Publications

For a full list of our work, visit Google Scholar

(you can also find the PDFs of our work in this folder)

• S.E. Kohrt, E.J. Novak, S. Tapadar, B. Wu, J. Strope, Y. Asante, H. Kim, M.S. Chang, D. Gurdak, A. Khalil, M. Rood, E. Raftery, D. Stavreva, H.M. Nguyen, L.G. Brown, M. Ramser, C. Peer, W.M. Meyers, N. Aboreden, M. Chakravortee, R. Sallari, P.S. Nelson, K.K. Kelly, T.G.W. Graham, X. Darzacq, W.D. Figg, A.K. Oyelere, E. Corey, R. Adelaiye-Ogala, & B.E. Gryder. Small-molecule disruption of androgen receptor–dependent chromatin clusters. Proceedings of the National Academy of Sciences, 2024

• Y. Asante, K. Benischke, I. Osman, Q.A. Ngo, J. Wurth, D. Laubscher, H. Kim, B. Udhayakumar, M.I.H. Khan, D.H. Chin, J. Porch, M. Chakraborty, R. Sallari, O. Delattre, S. Zaidi, S. Morice, D. Surdez, S.G. Danielli, B.W. Schäfer, B.E. Gryder*, & M. Wachtel*. PAX3-FOXO1 uses its activation domain to recruit CBP/P300 and shape RNA Pol2 cluster distribution. Nature Communications, 2023, *co-corresponding authors

• D.H. Chin, I. Osman, J. Porch, H. Kim, K.K. Buck, J. Rodriguez, B. Carapia, D. Yan, S.B. Moura, J. Sperry, J. Nakashima, K. Altman, D. Altman, & B.E. Gryder. BET Bromodomain Degradation Disrupts Function but Not 3D Formation of RNA Pol2 Clusters. Pharmaceuticals, 2023

• D. Laubscher^†, B.E. Gryder^†, B.D. Sunkel^†, T. Andresson, M. Wachtel, S. Das, B. Roschitzki, W. Wolski, X.S. Wu, H.-C. Chou, Y.K. Song, C. Wang, J.S. Wei, M. Wang, X. Wen, Q.A. Ngo, J.G. Marques, C.R. Vakoc, B.W. Schäfer, B.Z. Stanton, & J. Khan. BAF complexes drive proliferation and block myogenic differentiation in fusion-positive rhabdomyosarcoma. Nature Communications, 2021, ^†co-first authors

• A. M. Garzón-Porras, E. Chory, B. E. Gryder, Dynamic Opposition of Histone Modifications, ACS Chemical Biology, 2022

• C. F. Hays and B. E. Gryder, Epigenetic convergence in the rising tide of opioid overdose deaths, Molecular Psychiatry 2022

• Corradin, Sallari, Hoang, Kassim, Ben Hutta, Cuoto, Quach, Lovrenert, Hays, Gryder et al., Convergence of case-specific epigenetic alterations identify a confluence of genetic vulnerabilities tied to opioid overdose. Molecular Psychiatry, 2022

B.E. Gryder*, P.C. Scacheri, T. Ried* & J. Khan*. Chromatin Mechanisms Driving Cancer. Cold Spring Harb Perspect Biol, 2021. *co-corresponding

• S. Pomella^†, P. Sreenivas^†, B.E. Gryder^†, et. al., J. Khan*, R. Rota*, M. S. Ignatius*. Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma. Nature Comm., 2021 ^†co-first authors,^*co-corresponding authors

• D. Banerjee*, B.E. Gryder* et al., C. Thiele*, Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation. BioRxiv, 2020 *co-corresponding authors

• B.E. Gryder*, M. Wachtel, K. Chang, O. El Demerdash, N. G. Aboreden, W. Ewert, S. Pomella, W. Mohammed, R. Rota, J. S. Wei, Y. Song, B. Schaefer, C. R. Vakoc, J. Khan*. Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage. iScience, 2020 *co-corresponding authors (chosen for the journal’s cover artwork, June 26, 2020 issue)

• B.E. Gryder*, J. Khan*, B.Z. Stanton*. Absolute Quantification of Architecture (AQuA-HiChIP) Enables Measurement of Differential Chromatin Interactions. Nature Protocols, 2020 *co-corresponding authors 

• J. G. Marques, B.E. Gryder et al., NuRD subunit CHD4 regulates super-enhancer accessibility in Rhabdomyosarcoma and represents a general tumor dependency. eLife, 2020

• N. C. Whitlock, et al. B.E. Gryder, Capaldo, B., Ye, H., Sowalsky, A., MEIS1 down-regulation by MYC mediates prostate cancer development through elevated HOXB13 expression and AR activity. Oncogene,  2020.

• R. Adelaiye-Ogala, B.E. Gryder, et al., D. VanderWeele, Targeting the PI3K/AKT pathway overcomes enzalutamide resistance by inhibiting induction of the glucocorticoid receptor. Mol. Cancer Ther., 2020.

• B.E. Gryder*, S. Pomella, et. al., J. Khan*. Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nature Genetics, 2019 *co-corresponding authors

• A.M. Chiarella, K.V. Butler, B.E. Gryder, D. Lu, T.A. Wang, X. Yu, S. Pomella, J. Khan, J. Jin, N.A. Hathaway. Dose-dependent activation of gene expression is achieved using CRISPR and small molecules that recruit endogenous chromatin machinery. Nature Biotechnology, 2019

• B.E. Gryder^†, L. Wu^† et. al., J. Qi*, J. Khan*. Chemical genomics reveals histone deacetylases are required for core regulatory transcription. Nature Communications, 2019 ^†co-first authors,*co-corresponding authors

• M.E. Yohe^†, B.E. Gryder^†, et. al., C. Thomas, J. Khan. MEK inhibition induces MYOG and remodels super-enhancers in RAS-driven rhabdomyosarcoma. Science Translational Medicine, 2018 ^†co-first authors

• B.E. Gryder, M.E. Yohe, H.-C. Chou, et. al., K. Zhao, C.J. Thomas, J. Khan. PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability. Cancer Discovery, 2017

B.E. Gryder, Nelson C, and Shepard S, Biosemiotic Entropy of the Genome: Mutations and Epigenetic Imbalances Resulting in Cancer. Entropy. 2013; 15(1):234-261.