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Items: 15

1.

Oxido-reductive regulation of vascular remodeling by receptor tyrosine kinase ROS1.

Ali ZA, de Jesus Perez V, Yuan K, Orcholski M, Pan S, Qi W, Chopra G, Adams C, Kojima Y, Leeper NJ, Qu X, Zaleta-Rivera K, Kato K, Yamada Y, Oguri M, Kuchinsky A, Hazen SL, Jukema JW, Ganesh SK, Nabel EG, Channon K, Leon MB, Charest A, Quertermous T, Ashley EA.

J Clin Invest. 2014 Dec;124(12):5159-74. doi: 10.1172/JCI77484.

2.

enhancedGraphics: a Cytoscape app for enhanced node graphics.

Morris JH, Kuchinsky A, Ferrin TE, Pico AR.

F1000Res. 2014 Jul 1;3:147. doi: 10.12688/f1000research.4460.1.

3.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grünberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM.

Nat Biotechnol. 2014 Jun;32(6):545-50. doi: 10.1038/nbt.2891.

PMID:
24911500
4.

Mosaic: making biological sense of complex networks.

Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR.

Bioinformatics. 2012 Jul 15;28(14):1943-4. doi: 10.1093/bioinformatics/bts278.

5.

GLay: community structure analysis of biological networks.

Su G, Kuchinsky A, Morris JH, States DJ, Meng F.

Bioinformatics. 2010 Dec 15;26(24):3135-7. doi: 10.1093/bioinformatics/btq596.

6.

Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection.

Flórez AF, Park D, Bhak J, Kim BC, Kuchinsky A, Morris JH, Espinosa J, Muskus C.

BMC Bioinformatics. 2010 Sep 27;11:484. doi: 10.1186/1471-2105-11-484.

7.

Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors.

Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR.

PLoS Comput Biol. 2009 Nov;5(11):e1000553. doi: 10.1371/journal.pcbi.1000553.

8.

Exploring biological networks with Cytoscape software.

Yeung N, Cline MS, Kuchinsky A, Smoot ME, Bader GD.

Curr Protoc Bioinformatics. 2008 Sep;Chapter 8:Unit 8.13. doi: 10.1002/0471250953.bi0813s23.

PMID:
18819078
9.

VistaClara: an expression browser plug-in for Cytoscape.

Kincaid R, Kuchinsky A, Creech M.

Bioinformatics. 2008 Sep 15;24(18):2112-4. doi: 10.1093/bioinformatics/btn368.

10.

Cytoscape ESP: simple search of complex biological networks.

Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ.

Bioinformatics. 2008 Jun 15;24(12):1465-6. doi: 10.1093/bioinformatics/btn208.

11.

Integrating genetic, functional genomic, and bioinformatics data in a systems biology approach to complex diseases: application to schizophrenia.

Middleton FA, Rosenow C, Vailaya A, Kuchinsky A, Pato MT, Pato CN.

Methods Mol Biol. 2007;401:337-64. doi: 10.1007/978-1-59745-520-6_18. Review.

PMID:
18368374
12.

Integration of biological networks and gene expression data using Cytoscape.

Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD.

Nat Protoc. 2007;2(10):2366-82.

13.

Network analysis of human in-stent restenosis.

Ashley EA, Ferrara R, King JY, Vailaya A, Kuchinsky A, He X, Byers B, Gerckens U, Oblin S, Tsalenko A, Soito A, Spin JM, Tabibiazar R, Connolly AJ, Simpson JB, Grube E, Quertermous T.

Circulation. 2006 Dec 12;114(24):2644-54.

14.

Pathway analysis of coronary atherosclerosis.

King JY, Ferrara R, Tabibiazar R, Spin JM, Chen MM, Kuchinsky A, Vailaya A, Kincaid R, Tsalenko A, Deng DX, Connolly A, Zhang P, Yang E, Watt C, Yakhini Z, Ben-Dor A, Adler A, Bruhn L, Tsao P, Quertermous T, Ashley EA.

Physiol Genomics. 2005 Sep 21;23(1):103-18.

15.

An architecture for biological information extraction and representation.

Vailaya A, Bluvas P, Kincaid R, Kuchinsky A, Creech M, Adler A.

Bioinformatics. 2005 Feb 15;21(4):430-8.

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