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Publications

Bioinformatics & Biostatistics Core

Selected Publications

A full list of publications is available here.

2018

Carpenter BL*, Zhou W, Madaj Z, DeWitt AK, Ross JP, Grønbaek K, Liang G, Clark SJ, Molloy PL, Jones PA. 2018. Mother-child transmission of epigenetic information by tunable polymorphic imprinting. Proc Natl Acad Sci U S A
*Co-first authors

Liu M, Thomas SL, DeWitt AK, Zhou W, Madaj ZB, Ohtani H, Baylin SB, Liang G, Jones PA. 2018. Dual inhibition of DNA and histone methyltransferases increases viral mimicry in ovarian cancer cells. Cancer Res 78(20):5754–5766.

deCarvalho AC, Kim H, Poisson LM, Winn ME, Mueller C, Cherba D, Koeman J, Seth S, Protopopov A, Felicella M, Zheng S, Multani A, Jiang Y, Zhang J, Nam DH, Petricoin EF, Chin L, Mikkelsen T, Verhaak RGW. 2018. Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nat Genet 50(5):708–717.

Rey NL, George S, Steiner JA, Madaj Z, Luk KC, Trojanowski JQ, Lee VM, Brundin P. 2018. Spread of aggregates after olfactory bulb injection of α-synuclein fibrils is associated with early neuronal loss and is reduced long term. Acta Neuropathol 135(1):65–83.

Killinger BA*, Madaj Z*, Sikora JW, Rey N, Haas AJ, Vepa Y, Lindqvist D, Chen H, Thomas PM, Brundin P, Brundin L, Labrie V. 2018. The veriform appendix impacts the risk of developing Parkinson’s. Sci Transl Med 10(465):eaar5280.

Mukherjee A, Patterson AL, George JW, Carpenter TJ, Madaj ZB, Hostetter G, Risinger JI, Teixeira JM. 2018. Nuclear PTEN localization contributes to DNA damage response in endometrial adenocarcinoma and could have a diagnostic benefit for therapeutic management of the disease. Mol Cancer Ther.

Senchuk MM, Dues DJ, Schaar CE, Johnson BK, Madaj ZB, Bowman MJ, Winn ME, Van Raamsdonk JM. 2018. Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans. PLoS Genet 14(3):e1007268.

Beddows I, Rose LE. 2018. Factors determining hybridization rates in plants: A case study in Michigan.  Perspec Plant Ecol Sys 34:51–60.

Peacock JD, Pridgeon MG, Tovar EA, Essenburg CJ, Bowman MJ, Madaj ZB, Koeman J, Boguslawski EA, Grit J, Dodd RD, Khachaturov V, Cardona DM, Chen M, Kirsch DG, Maina F, Dono R, Winn ME, Graveel CR, Steensma. 2018. Genomic status of MET potentiates sensitivity to MET and MEK inhibition in NF1-related malignant peripheral nerve sheath tumors. Cancer Res 78(13):3672–3687.

2017

Waldhart AN, Dykstra H, Peck AS, Boguslawski EA, Madaj ZB, Wen J, Veldkamp K, Hollowell M, Zheng B, Cantley LC, McGraw TE, Wu N. 2017. Phosphorylation of TXNIP by AKT mediates acute influx of glucose in response to insulin. Cell Rep 19(10):2005–2013.

Dues DJ, Schaar CJ, Johnson BK, Bowman MJ, Winn ME, Senchuk MM, Van Raamsdonk JM. 2017. Uncoupling of oxidative stress resistance and lifespan in long-lived isp-1 mitochondrial mutants in Caenorhabditis elegans. Free Radic Biol Med 108:362–373.

Martin KR, Zhou W, Bowman MJ, Shih J, Au KS, Dittenhafer-Reed KE, Sisson KA, Koeman J, Weisenberger DJ, Cottingham SL, DeRoos ST, Devinsky O, Winn ME, Cherniak AD, Shen H, Northrup H, Krueger DA, MacKeigan JP. 2017. The genomic landscape of tuberous sclerosis complex. Nat Commun 8:15816. 

2016

Harlow ML, Maloney N, Roland J, Guillen Navarro MJ, Easton MK, Kitchen-Goosen SM, Boguslawski EA, Madaj ZB, Johnson BK, Bowman MJ, D’Incalci M, Winn ME, Turner L, Hostetter G, Galmarini CM, Aviles PM, Grohar PJ. 2016. Lurbinectedin inactivates the Ewing sarcoma oncoprotein EWS-FLI1 by redistributing it within the nucleus. Cancer Res 76(22):6657–6668.

Osgood CL, Tantawy MN, Maloney N, Madaj ZB, Peck A, Boguslawkski E, Jess J, Buck J, Winn ME, Manning HC, Grohar PJ. 2016. 18F-FLT positron emission tomography (PET) is a pharmacodynamic marker for EWS-FLI1 activity and Ewing sarcoma. Sci Rep 6:33926.

Osgood CL, Maloney N, Kidd CG, Kitchen-Goosen S, Segars L, Gebregiorigis M, Woldemichael GM, He M, Sankar S, Lessnick SL, Kang M, Smith M, Turner L, Madaj ZB, Winn ME, Núnez LE, González-Sabin J, Helman LJ, Moris F, Grohar PJ. 2016. Identification of mithramycin analogues with improved targeting of the EWS-FLI1 transcription factor. Clin Cancer Res 22(16):4105–4118.

2015

Foley JM, Scholten DJ 2nd, Monks NR, Cherba D, Monsma DJ, Davidson P, Dylewski D, Dykema K, Winn ME, Steensma MR. 2015. Anoikis-resistant subpopulations of human osteosarcoma display significant chemoresistance and are sensitive to targeted epigenetic therapies predicted by expression profilingJ Transl Med 13(1):110. 

Peacock JD, Dykema KJ, Toriello HV, Mooney MR, Scholten DJ 2nd, Winn ME, Borgman A, Duesbery NS, Hiemenga JA, Liu C, Campbell S, Nickoloff BP, Williams BO, Steensma MR. 2015. Oculoectodermal syndrome is a mosaic RASopathy associated with KRAS alterationsAm J Med Genet A 167(7):1429–1435.