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Biobase specifications


Unique identifier OMICS_29442
Name Biobase
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.40.0
Stability Stable
methods, utils, tools, R(>=2.10), RUnit, ALL, golubEsets, tkWidgets, BiocGenerics(>=0.3.2)
Maintained Yes




No version available



  • person_outline Wolfgang Huber

Publication for Biobase

Biobase citations


Exploring gene expression biomarker candidates for neurobehavioral impairment from total sleep deprivation

BMC Genomics
PMCID: 5941663
PMID: 29739334
DOI: 10.1186/s12864-018-4664-3

[…] lity of CLOCK/BMAL1 binding to the E-boxes on the next circadian cycle []. In the current study, not only was there a strong prediction of a regulatory role for USF1 in the RIF analysis, but also the Biobase F-match tool revealed over-representation of E-box binding sites in the differentially expressed genes.Other genes with regulatory roles supported by both RIF and F-match analyses were GABPA, […]


Exosome markers associated with immune activation and oxidative stress in HIV patients on antiretroviral therapy

Sci Rep
PMCID: 5940833
PMID: 29740045
DOI: 10.1038/s41598-018-25515-4

[…] st existing exosome database ( and the top 200 most abundant plasma proteins published previously. Functional annotation was performed by GO mapping using PANTHER ( and Biobase ( […]


Induction of muscle stem cell quiescence by the secreted niche factor Oncostatin M

Nat Commun
PMCID: 5906564
PMID: 29670077
DOI: 10.1038/s41467-018-03876-8
call_split See protocol

[…] 05088(+)01A, SA Bioscience) designed for quantitative RT-PCR analysis were used to amplify the putative Stat3 binding site adjacent to the mouse Pax7 locus (Chr4: 139387970-139388390), identified via Biobase Transfac analysis (Biobase Corp. MA). The Stat3 occupancy was calculated as a ratio of the amplification efficiency of Stat3 ChIP over input chromatin. […]


Srf destabilizes cellular identity by suppressing cell type specific gene expression programs

Nat Commun
PMCID: 5895821
PMID: 29643333
DOI: 10.1038/s41467-018-03748-1

[…] ify putative binding sites of DNA-binding proteins, the sequences were scanned with MATCH programs (cut-off = minFP) using vertebrate position weight matrices from the TRANSFAC Professional database (BioBase). For each matrix, the enrichment of the hit sequences in a set of sequences was compared with that in whole genomic regions and P-values were calculated by Fisher’s exact test. […]


Estrogen receptors orchestrate cell growth and differentiation to facilitate liver regeneration

PMCID: 5957001
PMID: 29774067
DOI: 10.7150/thno.23624
call_split See protocol

[…] databases were used including TFcheckpoint ( to identify transcription factors; AnimalTFDB ( to identify cofactors; TRANSFAC ( to identify eukaryotic transcription factors, consensus binding sequences (positional weight matrices), and regulated genes; and F […]


Human Adipose Derived Mesenchymal Stem/Stromal Cells Handling Protocols. Lipid Droplets and Proteins Double Staining

PMCID: 5894466
PMID: 29670879
DOI: 10.3389/fcell.2018.00033

[…] - ZEISS Primo Vert Inverted Microscope (Zeiss; Oberkochen, Baden-Württemberg, Germany)- Class II Biological Safety Cabinet (Biobase; Zhangqiu, Shandong, China)- Sanyo MCO-19AIC CO2 cell incubator (Sanyo; Moriguchi, Osaka, Japan)- Innova 4000 Incubator Shaker (New Brunswick Scientific, Enfield, CT, USA)- Jouan B4i Multifunc […]


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Biobase institution(s)
European Molecular Biology Laboratory, Heidelberg, Germany; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Harvard School of Public Health, Boston, MA, USA; Genentech, South San Francisco, CA, USA; Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Medical Genetics, School of Medical Sciences, State University of Campinas, Campinas, Brazil; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Biochemistry, University of Cambridge, Cambridge, UK; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Novartis Institutes for Biomedical Research, Basel, Switzerland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA; Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia; School of Urban Public Health at Hunter College, City University of New York, New York, NY, USA
Biobase funding source(s)
Supported by the National Human Genome Research Institute of the US National Institutes of Health (U41HG004059), the US National Science Foundation (1247813) and the European Commission FP7 project RADIANT.

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