PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data

по Zhang, Yanxiao, Lin, Yu-Hsuan, Johnson, Timothy D., Rozek, Laura S., Sartor, Maureen A.
Опубликовано 2014

Genomic binding and regulation of gene expression by the thyroid carcinoma-associated PAX8-PPARG fusion protein

по Zhang, Yanxiao, Yu, Jingcheng, Lee, Chee, Xu, Bin, Sartor, Maureen A., Koenig, Ronald J.
Опубликовано в: Oncotarget (2015)

A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis

по Xiong, Xiong, Zhang, Yanxiao, Yan, Jian, Jain, Surbhi, Chee, Sora, Ren, Bing, Zhao, Huimin
Опубликовано в: ACS Synth Biol (2017)

Joint profiling of histone modifications and transcriptome in single cells from mouse brain

по Zhu, Chenxu, Zhang, Yanxiao, Li, Yang Eric, Lucero, Jacinta, Behrens, M. Margarita, Ren, Bing
Опубликовано в: Nat Methods (2021)

Joint profiling of DNA methylation and chromatin architecture in single cells

по Li, Guoqiang, Liu, Yaping, Zhang, Yanxiao, Kubo, Naoki, Yu, Miao, Fang, Rongxin, Kellis, Manolis, Ren, Bing
Опубликовано в: Nat Methods (2019)

Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer

по Zhang, Yanxiao, Yu, Jingcheng, Grachtchouk, Vladimir, Qin, Tingting, Lumeng, Carey N, Sartor, Maureen A, Koenig, Ronald J
Опубликовано в: Oncotarget (2016)

Adipogenic Differentiation of Thyroid Cancer Cells Through the Pax8-PPARγ Fusion Protein Is Regulated by Thyroid Transcription Factor 1 (TTF-1)

по Xu, Bin, O'Donnell, Michael, O'Donnell, Jeffrey, Yu, Jingcheng, Zhang, Yanxiao, Sartor, Maureen A., Koenig, Ronald J.
Опубликовано в: J Biol Chem (2016)

Degeneration of Injured Axons and Dendrites Requires Restraint of a Protective JNK Signaling Pathway by the Transmembrane Protein Raw

по Hao, Yan, Waller, Thomas J., Nye, Derek M., Li, Jiaxing, Zhang, Yanxiao, Hume, Richard I., Rolls, Melissa M., Collins, Catherine A.
Опубликовано в: J Neurosci (2019)

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

по Juric, Ivan, Yu, Miao, Abnousi, Armen, Raviram, Ramya, Fang, Rongxin, Zhao, Yuan, Zhang, Yanxiao, Qiu, Yunjiang, Yang, Yuchen, Li, Yun, Ren, Bing, Hu, Ming
Опубликовано в: PLoS Comput Biol (2019)

HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers

по Koneva, Lada A., Zhang, Yanxiao, Virani, Shama, Hall, Pelle B., McHugh, Jonathan B., Chepeha, Douglas B., Wolf, Gregory T., Carey, Thomas E., Rozek, Laura S., Sartor, Maureen A.
Опубликовано в: Mol Cancer Res (2017)

Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure

по Arvanitis, Marios, Tampakakis, Emmanouil, Zhang, Yanxiao, Wang, Wei, Auton, Adam, Dutta, Diptavo, Glavaris, Stephanie, Keramati, Ali, Chatterjee, Nilanjan, Chi, Neil C., Ren, Bing, Post, Wendy S., Battle, Alexis
Опубликовано в: Nat Commun (2020)

Significant association between host transcriptome-derived HPV oncogene E6* influence score and carcinogenic pathways, tumor size, and survival in head and neck cancer

по Qin, Tingting, Koneva, Lada A., Liu, Yidan, Zhang, Yanxiao, Arthur, Anna E., Zarins, Katie R., Carey, Thomas E, Chepeha, Douglas, Wolf, Gregory T., Rozek, Laura S., Sartor, Maureen A.
Опубликовано в: Head Neck (2020)

Expressed HNSCC variants by HPV-status in a well-characterized Michigan cohort

по Qin, Tingting, Zhang, Yanxiao, Zarins, Katie R., Jones, Tamara R., Virani, Shama, Peterson, Lisa A., McHugh, Jonathan B., Chepeha, Douglas, Wolf, Gregory T., Rozek, Laura S., Sartor, Maureen A.
Опубликовано в: Sci Rep (2018)

