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Items: 1 to 20 of 81

1.

GeneDesign 3.0 is an updated synthetic biology toolkit.

Richardson SM, Nunley PW, Yarrington RM, Boeke JD, Bader JS.

Nucleic Acids Res. 2010 May;38(8):2603-6. doi: 10.1093/nar/gkq143. Epub 2010 Mar 8.

2.

Design-A-Gene with GeneDesign.

Richardson SM, Liu S, Boeke JD, Bader JS.

Methods Mol Biol. 2012;852:235-47. doi: 10.1007/978-1-61779-564-0_18.

PMID:
22328438
3.

GeneDesign: rapid, automated design of multikilobase synthetic genes.

Richardson SM, Wheelan SJ, Yarrington RM, Boeke JD.

Genome Res. 2006 Apr;16(4):550-6. Epub 2006 Feb 15.

4.

A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD.

Wilson ML, Hertzberg R, Adam L, Peccoud J.

Methods Enzymol. 2011;498:173-88. doi: 10.1016/B978-0-12-385120-8.00008-5.

PMID:
21601678
5.

The new protein topology graph library web server.

Schäfer T, Scheck A, Bruneß D, May P, Koch I.

Bioinformatics. 2016 Feb 1;32(3):474-6. doi: 10.1093/bioinformatics/btv574. Epub 2015 Oct 6.

PMID:
26446136
6.

The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications.

Moreland JL, Gramada A, Buzko OV, Zhang Q, Bourne PE.

BMC Bioinformatics. 2005 Feb 6;6:21.

7.

The Bioperl toolkit: Perl modules for the life sciences.

Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E.

Genome Res. 2002 Oct;12(10):1611-8.

8.

MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

Cai JJ, Smith DK, Xia X, Yuen KY.

BMC Bioinformatics. 2005 Mar 22;6:64.

9.

NeuroTerrain--a client-server system for browsing 3D biomedical image data sets.

Gustafson C, Bug WJ, Nissanov J.

BMC Bioinformatics. 2007 Feb 5;8:40.

10.

The design of Jemboss: a graphical user interface to EMBOSS.

Carver T, Bleasby A.

Bioinformatics. 2003 Sep 22;19(14):1837-43.

PMID:
14512356
11.

ArrayQuest: a web resource for the analysis of DNA microarray data.

Argraves GL, Jani S, Barth JL, Argraves WS.

BMC Bioinformatics. 2005 Dec 1;6:287.

12.

The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression.

Wu G, Bashir-Bello N, Freeland SJ.

Protein Expr Purif. 2006 Jun;47(2):441-5. Epub 2005 Nov 15.

PMID:
16376569
13.

CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.

Kohlhoff KJ, Sosnick MH, Hsu WT, Pande VS, Altman RB.

Bioinformatics. 2011 Aug 15;27(16):2322-3. doi: 10.1093/bioinformatics/btr386. Epub 2011 Jun 27.

14.

3Dmol.js: molecular visualization with WebGL.

Rego N, Koes D.

Bioinformatics. 2015 Apr 15;31(8):1322-4. doi: 10.1093/bioinformatics/btu829. Epub 2014 Dec 12.

15.

GoldenBraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology.

Sarrion-Perdigones A, Vazquez-Vilar M, Palací J, Castelijns B, Forment J, Ziarsolo P, Blanca J, Granell A, Orzaez D.

Plant Physiol. 2013 Jul;162(3):1618-31.

16.

GeneXplorer: an interactive web application for microarray data visualization and analysis.

Rees CA, Demeter J, Matese JC, Botstein D, Sherlock G.

BMC Bioinformatics. 2004 Oct 1;5:141.

17.

PlasMapper: a web server for drawing and auto-annotating plasmid maps.

Dong X, Stothard P, Forsythe IJ, Wishart DS.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W660-4.

18.

PEDANT genome database: 10 years online.

Riley ML, Schmidt T, Artamonova II, Wagner C, Volz A, Heumann K, Mewes HW, Frishman D.

Nucleic Acids Res. 2007 Jan;35(Database issue):D354-7. Epub 2006 Dec 5.

19.

A set of Macintosh computer programs for the design and analysis of synthetic genes.

Weiner MP, Scheraga HA.

Comput Appl Biosci. 1989 Jul;5(3):191-8.

PMID:
2569922
20.

PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy.

Müller P, Schwille P, Weidemann T.

Bioinformatics. 2014 Sep 1;30(17):2532-3. doi: 10.1093/bioinformatics/btu328. Epub 2014 May 13.

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