ChIP-Chip: Algorithms for Calling Binding Sites

Por Liu, X. Shirley, Meyer, Clifford A.
Publicado em 2009

Identifying and Mitigating Bias in Next-Generation Sequencing Methods for Chromatin Biology

Por Meyer, Clifford A., Liu, X. Shirley
Publicado no Nat Rev Genet (2014)

Minireview: Applications of Next-Generation Sequencing on Studies of Nuclear Receptor Regulation and Function

Por Meyer, Clifford A., Tang, Qianzi, Liu, X. Shirley
Publicado em 2012

MULTIPLE TESTING OF LOCAL MAXIMA FOR DETECTION OF PEAKS IN CHIP-SEQ DATA

Por Schwartzman, Armin, Jaffe, Andrew, Gavrilov, Yulia, Meyer, Clifford A.
Publicado no Ann Appl Stat (2013)

BINOCh: binding inference from nucleosome occupancy changes

Por Meyer, Clifford A., He, Housheng H., Brown, Myles, Liu, X. Shirley
Publicado em 2011

A closer look into DNase I hypersensitivity

Por He, Housheng Hansen, Meyer, Clifford A, Long, Henry, Liu, X Shirley, Brown, Myles
Publicado em 2013

Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription

Por Swinburne, Ian A., Meyer, Clifford A., Liu, X. Shirley, Silver, Pamela A., Brodsky, Alexander S.
Publicado em 2006

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data

Por Chen, Yiwen, Meyer, Clifford A, Liu, Tao, Li, Wei, Liu, Jun S, Liu, Xiaole Shirley
Publicado em 2011

A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer

Por Wang, Haiyun, Meyer, Clifford A, Fei, Teng, Wang, Gang, Zhang, Fan, Liu, X Shirley
Publicado em 2013

Model-based analysis of tiling-arrays for ChIP-chip

Por Johnson, W. Evan, Li, Wei, Meyer, Clifford A., Gottardo, Raphael, Carroll, Jason S., Brown, Myles, Liu, X. Shirley
Publicado em 2006

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

Por He, Housheng Hansen, Meyer, Clifford A., Chen, Mei Wei, Jordan, V. Craig, Brown, Myles, Liu, X. Shirley
Publicado em 2012

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers

Por Eeckhoute, Jérôme, Lupien, Mathieu, Meyer, Clifford A., Verzi, Michael P., Shivdasani, Ramesh A., Liu, X. Shirley, Brown, Myles
Publicado em 2009

Coactivator Function Defines the Active Estrogen Receptor Alpha Cistrome

Por Lupien, Mathieu, Eeckhoute, Jérôme, Meyer, Clifford A., Krum, Susan A., Rhodes, Daniel R., Liu, X. Shirley, Brown, Myles
Publicado em 2009

Computational inference of mRNA stability from histone modification and transcriptome profiles

Por Wang, Chengyang, Tian, Rui, Zhao, Qian, Xu, Han, Meyer, Clifford A., Li, Cheng, Zhang, Yong, Liu, X. Shirley
Publicado em 2012

FoxA1 translates epigenetic signatures into enhancer driven lineage-specific transcription

Por Lupien, Mathieu, Eeckhoute, Jérôme, Meyer, Clifford A., Wang, Qianben, Zhang, Yong, Li, Wei, Carroll, Jason S., Liu, X. Shirley, Brown, Myles
Publicado em 2008

Exon expression profiling reveals stimulus-mediated exon use in neural cells

Por McKee, Adrienne E, Neretti, Nicola, Carvalho, Luis E, Meyer, Clifford A, Fox, Edward A, Brodsky, Alexander S, Silver, Pamela A
Publicado em 2007

Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells

Por Brodsky, Alexander S, Meyer, Clifford A, Swinburne, Ian A, Hall, Giles, Keenan, Benjamin J, Liu, Xiaole S, Fox, Edward A, Silver, Pamela A
Publicado em 2005

A Comprehensive View of Nuclear Receptor Cancer Cistromes

Por Tang, Qianzi, Chen, Yiwen, Meyer, Clifford, Geistlinger, Tim, Lupien, Mathieu, Wang, Qian, Liu, Tao, Zhang, Yong, Brown, Myles, Liu, X. Shirley
Publicado em 2011

Target analysis by integration of transcriptome and ChIP-seq data with BETA

Por Wang, Su, Sun, Hanfei, Ma, Jian, Zang, Chongzhi, Wang, Chenfei, Wang, Juan, Tang, Qianzi, Meyer, Clifford A, Zhang, Yong, Liu, X Shirley
Publicado em 2013

Growth factor stimulation induces a distinct ERα cistrome underlying breast cancer endocrine resistance

Por Lupien, Mathieu, Meyer, Clifford A., Bailey, Shannon T., Eeckhoute, Jérôme, Cook, Jennifer, Westerling, Thomas, Zhang, Xiaoyang, Carroll, Jason S., Rhodes, Daniel R., Liu, X. Shirley, Brown, Myles
Publicado em 2010