2023
Hatthakarnkul P, Ammar A.et al. Protein expression of S100A2 reveals it association with patient prognosis and immune infiltration profile in colorectal cancer. J Cancer (2023); 14(10):1837-1847. doi:10.7150/jca.83910. https://www.jcancer.org/v14p1837.htm
Wang J, Harwood CA, et al. . Transcriptomic analysis of cutaneous squamous cell carcinoma reveals a multi-gene prognostic signature associated with metastasis. J Am Acad Dermatol. 2023 Aug 14:S0190-9622(23)02504-5. doi: 10.1016/j.jaad.2023.08.012
2022
Geronimo Matteo, Karen Leingartner, et al. In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals. Toxicological Sciences, Volume 191, Issue 2, February 2023, Pages 266–275, https://doi.org/10.1093/toxsci/kfac127
Ghosh, S., De Smedt, J., Tricot, T. et al. HiPSC-Derived Hepatocyte-like Cells Can Be Used as a Model for Transcriptomics-Based Study of Chemical Toxicity. Toxics 10, 1 (2022). https://doi.org/10.3390/toxics10010001
Black, M.B., Stern, A., Efremenko, A. et al. Biological system considerations for application of toxicogenomics in next-generation risk assessment and predictive toxicology. Toxicology in Vitro, Volume 80 (2022). https://doi.org/10.1016/j.tiv.2022.105311
Conley, J. M., Lambright, C. S., Evans, N. et al. Developmental toxicity of Nafion byproduct 2 (NBP2) in the Sprague-Dawley rat with comparisons to hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX) and perfluorooctane sulfonate (PFOS). Environmental International, Volume 160 (2022). https://doi.org/10.1016/j.envint.2021.107056
Vrijenhoek, N. G., Wehr, M. M., Kunnen, S.J. et al. Application of High-Throughput Transcriptomics for Mechanism-Based Biological Read-Across of Short-Chain Carboxylic Acid Analogues of Valproic Acid. ALTEX - Alternatives to animal experimentation (2022). https://doi.org/10.14573/altex.2107261
Nunes, C. Singh, P. Mazidi, Z. et al. An in vitro strategy using multiple human induced pluripotent stem cell-derived models to assess the toxicity of chemicals: A case study on paraquat. Toxicology in Vitro, Volume 81 (2022). https://doi.org/10.1016/j.tiv.2022.105333
Everett LJ, Mav D, Phadke DP, Balik-Meisner MR, Shah RR. Impact of Aligner, Normalization Method, and Sequencing Depth on TempO-seq Accuracy. Bioinformatics and Biology Insights (2022). doi:10.1177/11779322221095216
Murphy, C., Naderlinger, E., Mater, A., Kluin, R. J. C. and Wilmes, A. (2022) “Comparison of human recombinant protein coatings and fibroblast-ECM to Matrigel for induced pluripotent stem cell culture and renal podocyte differentiation”, ALTEX - Alternatives to animal experimentation. doi: 10.14573/altex.2112204.
2021
Joshua A Harrill, Logan J Everett, Derik E Haggard, Thomas Sheffield, Joseph L Bundy, Clinton M Willis, Russell S Thomas, Imran Shah, Richard S Judson, High-Throughput Transcriptomics Platform for Screening Environmental Chemicals, Toxicological Sciences, Volume 181, Issue 1, May 2021, Pages 68–89, https://doi.org/10.1093/toxsci/kfab009
Rowan-Carroll, A., Reardon, A, Leingartner, K. et al. High-Throughput Transcriptomic Analysis of Human Primary Hepatocyte Spheroids Exposed to Per- and Polyfluoroalkyl Substances as a Platform for Relative Potency Characterization. Toxicological Sciences, Volume 181, Issue 2 (2021). https://doi.org/10.1093/toxsci/kfab039
Wellens, S., Dehouck, L., Chandrasekaran, V. et al. Evaluation of a human iPSC-derived BBB model for repeated dose toxicity testing with cyclosporine A as model compound. Toxicology in Vitro, Volume 73 (2021). https://doi.org/10.1016/j.tiv.2021.105112
David M Crizer, Sreenivasa C Ramaiahgari. et al. Benchmark Concentrations for Untargeted Metabolomics Versus Transcriptomics for Liver Injury Compounds in In Vitro Liver Models . Toxicological Sciences, Volume 181, Issue 2, June 2021, Pages 175–186, https://doi.org/10.1093/toxsci/kfab036
2020
House JS, Bouzos E, Fahy KM, Francisco VM, Lloyd DT, Wright FA, Motsinger-Reif AA, Asuri P, Wheeler KE. Low-Dose Silver Nanoparticle Surface Chemistry and Temporal Effects on Gene Expression in Human Liver Cells. Small. 2020 May;16(21):e2000299. doi: 10.1002/smll.202000299. Epub 2020 Mar 29. PMID: 32227433; PMCID: PMC7446734.
