Below are examples of papers using the Short Time-series Expression Miner (STEM) software or method as part of the data analysis:

  • Wright J.A., Grant A.J., Hurd D., Harrison M., Guccione E.J., Kelly D.J., Maskell D.J. Metabolite and transcriptome analysis of Campylobacter jejuni in vitro growth revelas a stationary-phase physiological switch. Microbiology 2009; 155:80-94.

  • Yang L., Zhou D.S., Liu X.M., Han H.H., Zhan L.J., Guo Z.B., Zhang L.F., Qin C., Wong H.C., Yang R.F. Cold-induced gene expression profiles of Vibrio parahaemolyticus: a time-course analysis. FEMS Microbiology Letters 2009; 291:50-58.

  • Zhu L., Li M., Li X., Shuai S., Liu H., Wang J., Jiang A., Gu Y., Zhang K., Teng X., Jiang Z. Distinct Expression Patterns of Genes Associated with Muscle Growth and Adipose Deposition in Tibetan Pigs: A Possible Adaptive Mechanism for High Altitude Conditions. High Altitude Medicine & Biology. 2009; 10:45-55.

  • Shin J.W., Huggenberger R., and Detmar M. Transcriptional profiling of VEGF-A and VEGF-C target genes in lymphatic endothelium reveals endothelial-specific molecule-1 as a novel mediator of lymphangiogenesis. Blood 2008; 112: 2318-2326.

  • Capra E.J., Skrovanek S.M., Kruglyak L. Comparative Developmental Expression Profiling of Two C. elegans Isolates. PLoS One 2008; 3:e4055.

  • Sun R., Peng S., Chen X., Zhang H., Rizzolo L.J. Diffusible retinal secretions regulate the expression of tight junctions and other diverse functions of the retinal pigment epithelium. Molecular Vision 2008; 14:2237-2262.

  • Han SH, Yang S, Jung DS, Li JJ, Kim JJ, Kwak SJ, Kim DK, Moon SJ, Lee JE, Han D-S, Kan S-W. Gene expression patterns in glucose-stimulated podocytes. Biochemical and Biophysical Research Communications 2008; 370:514-518.

  • Scholz B, Svensson M, Alm H, Skold K, Falth M, Kultima K, Guigoni C, Doudnikoff E, Li Q, Crossman AR, Bezard E, Andren PE. Striatal Proteomic Analysis Suggests that First L-Dopa Dose Equates to Chronic Exposure. PLoS One 2008; 3:e1589.

  • Li MZ, Zhu L, Li XW, Shuai SR, Teng XK, Xiao HS, Li Q, Chen L, Guo YJ, Wang JY. Expression profiling analysis for genes related to meat quality and carcass traits during postnatal development of backfat in two pig breeds. Science in China Series C-Life Sciences 2008; 51:718-733.

  • Yang B, Srivastava S, Deyholos MK, Kav NNV. Transcriptional profiling of canola (Brassica napus L.) responses to the fungal pathogen Sclerotinia sclerotiorum. Plant Science 2007; 173:156-171.

  • Liu DY-T, Liu C-H, Lai M-T, Lin H-K, Hseu T-H. Global gene expression profiling of wild type and lysC knockout Escherichia coli W3110. FEMS Microbiol Lett 2007; 276: 202-206.

  • Rizzo LJ, Chen X, Weitzmann M, Sun R, Zhang H. Analysis of the RPE transcriptome reveals dynamic changes during the development of the outer blood-retinal barrier. Molecular Vision 2007; 13:1259-1273.

  • Lulko AT, Buist G, Kok J, Kuipers OP. Transcriptome Analysis of Temporal Regulation of Carbon Metabolism by CcpA in Bacillus subtilis Reveals Additional Target Genes. J Mol Microbiol Biotechnol 2007; 12:82-95.

  • Martinez I, Lombardia L, Garcia-Barreno B, Dominguez O, Melero JA. Distinct gene subsets are induced at different time points after human respiratory syncytial virus infection of A549 cells. J Gen Virol 2007; 88: 570-581.

  • Nymark P, Lindholm PM, Korpela MV, Lahti L, Ruosaari S, Kaski S, Hollmen J, Anttila S, Kinnula VL, Knuutila S. Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines. BMC Genomics 2007; 8:62.

  • Jiang Y and Deyholos MK. Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes. BMC Plant Biol 2006; 6:25.