Publications by authors named "Clifford A Meyer"

52Publications

Computational Approaches to Modeling Transcription Factor Activity and Gene Regulation.

Authors:
Clifford A Meyer X Shirley Liu

Trends Biochem Sci 2020 Dec 10;45(12):1094-1095. Epub 2020 Oct 10.

Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.

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December 2020

Integrative analyses of single-cell transcriptome and regulome using MAESTRO.

Authors:
Chenfei Wang Dongqing Sun Xin Huang Changxin Wan Ziyi Li Ya Han Qian Qin Jingyu Fan Xintao Qiu Yingtian Xie Clifford A Meyer Myles Brown Ming Tang Henry Long Tao Liu X Shirley Liu

Genome Biol 2020 08 7;21(1):198. Epub 2020 Aug 7.

Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.

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August 2020

Correction: Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells.

Authors:
Rong En Tay Olamide Olawoyin Paloma Cejas Yingtian Xie Clifford A Meyer Yoshinaga Ito Qing Yu Weng David E Fisher Henry W Long Myles Brown Hye-Jung Kim Kai W Wucherpfennig

J Exp Med 2020 Jul;217(7)

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July 2020

Determinants of transcription factor regulatory range.

Authors:
Chen-Hao Chen Rongbin Zheng Collin Tokheim Xin Dong Jingyu Fan Changxin Wan Qin Tang Myles Brown Jun S Liu Clifford A Meyer X Shirley Liu

Nat Commun 2020 05 18;11(1):2472. Epub 2020 May 18.

Department of Data Sciences, Dana-Farber Cancer Institute. Harvard T.H. Chan School of Public Health, Boston, MA, USA.

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May 2020

Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells.

Authors:
Rong En Tay Olamide Olawoyin Paloma Cejas Yingtian Xie Clifford A Meyer Qing Yu Weng David E Fisher Henry W Long Myles Brown Hye-Jung Kim Kai W Wucherpfennig

J Exp Med 2020 Jul;217(7)

Department of Immunology, Harvard Medical School, Boston, MA.

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July 2020

Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data.

Authors:
Qian Qin Jingyu Fan Rongbin Zheng Changxin Wan Shenglin Mei Qiu Wu Hanfei Sun Myles Brown Jing Zhang Clifford A Meyer X Shirley Liu

Genome Biol 2020 02 7;21(1):32. Epub 2020 Feb 7.

Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.

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February 2020

Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks.

Authors:
Shaojuan Li Changxin Wan Rongbin Zheng Jingyu Fan Xin Dong Clifford A Meyer X Shirley Liu

Nucleic Acids Res 2019 07;47(W1):W206-W211

Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

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July 2019

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.

Authors:
Rongbin Zheng Changxin Wan Shenglin Mei Qian Qin Qiu Wu Hanfei Sun Chen-Hao Chen Myles Brown Xiaoyan Zhang Clifford A Meyer X Shirley Liu

Nucleic Acids Res 2019 01;47(D1):D729-D735

Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

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January 2019

Improved design and analysis of CRISPR knockout screens.

Authors:
Chen-Hao Chen Tengfei Xiao Han Xu Peng Jiang Clifford A Meyer Wei Li Myles Brown X Shirley Liu

Bioinformatics 2018 12;34(23):4095-4101

Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.

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December 2018

ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D.

Authors:
Kazumasa Komura Yuki Yoshikawa Teppei Shimamura Goutam Chakraborty Travis A Gerke Kunihiko Hinohara Kalyani Chadalavada Seong Ho Jeong Joshua Armenia Shin-Yi Du Ying Z Mazzu Kohei Taniguchi Naokazu Ibuki Clifford A Meyer Gouri J Nanjangud Teruo Inamoto Gwo-Shu Mary Lee Lorelei A Mucci Haruhito Azuma Christopher J Sweeney Philip W Kantoff

J Clin Invest 2018 07 4;128(7):2979-2995. Epub 2018 Jun 4.

Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

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July 2018

Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer.

Authors:
Shenglin Mei Clifford A Meyer Rongbin Zheng Qian Qin Qiu Wu Peng Jiang Bo Li Xiaohui Shi Binbin Wang Jingyu Fan Celina Shih Myles Brown Chongzhi Zang X Shirley Liu

Cancer Res 2017 11;77(21):e19-e22

Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China.

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November 2017

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.

Authors:
Shenglin Mei Qian Qin Qiu Wu Hanfei Sun Rongbin Zheng Chongzhi Zang Muyuan Zhu Jiaxin Wu Xiaohui Shi Len Taing Tao Liu Myles Brown Clifford A Meyer X Shirley Liu

Nucleic Acids Res 2017 01 26;45(D1):D658-D662. Epub 2016 Oct 26.

Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China

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January 2017

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.

Authors:
Qian Qin Shenglin Mei Qiu Wu Hanfei Sun Lewyn Li Len Taing Sujun Chen Fugen Li Tao Liu Chongzhi Zang Han Xu Yiwen Chen Clifford A Meyer Yong Zhang Myles Brown Henry W Long X Shirley Liu

BMC Bioinformatics 2016 Oct 3;17(1):404. Epub 2016 Oct 3.

Shanghai Key laboratory of tuberculosis, Shanghai Pulmonary Hospital, Shanghai, China.

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October 2016

Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles.

Authors:
Su Wang Chongzhi Zang Tengfei Xiao Jingyu Fan Shenglin Mei Qian Qin Qiu Wu Xujuan Li Kexin Xu Housheng Hansen He Myles Brown Clifford A Meyer X Shirley Liu

Genome Res 2016 10 27;26(10):1417-1429. Epub 2016 Jul 27.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.

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October 2016

High-dimensional genomic data bias correction and data integration using MANCIE.

Authors:
Chongzhi Zang Tao Wang Ke Deng Bo Li Sheng'en Hu Qian Qin Tengfei Xiao Shihua Zhang Clifford A Meyer Housheng Hansen He Myles Brown Jun S Liu Yang Xie X Shirley Liu

Nat Commun 2016 Apr 13;7:11305. Epub 2016 Apr 13.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.

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April 2016

Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer.

Authors:
Shaokun Shu Charles Y Lin Housheng Hansen He Robert M Witwicki Doris P Tabassum Justin M Roberts Michalina Janiszewska Sung Jin Huh Yi Liang Jeremy Ryan Ernest Doherty Hisham Mohammed Hao Guo Daniel G Stover Muhammad B Ekram Jonathan Brown Clive D'Santos Ian E Krop Deborah Dillon Michael McKeown Christopher Ott Jun Qi Min Ni Prakash K Rao Melissa Duarte Shwu-Yuan Wu Cheng-Ming Chiang Lars Anders Richard A Young Eric Winer Antony Letai William T Barry Jason S Carroll Henry Long Myles Brown X Shirley Liu Clifford A Meyer James E Bradner Kornelia Polyak

Nature 2016 Jan 6;529(7586):413-417. Epub 2016 Jan 6.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

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January 2016

Sequence determinants of improved CRISPR sgRNA design.

Authors:
Han Xu Tengfei Xiao Chen-Hao Chen Wei Li Clifford A Meyer Qiu Wu Di Wu Le Cong Feng Zhang Jun S Liu Myles Brown X Shirley Liu

Genome Res 2015 Aug 10;25(8):1147-57. Epub 2015 Jun 10.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;

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August 2015

Cyclin C is a haploinsufficient tumour suppressor.

Authors:
Na Li Anne Fassl Joel Chick Hiroyuki Inuzuka Xiaoyu Li Marc R Mansour Lijun Liu Haizhen Wang Bryan King Shavali Shaik Alejandro Gutierrez Alban Ordureau Tobias Otto Taras Kreslavsky Lukas Baitsch Leah Bury Clifford A Meyer Nan Ke Kristin A Mulry Michael J Kluk Moni Roy Sunkyu Kim Xiaowu Zhang Yan Geng Agnieszka Zagozdzon Sarah Jenkinson Rosemary E Gale David C Linch Jean J Zhao Charles G Mullighan J Wade Harper Jon C Aster Iannis Aifantis Harald von Boehmer Steven P Gygi Wenyi Wei A Thomas Look Piotr Sicinski

Nat Cell Biol 2014 Nov 26;16(11):1080-91. Epub 2014 Oct 26.

1] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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November 2014

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.

Authors:
Clifford A Meyer X Shirley Liu

Nat Rev Genet 2014 Nov 16;15(11):709-21. Epub 2014 Sep 16.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA; and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.

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November 2014

MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes.

Authors:
Xiaoqi Zheng Qian Zhao Hua-Jun Wu Wei Li Haiyun Wang Clifford A Meyer Qian Alvin Qin Han Xu Chongzhi Zang Peng Jiang Fuqiang Li Yong Hou Jianxing He Jun Wang Jun Wang Peng Zhang Yong Zhang Xiaole Shirley Liu

Genome Biol 2014 Aug 7;15(8):419. Epub 2014 Aug 7.

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August 2014