Search Results - "Chen, Duojiao"

Nonlinear relationship between chromatin accessibility and estradiol-regulated gene expression by Chen, Duojiao, Parker, Taylor M., Bhat-Nakshatri, Poornima, Chu, Xiaona, Liu, Yunlong, Wang, Yue, Nakshatri, Harikrishna

“…Chromatin accessibility is central to basal and inducible gene expression. Through ATAC-seq experiments in estrogen receptor-positive (ER+) breast cancer cell…”
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Prediction of functional microexons by transfer learning by Cheng, Qi, He, Bo, Zhao, Chengkui, Bi, Hongyuan, Chen, Duojiao, Han, Shuangze, Gao, Haikuan, Feng, Weixing

“…Abstract Background Microexons are a particular kind of exon of less than 30 nucleotides in length. More than 60% of annotated human microexons were found to…”
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Loss of succinyl-CoA synthetase in mouse forebrain results in hypersuccinylation with perturbed neuronal transcription and metabolism by Lancaster, Makayla S., Kim, Byungwook, Doud, Emma H., Tate, Mason D., Sharify, Ahmad D., Gao, Hongyu, Chen, Duojiao, Simpson, Ed, Gillespie, Patrick, Chu, Xiaona, Miller, Marcus J., Wang, Yue, Liu, Yunlong, Mosley, Amber L., Kim, Jungsu, Graham, Brett H.

“…Lysine succinylation is a subtype of protein acylation associated with metabolic regulation of succinyl-CoA in the tricarboxylic acid cycle. Deficiency of…”
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Improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies by Feng, Weixing, Zhao, Sen, Xue, Dingkai, Song, Fengfei, Li, Ziwei, Chen, Duojiao, He, Bo, Hao, Yangyang, Wang, Yadong, Liu, Yunlong

“…Ion Torrent and Ion Proton are semiconductor-based sequencing technologies that feature rapid sequencing speed and low upfront and operating costs, thanks to…”
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Cryopreservation Preserves Cell-Type Composition and Gene Expression Profiles in Bone Marrow Aspirates From Multiple Myeloma Patients by Chen, Duojiao, Abu Zaid, Mohammad I, Reiter, Jill L, Czader, Magdalena, Wang, Lin, McGuire, Patrick, Xuei, Xiaoling, Gao, Hongyu, Huang, Kun, Abonour, Rafat, Walker, Brian A, Liu, Yunlong

“…Single-cell RNA sequencing reveals gene expression differences between individual cells and also identifies different cell populations that are present in the…”
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A human skeletal muscle stem/myotube model reveals multiple signaling targets of cancer secretome in skeletal muscle by Wang, Ruizhong, Kumar, Brijesh, Bhat-Nakshatri, Poornima, Khatpe, Aditi S., Murphy, Michael P., Wanczyk, Kristen E., Simpson, Edward, Chen, Duojiao, Gao, Hongyu, Liu, Yunlong, Doud, Emma H., Mosley, Amber L., Nakshatri, Harikrishna

“…Skeletal muscle dysfunction or reprogramming due to the effects of the cancer secretome is observed in multiple malignancies. Although mouse models are…”
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Author Correction: Lipid exposure activates gene expression changes associated with estrogen receptor negative breast cancer by Yadav, Shivangi, Virk, Ranya, Chung, Carolina H., Eduardo, Mariana Bustamante, VanDerway, David, Chen, Duojiao, Burdett, Kirsten, Gao, Hongyu, Zeng, Zexian, Ranjan, Manish, Cottone, Gannon, Xuei, Xiaoling, Chandrasekaran, Sriram, Backman, Vadim, Chatterton, Robert, Khan, Seema Ahsan, Clare, Susan E.

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Lipid exposure activates gene expression changes associated with estrogen receptor negative breast cancer by Yadav, Shivangi, Virk, Ranya, Chung, Carolina H., Eduardo, Mariana Bustamante, VanDerway, David, Chen, Duojiao, Burdett, Kirsten, Gao, Hongyu, Zeng, Zexian, Ranjan, Manish, Cottone, Gannon, Xuei, Xiaoling, Chandrasekaran, Sriram, Backman, Vadim, Chatterton, Robert, Khan, Seema Ahsan, Clare, Susan E.

“…Improved understanding of local breast biology that favors the development of estrogen receptor negative (ER−) breast cancer (BC) would foster better…”
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A method for homopolymer length discrimination in ion torrent sequencing by Feng, Weixing, Xue, Dingkai, Song, Fengfei, Chen, Duojiao, Li, Ziwei, Wang, Xueying

“…Ion torrent is a novel semiconductor long sequencing platform and advantages in faster and cheaper sequencing calls, but its raw data analysis is far from…”
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Deciphering Gene Regulatory Mechanisms Through Multi-Omics Integration by Chen, Duojiao

“…Complex biological systems are composed of many regulatory components, which can be measured with the advent of genomics technology. Each molecular assay is…”
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Abstract 1006: Non-linear relationship between estradiol-regulated changes in chromatin architecture and gene expression by Parker, Taylor M., Chen, Duojiao, Bhat-Nakshatri, Poornima, Chu, Xiaona, Liu, Yunlong, Wang, Yue, Nakshatri, Harikrishna

