OpenURL Connection Search

Select item for more details and to access through your institution.

CircularLogo: A lightweight web application to visualize intra-motif dependencies.
Published in:
BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1680-2
By:
- Zhenqing Ye;
- Tao Ma;
- Kalmbach, Michael T.;
- Dasari, Surendra;
- Kocher, Jean-Pierre A.;
- Liguo Wang
Publication type:
Article
Androgen receptor splice variants bind to constitutively open chromatin and promote abiraterone-resistant growth of prostate cancer.
Published in:
Nucleic Acids Research, 2018, v. 46, n. 4, p. 1895, doi. 10.1093/nar/gkx1306
By:
- He, Yundong;
- Lu, Ji;
- Ye, Zhenqing;
- Hao, Siyuan;
- Wang, Liewei;
- Kohli, Manish;
- Tindall, Donald J;
- Li, Benyi;
- Zhu, Runzhi;
- Wang, Liguo
Publication type:
Article
Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 16, p. 7540, doi. 10.1093/nar/gkw659
By:
- Zhenqing Ye;
- Zhong Chen;
- Sunkel, Benjamin;
- Frietze, Seth;
- Huang, Tim H.-M.;
- Qianben Wang;
- Jin, Victor X.
Publication type:
Article
Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 9, p. 4105, doi. 10.1093/nar/gkv1528
By:
- Sunkel, Benjamin;
- Dayong Wu;
- Zhong Chen;
- Chiou-Miin Wang;
- Xiangtao Liu;
- Zhenqing Ye;
- Horning, Aaron M.;
- Liu, Joseph;
- Mahalingam, Devalingam;
- Lopez-Nicora, Horacio;
- Chun-Lin Lin;
- Goodfellow, Paul J.;
- Clinton, Steven K.;
- Jin, Victor X.;
- Chun-Liang Chen;
- Tim H.-M. Huang;
- Qianben Wang
Publication type:
Article
Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer.
Published in:
Nucleic Acids Research, 2014, v. 42, n. 6, p. 3607, doi. 10.1093/nar/gkt1382
By:
- Wu, Dayong;
- Sunkel, Benjamin;
- Chen, Zhong;
- Liu, Xiangtao;
- Ye, Zhenqing;
- Li, Qianjin;
- Grenade, Cassandra;
- Ke, Jingdong;
- Zhang, Chunpeng;
- Chen, Hongyan;
- Nephew, Kenneth P.;
- Huang, Tim H.-M.;
- Liu, Zhihua;
- Jin, Victor X.;
- Wang, Qianben
Publication type:
Article
Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.
Published in:
Nucleic Acids Research, 2014, v. 42, n. 5, p. 2856
By:
- Ye, Zhenqing;
- Chen, Zhong;
- Lan, Xun;
- Hara, Stephen;
- Sunkel, Benjamin;
- Huang, Tim H.-M.;
- Elnitski, Laura;
- Wang, Qianben;
- Jin, Victor X.
Publication type:
Article
Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.
Published in:
Nucleic Acids Research, 2012, v. 40, n. 16, p. 7690, doi. 10.1093/nar/gks501
By:
- Lan, Xun;
- Witt, Heather;
- Katsumura, Koichi;
- Ye, Zhenqing;
- Wang, Qianben;
- Bresnick, Emery H.;
- Farnham, Peggy J.;
- Jin, Victor X.
Publication type:
Article
A noncanonical AR addiction drives enzalutamide resistance in prostate cancer.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21860-7
By:
- He, Yundong;
- Wei, Ting;
- Ye, Zhenqing;
- Orme, Jacob J.;
- Lin, Dong;
- Sheng, Haoyue;
- Fazli, Ladan;
- Jeffrey Karnes, R.;
- Jimenez, Rafael;
- Wang, Liguo;
- Wang, Liewei;
- Gleave, Martin E.;
- Wang, Yuzhuo;
- Shi, Lei;
- Huang, Haojie
Publication type:
Article
CpGtools: a python package for DNA methylation analysis.
Published in:
Bioinformatics, 2021, v. 37, n. 11, p. 1598, doi. 10.1093/bioinformatics/btz916
By:
- Wei, Ting;
- Nie, Jinfu;
- Larson, Nicholas B;
- Ye, Zhenqing;
- Eckel-Passow, Jeanette E;
- Robertson, Keith D;
- Kocher, Jean-Pierre A;
- Wang, Liguo
Publication type:
Article
Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-45097-2
By:
- Xu, Yi;
- Nipper, Michael H.;
