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Items: 11

1.

The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research.

Reynolds SM, Miller M, Lee P, Leinonen K, Paquette SM, Rodebaugh Z, Hahn A, Gibbs DL, Slagel J, Longabaugh WJ, Dhankani V, Reyes M, Pihl T, Backus M, Bookman M, Deflaux N, Bingham J, Pot D, Shmulevich I.

Cancer Res. 2017 Nov 1;77(21):e7-e10. doi: 10.1158/0008-5472.CAN-17-0617.

2.

Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network.

Longabaugh WJR, Zeng W, Zhang JA, Hosokawa H, Jansen CS, Li L, Romero-Wolf M, Liu P, Kueh HY, Mortazavi A, Rothenberg EV.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5800-5807. doi: 10.1073/pnas.1610617114.

3.

BioTapestry now provides a web application and improved drawing and layout tools.

Paquette SM, Leinonen K, Longabaugh WJ.

F1000Res. 2016 Jan 8;5:39. doi: 10.12688/f1000research.7620.1. eCollection 2016.

4.

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.

Peterson EJ, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJ, Sherman DR, Baliga NS.

Nucleic Acids Res. 2014 Oct;42(18):11291-303. doi: 10.1093/nar/gku777. Epub 2014 Sep 17.

5.

Combing the hairball with BioFabric: a new approach for visualization of large networks.

Longabaugh WJ.

BMC Bioinformatics. 2012 Oct 27;13:275. doi: 10.1186/1471-2105-13-275.

6.

BioTapestry: a tool to visualize the dynamic properties of gene regulatory networks.

Longabaugh WJ.

Methods Mol Biol. 2012;786:359-94. doi: 10.1007/978-1-61779-292-2_21.

PMID:
21938637
7.

A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo.

Su YH, Li E, Geiss GK, Longabaugh WJ, Krämer A, Davidson EH.

Dev Biol. 2009 May 15;329(2):410-21. doi: 10.1016/j.ydbio.2009.02.029. Epub 2009 Mar 4.

8.

A gene regulatory network armature for T lymphocyte specification.

Georgescu C, Longabaugh WJ, Scripture-Adams DD, David-Fung ES, Yui MA, Zarnegar MA, Bolouri H, Rothenberg EV.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20100-5. doi: 10.1073/pnas.0806501105. Epub 2008 Dec 22.

9.

Visualization, documentation, analysis, and communication of large-scale gene regulatory networks.

Longabaugh WJ, Davidson EH, Bolouri H.

Biochim Biophys Acta. 2009 Apr;1789(4):363-74. doi: 10.1016/j.bbagrm.2008.07.014. Epub 2008 Aug 6. Review.

10.

Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning.

Vokes SA, Ji H, McCuine S, Tenzen T, Giles S, Zhong S, Longabaugh WJ, Davidson EH, Wong WH, McMahon AP.

Development. 2007 May;134(10):1977-89. Epub 2007 Apr 18.

11.

Computational representation of developmental genetic regulatory networks.

Longabaugh WJ, Davidson EH, Bolouri H.

Dev Biol. 2005 Jul 1;283(1):1-16. Review.

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