CisGenome Browser statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CisGenome Browser

Tool usage distribution map

This map represents all the scientific publications referring to CisGenome Browser per scientific context
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Associated diseases

This word cloud represents CisGenome Browser usage per disease context

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CisGenome Browser specifications


Unique identifier OMICS_22151
Name CisGenome Browser
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data A sample file.
Input format BAR,TSV,BAM,refFlat,UCSC BED,WIG
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Medium
Version 1.0.14
Stability Stable
Source code URL
Maintained Yes




No version available


  • person_outline Hui Jiang
  • person_outline Hui Jang

Additional information

Publication for CisGenome Browser

CisGenome Browser citations


Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth

PMCID: 5634782
PMID: 28949295
DOI: 10.7554/eLife.29938.025

[…] ed and quantified on an Agilent Bioanalyzer. Sequencing was performed on Illumina Hiseq platform. Raw reads were mapped to the reference genome (sacCer2) by bowtie () and peaks were visualized by the CisGenome Browser (). […]


TNF α modulates genome wide redistribution of ΔNp63α/TAp73 and NF κB c REL interactive binding on TP53 and AP 1 motifs to promote an oncogenic gene program in squamous cancer

PMCID: 5093089
PMID: 27132513
DOI: 10.1038/onc.2016.112
call_split See protocol

[…] within a few hundred DNA base pairs. In our study, the default setting was selected, which is commonly utilized and suitable to our datasets. Detected peak regions were visualized mainly by using the CisGenome browser () together with gene structure, DNA sequences and conservation scores. We compared the fraction of peaks residing in various genomic features with the corresponding genome backgroun […]


High temporal resolution view of transcription and chromatin states across distinct metabolic states in budding yeast

PMCID: 4190017
PMID: 25173176
DOI: 10.1038/nsmb.2881
call_split See protocol

[…] fied on an Agilent Bioanalyzer. Sequencing was performed on an Illumina GXII or Hiseq 2000 or Solid. Raw reads were mapped to the reference genome (sacCer2) by bowtie and peaks were visualized by the CisGenome Browser as described above. […]


Genome Wide Effects of Selenium and Translational Uncoupling on Transcription in the Termite Gut Symbiont Treponema primitia

PMCID: 3892789
PMID: 24222491
DOI: 10.1128/mBio.00869-13

[…] justed hits per kb of coding DNA were considered in analyses. Signal intensities were visualized graphically by converting Maq-aligned reads into a BAR file using Cisgenome software and viewed on the Cisgenome browser (Stanford University, Stanford, CA) (). For a smoother graphical display of data, a moving average of reads per 200-bp sliding nucleotide window was generated using the MATLAB softwa […]


Modeling Truncated AR Expression in a Natural Androgen Responsive Environment and Identification of RHOB as a Direct Transcriptional Target

PLoS One
PMCID: 3510170
PMID: 23209612
DOI: 10.1371/journal.pone.0049887

[…] e . TC-AR binding regions were identified by comparison to total input control as well as IgG control using the TileMap peak detection tool . Genomic locations of binding peaks were visualized in the CisGenome browser. […]

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CisGenome Browser institution(s)
Department of Statistics, Stanford University, Stanford, CA, USA; Stanford Genome Technology Center, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Systems Biology Centre, Coventry House, the University of Warwick, Coventry, UK; Department of Health Research and Policy, Stanford University, Stanford, CA, USA
CisGenome Browser funding source(s)
Supported by National Institute of Health grant R01-HG004634; in part by National Institute of Health grant 2P01-HG000205; and Agilent Technologies.

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