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Items: 1 to 20 of 110

1.

Semantic integration of data on transcriptional regulation.

Baitaluk M, Ponomarenko J.

Bioinformatics. 2010 Jul 1;26(13):1651-61. doi: 10.1093/bioinformatics/btq231.

2.

An integrative approach to inferring gene regulatory module networks.

Baitaluk M, Kozhenkov S, Ponomarenko J.

PLoS One. 2012;7(12):e52836. doi: 10.1371/journal.pone.0052836.

3.

IntegromeDB: an integrated system and biological search engine.

Baitaluk M, Kozhenkov S, Dubinina Y, Ponomarenko J.

BMC Genomics. 2012 Jan 19;13:35. doi: 10.1186/1471-2164-13-35.

4.

BiologicalNetworks 2.0--an integrative view of genome biology data.

Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M.

BMC Bioinformatics. 2010 Dec 29;11:610. doi: 10.1186/1471-2105-11-610.

5.

Learning protein-DNA interaction landscapes by integrating experimental data through computational models.

Zhong J, Wasson T, Hartemink AJ.

Bioinformatics. 2014 Oct 15;30(20):2868-74. doi: 10.1093/bioinformatics/btu408.

6.

BiologicalNetworks: visualization and analysis tool for systems biology.

Baitaluk M, Sedova M, Ray A, Gupta A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W466-71.

7.

Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data.

Ma S, Jiang T, Jiang R.

Bioinformatics. 2015 Feb 15;31(4):563-71. doi: 10.1093/bioinformatics/btu672.

PMID:
25322838
8.

A new method to measure the semantic similarity of GO terms.

Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF.

Bioinformatics. 2007 May 15;23(10):1274-81.

PMID:
17344234
9.

BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies.

Kozhenkov S, Sedova M, Dubinina Y, Gupta A, Ray A, Ponomarenko J, Baitaluk M.

BMC Syst Biol. 2011 Jan 14;5:7. doi: 10.1186/1752-0509-5-7.

10.

EGAN: exploratory gene association networks.

Paquette J, Tokuyasu T.

Bioinformatics. 2010 Jan 15;26(2):285-6. doi: 10.1093/bioinformatics/btp656.

11.

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

12.

Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic.

Gu J, Xuan J, Riggins RB, Chen L, Wang Y, Clarke R.

Bioinformatics. 2012 Aug 1;28(15):1990-7. doi: 10.1093/bioinformatics/bts296. Erratum in: Bioinformatics. 2014 Aug 1;30(15):2242.

13.

Finding gene regulatory network candidates using the gene expression knowledge base.

Venkatesan A, Tripathi S, Sanz de Galdeano A, Blondé W, Lægreid A, Mironov V, Kuiper M.

BMC Bioinformatics. 2014 Dec 10;15:386. doi: 10.1186/s12859-014-0386-y.

14.

Discriminating response groups in metabolic and regulatory pathway networks.

Van Hemert JL, Dickerson JA.

Bioinformatics. 2012 Apr 1;28(7):947-54. doi: 10.1093/bioinformatics/bts039.

PMID:
22308149
15.

PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning.

Melott JM, Weinstein JN, Broom BM.

Bioinformatics. 2016 Jan 15;32(2):312-4. doi: 10.1093/bioinformatics/btv554.

16.

Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival.

Suo C, Hrydziuszko O, Lee D, Pramana S, Saputra D, Joshi H, Calza S, Pawitan Y.

Bioinformatics. 2015 Aug 15;31(16):2607-13. doi: 10.1093/bioinformatics/btv164.

PMID:
25810432
17.

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.

18.

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.

19.

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.

Park CY, Krishnan A, Zhu Q, Wong AK, Lee YS, Troyanskaya OG.

Bioinformatics. 2015 Apr 1;31(7):1093-101. doi: 10.1093/bioinformatics/btu786.

20.

Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources.

Blom EJ, Breitling R, Hofstede KJ, Roerdink JB, van Hijum SA, Kuipers OP.

BMC Genomics. 2008 Oct 21;9:495. doi: 10.1186/1471-2164-9-495.

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