Berkley E Gryder (Berkley Gryder)

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 33

Top Topics

Transcription Factor

Histone Deacetylase

Gene Expression

Top Venues

Nature communications

Molecular psychiatry

Nature biotechnology

This page only lists publications with an associated author ORCID identifier.

Publications

Deblina Banerjee, Sukriti Bagchi, Zhihui Liu, Hsien-Chao Chou, Man Xu, Ming Sun, Sara Aloisi, Zalman Vaksman, Sharon J Diskin, Mark Zimmerman, Javed Khan, Berkley E Gryder, Carol J Thiele
Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation. Nature communications 15 (1) (2024)
Deblina Banerjee, Sukriti Bagchi, Zhihui Liu, Hsien-Chao Chou, Man Xu, Ming Sun, Sara Aloisi, Zalman Vaksman, Sharon J Diskin, Mark Zimmerman, Javed Khan, Berkley E Gryder, Carol J Thiele
Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation. Nature communications 15 (1) (2024)
Yong Yean Kim, Berkley E Gryder, Ranuka Sinniah, Megan L Peach, Jack F Shern, Abdalla Abdelmaksoud, Silvia Pomella, Girma M Woldemichael, Benjamin Z Stanton, David Milewski, Joseph J Barchi, John S Schneekloth, Raj Chari, Joshua T Kowalczyk, Shilpa R Shenoy, Jason R Evans, Young K Song, Chaoyu Wang, Xinyu Wen, Hsien-Chao Chou, Vineela Gangalapudi, Dominic Esposito, Jane Jones, Lauren Procter, Maura O'Neill, Lisa M Miller Jenkins, Nadya I Tarasova, Jun S Wei, James B McMahon, Barry R Oâ Keefe, Robert G Hawley, Javed Khan
KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. Nature communications 15 (1) (2024)
Yong Yean Kim, Berkley E Gryder, Ranuka Sinniah, Megan L Peach, Jack F Shern, Abdalla Abdelmaksoud, Silvia Pomella, Girma M Woldemichael, Benjamin Z Stanton, David Milewski, Joseph J Barchi, John S Schneekloth, Raj Chari, Joshua T Kowalczyk, Shilpa R Shenoy, Jason R Evans, Young K Song, Chaoyu Wang, Xinyu Wen, Hsien-Chao Chou, Vineela Gangalapudi, Dominic Esposito, Jane Jones, Lauren Procter, Maura O'Neill, Lisa M Miller Jenkins, Nadya I Tarasova, Jun S Wei, James B McMahon, Barry R Oâ Keefe, Robert G Hawley, Javed Khan
KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. Nature communications 15 (1) (2024)
Yong Yean Kim, Berkley E Gryder, Ranuka Sinniah, Megan L Peach, Jack F Shern, Abdalla Abdelmaksoud, Silvia Pomella, Girma M Woldemichael, Benjamin Z Stanton, David Milewski, Joseph J Barchi, John S Schneekloth, Raj Chari, Joshua T Kowalczyk, Shilpa R Shenoy, Jason R Evans, Young K Song, Chaoyu Wang, Xinyu Wen, Hsien-Chao Chou, Vineela Gangalapudi, Dominic Esposito, Jane Jones, Lauren Procter, Maura O'Neill, Lisa M Miller Jenkins, Nadya I Tarasova, Jun S Wei, James B McMahon, Barry R Oâ Keefe, Robert G Hawley, Javed Khan
KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. Nature communications 15 (1) (2024)
Deblina Banerjee, Sukriti Bagchi, Zhihui Liu, Hsien-Chao Chou, Man Xu, Ming Sun, Sara Aloisi, Zalman Vaksman, Sharon J Diskin, Mark Zimmerman, Javed Khan, Berkley E Gryder, Carol J Thiele
Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation. Nature communications 15 (1) (2024)
