TEAM PUBLICATIONS

Articles co-authored by members of the GENEVESTIGATOR team. For articles that have cited GENEVESTIGATOR, please check Google Scholar using the keyword "GENEVESTIGATOR".

Zimmermann P, Bleuler S, Laule O, Martin F, Ivanov NV, Campanoni P, Oishi K, Lugon-Moulin N, Wyss M, Hruz T and W Gruissem (2014) ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions.BioData Mining 2014, 7:18. [ Abstract ]

Prasad A, Suresh Kumar S, Dessimoz C, Bleuler S, Laule O, Hruz T, Gruissem W, and P Zimmermann (2013) Global regulatory architecture of human, mouse and rat tissue transcriptomes.BMC Genomics 2013, 14:716. [ Abstract ]

Meskauskiene R, Laule O, Ivanov NV, Martin F, Wyss M, Gruissem W, and P Zimmermann (2013) Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. Plant Methods 2013, 9:33. [ Abstract ]

Hruz T, Wyss M, Lucas C, Laule O, von Rohr P, Zimmermann P, and S Bleuler (2013) A Multilevel Gamma-Clustering Layout Algorithm for Visualization of Biological Networks. Advances in Bioinformatics, vol. 2013, Article ID 920325, 10 pages, 2013. doi:10.1155/2013/920325. [ Full text ]

Hruz T, Wyss M, Docquier M, Pfaffl MW, Masanetz S, Borghi L, Verbrugge P, Kalaydjieva L, Bleuler S, Laule O, Descombes P, Gruissem W and P Zimmermann (2011) RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. BMC Genomics 2011, 12:156. [ Abstract ]

Zimmermann P, Laule O, Schmitz J, Hruz T, Bleuler S, and W Gruissem (2008) Genevestigator Transcriptome Meta-Analysis and Biomarker Search Using Rice and Barley Gene Expression Databases. Molecular Plant 1 (5), 851-857. [ Abstract ]

Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W and P Zimmermann (2008) Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Advances in Bioinformatics 2008, 420747 [Full Text ]

Bleuler S, Zimmermann P, Friberg M, and E Zitzler (2007) Discovering Trends in Gene Expression Data Using a Hybrid Evolutionary Algorithm Algorithmic Operations Research, Vol 3(2)

Grennan AK (2006) Genevestigator. Facilitating web-based gene-expression analysis. Plant Physiology 141(4):1164-6 [PubMed ]

Hruz T, Hirsch-Hoffmann M, Gruissem W, and P Zimmermann (2006) Reducing Java Internet project risks: a case study of public measurement of client component functionality in the user community PPPJ06, pp. 199-202 

Laule O, Hirsch-Hoffmann M, Hruz T, Gruissem W, and P Zimmermann (2006) Web-based analysis of the mouse transcriptome using Genevestigator BMC Bioinformatics 7, 311 [Full text ]

Schöner D, Barkow S, Bleuler S, Bühlmann P, Gruissem W, Hennig L, Wille A, Zimmermmann P, and E Zitzler (2006) Network analysis of systems elements In: Plant Systems Biology (ed. S. Baginsky and A. Fernie), Birkhäuser Verlag.

Hennig L and P Zimmermann (2006) Data warehouses - Your one-stop-shops for microarray data In: European Training and Networking Activity. Plant Genomics and Bioinformatics Expression Micro Arrays and Beyond – a course book (ed. J. Freitag), MPI-MPP 2006, Potsdam-Golm, pp. 211-217

Zimmermann P, Schildknecht B, Garcia-Hernandez M, Gruissem W, Craigon D, Mukherjee G, May S, Parkinson H, Rhee S, Wagner U, and L Hennig (2006) MIAME/Plant - adding value to plant microarrray experiments Plant Methods  2 , 1 [PubMed ]

Prelic A, Bleuler S, Zimmermann P, Wille A, Bühlmann P, Gruissem W, Hennig L, Thiele L, and E Zitzler (2006) A systematic comparison and evaluation of biclustering methods for gene expression data Bioinformatics  22 , 1122-112 [PubMed ]

Barkow S, Bleuler S, Prelic A, Zimmermann P, and E Zitzler (2006) BicAT: a biclustering analysis toolbox Bioinformatics 22(10): 1282-1283 [PubMed ]

Zimmermann P, Hennig L, and W Gruissem (2005) Gene expression analysis and network discovery using Genevestigator Trends in Plant Science 9 10 , 407-409 [PubMed ]

Zimmermann P, Hirsch-Hoffmann M, Hennig L, and W Gruissem (2004) GENEVESTIGATOR: Arabidopsis Microarray Database and Analysis Toolbox Plant Physiology 136 1 , 2621-2632 [PubMed ] (most frequently cited GENEVESTIGATOR paper)

Wille A, Zimmermann P, Vranová E, Bleuler S, Fürholz A, Hennig L, Laule O, Prelíc A, von Rohr P, Thiele L, Zitzler E, Gruissem W, and P Bühlmann (2004) Sparse graphical gaussian modeling for genetic regulatory network inference Genome Biology  5 , R92.1-R92.13 [PubMed ]