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Analysis of a single Helicobacter pylori strain over a 10-year period in a primate model.

Liu H, Fero JB, Mendez M, Carpenter BM, Servetas SL, Rahman A, Goldman MD, Boren T, Salama NR, Merrell DS, Dubois A.

Int J Med Microbiol. 2015 May;305(3):392-403. doi: 10.1016/j.ijmm.2015.03.002. Epub 2015 Mar 6.


BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data.

Wu H, Fujiwara T, Yamamoto Y, Bolleman J, Yamaguchi A.

J Biomed Semantics. 2014 Jul 10;5:32. doi: 10.1186/2041-1480-5-32. eCollection 2014.


Review of biological network data and its applications.

Yu D, Kim M, Xiao G, Hwang TH.

Genomics Inform. 2013 Dec;11(4):200-10. doi: 10.5808/GI.2013.11.4.200. Epub 2013 Dec 31. Review.


The putative Poc complex controls two distinct Pseudomonas aeruginosa polar motility mechanisms.

Cowles KN, Moser TS, Siryaporn A, Nyakudarika N, Dixon W, Turner JJ, Gitai Z.

Mol Microbiol. 2013 Dec;90(5):923-38. doi: 10.1111/mmi.12403. Epub 2013 Oct 16.


A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology.

Seidl MF, Schneider A, Govers F, Snel B.

BMC Genomics. 2013 Jul 17;14:483. doi: 10.1186/1471-2164-14-483.


Loss of a 20S proteasome activator in Saccharomyces cerevisiae downregulates genes important for genomic integrity, increases DNA damage, and selectively sensitizes cells to agents with diverse mechanisms of action.

Doherty KM, Pride LD, Lukose J, Snydsman BE, Charles R, Pramanik A, Muller EG, Botstein D, Moore CW.

G3 (Bethesda). 2012 Aug;2(8):943-59. doi: 10.1534/g3.112.003376. Epub 2012 Aug 1.


eXframe: reusable framework for storage, analysis and visualization of genomics experiments.

Sinha AU, Merrill E, Armstrong SA, Clark TW, Das S.

BMC Bioinformatics. 2011 Nov 21;12:452. doi: 10.1186/1471-2105-12-452.


The collagen chaperone HSP47 is a new interactor of APP that affects the levels of extracellular beta-amyloid peptides.

Bianchi FT, Camera P, Ala U, Imperiale D, Migheli A, Boda E, Tempia F, Berto G, Bosio Y, Oddo S, LaFerla FM, Taraglio S, Dotti CG, Di Cunto F.

PLoS One. 2011;6(7):e22370. doi: 10.1371/journal.pone.0022370. Epub 2011 Jul 28.


Data standards for Omics data: the basis of data sharing and reuse.

Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ Jr, Taylor CF, Taylor R, Ball CA.

Methods Mol Biol. 2011;719:31-69. doi: 10.1007/978-1-61779-027-0_2. Review.


AphA and LuxR/HapR reciprocally control quorum sensing in vibrios.

Rutherford ST, van Kessel JC, Shao Y, Bassler BL.

Genes Dev. 2011 Feb 15;25(4):397-408. doi: 10.1101/gad.2015011.


Quality assessment of transcriptome data using intrinsic statistical properties.

Brysbaert G, Pellay FX, Noth S, Benecke A.

Genomics Proteomics Bioinformatics. 2010 Mar;8(1):57-71. doi: 10.1016/S1672-0229(10)60006-X.


The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database.

Tagmount A, Wang M, Lindquist E, Tanaka Y, Teranishi KS, Sunagawa S, Wong M, Stillman JH.

PLoS One. 2010 Feb 19;5(2):e9327. doi: 10.1371/journal.pone.0009327.


Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments.

Celton M, Malpertuy A, Lelandais G, de Brevern AG.

BMC Genomics. 2010 Jan 7;11:15. doi: 10.1186/1471-2164-11-15.


Cordycepin interferes with 3' end formation in yeast independently of its potential to terminate RNA chain elongation.

Holbein S, Wengi A, Decourty L, Freimoser FM, Jacquier A, Dichtl B.

RNA. 2009 May;15(5):837-49. doi: 10.1261/rna.1458909. Epub 2009 Mar 26.


A complex-based reconstruction of the Saccharomyces cerevisiae interactome.

Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walther TC, Krogan NJ, Koller D.

Mol Cell Proteomics. 2009 Jun;8(6):1361-81. doi: 10.1074/mcp.M800490-MCP200. Epub 2009 Jan 27.


MiMiR--an integrated platform for microarray data sharing, mining and analysis.

Tomlinson C, Thimma M, Alexandrakis S, Castillo T, Dennis JL, Brooks A, Bradley T, Turnbull C, Blaveri E, Barton G, Chiba N, Maratou K, Soutter P, Aitman T, Game L.

BMC Bioinformatics. 2008 Sep 18;9:379. doi: 10.1186/1471-2105-9-379.


Navigating public microarray databases.

Penkett CJ, Bähler J.

Comp Funct Genomics. 2004;5(6-7):471-9. doi: 10.1002/cfg.427.


Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy.

Kim WK, Krumpelman C, Marcotte EM.

Genome Biol. 2008;9 Suppl 1:S5. doi: 10.1186/gb-2008-9-s1-s5. Epub 2008 Jun 27.

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