Baltazar, M.T., Cable, S., Carmichael, P.L. et al. A next generation risk assessment case study for courmarin in cosmetic products. Toxicological Sciences kfaa048 (2020). https://doi.org/10.1093/toxsci/kfaa048
Verheijen, M., Tong, W., Shi, L. et al. Towards the development of an omics data analysis framework. Toxicology and Pharmacology 112, 106621. https://doi.org/10.1016/j.yrtph.2020.104621
Turnbull, A.K., Selli, C., Martinez-Perez, C. et al. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches. BMC Bioinformatics 21, 30 (2020). https://doi.org/10.1186/s12859-020-3365-5
Piras, I.S., Bleul, C., Schrauwen, I., et al. 2020. Transcriptional profiling of Multiple System Atrophy cerebellar tissue highlights differences between the parkinsonian and cerebellar sub-types of the disease. bioRxiv (2020). https://doi.org/10.1101/2020.02.11.944306
Yang, H., Niemeijer, M., van de Water, B., Beltman, J.B. ATF6 is a critical determinant of CHOP dynamics during the unfolded protein response. iSCIENCE 23, 2 (2020). https:// doi.org/10.1016/j.isci.2020.100860.
Bushel PR, Auerbach SS. Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data. Front Genet. 2020 Jun 23;11:594. doi: 10.3389/fgene.2020.00594. Erratum in: Front Genet. 2020 Aug 11;11:943. PMID: 32655620; PMCID: PMC7325690.
2019
Trejo, C.L., Babić, M., Imler, E., Gonzalez, M., Bibikov, S.I., Shepard, P.J., VanSteenhouse, H.C., Yeakley, J.M. and Seligmann, B.E. Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue. PloS one 14, 2 (2019): e0212031. https://doi.org/10.1371/journal.pone.0212031
Ramaiahgari, S.C., Auerbach, S.S., Saddler, et al. The power of resolution: contextualized understanding of biological responses to liver injury chemicals using high-throughput transcriptomics and benchmark concentration modeling. Toxicological Sciences 169, 2 (2019). https://doi.org/10.1093/toxsci/kfz065
Balik-Meisner, M.R., Mav, D., et al. Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics. Zebrafish 16, 4 (2019). https://doi.org/10.1089/zeb.2018.1720
Chappell, G.A., Rager, J.E., Wolf, J., et al. Comparison of Gene Expression Responses in the Small Intestine of Mice Following Exposure to 3 Carcinogens Using the S1500+ Gene Set Informs a Potential Common Adverse Outcome Pathway. Toxicologic Pathology 47, 7 (2019). https://doi.org/10.1177/0192623319873882
Bischoff, L.J., Kuijper, I.A., Schimming, J.P., et al. A systematic analysis of Nrf2 pathway activation dynamics during repeated xenobiotic exposure. Archives of Toxicology 93, 2 (2019). https://doi.org/10.1007/s00204-018-2353-2
van der Wel, T., Hilhorst, R., den Dulk, H., et al. Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis via SYK activation. bioRxiv (2019). https://doi.org/10.1101/841189
Trejo, C., Imler, E., Babic, M., et al. Whole transcriptome TempO-Seq profiling of focal areas of H&E stained FFPE: Differentiation of normal colon and cancer phenotypes between donors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; Abstract # 5241. Cancer Research 79, 13 (2019). https://doi.org/10.1158/1538-7445.AM2019-5241
Imler, E., Nagle, R. and Seligmann, B. Digital Spatial Molecular Profiling evidence from H&E stained FFPE that the tumor microenvironment confers gene expression phenotype specificity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; Abstract # 125. Cancer Research 79, 13 (2019). https://doi.org/10.1158/1538-7445.AM2019-125
Raghunathan, M., Imler, E., Trejo, C., et al. Whole transcriptome dose response profiling enables characterization of efficacy, metabolism, side effects and cytotoxicity in a single comprehensive assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; Abstract # LB-097. Cancer Research 79, 13 (2019). https://doi.org/10.1158/1538-7445.AM2019-LB-097
Turnbull, A.K., Selli, C., Martinez-Perez, C., et al. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium 2018; Abstract # P3-06-17. Cancer Research 79, 4 (2019). https://doi.org/10.1158/1538-7445.SABCS18-P3-06-17
Carleo, A., Terwolbeck, O. and Prasse, A. Transciptomic Profile TGF-β Inhibitor Treatment in BAL Cells from IPF Patients [abstract]. Pneumologie 73, 02, p. A12. https://doi.org/10.1055/s-0039-1678392
