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Items: 1 to 20 of 73

1.

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.

Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP.

Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18.

2.

Data integration in biological research: an overview.

Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV.

J Biol Res (Thessalon). 2015 Sep 2;22(1):9. doi: 10.1186/s40709-015-0032-5. eCollection 2015 Dec. Review.

3.

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I.

Gigascience. 2015 Aug 25;4:38. doi: 10.1186/s13742-015-0077-2. eCollection 2015. Review.

4.

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

Guardia GD, Pires LF, Vêncio RZ, Malmegrim KC, de Farias CR.

PLoS One. 2015 Jul 24;10(7):e0134011. doi: 10.1371/journal.pone.0134011. eCollection 2015.

5.

SEEK: a systems biology data and model management platform.

Wolstencroft K, Owen S, Krebs O, Nguyen Q, Stanford NJ, Golebiewski M, Weidemann A, Bittkowski M, An L, Shockley D, Snoep JL, Mueller W, Goble C.

BMC Syst Biol. 2015 Jul 11;9:33. doi: 10.1186/s12918-015-0174-y.

6.

Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome.

Marin TL, Gongol B, Martin M, King SJ, Smith L, Johnson DA, Subramaniam S, Chien S, Shyy JY.

BMC Syst Biol. 2015 Mar 11;9:13. doi: 10.1186/s12918-015-0156-0.

7.

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.

Reiss DJ, Plaisier CL, Wu WJ, Baliga NS.

Nucleic Acids Res. 2015 Jul 27;43(13):e87. doi: 10.1093/nar/gkv300. Epub 2015 Apr 14.

8.

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA.

Proteomics. 2015 Mar;15(5-6):930-49. doi: 10.1002/pmic.201400302. Review.

9.

A digital repository with an extensible data model for biobanking and genomic analysis management.

Izzo M, Mortola F, Arnulfo G, Fato MM, Varesio L.

BMC Genomics. 2014;15 Suppl 3:S3. doi: 10.1186/1471-2164-15-S3-S3. Epub 2014 May 6.

10.

R-based software for the integration of pathway data into bioinformatic algorithms.

Kramer F, Bayerlová M, Beißbarth T.

Biology (Basel). 2014 Feb 7;3(1):85-100. doi: 10.3390/biology3010085.

11.

FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.

Mader M, Simon R, Kurtz S.

J Clin Bioinforma. 2014 Mar 31;4(1):5. doi: 10.1186/2043-9113-4-5.

12.

Semantic integration of gene expression analysis tools and data sources using software connectors.

Miyazaki FA, Guardia GD, Vêncio RZ, de Farias CR.

BMC Genomics. 2013 Oct 25;14 Suppl 6:S2. doi: 10.1186/1471-2164-14-S6-S2.

13.

Network portal: a database for storage, analysis and visualization of biological networks.

Turkarslan S, Wurtmann EJ, Wu WJ, Jiang N, Bare JC, Foley K, Reiss DJ, Novichkov P, Baliga NS.

Nucleic Acids Res. 2014 Jan;42(Database issue):D184-90. doi: 10.1093/nar/gkt1190. Epub 2013 Nov 23.

14.

Evolutionary etiology of high-grade astrocytomas.

Song Y, Zhang Q, Kutlu B, Difilippantonio S, Bash R, Gilbert D, Yin C, O'Sullivan TN, Yang C, Kozlov S, Bullitt E, McCarthy KD, Kafri T, Louis DN, Miller CR, Hood L, Van Dyke T.

Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17933-8. doi: 10.1073/pnas.1317026110. Epub 2013 Oct 10.

15.

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen.

Yoon SH, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie TJ, Slagel J, Moritz RL, Hackett M, Leigh JA, Baliga NS.

Genome Res. 2013 Nov;23(11):1839-51. doi: 10.1101/gr.153916.112. Epub 2013 Oct 2.

16.

STAR: an integrated solution to management and visualization of sequencing data.

Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W.

Bioinformatics. 2013 Dec 15;29(24):3204-10. doi: 10.1093/bioinformatics/btt558. Epub 2013 Sep 27.

17.

JBioWH: an open-source Java framework for bioinformatics data integration.

Vera R, Perez-Riverol Y, Perez S, Ligeti B, Kertész-Farkas A, Pongor S.

Database (Oxford). 2013 Jul 11;2013:bat051. doi: 10.1093/database/bat051. Print 2013.

18.

Review of software tools for design and analysis of large scale MRM proteomic datasets.

Colangelo CM, Chung L, Bruce C, Cheung KH.

Methods. 2013 Jun 15;61(3):287-98. doi: 10.1016/j.ymeth.2013.05.004. Epub 2013 May 21. Review.

19.

Architecture for interoperable software in biology.

Bare JC, Baliga NS.

Brief Bioinform. 2014 Jul;15(4):626-36. doi: 10.1093/bib/bbs074. Epub 2012 Dec 11.

20.

Bioinformatics Resource Manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools.

Tilton SC, Tal TL, Scroggins SM, Franzosa JA, Peterson ES, Tanguay RL, Waters KM.

BMC Bioinformatics. 2012 Nov 23;13:311. doi: 10.1186/1471-2105-13-311.

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