Yong Yean Kim, Berkley E Gryder, Ranuka Sinniah, Megan L Peach, Jack F Shern, Abdalla Abdelmaksoud, Silvia Pomella, Girma M Woldemichael, Benjamin Z Stanton, David Milewski, Joseph J Barchi, John S Schneekloth, Raj Chari, Joshua T Kowalczyk, Shilpa R Shenoy, Jason R Evans, Young K Song, Chaoyu Wang, Xinyu Wen, Hsien-Chao Chou, Vineela Gangalapudi, Dominic Esposito, Jane Jones, Lauren Procter, Maura O'Neill, Lisa M Miller Jenkins, Nadya I Tarasova, Jun S Wei, James B McMahon, Barry R Oâ Keefe, Robert G Hawley, Javed Khan
KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. Nature communications 15 (1) (2024)
Yaw Asante, Katharina Benischke, Issra Osman, Quy A Ngo, Jakob Wurth, Dominik Laubscher, Hyun Min Kim, Bhavatharini Udhayakumar, Md Imdadul H Khan, Diana H Chin, Jadon Porch, Maharshi Chakraborty, Richard Sallari, Olivier O Delattre, Sakina Zaidi, Sarah Morice, Didier Surdez, Sara G Danielli, Beat W Schäfer, Berkley E Gryder, Marco Wachtel
PAX3-FOXO1 uses its activation domain to recruit CBP/P300 and shape RNA Pol2 cluster distribution. Nature communications 14 (1) (2023)
Silvia Pomella, Matteo Cassandri, Lucrezia D'Archivio, Antonella Porrazzo, Cristina Cossetti, Doris Phelps, Clara Perrone, Michele Pezzella, Antonella Cardinale, Marco Wachtel, Sara Aloisi, David Milewski, Marta Colletti, Prethish Sreenivas, Zoë S Walters, Giovanni Barillari, Angela Di Giannatale, Giuseppe Maria Milano, Cristiano De Stefanis, Rita Alaggio, Sonia Rodriguez-Rodriguez, Nadia Carlesso, Christopher R Vakoc, Enrico Velardi, Beat W Schäfer, Ernesto Guccione, Susanne Andrea Gatz, Ajla Wasti, Marielle Yohe, Myron S Ignatius, Concetta Quintarelli, Janet M Shipley, Lucio Miele, Javed Khan, Peter J Houghton, Francesco Marampon, Berkley E Gryder, Biagio De Angelis, Franco Locatelli, Rossella Rota
MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57 Kip2 targeting. Nature communications 14 (1) (2023)
Yaw Asante, Katharina Benischke, Issra Osman, Quy A Ngo, Jakob Wurth, Dominik Laubscher, Hyun Min Kim, Bhavatharini Udhayakumar, Md Imdadul H Khan, Diana H Chin, Jadon Porch, Maharshi Chakraborty, Richard Sallari, Olivier O Delattre, Sakina Zaidi, Sarah Morice, Didier Surdez, Sara G Danielli, Beat W Schäfer, Berkley E Gryder, Marco Wachtel
PAX3-FOXO1 uses its activation domain to recruit CBP/P300 and shape RNA Pol2 cluster distribution. Nature communications 14 (1) (2023)
Silvia Pomella, Matteo Cassandri, Lucrezia D'Archivio, Antonella Porrazzo, Cristina Cossetti, Doris Phelps, Clara Perrone, Michele Pezzella, Antonella Cardinale, Marco Wachtel, Sara Aloisi, David Milewski, Marta Colletti, Prethish Sreenivas, Zoë S Walters, Giovanni Barillari, Angela Di Giannatale, Giuseppe Maria Milano, Cristiano De Stefanis, Rita Alaggio, Sonia Rodriguez-Rodriguez, Nadia Carlesso, Christopher R Vakoc, Enrico Velardi, Beat W Schäfer, Ernesto Guccione, Susanne Andrea Gatz, Ajla Wasti, Marielle Yohe, Myron S Ignatius, Concetta Quintarelli, Janet M Shipley, Lucio Miele, Javed Khan, Peter J Houghton, Francesco Marampon, Berkley E Gryder, Biagio De Angelis, Franco Locatelli, Rossella Rota
MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57 Kip2 targeting. Nature communications 14 (1) (2023)
