Publications using ermineJ

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Here are the publications we know about that involved the use of ermineJ:

• Li M, Zhu L, Li X, Shuai S, Teng X, Xiao H, Li Q, Chen L, Guo Y, Wang J. Sci China C Life Sci. 2008 Expression profiling analysis for genes related to meat quality and carcass traits during postnatal development of backfat in two pig breeds.Aug;51(8):718-33.
• Kant P, Gordon M, Kant S, Zolla G, Davydov O, Heimer YM, Chalifa-Caspi V, Shaked R, Barak S. Plant Cell Environ. 2008 Functional-genomics-based identification of genes that regulate Arabidopsis responses to multiple abiotic stresses. Jun;31(6):697-714.
• Baron CA, Tepper CG, Liu SY, Davis RR, Wang NJ, Schanen NC, Gregg JP. Genomic and functional profiling of duplicated chromosome 15 cell lines reveal regulatory alterations in UBE3A-associated ubiquitin-proteasome pathway processes. Hum Mol Genet. 2006 Mar 15;15(6):853-69.
• Huang Y, Yan J, Lubet R, Kensler TW, Sutter TR. Identification of novel transcriptional networks in response to treatment with the anticarcinogen 3H-1,2-dithiole-3-thione. Physiol Genomics. 2006 Jan 12;24(2):144-53.
• AE Loraine, ML Salmi, SC Stout, SJ Roux. Gene-Ontology-based analysis of gene expression changes in early development of Ceratopteris spores. 2005 IEEE Computational Systems Bioinformatics Conference.
• Katsel P, Davis KL, Haroutunian V. Variations in myelin and oligodendrocyte-related gene expression across multiple brain regions in schizophrenia: A gene ontology study. Schizophr Res. 2005
• Kong SW, Bodyak N, Yue P, Liu Z, Brown J, Izumo S, Kang PM. Genetic expression profiles during physiological and pathological cardiac hypertrophy and heart failure in rats. Physiol. Genomics 21: 34-42, 2005
• Erraji-Benchekroun L, Underwood MD, Arango V, et al. Molecular aging in human prefrontal cortex is selective and continuous throughout adult life BIOLOGICAL PSYCHIATRY 57 (5): 549-558 MAR 1 2005
• Barr, G.A., Gao, P. Wang, S., Cheng, J. Qin, J., Sibille, E. and Pavlidis, P. Developmental changes in gene expression induced by injury in the rat. Pain, 2005, 117:6-18.
• Verbitsky M, Yonan AL, Malleret G, et al. Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in mice LEARNING & MEMORY 11 (3): 253-260 MAY-JUN 2004
• Pavlidis, Lewis and Noble, Proceedings of the Pacific Symposium on Biocomputing 7. pp 474-485, 2002. ( Download a reprint) .
• Sibille, E., Arango, V., Galfalvy, H.C., Pavlidis, P., Ellis, S.P. and Mann, J.J. (2004) Genomic analysis of depression and suicide in human prefrontal cortex. Neuropsychopharmacology 29:351-361 .
• Pavlidis P., Qin J, Arango V, Mann J, Sibille E. (2004) Using the Gene Ontology for microarray data mining: A comparison of methods and application to age effects in human prefrontal cortex. Neurochemical Research, 29(6) 1213-1222 .
• Pavlidis, P., Qin, J and Sibille E (2003) Statistical analysis of Gene Ontology classes as tools for understanding gene expression changes in the brain. Society for neuroscience Annual Meeting Abstract 758.12. ( download the powerpoint version of the poster )