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Results: 13

1.

FIGG: simulating populations of whole genome sequences for heterogeneous data analyses.

Killcoyne S, del Sol A.

BMC Bioinformatics. 2014 May 19;15:149. doi: 10.1186/1471-2105-15-149.

2.

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.

Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.

BMC Bioinformatics. 2012 Dec 5;13:324. doi: 10.1186/1471-2105-13-324.

3.

Interfaces to PeptideAtlas: a case study of standard data access systems.

Killcoyne S, Handcock J, Robinson T, Deutsch EW, Boyle J.

Brief Bioinform. 2012 Sep;13(5):615-26. doi: 10.1093/bib/bbr067. Epub 2011 Nov 22.

4.

Methods for visual mining of genomic and proteomic data atlases.

Boyle J, Kreisberg R, Bressler R, Killcoyne S.

BMC Bioinformatics. 2012 Apr 23;13:58. doi: 10.1186/1471-2105-13-58.

5.

Mining PeptideAtlas for biomarkers and therapeutics in human disease.

Killcoyne S, Deutsch EW, Boyle J.

Curr Pharm Des. 2012;18(6):748-54.

6.

SAMQA: error classification and validation of high-throughput sequenced read data.

Robinson T, Killcoyne S, Bressler R, Boyle J.

BMC Genomics. 2011 Aug 18;12:419. doi: 10.1186/1471-2164-12-419.

7.

Managing Chaos: Lessons Learned Developing Software in the Life Sciences.

Killcoyne S, Boyle J.

Comput Sci Eng. 2009 Nov;11(6):20-29. No abstract available.

8.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

Burdick DB, Cavnor CC, Handcock J, Killcoyne S, Lin J, Marzolf B, Ramsey SA, Rovira H, Bressler R, Shmulevich I, Boyle J.

BMC Bioinformatics. 2010 Jul 14;11:377. doi: 10.1186/1471-2105-11-377.

9.

Cytoscape: a community-based framework for network modeling.

Killcoyne S, Carter GW, Smith J, Boyle J.

Methods Mol Biol. 2009;563:219-39. doi: 10.1007/978-1-60761-175-2_12.

PMID:
19597788
10.

Adaptable data management for systems biology investigations.

Boyle J, Rovira H, Cavnor C, Burdick D, Killcoyne S, Shmulevich I.

BMC Bioinformatics. 2009 Mar 6;10:79. doi: 10.1186/1471-2105-10-79.

11.

Systems biology driven software design for the research enterprise.

Boyle J, Cavnor C, Killcoyne S, Shmulevich I.

BMC Bioinformatics. 2008 Jun 25;9:295. doi: 10.1186/1471-2105-9-295.

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.

T1DBase: integration and presentation of complex data for type 1 diabetes research.

Hulbert EM, Smink LJ, Adlem EC, Allen JE, Burdick DB, Burren OS, Cassen VM, Cavnor CC, Dolman GE, Flamez D, Friery KF, Healy BC, Killcoyne SA, Kutlu B, Schuilenburg H, Walker NM, Mychaleckyj J, Eizirik DL, Wicker LS, Todd JA, Goodman N.

Nucleic Acids Res. 2007 Jan;35(Database issue):D742-6. Epub 2006 Dec 14. Erratum in: Nucleic Acids Res. 2007;35(18):6338. Cassen, Victor M [added].

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