- Dominguez, Angel A.;
- Ye, Zhenqing;
- Akanuma, Naoki;
- Lopez, Kevin;
- Deng, Janice J.;
- Arenas, Destiny;
- Sanchez, Ava;
- Sharkey, Francis E.;
- Court, Colin M.;
- Singhi, Aatur D.;
- Wang, Huamin;
- Fernandez-Zapico, Martin E.;
- Sun, Lu-Zhe;
- Zheng, Siyuan;
- Chen, Yidong;
- Liu, Jun;
- Wang, Pei
Publication type:
Article
Maternal Transmission Effect of a PDGF-C SNP on Nonsyndromic Cleft Lip with or without Palate from a Chinese Population.
Published in:
PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0046477
By:
- Di Wu;
- Mei Wang;
- Xingang Wang;
- Ningbei Yin;
- Tao Song;
- Haidong Li;
- Feng Zhang;
- Yongbiao Zhang;
- Zhenqing Ye;
- Jun Yu;
- Duen-Mei Wang;
- Zhenmin Zhao;
- Zongli Xu
Publication type:
Article
On the Origin of Tibetans and Their Genetic Basis in Adapting High-Altitude Environments.
Published in:
PLoS ONE, 2011, v. 6, n. 2, p. 1, doi. 10.1371/journal.pone.0017002
By:
- Binbin Wang;
- Yong-Biao Zhang;
- Feng Zhang;
- Hongbin Lin;
- Xumin Wang;
- Ning Wan;
- Zhenqing Ye;
- Haiyu Weng;
- Lili Zhang;
- Xin Li;
- Jiangwei Yan;
- Panpan Wang;
- Tingting Wu;
- Longfei Cheng;
- Jing Wang;
- Wang, Duen-Mei;
- Xu Ma;
- Jun Yu
Publication type:
Article
Loss of BRD4 induces cell senescence in HSC/HPCs by deregulating histone H3 clipping.
Published in:
EMBO Reports, 2023, v. 24, n. 10, p. 1, doi. 10.15252/embr.202357032
By:
- Yang, Hui;
- Sui, Pinpin;
- Guo, Ying;
- Chen, Shi;
- Maloof, Marie E;
- Ge, Guo;
- Nihozeko, Francine;
- Delma, Caroline R;
- Zhu, Ganqian;
- Zhang, Peng;
- Ye, Zhenqing;
- Medina, Edward A;
- Ayad, Nagi G;
- Mesa, Ruben;
- Nimer, Stephen D;
- Chiang, Cheng‐Ming;
- Xu, Mingjiang;
- Chen, Yidong;
- Yang, Feng‐Chun
Publication type:
Article
Estrogen receptor beta repurposes EZH2 to suppress oncogenic NFκB/p65 signaling in triple negative breast cancer.
Published in:
NPJ Breast Cancer, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41523-022-00387-0
By:
- Aspros, Kirsten G. M.;
- Carter, Jodi M.;
- Hoskin, Tanya L.;
- Suman, Vera J.;
- Subramaniam, Malayannan;
- Emch, Michael J.;
- Ye, Zhenqing;
- Sun, Zhifu;
- Sinnwell, Jason P.;
- Thompson, Kevin J.;
- Tang, Xiaojia;
- Rodman, Esther P. B.;
- Wang, Xiyin;
- Nelson, Adam W.;
- Chernukhin, Igor;
- Hamdan, Feda H.;
- Bruinsma, Elizabeth S.;
- Carroll, Jason S.;
- Fernandez-Zapico, Martin E.;
- Johnsen, Steven A.
Publication type:
Article
Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data.
Published in:
eLife, 2022, p. 1, doi. 10.7554/eLife.71994
By:
- Noureen, Nighat;
- Zhenqing Ye;
- Yidong Chen;
- Xiaojing Wang;
- Siyuan Zheng
Publication type:
Article
EZH2 cooperates with gain‐of‐function p53 mutants to promote cancer growth and metastasis.
Published in:
EMBO Journal, 2019, v. 38, n. 5, p. N.PAG, doi. 10.15252/embj.201899599
By:
- Zhao, Yu;
- Ding, Liya;
- Wang, Dejie;
- Ye, Zhenqing;
- He, Yundong;
- Ma, Linlin;
- Zhu, Runzhi;
- Pan, Yunqian;
- Wu, Qiang;
- Pang, Kun;
- Hou, Xiaonan;
- Weroha, Saravut J;
- Han, Conghui;
- Coleman, Roger;
- Coleman, Ilsa;
- Karnes, R Jeffery;
- Zhang, Jun;
- Nelson, Peter S;
- Wang, Liguo;
- Huang, Haojie
Publication type:
Article
Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer.
Published in:
EMBO Journal, 2015, v. 34, n. 4, p. 502, doi. 10.15252/embj.201490306
By:
- Chen, Zhong;
- Lan, Xun;
- Thomas‐Ahner, Jennifer M;
- Wu, Dayong;
- Liu, Xiangtao;
- Ye, Zhenqing;
- Wang, Liguo;
- Sunkel, Benjamin;