2018
Batai, K., Imler, E., Pangilinan, J., et al. Whole-transcriptome sequencing identified gene expression signatures associated with aggressive clear cell renal cell carcinoma. Genes & Cancer 9, 5-6 (2019). https://doi.org/10.18632/genesandcancer.183
Limonciel, A., Ates, G., Carta, G., et al. Comparison of base-line and chemical-induced transcriptomic responses in HepaRG and RPTEC/TERT1 cells using TempO-Seq. Archives of Toxicology 92, 8 (2018). https://doi.org/10.1007/s00204-018-2256-2
Bushel, P.R., Paules, R.S. and Auerbach, S.S. A comparison of the TempO-Seq S1500+ platform to RNA-Seq and microarray using rat liver mode of action samples. Frontiers in Genetics 9 (2018). https://doi.org/10.3389/fgene.2018.00485
Grimm, F.A., Blanchette, A., House, J.S., et al. A human population-based organotypic in vitro model for cardiotoxicity screening. ALTEX 35, 4 (2018). https://doi.org/10.14573/altex.1805301
Hanke, N.T., Imler, E., Marron, M.T., et al. Characterization of carfilzomib-resistant non-small cell lung cancer cell lines. Journal of Cancer Research and Clinical Oncology 144, 7 (2018). https://doi.org/10.1007/s00432-018-2662-0
Argenziano, M., Lambers, E., Hong, L., et al. Electrophysiologic characterization of calcium handling in human induced pluripotent stem cell-derived atrial cardiomyocytes. Stem Cell Reports 10, 6 (2018). https://doi.org/10.1016/j.stemcr.2018.04.005
Imler, E., Babic, M., Adams, D., et al. Focal gene expression profiling of counterstained FFPE with correlation to morphology using TempO-Seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; Abstract # 2106. Cancer Research 78, 13. https://doi.org/10.1158/1538-7445.AM2018-2106
Mav D, Shah RR, Howard BE, Auerbach SS, Bushel PR, Collins JB, et al. (2018) A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. PLoS ONE 13(2): e0191105. https://doi.org/10.1371/journal.pone.0191105
Judson, R. Rapid toxicity screening of chemicals combining in vitro high-throughput transcriptomics, toxicokinetics and exposure estimates. In Toxicology Letters (Vol. 295, pp. S28-S28). Eurotox (2018).
2017
Yeakley, J.M., Shepard, P.J., Goyena, D.E., et al. A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling. PLoS One 12, 5 (2017). https://doi.org/10.1371/journal.pone.0178302
Rooney, J.P., Ryan, N., Chorley, B.N., et al. From the cover: genomic effects of androstenedione and sex-specific liver cancer susceptibility in mice. Toxicological Sciences 160, 1 (2017). https://doi.org/10.1093/toxsci/kfx153
House, J.S., Grimm, F.A., Jima, et al. A pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics. Frontiers in Genetics 8 (2017). https://doi.org/10.3389/fgene.2017.00168
Seligmann, B., Marron, M., Babic, M., et al. Detection of gene expression biomarkers from enriched CTC preparations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; Abstract # 1729. Cancer Research 77, 13 (2017). https://doi.org/10.1158/1538-7445.AM2017-1729
Babic, M., Imler, E., Shepard, P., et al. Changes in gene expression of stromal and epithelial cells during prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; Abstract # 1992. Cancer Research 77, 13 (2017). https://doi.org/10.1158/1538-7445.AM2017-1992
VanSteenhouse, H., Shepard, P., Yeakley, J. et al. Targeted whole transcriptome gene expression profiling for mechanistic toxicology [abstract]. Toxicology Letters 280 (2017). http://dx.doi.org/10.1016/j.toxlet.2017.07.827
Harrill, J.A. High-Throughput Transcriptomics (HTTr) Concentration-Response Screening in MCF7 cells. EPA (2017.)
2016
Grimm, F.A., Iwata, Y., Sirenko, O., et al. A chemical–biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives. Green Chemistry 18, 16 (2016). https://doi.org/10.1039/C6GC01147K
Babic, M., Shepard, P., Yeakley, J., et al. Differential expression and mechanistic pathways of prostate cancer identified from FFPE tissue using surrogate or whole transcriptome TempO-Seq targeted gene expression assays [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; Abstract # 1840. Cancer Research 76, 14 (2016). https://doi.org/10.1158/1538-7445.AM2016-1840