Zhi John Lu
Zhi John Lu
Verified email at biomed.tsinghua.edu.cn - Homepage
TitleCited byYear
An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature, 2012
51922012
A user’s guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium
PLoS Biol 9 (4), e1001046, 2011
11112011
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), 1775-1787, 2010
8582010
Comparative analysis of the transcriptome across distant species
MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, ...
Nature 512 (7515), 445-448, 2014
2212014
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 Chen, ...
Genome research 21 (2), 245-254, 2011
1952011
Divergent lncRNAs regulate gene expression and lineage differentiation in pluripotent cells
S Luo, JY Lu, L Liu, Y Yin, C Chen, X Han, B Wu, R Xu, W Liu, P Yan, ...
Cell stem cell 18 (5), 637-652, 2016
1812016
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response
M Zhong, W Niu, ZJ Lu, M Sarov, JI Murray, J Janette, D Raha, ...
PLoS genetics 6 (2), 2010
1612010
Improved RNA secondary structure prediction by maximizing expected pair accuracy
ZJ Lu, JW Gloor, DH Mathews
Rna 15 (10), 1805-1813, 2009
1542009
Characterization of Stress‐responsive lncRNAs in Arabidopsis thaliana by Integrating Expression, Epigenetic and Structural Features
C Di, J Yuan, Y Wu, J Li, H Lin, L Hu, T Zhang, Y Qi, MB Gerstein, Y Guo, ...
The Plant Journal, 2014
1322014
CLIPdb: a CLIP-seq database for protein-RNA interactions
YCT Yang, C Di, B Hu, M Zhou, Y Liu, N Song, Y Li, J Umetsu, ZJ Lu
BMC genomics 16 (1), 51, 2015
1282015
Efficient siRNA selection using hybridization thermodynamics
ZJ Lu, DH Mathews
Nucleic acids research 36 (2), 640-647, 2008
1182008
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
ZJ Lu, DH Turner, DH Mathews
Nucleic acids research 34 (17), 4912-4924, 2006
1092006
Recurrently deregulated lncRNAs in hepatocellular carcinoma
Y Yang, L Chen, J Gu, H Zhang, J Yuan, Q Lian, G Lv, S Wang, Y Wu, ...
Nature communications 8, 14421, 2017
1002017
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data
C Cheng, KK Yan, W Hwang, J Qian, N Bhardwaj, J Rozowsky, ZJ Lu, ...
PLoS computational biology 7 (11), 2011
952011
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
XJ Mu, ZJ Lu, Y Kong, HYK Lam, MB Gerstein
Nucleic acids research 39 (16), 7058-7076, 2011
842011
Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae
MA Freeberg, T Han, JJ Moresco, A Kong, YC Yang, ZJ Lu, JR Yates, ...
Genome Biology 14 (2), R13, 2013
782013
Systematic identification of synergistic drug pairs targeting HIV
X Tan, L Hu, LJ Luquette III, G Gao, Y Liu, H Qu, R Xi, ZJ Lu, PJ Park, ...
Nature Biotechnology, 2012
762012
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
ZJ Lu, KY Yip, G Wang, C Shou, LDW Hillier, E Khurana, A Agarwal, ...
Genome research 21 (2), 276-285, 2011
762011
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics
ZJ Lu, DH Mathews
Nucleic acids research 36 (suppl_2), W104-W108, 2008
712008
Critical roles of long noncoding RNAs in Drosophila spermatogenesis
K Wen, L Yang, T Xiong, C Di, D Ma, M Wu, Z Xue, X Zhang, L Li, ...
Genome Research 26 (9), 1233-1244, 2016
582016
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