- Grenade, Cassandra;
- Chen, Junsheng;
- Zynger, Debra L;
- Yan, Pearlly S;
- Huang, Jiaoti;
- Nephew, Kenneth P;
- Huang, Tim H‐M;
- Lin, Shili;
- Clinton, Steven K;
- Li, Wei;
- Jin, Victor X;
- Wang, Qianben
Publication type:
Article
Hippo pathway-mediated YAP1/ TAZ inhibition is essential for proper pancreatic endocrine specification and differentiation.
Published in:
eLife, 2024, p. 1, doi. 10.7554/eLife.84532
By:
- Yifan Wu;
- Kunhua Qin;
- Yi Xu;
- Rajhans, Shreya;
- Vo, Truong;
- Lopez, Kevin M;
- Jun Liu;
- Nipper, Michael H;
- Deng, Janice;
- Xue Yin;
- Ramjit, Logan R;
- Zhenqing Ye;
- Yu Luan;
- Arda, H. Efsun;
- Pei Wang
Publication type:
Article
A survey of computational methods in transcriptome-wide alternative splicing analysis.
Published in:
Biomolecular Concepts, 2015, v. 6, n. 1, p. 59, doi. 10.1515/bmc-2014-0040
By:
- Jianbo Wang;
- Zhenqing Ye;
- Huang, Tim H.-M.;
- Huidong Shi;
- Victor Jin
Publication type:
Article
ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes.
Published in:
Epigenetics & Chromatin, 2013, v. 6, n. 1, p. 1, doi. 10.1186/1756-8935-6-13
By:
- Blattler, Adam;
- Lijing Yao;
- Yao Wang;
- Zhenqing Ye;
- Jin, Victor X.;
- Farnham, Peggy J.
Publication type:
Article
BMI1 maintains the Treg epigenomic landscape to prevent inflammatory bowel disease.
Published in:
2021
By:
- Gonzalez, Michelle M.;
- Bamidele, Adebowale O.;
- Svingen, Phyllis A.;
- Sagstetter, Mary R.;
- Smyrk, Thomas C.;
- Gaballa, Joseph M.;
- Hamdan, Feda H.;
- Kosinsky, Robyn Laura;
- Gibbons, Hunter R.;
- Zhifu Sun;
- Zhenqing Ye;
- Nair, Asha;
- Ramos, Guilherme P.;
- Neto, Manuel B. Braga;
- Wixom, Alexander Q.;
- Mathison, Angela J.;
- Johnsen, Steven A.;
- Urrutia, Raul;
- Faubion Jr., William A.;
- Sun, Zhifu
Publication type:
journal article
PD-1hi CD8+ resident memory T cells balance immunity and fibrotic sequelae.
Published in:
Science Immunology, 2019, v. 4, n. 36, p. 1, doi. 10.1126/sciimmunol.aaw1217
By:
- Zheng Wang;
- Shaohua Wang;
- Goplen, Nick P.;
- Chaofan Li;
- In Su Cheon;
- Qigang Dai;
- Su Huang;
- Jinjun Shan;
- Chaoyu Ma;
- Zhenqing Ye;
- Min Xiang;
- Limper, Andrew H.;
- Porquera, Eva-Carmona;
- Kohlmeier, Jacob E.;
- Kaplan, Mark H.;
- Nu Zhang;
- Johnson, Aaron J.;
- Vassallo, Robert;
- Jie Sun
Publication type:
Article
Deep learning tackles single-cell analysis—a survey of deep learning for scRNA-seq analysis.
Published in:
Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab531
By:
- Flores, Mario;
- Liu, Zhentao;
- Zhang, Tinghe;
- Hasib, Md Musaddaqui;
- Chiu, Yu-Chiao;
- Ye, Zhenqing;
- Paniagua, Karla;
- Jo, Sumin;
- Zhang, Jianqiu;
- Gao, Shou-Jiang;
- Jin, Yu-Fang;
- Chen, Yidong;
- Huang, Yufei
Publication type:
Article
Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer.
Published in:
Nature Communications, 2015, v. 6, n. 9, p. 8323, doi. 10.1038/ncomms9323
By:
- Zhong Chen;
- Xun Lan;
- Dayong Wu;
- Benjamin Sunkel;
- Zhenqing Ye;
- Jiaoti Huang;
- Zhihua Liu;
- Clinton, Steven K.;
- Jin, Victor X.;
- Qianben Wang
Publication type:
Article
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.
Published in:
Genome Biology, 2012, v. 13, n. 9, p. 1, doi. 10.1186/gb-2012-13-9-r52
By:
- Frietze, Seth;
- Rui Wang;
- Lijing Yao;
- Yu Gyoung Tak;
- Zhenqing Ye;
- Gaddis, Malaina;
- Witt, Heather;
- Farnham, Peggy J.;
- Jin, Victor X.
Publication type:
Article
Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application.
Published in:
BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4371-5
By:
- Jian Zhong;
- Zhenqing Ye;
- Lenz, Samuel W.;
- Clark, Chad R.;
- Bharucha, Adil;
- Farrugia, Gianrico;
- Robertson, Keith D.;
- Zhiguo Zhang;
- Tamas Ordog;
- Jeong-Heon Lee
Publication type:
Article
Glucocorticoids unmask silent non-coding genetic risk variants for common diseases.
Published in:
Nucleic Acids Research, 2022, v. 50, n. 20, p. 11635, doi. 10.1093/nar/gkac1045
By:
- Nguyen, Thanh Thanh L;
- Gao, Huanyao;
- Liu, Duan;
- Philips, Trudy Janice;
- Ye, Zhenqing;
- Lee, Jeong-Heon;
- Shi, Geng-xian;
- Copenhaver, Kaleigh;
- Zhang, Lingxin;
- Wei, Lixuan;
- Yu, Jia;
- Zhang, Huan;
- Barath, Abhijeet;
- Luong, Maggie;
- Zhang, Cheng;
- Gaspar-Maia, Alexandre;
- Li, Hu;
- Wang, Liewei;
- Ordog, Tamas;
- Weinshilboum, Richard M
Publication type:
Article
Phosphorylated MED1 links transcription recycling and cancer growth.
Published in:
Nucleic Acids Research, 2022, v. 50, n. 8, p. 4450, doi. 10.1093/nar/gkac246
By:
- Chen, Zhong;
- Ye, Zhenqing;
- Soccio, Raymond E;
- Nakadai, Tomoyoshi;
- Hankey, William;
- Zhao, Yue;
- Huang, Furong;
- Yuan, Fuwen;
- Wang, Hongyan;
- Cui, Zhifen;
- Sunkel, Benjamin;
- Wu, Dayong;
- Dzeng, Richard K;
- Thomas-Ahner, Jennifer M;
- Huang, Tim H M;
- Clinton, Steven K;
- Huang, Jiaoti;
- Lazar, Mitchell A;
- Jin, Victor X;
- Roeder, Robert G
Publication type:
Article
Glucocorticoids mediate transcriptome‐wide alternative polyadenylation: Potential mechanistic and clinical implications.
Published in:
CTS: Clinical & Translational Science, 2022, v. 15, n. 11, p. 2758, doi. 10.1111/cts.13402
By:
- Nguyen, Thanh Thanh L.;
- Liu, Duan;
- Gao, Huanyao;
- Ye, Zhenqing;
- Lee, Jeong‐Heon;
- Wei, Lixuan;
- Yu, Jia;
- Zhang, Lingxin;
- Wang, Liewei;
- Ordog, Tamas;
- Weinshilboum, Richard M.
Publication type:
Article
Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq.
Published in:
BMC Genomics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12864-019-5639-8
By:
- Zhong, Jian;
- Ye, Zhenqing;
- Clark, Chad R.;
- Lenz, Samuel W.;
- Nguyen, Justin H.;
- Yan, Huihuang;
- Robertson, Keith D.;
- Farrugia, Gianrico;
- Zhang, Zhiguo;
- Ordog, Tamas;
- Lee, Jeong-Heon
Publication type:
Article
Lysine-specific histone demethylase 1A (KDM1A/LSD1) inhibition attenuates DNA double-strand break repair and augments the efficacy of temozolomide in glioblastoma.
Published in:
Neuro-Oncology, 2023, v. 25, n. 7, p. 1249, doi. 10.1093/neuonc/noad018
By:
- Alejo, Salvador;
- Palacios, Bridgitte E;
- Venkata, Prabhakar Pitta;
- He, Yi;
- Li, Wenjing;
- Johnson, Jessica D;
- Chen, Yihong;
- Jayamohan, Sridharan;
- Pratap, Uday P;
- Clarke, Kyra;
- Zou, Yi;
- Lv, Yingli;
- Weldon, Korri;
- Viswanadhapalli, Suryavathi;
- Lai, Zhao;
- Ye, Zhenqing;
- Chen, Yidong;
- Gilbert, Andrea R;
- Suzuki, Takayoshi;
- Tekmal, Rajeshwar R
Publication type:
Article
Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4+ Lymphocytes in Crohn's Disease.
Published in:
Journal of Crohn's & Colitis, 2023, v. 17, n. 11, p. 1847, doi. 10.1093/ecco-jcc/jjad093
By:
- Sun, Zhifu;
- Braga-Neto, Manuel B;
- Xiong, Yuning;
- Bhagwate, Adytia V;
- Gibbons, Hunter R;
- Sagstetter, Mary R;
- Hamdan, Feda H;
- Baheti, Saurabh;
- Friton, Jessica;
- Nair, Asha;
- Ye, Zhenqing;
- Faubion, William A
Publication type:
Article

