Wenxiu Ma
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An integrated software system for analyzing ChIP-chip and ChIP-seq data
H Ji, H Jiang, W Ma, DS Johnson, RM Myers, WH Wong
Nature biotechnology 26 (11), 1293-1300, 2008
TERT promotes epithelial proliferation through transcriptional control of a Myc-and Wnt-related developmental program
J Choi, LK Southworth, KY Sarin, AS Venteicher, W Ma, W Chang, ...
PLoS Genet 4 (1), e10, 2008
Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks
JS Park, W Ma, LL O'Brien, E Chung, JJ Guo, JG Cheng, MT Valerius, ...
Developmental cell 23 (3), 637-651, 2012
The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation
F Yang, X Deng, W Ma, JB Berletch, N Rabaia, G Wei, JM Moore, ...
Genome biology 16 (1), 52, 2015
Bipartite structure of the inactive mouse X chromosome
X Deng, W Ma, V Ramani, A Hill, F Yang, F Ay, JB Berletch, CA Blau, ...
Genome biology 16 (1), 152, 2015
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
W Ma, F Ay, C Lee, G Gulsoy, X Deng, S Cook, J Hesson, C Cavanaugh, ...
Nature methods 12 (1), 71-78, 2015
Escape from X Inactivation Varies in Mouse Tissues
JB Berletch, W Ma, F Yang, J Shendure, WS Noble, CM Disteche, X Deng
PLOS Genetics 11 (3), e1005079, 2015
Motif-based analysis of large nucleotide data sets using MEME-ChIP
W Ma, WS Noble, TL Bailey
Nature protocols 9 (6), 1428-1450, 2014
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning
KA Peterson, Y Nishi, W Ma, A Vedenko, L Shokri, X Zhang, M McFarlane, ...
Genes & Development 26 (24), 2802-2816, 2012
Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis
EY Lee, H Ji, Z Ouyang, B Zhou, W Ma, SA Vokes, AP McMahon, ...
Proceedings of the National Academy of Sciences 107 (21), 9736-9741, 2010
Mapping 3D genome architecture through in situ DNase Hi-C
V Ramani, DA Cusanovich, RJ Hause, W Ma, R Qiu, X Deng, CA Blau, ...
Nature protocols 11 (11), 2104-2121, 2016
Mammalian X Upregulation Is Associated with Enhanced Transcription Initiation, RNA Half-Life, and MOF-Mediated H4K16 Acetylation
X Deng, JB Berletch, W Ma, DK Nguyen, JB Hiatt, WS Noble, J Shendure, ...
Developmental Cell, 2013
Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B
Y Qiu, EK Pasoreck, AK Reddy, A Nagatani, W Ma, J Chory, M Chen
Nature communications 8 (1), 1905, 2017
Using CisGenome to Analyze ChIP‐chip and ChIP‐seq Data
H Ji, H Jiang, W Ma, WH Wong
Current Protocols in Bioinformatics 2, 2, 2011
The analysis of ChIP-Seq data
W Ma, WH Wong
Methods in enzymology 497, 51-73, 2011
Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates
T Barr, S Sureshchandra, P Ruegger, J Zhang, W Ma, J Borneman, ...
Gut microbes 9 (4), 338-356, 2018
Insight into Insulin Secretion from Transcriptome and Genetic Analysis of Insulin-Producing Cells of Drosophila
J Cao, J Ni, W Ma, V Shiu, LA Milla, S Park, ML Spletter, S Tang, J Zhang, ...
Genetics 197 (1), 175-192, 2014
Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution
W Ma, F Ay, C Lee, G Gulsoy, X Deng, S Cook, J Hesson, C Cavanaugh, ...
Methods 142, 59-73, 2018
DNA sequence+ shape kernel enables alignment-free modeling of transcription factor binding
W Ma, L Yang, R Rohs, WS Noble
Bioinformatics 33 (19), 3003-3010, 2017
Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomes
AZ Virji, J Thekkiniath, W Ma, L Lawres, J Knight, A Swei, K Le Roch, ...
International journal for parasitology 49 (2), 105-113, 2019
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