.1016/j.tig.2003.10.011. View

19.

Hoffmann R, Valencia A . A gene network for navigating the literature. Nat Genet. 2004; 36(7):664. DOI: 10.1038/ng0704-664. View

20.

Guimera R, Uzzi B, Spiro J, Nunes Amaral L . Team assembly mechanisms determine collaboration network structure and team performance. Science. 2005; 308(5722):697-702. PMC: 2128751. DOI: 10.1126/science.1106340. View