Found: 32

CircularLogo: A lightweight web application to visualize intra-motif dependencies.

Androgen receptor splice variants bind to constitutively open chromatin and promote abiraterone-resistant growth of prostate cancer.

Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.

Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence.

Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer.

Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.

A noncanonical AR addiction drives enzalutamide resistance in prostate cancer.

CpGtools: a python package for DNA methylation analysis.

Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset.

Maternal Transmission Effect of a PDGF-C SNP on Nonsyndromic Cleft Lip with or without Palate from a Chinese Population.

On the Origin of Tibetans and Their Genetic Basis in Adapting High-Altitude Environments.

Loss of BRD4 induces cell senescence in HSC/HPCs by deregulating histone H3 clipping.

Estrogen receptor beta repurposes EZH2 to suppress oncogenic NFκB/p65 signaling in triple negative breast cancer.

Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data.

EZH2 cooperates with gain‐of‐function p53 mutants to promote cancer growth and metastasis.

Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer.

Hippo pathway-mediated YAP1/ TAZ inhibition is essential for proper pancreatic endocrine specification and differentiation.

A survey of computational methods in transcriptome-wide alternative splicing analysis.

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes.

BMI1 maintains the Treg epigenomic landscape to prevent inflammatory bowel disease.

PD-1<sup>hi</sup> CD8<sup>+</sup> resident memory T cells balance immunity and fibrotic sequelae.

Deep learning tackles single-cell analysis—a survey of deep learning for scRNA-seq analysis.

Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer.

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.

Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application.

Glucocorticoids unmask silent non-coding genetic risk variants for common diseases.

Phosphorylated MED1 links transcription recycling and cancer growth.

Glucocorticoids mediate transcriptome‐wide alternative polyadenylation: Potential mechanistic and clinical implications.

Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq.

Lysine-specific histone demethylase 1A (KDM1A/LSD1) inhibition attenuates DNA double-strand break repair and augments the efficacy of temozolomide in glioblastoma.

Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4<sup>+</sup> Lymphocytes in Crohn's Disease.