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

по Preissl, Sebastian, Fang, Rongxin, Huang, Hui, Zhao, Yuan, Raviram, Ramya, Gorkin, David U., Zhang, Yanxiao, Sos, Brandon C., Afzal, Veena, Dickel, Diane E., Kuan, Samantha, Visel, Axel, Pennacchio, Len A., Zhang, Kun, Ren, Bing
Опубликовано в: Nat Neurosci (2018)

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

по Fang, Rongxin, Preissl, Sebastian, Li, Yang, Hou, Xiaomeng, Lucero, Jacinta, Wang, Xinxin, Motamedi, Amir, Shiau, Andrew K., Zhou, Xinzhu, Xie, Fangming, Mukamel, Eran A., Zhang, Kai, Zhang, Yanxiao, Behrens, M. Margarita, Ecker, Joseph R., Ren, Bing
Опубликовано в: Nat Commun (2021)

Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number alterations, PIK3CA mutation, and pathway signatures

по Zhang, Yanxiao, Koneva, Lada A., Virani, Shama, Arthur, Anna E., Virani, Alisha, Hall, Pelle B., Warden, Charles D., Carey, Thomas E., Chepeha, Douglas B., Prince, Mark E., McHugh, Jonathan B., Wolf, Gregory T., Rozek, Laura S., Sartor, Maureen A.
Опубликовано в: Clin Cancer Res (2016)

Cardiac cell type–specific gene regulatory programs and disease risk association

по Hocker, James D., Poirion, Olivier B., Zhu, Fugui, Buchanan, Justin, Zhang, Kai, Chiou, Joshua, Wang, Tsui-Min, Zhang, Qingquan, Hou, Xiaomeng, Li, Yang E., Zhang, Yanxiao, Farah, Elie N., Wang, Allen, McCulloch, Andrew D., Gaulton, Kyle J., Ren, Bing, Chi, Neil C., Preissl, Sebastian
Опубликовано в: Sci Adv (2021)

Transcriptionally Active HERV-H Retrotransposons Demarcate Topologically Associating Domains in Human Pluripotent Stem Cells

по Zhang, Yanxiao, Li, Ting, Preissl, Sebastian, Amaral, Maria Luisa, Grinstein, Jonathan, Farah, Elie N., Destici, Eugin, Qiu, Yunjiang, Hu, Rong, Lee, Ah Young, Chee, Sora, Ma, Kaiyue, Ye, Zhen, Zhu, Quan, Huang, Hui, Fang, Rongxin, Yu, Leqian, Belmonte, Juan Carlos Izpisua, Wu, Jun, Evans, Sylvia M., Chi, Neil C., Ren, Bing
Опубликовано в: Nat Genet (2019)

Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation

по Zhang, Zeda, Zhou, Chuanli, Li, Xiaoling, Barnes, Spencer D., Deng, Su, Hoover, Elizabeth, Chen, Chi-Chao, Lee, Young Sun, Zhang, Yanxiao, Wang, Choushi, Metang, Lauren A., Wu, Chao, Tirado, Carla Rodriguez, Johnson, Nickolas A., Wongvipat, John, Navrazhina, Kristina, Cao, Zhen, Choi, Danielle, Huang, Chun-Hao, Linton, Eliot, Chen, Xiaoping, Liang, Yupu, Mason, Christopher E., de Stanchina, Elisa, Abida, Wassim, Lujambio, Amaia, Li, Sheng, Lowe, Scott W., Mendell, Joshua T., Malladi, Venkat S., Sawyers, Charles L., Mu, Ping
Опубликовано в: Cancer Cell (2020)

An atlas of dynamic chromatin landscapes in mouse fetal development

по Gorkin, David U., Barozzi, Iros, Zhao, Yuan, Zhang, Yanxiao, Huang, Hui, Lee, Ah Young, Li, Bin, Chiou, Joshua, Wildberg, Andre, Ding, Bo, Zhang, Bo, Wang, Mengchi, Strattan, J. Seth, Davidson, Jean M., Qiu, Yunjiang, Afzal, Veena, Akiyama, Jennifer A., Plajzer-Frick, Ingrid, Novak, Catherine S., Kato, Momoe, Garvin, Tyler H., Pham, Quan T., Harrington, Anne N., Mannion, Brandon J., Lee, Elizabeth A., Fukuda-Yuzawa, Yoko, He, Yupeng, Preissl, Sebastian, Chee, Sora, Han, Jee Yun, Williams, Brian A., Trout, Diane, Amrhein, Henry, Yang, Hongbo, Cherry, J. Michael, Wang, Wei, Gaulton, Kyle, Ecker, Joseph R., Shen, Yin, Dickel, Diane E., Visel, Axel, Pennacchio, Len A., Ren, Bing
Опубликовано в: Nature (2020)