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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.

PMID:
24885193
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
23216909
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
22941959
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
22524279
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Mining PeptideAtlas for biomarkers and therapeutics in human disease.

Killcoyne S, Deutsch EW, Boyle J.

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

PMID:
22236120
[PubMed - indexed for MEDLINE]
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.

PMID:
21851633
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
20700479
[PubMed]
Free PMC Article
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.

PMID:
20630057
[PubMed - indexed for MEDLINE]
Free PMC Article
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
[PubMed - indexed for MEDLINE]
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.

PMID:
19265554
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
18578887
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
17947979
[PubMed - indexed for MEDLINE]
Free PMC Article
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].

PMID:
17169983
[PubMed - indexed for MEDLINE]
Free PMC Article

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