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

  • M. Chamankhah, E. Eftekharpour, S. Karimi-Abdolrezaee, P.C. Boutros, S. San-Marina, M.G. Fehlings. Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. BMC Genomics, 14:583, 2013.

  • C.C. Lutz, S.L. Rodriguez-Zas, S.E. Fahrbach, G.E. Robinson. Transcriptional response to foraging experience in the honey bee mushroom bodies-R1. Developmental Biology, 72: 153-166, 2011.

  • B.-Y. Kim, L.H. Cao, J.Y. Kim. Common Responses in Gene Expression by Ephedra herba in Brain and Heart of Mouse Phytotherapy Research, 25: 1440-1446, 2011.

  • J. Yang, D. An, P. Zhang. Expression Profiling of Cassava Storage Roots Reveals an Active Process of Glycolysis/Gluconeogenesis Journal of Integrative Biology. 53: 193-211, 2011.

  • J. Zhang, Y. Yang, Y. Wang, J. Zhang, Z. Wang, M. Yin, X. Shen. Identification of Hub Genes Related to the Recovery Phase of Irradiation Injury by Microarray and Integrated Gene Network Analysis PLoS One 6: e24680, 2011.

  • B. Yu, S. Zhou, Y. Wang, G. Ding, F. Ding, X. Gu. Profile of MicroRNAs following Rat Sciatic Nerve Injury by Deep Sequencing: Implication for Mechanisms of Nerve Regeneration. PLoS One, 6: e24612, 2011.

  • S. Mourlevata, J.-P. Galizzia, N. Guigal-Sthana, S. Courtade-Gania, G. Rolland-Valognesa, M. Rodrigueza, F. Barbeta, C. Bourriera, S. Catessona, A. Chomela, L. Danobera, N. Villaina, D.-H. Caignarda, B. Pirotteb, P. Lestagea and B.P. Lockharta. Molecular characterization of the AMPA-receptor potentiator S70340 in rat primary cortical culture: Whole-genome expression profiling. Neuorscience Research, 70:349-360, 2011.

  • Sharma P.K., Mittal N., Deswal S., Roy N. Calorie restriction up-regulates iron and copper transport genes in Saccharomyces cerevisiae. Mol Biosyst 2011; 7:394-402.

  • R. Li, W.E. Ackerman, T.L. Summerfield, L. Yu, P. Gulati, J. Zhang, K. Huang, R. Romero, D.A. Kniss. Inflammatory Gene Regulatory Networks in Amnion Cells Following Cytokine Stimulation: Translational Systems Approach to Modeling Human Parturition. PLoS One, 2011, 6: e20560.

  • Y. Zhang, D. Handley, T. Kaplan, H. Yu, A.S. Bais, T. Richards, K.V. Pandit, Q. Zeng, P.V. Benos, N. Friedman, O. Eickelberg, N. Kaminski. High Throughput Determination of TGF.1/SMAD3 Targets in A549 Lung Epithelial Cells. PLoS One 2011; 6: e20319.

  • Ge Y., Li Y., Lv D-K., Bai X., Ji W., Cai H., Wang A-X and Zhu Y-M. Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors. Functional & Integrative Genomics 2011; 11:369-79.

  • Wieczorek L., Maas J.W., Muglia L.M., Vogt S.K., Muglia L.J. Temporal and Regional Regulation of Gene Expression by Calcium-Stimulated Adenylyl Cyclase Activity during Fear Memory. PLoS One 2010; 5:e13385.

  • van Delft J.H.M., Mathijs K., Staal Y.C.M., van Herwijnen M.H.M., Brauers K.J.J., Boorsma A., Kleinjans J.C.S. Time Series Analysis of Benzo[A]Pyrene-Induced Transcriptome Changes Suggests That A Network Of Transcription Factors Regulates The Effects on Functional Gene Sets. Toxicological Sciences, 2010; 17:381-392.

  • Gricea E.A., Snitkina E.S., Yockeya L.J., Bermudezb D.M., NISC Comparative Sequencing Program, Liechtyd K.W., Segrea J.A. Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response. Proc. Natl Acad Sci 2010; 107:14799-14804.

  • Sharbel T.F., Voigt M.L., Corral J.M., Galla G., Kumlehn J., Klukas C., Screiber F., Vogel H. and Rotter B. Apomictic and Sexual Ovules of Boechera Display Heterochronic Global Gene Expression Patterns. Plant Cell 2010; 22: 655-671.

  • Wozniak M.B., Villendas R., Bischoff J.R., Blanco-Aparicio C.B., Martinez Leal J.F., de La Cueval P., Rodriguez M.E., Herreros B., Martin-Perez D., Longo M.I., Herrera M., Piris M.A., Ortiz-Romero P.L. Vorinostat interferes with the signaling transduction pathway of T cell receptor and synergizes with PI3K inhibitors in cutaneous T-cell lymphoma. Haematologica, 2010; 95: 613-621.

  • Bried J.J., Delft J.M.H., Kok, T.M.C.M, Herwijnen M.H.M., Mass L.M., Gottschalk R.W.H., and Klienjans J.C.S. Global Gene Expression Analysis Reveals Differences in Cellular Responses to Hydroxyl- and Superoxide Anion Radical-induced Oxidative Stress in Caco-2 Cells. Toxicological Sciences, 2010; 114:193-203.

  • Waddell S.J., Popper S.J., Rubins K.H., Griffiths M.J., Brown P.O., Levin M., Relman D.A. Dissecting Interferon-Induced Transcriptional Programs in Human Peripheral Blood Cells. PloS One 2010; 5: e9753.

  • Kim B.Y., Cao L.H., Park H., Jeong S. Reciprocal regulation of gene expression by Ephedra herba in mouse brain. Phytotherapy Research, 2010; 24: 531-537.

  • Ozbudak E., Tassy O., Pourquie O. Spatiotemporal compartmentalization of key physiological processes during muscle precursor differentiation. Proc. Natl Acad Sci 2010; 107: 4224-4229.

  • Alm H., Scholz B., Kultima K., Nilsson A., Andren P.E., Savitski M.M., Bergman A., Stigson M., Fex-Svenningsen A., Dencker L. In vitro neurotxicity of PBDE-99: immediate and concentration-dependent effects on prtein expression in cerebral cortex cells. J. Proteome Res. 2010; 9: 1226-1235.

  • You Y.H., Song Y.Y., Meng F.L., He L.H., Zhang M.J., Yan X.M., Zhang J.Z. Time-series gene expression profiles in AGS cells stimulated with Helicobacter pylori. World J Gastroenterol 2010; 16: 1385-1396.

  • Baker D.A and Russell S. Gene expression during Drosophila melanogaster egg development before and after reproductive diapause. BMC Genomics 2009; 10:242.

  • Li D., Su Z., Dong J., Wang T. An expression database for roots of the model legume Medicago truncatula under salt stress. BMC Genomics 2009; 10:517.

  • 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.

  • Pelechano V., Jimeno-Gonzalez S., Rodriguez-Gil A., Garcia-Martinez J., Perez-Ortin J.E., Chavez S. Regulon-Specific Control of Transcription Elongation across the Yeast Genome. PLoS Genetics 2009; 5:e1000614.

  • 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.

  • Synnergren, J., Adak, S., Englund, M.C.O., Giesler, T.L., Noaksson, K., Lindahl, A., Nilsson, P., Nelson, D., Abbot, S., Olsson, B., Sartipy, P. Cardiomyogenic gene expression profiling of differentiating human embryonic stem cells. Journal of Biotechnology 2008; 134: 162-170.

  • 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.