PubMed

MIAME/Plant - adding value to plant microarrray experiments.

Zimmermann P, Schildknecht B, Craigon D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee S, Wagner U, Hennig L.

Plant Methods. 2006 Jan 9;2:1.PMID: 16401339 [PubMed - in process]Related articlesFree article

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.PMID: 18801157 [PubMed - indexed for MEDLINE]Related articlesFree article

The MGED Ontology: a resource for semantics-based description of microarray experiments.

Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr.

Bioinformatics. 2006 Apr 1;22(7):866-73. Epub 2006 Jan 21.PMID: 16428806 [PubMed - indexed for MEDLINE]Related articlesFree article

KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours.

Draghici S, Tarca AL, Yu L, Ethier S, Romero R.

Bioinformatics. 2008 Mar 1;24(5):738-40. Epub 2007 Nov 17.PMID: 18024967 [PubMed - indexed for MEDLINE]Related articlesFree article

Annotation of environmental OMICS data: application to the transcriptomics domain.

Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, Allen MJ, Wilson WH, Olive P, Last K, Kramer C, Bailhache T, Reeves J, Pallett D, Warne J, Nashar K, Parkinson H, Sansone SA, Rocca-Serra P, Stevens R, Snape J, Brass A, Field D.

OMICS. 2006 Summer;10(2):172-8. Review.PMID: 16901223 [PubMed - indexed for MEDLINE]Related articles

MGED standards: work in progress.

Ball CA, Brazma A.

OMICS. 2006 Summer;10(2):138-44. Review.PMID: 16901218 [PubMed - indexed for MEDLINE]Related articles

The MGED Ontology: A Framework for Describing Functional Genomics Experiments.

Stoeckert CJ, Parkinson H.

Comp Funct Genomics. 2003;4(1):127-32.PMID: 18629093 [PubMed - in process]Related articlesFree article

SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data.

Menssen A, Edinger G, Grün JR, Haase U, Baumgrass R, Grützkau A, Radbruch A, Burmester GR, Häupl T.

BMC Genomics. 2009 Mar 5;10:98.PMID: 19265543 [PubMed - indexed for MEDLINE]Related articlesFree article

Web-based analysis of the mouse transcriptome using Genevestigator.

Laule O, Hirsch-Hoffmann M, Hruz T, Gruissem W, Zimmermann P.

BMC Bioinformatics. 2006 Jun 21;7:311.PMID: 16790046 [PubMed - indexed for MEDLINE]Related articlesFree article

MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation.

Hermida L, Schaad O, Demougin P, Descombes P, Primig M.

BMC Bioinformatics. 2006 Apr 5;7:190.PMID: 16597336 [PubMed - indexed for MEDLINE]Related articlesFree article

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.

BMC Bioinformatics. 2006 Nov 6;7:489.PMID: 17087822 [PubMed - indexed for MEDLINE]Related articlesFree article

A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research.

Köhl KI, Basler G, Lüdemann A, Selbig J, Walther D.

Plant Methods. 2008 May 21;4:11.PMID: 18495032 [PubMed - in process]Related articlesFree article

MADIBA: a web server toolkit for biological interpretation of Plasmodium and plant gene clusters.

Law PJ, Claudel-Renard C, Joubert F, Louw AI, Berger DK.

BMC Genomics. 2008 Feb 28;9:105.PMID: 18307768 [PubMed - indexed for MEDLINE]Related articlesFree article

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.

Brazma A.

ScientificWorldJournal. 2009 May 29;9:420-3.PMID: 19484163 [PubMed - indexed for MEDLINE]Related articles

Applications of carboxylesterase activity in environmental monitoring and toxicity identification evaluations (TIEs).

Wheelock CE, Phillips BM, Anderson BS, Miller JL, Miller MJ, Hammock BD.

Rev Environ Contam Toxicol. 2008;195:117-78. Review.PMID: 18418956 [PubMed - indexed for MEDLINE]Related articles

An ontology of scientific experiments.

Soldatova LN, King RD.

J R Soc Interface. 2006 Dec 22;3(11):795-803.PMID: 17015305 [PubMed - indexed for MEDLINE]Related articlesFree article

AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips.

Frickey T, Benedito VA, Udvardi M, Weiller G.

Plant Physiol. 2008 Feb;146(2):377-86. Epub 2007 Dec 7.PMID: 18065560 [PubMed - indexed for MEDLINE]Related articlesFree article

Using ontologies to annotate microarray experiments.

Whetzel PL, Parkinson H, Stoeckert CJ Jr.

Methods Enzymol. 2006;411:325-39. Review.PMID: 16939798 [PubMed - indexed for MEDLINE]Related articles

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Kuhn A, Luthi-Carter R, Delorenzi M.

BMC Bioinformatics. 2008 Jan 17;9:26.PMID: 18201381 [PubMed - indexed for MEDLINE]Related articlesFree article

Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes.

Brock GN, Shaffer JR, Blakesley RE, Lotz MJ, Tseng GC.

BMC Bioinformatics. 2008 Jan 10;9:12.PMID: 18186917 [PubMed - indexed for MEDLINE]Related articlesFree article