Topic-Driven Bibliometrics and Trend Intelligence for Stem Cell and Cancer Research.

Bibliographic Details
Title:	Topic-Driven Bibliometrics and Trend Intelligence for Stem Cell and Cancer Research.
Authors:	Kidder BL; Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. benjamin.kidder@wayne.edu.; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA. benjamin.kidder@wayne.edu.
Source:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2027; Vol. 3074, pp. 53-67.
Publication Type:	Journal Article
Language:	English
Journal Info:	Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE
Imprint Name(s):	Publication: Totowa, NJ : Humana Press Original Publication: Clifton, N.J. : Humana Press
MeSH Terms:	Computational Biology/methods , Neoplastic Stem Cells/metabolism , Bibliometrics* , Neoplasms* , Stem Cell Research*, Data Mining/methods ; Humans ; PubMed ; Software
Abstract:	The rapid growth of biomedical literature has created an urgent need for computational tools that enable researchers to systematically analyze publication trends, identify emerging research themes, and map the evolution of scientific fields. PubMed Atlas is a command-line and web-enabled workflow for topic-driven bibliometrics and trend intelligence using PubMed E-utilities. The pipeline executes PubMed queries, retrieves matching PMIDs, downloads full metadata records in batches, parses structured information (title, abstract, authors/affiliations, MeSH terms, publication types, grants, keywords, DOI), and stores normalized data in a local SQLite database for rapid querying and visualization. A Streamlit dashboard provides interactive exploration of publication trends, journal distributions, MeSH term summaries, geographic distributions, and recent article browsing with direct PubMed links. This protocol describes the installation, configuration, and operation of PubMed Atlas for cancer stem cell and stem cell transcriptional network research, and other fields, enabling investigators to conduct reproducible bibliometric analyses and identify knowledge gaps in rapidly evolving fields. (© 2027. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
References:	Canese K, Weis S (2013). PubMed: the bibliographic database. NCBI Handbook 2013. Landhuis E (2016) Scientific literature: Information overload. Nature. 535(7612):457–458. (PMID: 10.1038/nj7612-457a27453968) Pautasso M (2013) Ten simple rules for writing a literature review. PLoS Comput Biol 9(7):e1003149. (PMID: 10.1371/journal.pcbi.1003149238741893715443) Hoang AD (2025) Evaluating bibliometrics reviews: a practical guide for peer review and critical reading. Eval Rev 49(6):1074–1102. (PMID: 10.1177/0193841X2513368394025151112476466) Romanelli JP, Goncalves MCP, de Abreu Pestana LF, Soares JAH, Boschi RS, Andrade DF (2021) Four challenges when conducting bibliometric reviews and how to deal with them. Environ Sci Pollut Res Int 28(43):60448–60458. (PMID: 10.1007/s11356-021-16420-x34545520) Donthu N, Kumar S, Mukherjee D, Pandey N, Lim WM (2021) How to conduct a bibliometric analysis: an overview and guidelines. J Bus Res 133:285–296. (PMID: 10.1016/j.jbusres.2021.04.070) Aria M, Cuccurullo C (2017) bibliometrix: an R-tool for comprehensive science mapping analysis. J Informet 11(4):959–975. (PMID: 10.1016/j.joi.2017.08.007) Moral-Muñoz JA, Herrera-Viedma E, Santisteban-Espejo A, Cobo MJ (2020) Software tools for conducting bibliometric analysis in science: An up-to-date review. Profesional de la Información 29(1), e290103. https://doi.org/10.3145/epi.2020.ene.03. (PMID: 10.3145/epi.2020.ene.03) Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 126(4):663–676. (PMID: 10.1016/j.cell.2006.07.02416904174) Huch M, Knoblich JA, Lutolf MP, Martinez-Arias A (2017) The hope and the hype of organoid research. Development. 144(6):938–941. (PMID: 10.1242/dev.15020128292837) Chen W, Dong J, Haiech J, Kilhoffer MC, Zeniou M (2016) Cancer stem cell quiescence and plasticity as major challenges in cancer therapy. Stem Cells Int 2016:1740936. (PMID: 10.1155/2016/1740936274189314932171) Kreso A, Dick JE (2014) Evolution of the cancer stem cell model. Cell Stem Cell 14(3):275–291. (PMID: 10.1016/j.stem.2014.02.00624607403) Zhu J, Liu W (2020) A tale of two databases: the use of Web of Science and Scopus in academic papers. Scientometrics. 123(1):321–335. (PMID: 10.1007/s11192-020-03387-8) Hook DW, Porter SJ, Herzog C (2018) Dimensions: building context for search and evaluation. Front Res Met Anal 3:23. (PMID: 10.3389/frma.2018.00023) Van Eck N, Waltman L (2010) Software survey: VOSviewer, a computer program for bibliometric mapping. Scientometrics 84(2):523–538. (PMID: 10.1007/s11192-009-0146-320585380) Cobo MJ, López-Herrera AG, Herrera-Viedma E, Herrera F (2011) Science mapping software tools: review, analysis, and cooperative study among tools. J Am Soc Inform Science Technol 62(7):1382–1402. (PMID: 10.1002/asi.21525) Coordinators NR (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 41(Database issue):D8. Sayers EW, Beck J, Bolton EE et al. (2021) Database resources of the National Centre for Biotechnology Information. Nucleic Acids Res 49(D1):D10–D17. (PMID: 10.1093/nar/gkaa892330958707778943)
Contributed Indexing:	Keywords: Bibliometrics; Cancer stem cells; Computational biology; E-utilities; Literature mining; PubMed; SQLite; Stem cells; Streamlit; Trend analysis
Entry Date(s):	Date Created: 20260914 Date Completed: 20260914 Latest Revision: 20260914
Update Code:	20260915
DOI:	10.1007/978-1-0716-5539-9_4
PMID:	42734744
Database:	MEDLINE

Description
ISSN:	1940-6029
DOI:	10.1007/978-1-0716-5539-9_4