Jain S, Rick JW, Joshi R, Beniwal A, Spatz J, Chih-Chieh Chang A, Nguyen AT, Sudhir S, Chandra A, Haddad A, Wadhwa H, Shah SS, Choi S, Hayes JL, Wang L, Yagnik G, Costello JF, Diaz A, Aghi MK. Single-cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma with protumoral effects. J Clin Invest. 2023 doi: 10.1172/JCI147087

Boissinot M, King H, Adams M, Higgins J, Shaw G, Ward TA, Steele LP, Tams D, Morton R, Polson E, da Silva B, Droop A, Hayes JL, Martin H, Laslo P, Morrison E, Tomlinson DC, Wurdak H, Bond J, Lawler SE & Short SC. Profiling cytotoxic microRNAs in pediatric and adult glioblastoma cells by high-content screening, identification, and validation of miR-1300. Oncogene. 2020 https://doi.org/10.1038/s41388-020-1360-y

Schiffman C, Petrick L, Perttula K, Yano Y, Carlsson H, Whitehead T, Metayer C, Hayes J, Rappaport S, Dudoit S. Filtering procedures for untargeted LC-MS metabolomics data. BMC Bioinformatics. 2019 20(334). PMID: 31200644 https://doi.org/10.1186/s12859-019-2871-9

Yano Y, Schiffman C, Grigoryan H, Hayes J, Edmands W, Petrick L, Whitehead T, Metayer C, Dudoit S, Rappaport S. Untargeted Adductomics of Newborn Dried Blood Spots Identifies Modifications to Human Serum Albumin Associated with Childhood Leukemia. Leukemia Research. 2019 88:106268. PMID: 31760269 https://doi.org/10.1016/j.leukres.2019.106268

Bhaskaran V, Nowicki MO, Idriss M, Jimenez MA, Lugli G, Hayes JL, Mahmoud AB Zane, Passaro C, Ligon KL, Haas-Kogan D, Bronisz A, Godlewski J, Lawler SE, Chiocca EA, Peruzzi P. Nature Communications. 2019 10(1):442. PMID: 30683859

Thorne JL, Battaglia S, Baxter DE, Hayes JL, Hutchinson SA, Janace S, Millican-Slater RA, Smith L, Teske MC, Wastall LM, Hughes TA. MiR-19b non-canonical binding is directed by HuR and confers chemosensitivity through regulation of P-glycoprotein in breast cancer. BBA - Gene Regulatory Mechanisms. 2018 1861(11). PMID: 30343695

Mancini A, Xavier-Magalhaes A, Woods WS, Nguyen KT, Amen, AM, Hayes JL, Fellman C, Gapinske M, McKinney AM, Hong C, Jones LE, Walsh KM, Nell RJA, Doudna JA, Costa BM, Song JS, Perez-Pinera P, Costello JF. Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner. Cancer Cell 2018 34(3). PMID: 30205050

Ricklefs FL, Alayo Q, Krenzlin H, Mahmoud AB, Speranza MC, Nakashima H, Hayes JL, Lee K, Balaj L, Passaro C, Rooj AK, Krasemann S, Carter BS, Chen CC, Steed T, Treiber J, Rodig S, Yang K, Nakano I, Lee H, Weissleder R, Breakefield XO, Godlewski J, Westphal M, Lamszus K, Freeman GJ, Bronisz A, Lawler SE, Chiocca EA. Immune evasion mediated by PD-L1 on glioblastoma-derived extracellular vesicles. Science Advances 2018 4(3): eaar2766. PMID: 29532035

Edmands WMB, Hayes J, Rappaport SM. SimExTargId: A comprehensive package for real-time LC-MS data acquisition and analysis. Bioinformatics 2018. PMID: 29790936

Hayes J, Yu Y, Jalbert LE, Mazor T, Jones LE, Wood MD, Walsh KM, Bengtsson H, Hong C, Oberndorfer S, Roetzer T, Smirnov IV, Clarke JL, Aghi M, Chang SM, Nelson SJ, Woehrer A, Phillips JJ, Solomon D, Costello JF. Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas. Neuro Oncol. 2017. PMID: 29077933

Mazor T., Chesnelong C., Pankov A., Jalbert LE., Hong C., Hayes J., Smirnov IV., Marshall R., Souza C., Shen Y., Viswanath P., Noushmehr H., Ronen SM., Jones SJ., Marra MA., Cairncross JG, Perry A., Nelson SJ., Chang SM., Bollen AW., Molinaro AM., Bengtsson H., Olshen AB, Weiss S., Phillips JJ., Luchman HA., Costello JF. Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1. PNAS 2017 114(40):10743-10748.

Mohan N., Kwiatkowska A., Bhaskaran V., Hayes J., Hu Bin. and Viapiano M. S. Tumor-derived fibulin-3 activates pro-invasive NF-kappa B signaling in glioblastoma cells and their microenvironment. Oncogene 2017 36(34):4875-4886.

Kuang R., Jahangiri A., Mascharak S., Nguyen A., Ankush, Flanigan CPM., Yagnik G., Wagner JR., De Lay M., Carrera D., Castro BA., Hayes J., Sidorov M., and Aghi MK. et al. GLUT3 upregulation promotes metabolic reprogramming associated with antiangiogenic therapy resistance. JCI insight 2017, 2(2):e88815.

Hayes J., Thygesen H., Gregory W., Westhead DR., French P., Van Den Bent M., Lawler SE., Short S., et al. A validated microRNA profile with predictive potential in glioblastoma patients treated with bevacizumab. Molecular Oncology 2016, 10(8):1296-304.

Hayes J., Thygesen H., Droop A., Hughes TA., Westhead DR., Lawler SE., Wurdak H., Short S. Prognostic microRNAs in high-grade glioma reveal a link to OP differentiation. Oncoscience 2014, 2(3):252-62.

Hayes J., Thygesen H., Tumilson C., and Lawler SE. et al. Prediction of clinical outcome in glioblastoma using a biologically relevant nine-microRNA signature. Molecular Oncology 2014, 9(3):704-14.

Hayes J., Peruzzi P., Lawler SE. MicroRNAs in cancer: biomarkers, functions and therapy. Trends Mol Med 2014, 20:460-469. (One of TMMs top ten articles for 2014).

Peruzzi P, Bronisz A, Nowicki MO, Wang Y, Ogawa D, Price R, Nakano I, Kwon CH, Hayes J, Lawler SE, Ostrowski MC, Chiocca EA, Godlewski J. MicroRNA-128 coordinately targets Polycomb Repressor Complexes in glioma stem cells. Neuro-oncology. 2013;74:1541-53.

Kim J, Zhang Y, Skalski M, Hayes J, Kefas B, Schiff D, et al. microRNA-148a is a prognostic oncomiR that targets MIG6 and BIM to regulate EGFR and apoptosis in glioblastoma. Cancer Res. 2012, 5:1212-24.

Hayes JL, Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, et al. Diagnosis of copy number variation by Illumina next generation sequencing is comparable in performance to oligonucleotide array comparative genomic hybridisation. Genomics. 2013;102:174–81.

Hope IA, Stevens J, Garner A, Hayes J, Cheo DL, Brasch MA, et al. Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system. Genome Research. 2004;14:2070–5.

Preprints

Hayes et al. 2018 adductomicsR: A package for detection and quantification of protein adducts from mass spectra of tryptic digests. BioRxiv. doi: https://doi.org/10.1101/463331 Also available on Github https://github.com/JosieLHayes/adductomicsR and in Bioconductor http://www.bioconductor.org/packages/release/bioc/html/adductomicsR.html