Silvia Pomella, Matteo Cassandri, Lucrezia D'Archivio, Antonella Porrazzo, Cristina Cossetti, Doris Phelps, Clara Perrone, Michele Pezzella, Antonella Cardinale, Marco Wachtel, Sara Aloisi, David Milewski, Marta Colletti, Prethish Sreenivas, Zoë S Walters, Giovanni Barillari, Angela Di Giannatale, Giuseppe Maria Milano, Cristiano De Stefanis, Rita Alaggio, Sonia Rodriguez-Rodriguez, Nadia Carlesso, Christopher R Vakoc, Enrico Velardi, Beat W Schäfer, Ernesto Guccione, Susanne Andrea Gatz, Ajla Wasti, Marielle Yohe, Myron S Ignatius, Concetta Quintarelli, Janet M Shipley, Lucio Miele, Javed Khan, Peter J Houghton, Francesco Marampon, Berkley E Gryder, Biagio De Angelis, Franco Locatelli, Rossella Rota
MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57 Kip2 targeting. Nature communications 14 (1) (2023)
Silvia Pomella, Matteo Cassandri, Lucrezia D'Archivio, Antonella Porrazzo, Cristina Cossetti, Doris Phelps, Clara Perrone, Michele Pezzella, Antonella Cardinale, Marco Wachtel, Sara Aloisi, David Milewski, Marta Colletti, Prethish Sreenivas, Zoë S Walters, Giovanni Barillari, Angela Di Giannatale, Giuseppe Maria Milano, Cristiano De Stefanis, Rita Alaggio, Sonia Rodriguez-Rodriguez, Nadia Carlesso, Christopher R Vakoc, Enrico Velardi, Beat W Schäfer, Ernesto Guccione, Susanne Andrea Gatz, Ajla Wasti, Marielle Yohe, Myron S Ignatius, Concetta Quintarelli, Janet M Shipley, Lucio Miele, Javed Khan, Peter J Houghton, Francesco Marampon, Berkley E Gryder, Biagio De Angelis, Franco Locatelli, Rossella Rota
MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57 Kip2 targeting. Nature communications 14 (1) (2023)
Yaw Asante, Katharina Benischke, Issra Osman, Quy A Ngo, Jakob Wurth, Dominik Laubscher, Hyun Min Kim, Bhavatharini Udhayakumar, Md Imdadul H Khan, Diana H Chin, Jadon Porch, Maharshi Chakraborty, Richard Sallari, Olivier O Delattre, Sakina Zaidi, Sarah Morice, Didier Surdez, Sara G Danielli, Beat W Schäfer, Berkley E Gryder, Marco Wachtel
PAX3-FOXO1 uses its activation domain to recruit CBP/P300 and shape RNA Pol2 cluster distribution. Nature communications 14 (1) (2023)
Martyna W Sroka, Damianos Skopelitis, Marit W Vermunt, Jonathan B Preall, Osama El Demerdash, Larissa M N de Almeida, Kenneth Chang, Raditya Utama, Berkley E Gryder, Giuseppina Caligiuri, Diqiu Ren, Benan Nalbant, Joseph P Milazzo, David A Tuveson, Alexander Dobin, Scott W Hiebert, Kristy R Stengel, Roberto Mantovani, Javed Khan, Rahul M Kohli, Junwei Shi, Gerd A Blobel, Christopher R Vakoc
Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma. Proceedings of the National Academy of Sciences of the United States of America 120 (36) (2023)
Royce W Zhou, Jia Xu, Tiphaine C Martin, Alexis L Zachem, John He, Sait Ozturk, Deniz Demircioglu, Ankita Bansal, Andrew P Trotta, Bruno Giotti, Berkley E Gryder, Yao Shen, Xuewei Wu, Saul Carcamo, Kaitlyn Bosch, Benjamin D Hopkins, Alexander M Tsankov, Randolph Steinhagen, Drew R Jones, John Asara, Jerry E Chipuk, Rachel Brody, Steven Itzkowitz, Iok In Christine Chio, Dan Hasson, Emily Bernstein, Ramon E Parsons
Author Correction: A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma. Nature communications 14 (1) (2023)
Ana María Garzón-Porras, Emma J Chory, Berkley E Gryder
Dynamic Opposition of Histone Modifications. ACS chemical biology (2022)
Cameron F Hays, Berkley E Gryder
