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PubMatrix specifications


Unique identifier OMICS_15627
Name PubMatrix
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Kevin Becker

Publication for PubMatrix

PubMatrix citations


Transcriptional profiling of human bronchial epithelial cell BEAS 2B exposed to diesel and biomass ultrafine particles

BMC Genomics
PMCID: 5923024
PMID: 29703138
DOI: 10.1186/s12864-018-4679-9

[…] nrichment of 4 manually selected significant gene sets from GSEA analysis (TNF-α signaling via NF-κB; inflammatory response, epithelial mesenchymal transition(EMT); and xenobiotic metabolism); iii) a PubMatrix total score higher or equal to 15, corresponding to at least 15 publications containing both the gene name and the terms cardiovascular diseases, lung cancer, or lung diseases. The gene netw […]


RNA SEQ Analysis Indicates that the AE3 Cl−/HCO3− Exchanger Contributes to Active Transport Mediated CO2 Disposal in Heart

Sci Rep
PMCID: 5544674
PMID: 28779178
DOI: 10.1038/s41598-017-07585-y

[…] ilation, Angiogenesis (Supplementary Table ) and (2) Energy Metabolism (Supplementary Table ), additional genes were included in the lists based on PubMed literature searches, which relied heavily on PubMatrix. Those searches can be publicly accessed as described below. […]


Novel Genetic Variants Associated with Child Refractory Esophageal Stricture with Food Allergy by Exome Sequencing

PMCID: 5409729
PMID: 28420126
DOI: 10.3390/nu9040390

[…] y Sift and Polyphen 2 [,]. DAVID was utilized to perform Gene Ontology to identify the cellular biological processes of genes with pediatric refractory esophageal stricture with food allergy SNPs []. PubMatrix analysis [], a multiplex literature mining tool, was used as described previously [] to build the relationship between genes with milk-protein allergy variations and allergy-associated disea […]


Therapeutic properties of Scutellaria baicalensis in db/db mice evaluated using Connectivity Map and network pharmacology

Sci Rep
PMCID: 5282526
PMID: 28139721
DOI: 10.1038/srep41711

[…] rmutated p-value < 0.01 were used as search keywords. The numbers of papers with keywords in the title or abstract published in 1990–2016 were collectively obtained from the PubMed database using the PubMatrix algorithm. The numbers of papers were indicated by different colours on a scale bar. For a random permutation-based test, we used all the chemicals (1309 chemicals) present in the cmap datab […]


Inducible and reversible phenotypes in a novel mouse model of Friedreich’s Ataxia

PMCID: 5736353
PMID: 29257745
DOI: 10.7554/eLife.30054.055

[…] les were utilized for enrichment analyses. All included terms exhibited significant Benjamini corrected P-values for enrichment and generally contained greater than five members per category. We used PubMatrix (); RRID:SCR_008236) to examine each differentially expressed gene’s association with the observed phenotypes of FRDAkd mice in the published literature by testing association with the key-w […]


Development and Validation of a Computational Model for Androgen Receptor Activity

Chem Res Toxicol
PMCID: 5396026
PMID: 27933809
DOI: 10.1021/acs.chemrestox.6b00347

[…] )• Korean Center for Validation of Alternative Methods (KoCVAM, ongoing)We conducted semiautomated literature searches for in vitro androgen activity data on the superset of chemicals (n = 158) using PubMatrix ( and Scopus ( Data from in vitro AR binding and TA assays were extracted from identified references and compiled into a single data […]


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