“…Abstract Gene expression in estrogen receptor (ER)-positive breast cancer cells is predominantly driven by ER-estradiol (E2) signaling. However, the effects of…”
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Single-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry by Bhat-Nakshatri, Poornima, Gao, Hongyu, Khatpe, Aditi S, Adebayo, Adedeji K, McGuire, Patrick C, Erdogan, Cihat, Chen, Duojiao, Jiang, Guanglong, New, Felicia, German, Rana, Emmert, Lydia, Sandusky, George, Storniolo, Anna Maria, Liu, Yunlong, Nakshatri, Harikrishna

“…Single-nucleus analysis allows robust cell-type classification and helps to establish relationships between chromatin accessibility and cell-type-specific gene…”
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Abstract P3-07-09: Single cell transcriptomic analysis reveals the effects of BRCA1 and BRCA2 mutations on distinct signaling networks and cancer susceptibility by Nakshatri, Harikrishna, Bhat-Nakshatri, Poornima, Chen, Duojiao, Chen, Katie, Mang, Henry, Herodotou, Christopher A, Khatpe, Aditi S, McGuire, Patrick C, Xuei, Xiaoling, Liu, Yunlong, Sandusky, George, Storniolo, Anna Maria

“…Abstract Background: Inheritance of BRCA1 and BRCA2 mutations is associated with increased risk of breast and ovarian cancers. Previous studies with…”
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TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer by Khatpe, Aditi S, Dirks, Rebecca, Bhat-Nakshatri, Poornima, Mang, Henry, Batic, Katie, Swiezy, Sarah, Olson, Jacob, Rao, Xi, Wang, Yue, Tanaka, Hiromi, Liu, Sheng, Wan, Jun, Chen, Duojiao, Liu, Yunlong, Fang, Fang, Althouse, Sandra, Hulsey, Emily, Granatir, Maggie M, Addison, Rebekah, Temm, Constance J, Sandusky, George, Lee-Gosselin, Audrey, Nephew, Kenneth, Miller, Kathy D, Nakshatri, Harikrishna

“…Study of genomic aberrations leading to immortalization of epithelial cells has been technically challenging due to the lack of isogenic models. To address…”
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A new method for alleviating sequence-specific biases in DNase-seq by Siwen Xu, Ying Wang, Huan Liu, Duojiao Chen, Hongyuan Bi, Weixing Feng

“…DNasel footprinting is an established approach for recognizing transcription factor binding sites. High-throughput DNase-seq arrays have been used to depict in…”
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Identification method of transcription factor binding sites based on DNase-Seq signal by Peichao Sang, Duojiao Chen, Siwen Xu, Weixing Feng

“…Revealing the mechanism of gene regulation is one of central challenge in modern genomics research. Since transcription factors play vital roles in process of…”
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Osteogenic Differentiation Potential of Mesenchymal Stem Cells Using Single Cell Multiomic Analysis by Chen, Duojiao, Liu, Sheng, Chu, Xiaona, Reiter, Jill, Gao, Hongyu, McGuire, Patrick, Yu, Xuhong, Xuei, Xiaoling, Liu, Yichen, Wan, Jun, Fang, Fang, Liu, Yunlong, Wang, Yue

“…Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes, and adipocytes…”
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Abstract IA024: Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry by Bhat-Nakshatri, Poornima, Chen, Duojiao, Khatpe, Aditi, Gao, Hongyu, Liu, Yunlong, Storniolo, Anna Maria, Nakshatri, Harikrishna

“…Abstract Single nuclei analysis is allowing robust classification of cell types in an organ that helps to establish relationships between cell-type specific…”
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Abstract 1458: Single cell resolution chromatin accessibility and transcriptomic atlas of genetic ancestry mapped healthy breast tissues by Bhat-Nakshatri, Poornima, Chen, Duojiao, Gao, Hongyu, Liu, Yunlong, Storniolo, Anna Maria, Nakshatri, Harikrishna

“…Abstract Single cell mRNA atlases of multiple organs have been reported using scRNA-seq. We had previously reported single cell mRNA atlas of the breast. In…”
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Tumor collection/processing under physioxia uncovers highly relevant signaling networks and drug sensitivity by Kumar, Brijesh, Adebayo, Adedeji K, Prasad, Mayuri, Capitano, Maegan L, Wang, Ruizhong, Bhat-Nakshatri, Poornima, Anjanappa, Manjushree, Simpson, Edward, Chen, Duojiao, Liu, Yunlong, Schilder, Jeanne M, Colter, Austyn B, Maguire, Callista, Temm, Constance J, Sandusky, George, Doud, Emma H, Wijeratne, Aruna B, Mosley, Amber L, Broxmeyer, Hal E, Nakshatri, Harikrishna

“…Preclinical studies of primary cancer cells are typically done after tumors are removed from patients or animals at ambient atmospheric oxygen (O , ~21%)…”
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