Epigenetic convergence in the rising tide of opioid overdose deaths. Molecular psychiatry 27 (6) (2022)
Olivia Corradin, Richard Sallari, An T Hoang, Bibi S Kassim, Gabriella Ben Hutta, Lizette Cuoto, Bryan C Quach, Katreya Lovrenert, Cameron Hays, Berkley E Gryder, Marina Iskhakova, Hannah Cates, Yanwei Song, Cynthia F Bartels, Dana B Hancock, Deborah C Mash, Eric O Johnson, Schahram Akbarian, Peter C Scacheri
Convergence of case-specific epigenetic alterations identify a confluence of genetic vulnerabilities tied to opioid overdose. Molecular psychiatry 27 (4) (2022)
Royce W Zhou, Jia Xu, Tiphaine C Martin, Alexis L Zachem, John He, Sait Ozturk, Deniz Demircioglu, Ankita Bansal, Andrew P Trotta, Bruno Giotti, Berkley E Gryder, Yao Shen, Xuewei Wu, Saul Carcamo, Kaitlyn Bosch, Benjamin D Hopkins, Alexander M Tsankov, Randolph Steinhagen, Drew R Jones, John Asara, Jerry E Chipuk, Rachel Brody, Steven Itzkowitz, Iok In Christine Chio, Dan Hasson, Emily Bernstein, Ramon E Parsons
A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma. Nature communications 13 (1) (2022)
David Milewski, Samriddhi Shukla, Berkley E Gryder, Arun Pradhan, Johnny Donovan, Parvathi Sudha, Sushmitha Vallabh, Athena Pyros, Yan Xu, Artem Barski, Sara Szabo, Brian Turpin, Joseph G Pressey, Douglas P Millay, Javed Khan, Vladimir V Kalinichenko, Tanya V Kalin
FOXF1 is required for the oncogenic properties of PAX3-FOXO1 in rhabdomyosarcoma. Oncogene 40 (12) (2021)
Dominik Laubscher, Berkley E Gryder, Benjamin D Sunkel, Thorkell Andresson, Marco Wachtel, Sudipto Das, Bernd Roschitzki, Witold Wolski, Xiaoli S Wu, Hsien-Chao Chou, Young K Song, Chaoyu Wang, Jun S Wei, Meng Wang, Xinyu Wen, Quy Ai Ngo, Joana G Marques, Christopher R Vakoc, Beat W Schäfer, Benjamin Z Stanton, Javed Khan
BAF complexes drive proliferation and block myogenic differentiation in fusion-positive rhabdomyosarcoma. Nature communications 12 (1) (2021)
Robert Kupp, Lisa Ruff, Sabrina Terranova, Erica Nathan, Stephane Ballereau, Rory Stark, Chandra Sekhar Reddy Chilamakuri, Nadin Hoffmann, Katherine Wickham-Rahrmann, Marcus Widdess, Amir Arabzade, Yanhua Zhao, Srinidhi Varadharajan, Tuyu Zheng, Mohankumar Murugesan, Stefan M Pfister, Daisuke Kawauchi, Kristian W Pajtler, Benjamin Deneen, Stephen C Mack, Katherine E Masih, Berkley E Gryder, Javed Khan, Richard J Gilbertson
ZFTA Translocations Constitute Ependymoma Chromatin Remodeling and Transcription Factors. Cancer discovery 11 (9) (2021)
Long Wang, Nicole Rae Hensch, Kathryn Bondra, Prethish Sreenivas, Xiang R Zhao, Jiangfei Chen, Rodrigo Moreno Campos, Kunal Baxi, Angelina V Vaseva, Benjamin D Sunkel, Berkley E Gryder, Silvia Pomella, Benjamin Z Stanton, Siyuan Zheng, Eleanor Y Chen, Rossella Rota, Javed Khan, Peter J Houghton, Myron S Ignatius
SNAI2-Mediated Repression of BIM Protects Rhabdomyosarcoma from Ionizing Radiation. Cancer research 81 (21) (2021)
Silvia Pomella, Prethish Sreenivas, Berkley E Gryder, Long Wang, David Milewski, Matteo Cassandri, Kunal Baxi, Nicole Rae Hensch, Elena Carcarino, Young Song, Hsien-Chao Chou, Marielle E Yohe, Benjamin Z Stanton, Bruno Amadio, Ignazio Caruana, Cristiano De Stefanis, Rita De Vito, Franco Locatelli, Yidong Chen, Eleanor Y Chen, Peter Houghton, Javed Khan, Rossella Rota, Myron S Ignatius
Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma. Nature communications 12 (1) (2021)
Nichelle C Whitlock, Shana Y Trostel, Scott Wilkinson, Nicholas T Terrigino, S Thomas Hennigan, Ross Lake, Nicole V Carrabba, Rayann Atway, Elizabeth D Walton, Berkley E Gryder, Brian J Capaldo, Huihui Ye, Adam G Sowalsky
MEIS1 down-regulation by MYC mediates prostate cancer development through elevated HOXB13 expression and AR activity. Oncogene 39 (34) (2020)
Richard K Yang, Igor B Kuznetsov, Erik A Ranheim, Jun S Wei, Sivasish Sindiri, Berkley E Gryder, Vineela Gangalapudi, Young K Song, Viharkumar Patel, Jacquelyn A Hank, Cindy Zuleger, Amy K Erbe, Zachary S Morris, Renae Quale, KyungMann Kim, Mark R Albertini, Javed Khan, Paul M Sondel
Outcome-Related Signatures Identified by Whole Transcriptome Sequencing of Resectable Stage III/IV Melanoma Evaluated after Starting Hu14.18-IL2. Clinical cancer research : an official journal of the American Association for Cancer Research 26 (13) (2020)
Berkley E Gryder, Javed Khan, Benjamin Z Stanton
Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP). Nature protocols 15 (3) (2020)
Remi Adelaiye-Ogala, Berkley E Gryder, Yen Thi Minh Nguyen, Aian Neil Alilin, Adlai R Grayson, Wardah Bajwa, Keith H Jansson, Michael L Beshiri, Supreet Agarwal, Jose Antonio Rodriguez-Nieves, Brian Capaldo, Kathleen Kelly, David J VanderWeele
Targeting the PI3K/AKT Pathway Overcomes Enzalutamide Resistance by Inhibiting Induction of the Glucocorticoid Receptor. Molecular cancer therapeutics 19 (7) (2020)
Berkley E Gryder, Silvia Pomella, Carly Sayers, Xiaoli S Wu, Young Song, Anna M Chiarella, Sukriti Bagchi, Hsien-Chao Chou, Ranu S Sinniah, Ashley Walton, Xinyu Wen, Rossella Rota, Nathaniel A Hathaway, Keji Zhao, Jiji Chen, Christopher R Vakoc, Jack F Shern, Benjamin Z Stanton, Javed Khan
Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nature genetics 51 (12) (2019)
Marielle E Yohe, Berkley E Gryder, Jack F Shern, Young K Song, Hsien-Chao Chou, Sivasish Sindiri, Arnulfo Mendoza, Rajesh Patidar, Xiaohu Zhang, Rajarashi Guha, Donna Butcher, Kristine A Isanogle, Christina M Robinson, Xiaoling Luo, Jin-Qiu Chen, Ashley Walton, Parirokh Awasthi, Elijah F Edmondson, Simone Difilippantonio, Jun S Wei, Keji Zhao, Marc Ferrer, Craig J Thomas, Javed Khan
MEK inhibition induces MYOG and remodels super-enhancers in RAS-driven rhabdomyosarcoma. Science translational medicine 10 (448) (2019)
Anna M Chiarella, Kyle V Butler, Berkley E Gryder, Dongbo Lu, Tiffany A Wang, Xufen Yu, Silvia Pomella, Javed Khan, Jian Jin, Nathaniel A Hathaway
Dose-dependent activation of gene expression is achieved using CRISPR and small molecules that recruit endogenous chromatin machinery. Nature biotechnology 38 (1) (2019)
Berkley E Gryder, Lei Wu, Girma M Woldemichael, Silvia Pomella, Taylor R Quinn, Paul M C Park, Abigail Cleveland, Benjamin Z Stanton, Young Song, Rossella Rota, Olaf Wiest, Marielle E Yohe, Jack F Shern, Jun Qi, Javed Khan
Chemical genomics reveals histone deacetylases are required for core regulatory transcription. Nature communications 10 (1) (2019)