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How to cite GREAT

Please cite GREAT as follows:

Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, and Gill Bejerano. "GREAT improves functional interpretation of cis-regulatory regions". Nat. Biotechnol. 28(5):495-501, 2010.

A stable link to the publication is

Why Cite GREAT

Over the long run, the best way to assure the continued availability and development of GREAT is for us to be able to show its relevance and contribution to biomedical research. We thank you for your support!

Publications & Reprints

The above Nature Biotechnology paper is currently the inaugural GREAT publication. Reprints are available at

Papers that cite GREAT

  1. Fujita, P.A. et al., The UCSC Genome Browser database: update 2011, Nucleic Acids Res., 39(Database issue):D876-882, 2011.
  2. Mak, H.C., Trends in computational biology--2010, Nature Biotechnol., 29(1):45-49, 2011.
  3. Novershtern, N. et al, Densely interconnected transcriptional circuits control cell states in human hematopoiesis, Cell, 144(2):296-309, 2011.
  4. Cullum, R. et al., The next generation: using new sequencing technologies to analyze gene regulation, Respirology, 16(2):210-222, 2011.
  5. Rada-Iglesias, A. et al., A unique chromatin signature uncovers early developmental enhancers in humans, Nature, 470(7333):279-283, 2011.
  6. Sullivan, A.L. et al., Serum Response Factor utilizes distinct promoter- and enhancer-based mechanisms to regulate cytoskeletal gene expression in macrophages, Mol. Cell. Biol., 31(4):861-875, 2011.
  7. Ma, Z.Y. et al., Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates, Nature Struct. Mol. Biol., 18(2):120-127, 2011.
  8. McLean, C.Y. et al., Human-specific loss of regulatory DNA and the evolution of human-specific traits, Nature, 471(7337):216-219, 2011.
  9. Soccio, R.E. et al., Species-specific strategies underlying conserved functions of metabolic transcription factors, Mol. Endocrinol., 25(4):694-706, 2011.
  10. Capellini, T.D. et al., Pbx homeodomain proteins: TALEnted regulators of limb patterning and outgrowth, Dev. Dyn., 240(5):1063-1086, 2011.
  11. Capellini, T.D. et al., Control of pelvic girdle development by genes of the Pbx family and Emx2, Dev. Dyn., 240(5):1173-1189, 2011.
  12. Tijssen, M.R. et al., Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators, Dev. Cell, 20(5):597-609, 2011.
  13. LePendu, P. et al., Enabling enrichment analysis with the Human Disease Ontology, Journal of Biomedical Informatics, Available online 29 April 2011.
  14. Zentner, G.E. et al., Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions, Genome Research, 21(8):1273-1283, 2011.
  15. Sandve, G.K. et al., The differential disease regulome, BMC Genomics, 12:353, 2011.
  16. Yoon, S.J. et al., HEB and E2A function as SMAD/FOXH1 cofactors, Genes Dev., 25(15):1654-1661, 2011.
  17. Ryu, S.H. et al., Transcriptional changes of secreted Wnt antagonists in hindlimb skeletal muscle during the lifetime of the C57BL/6J mouse, Mech. Ageing Dev., Epub ahead of print 9 Aug 2011.
  18. Lowe, C.B. et al., Three periods of regulatory innovation during vertebrate evolution, Science, 333(6045):1019-1024, 2011.
  19. Karczewski, K.J. et al., Cooperative transcription factor associations discovered using regulatory variation, Proc. Natl. Acad. Sci. USA, 108(32):13353-13358, 2011.


We really appreciate people's supportive e-mails and re-cap a handful of them here to encourage folks to take the plunge.

Date: April 21, 2011
Hi Gill,
Just wanted to let you know that we tried GREAT on a new kind of genomic data set
after your talk. It worked amazingly well and made sense with respect to known biology.
Keep up the good work!
Subject: your tool is cool

Date: October 19, 2010

Dear GREAT developers
I find this tool very useful in analyzing my ChIP-seq peaks, especially
after being quite frustrated using other tools to get insight into the
functions/pathways associated with my TF. ...

Subject: Re: great

Date: May 5, 2010
Hey guys, I had a chance to try out GREAT for a bit with our ...
chip-seq data. It looks like an amazing tool and it's way ahead
of anything else out there for chipseq-related functional analysis. My
favorite part is being able to click through each annotation and
seeing the actual genes that were assigned.. very fancy and cool. That
and the integration with the mouse phenotype ontologies--a big thing
that other tools dont' have. Anyway we'll definitely be using it and
I'll be sure to spread the word!

Date: May 4, 2010

Hi ...
This is not a ... ad. GREAT is awesome, we have been playing
around with it quite a bit.
you certainly will be referenced in a paper that we want to submit by
the end of this month. And I suspect many more after that.

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