Chao Cheng
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An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature 489 (7414), 57, 2012
Architecture of the human regulatory network derived from ENCODE data
MB Gerstein, A Kundaje, M Hariharan, SG Landt, KK Yan, C Cheng, ...
Nature 489 (7414), 91-100, 2012
A user's guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium
PLoS Biol 9 (4), e1001046, 2011
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng, BI Arshinoff, T Liu, ...
Science 330 (6012), 1775, 2010
Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9
M Wei, P Fabrizio, J Hu, H Ge, C Cheng, L Li, VD Longo
PLoS Genetics 4 (1), e13, 2008
A cis-regulatory map of the Drosophila genome
N Nègre, CD Brown, L Ma, CA Bristow, SW Miller, U Wagner, ...
Nature 471 (7339), 527-531, 2011
Sir2 blocks extreme life-span extension
P Fabrizio, C Gattazzo, L Battistella, M Wei, C Cheng, K McGrew, ...
Cell 123 (4), 655-667, 2005
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
KY Yip, C Cheng, N Bhardwaj, JB Brown, J Leng, A Kundaje, J Rozowsky, ...
Genome biology 13 (9), 1-22, 2012
Comparative analysis of the transcriptome across distant species
M Gerstein, J Rozowsky, K Yan, D Wang, C Cheng, B Brown, C Davis, ...
Nature 512, 445–448, 2014
Modeling gene expression using chromatin features in various cellular contexts
X Dong, MC Greven, A Kundaje, S Djebali, JB Brown, C Cheng, ...
Genome biology 13 (9), 1-17, 2012
CircNet: a database of circular RNAs derived from transcriptome sequencing data
YC Liu, JR Li, CH Sun, E Andrews, RF Chao, FM Lin, SL Weng, SD Hsu, ...
Nucleic Acids Res., pii: gkv940, 2015
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.
W Niu, ZJ Lu, M Zhong, M Sarov, JI Murray, CM Brdlik, J Janette, C Cheng, ...
Genome Res. 21 (2), 245-254, 2011
Comparative analysis of regulatory information and circuits across diverse species
A Boyle, C Araya, C Brdlik, P Cayting, C Cheng, Y Cheng, K Gardner, ...
Nature 512, 453–456, 2014
A deep learning framework for modeling structural features of RNA-binding protein targets
S Zhang, J Zhou, H H, H Gong, L Chen, C Cheng, J Zeng
Nucleic Acids Res., gkv1025, 2015
Big data bioinformatics
C Greene, J Tan, M Ung, J Moore, C Cheng
J. Cell. Physiol., 2014
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
C Cheng, R Alexander, R Min, J Leng, KY Yip, J Rozowsky, KK Yan, ...
Genome Research 22 (9), 1658-1667, 2012
Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis.
Y Lee, X Yang, Y Huang, H Fan, Q Zhang, Y Wu, J Li, R Hasina, C Cheng, ...
PLoS computational biology 6 (4), 2010
Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization
Y Mishima, C Abreu-Goodger, AA Staton, C Stahlhut, C Shou, C Cheng, ...
Genes & development 23 (5), 619-632, 2009
Identification of cell cycle–regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
GD Grant, L Brooks 3rd, X Zhang, JM Mahoney, V Martyanov, TA Wood, ...
Molecular biology of the cell 24 (23), 3634-3650, 2013
Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines
Q Cao, C Anyansi, X Hu, L Xu, L Xiong, W Tang, MTS Mok, C Cheng, ...
Nature genetics 49 (10), 1428-1436, 2017
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