Search Results - "Ouyang, Zhengyu"

Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis by Seidman, Jason S., Troutman, Ty D., Sakai, Mashito, Gola, Anita, Spann, Nathanael J., Bennett, Hunter, Bruni, Cassi M., Ouyang, Zhengyu, Li, Rick Z., Sun, Xiaoli, Vu, BaoChau T., Pasillas, Martina P., Ego, Kaori M., Gosselin, David, Link, Verena M., Chong, Ling-Wa, Evans, Ronald M., Thompson, Bonne M., McDonald, Jeffrey G., Hosseini, Mojgan, Witztum, Joseph L., Germain, Ronald N., Glass, Christopher K.

“…Tissue-resident and recruited macrophages contribute to both host defense and pathology. Multiple macrophage phenotypes are represented in diseased tissues,…”
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Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung by Sajti, Eniko, Link, Verena M., Ouyang, Zhengyu, Spann, Nathanael J., Westin, Emma, Romanoski, Casey E., Fonseca, Gregory J., Prince, Lawrence S., Glass, Christopher K.

“…The lung is inhabited by resident alveolar and interstitial macrophages as well as monocytic cells that survey lung tissues. Each cell type plays distinct…”
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Transient genomic instability drives tumorigenesis through accelerated clonal evolution by Shoshani, Ofer, Bakker, Bjorn, de Haan, Lauren, Tijhuis, Andréa E, Wang, Yin, Kim, Dong Hyun, Maldonado, Marcus, Demarest, Matthew A, Artates, Jon, Zhengyu, Ouyang, Mark, Adam, Wardenaar, René, Sasik, Roman, Spierings, Diana C J, Vitre, Benjamin, Fisch, Kathleen, Foijer, Floris, Cleveland, Don W

“…Abnormal numerical and structural chromosome content is frequently found in human cancer. To test the role of aneuploidy in tumor initiation and progression,…”
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Chronic Peripheral Inflammation Causes a Region-Specific Myeloid Response in the Central Nervous System by Süß, Patrick, Hoffmann, Alana, Rothe, Tobias, Ouyang, Zhengyu, Baum, Wolfgang, Staszewski, Ori, Schett, Georg, Prinz, Marco, Krönke, Gerhard, Glass, Christopher K., Winkler, Jürgen, Schlachetzki, Johannes C.M.

“…Systemic immune dysregulation contributes to the development of neuropsychiatric and neurodegenerative diseases. The precise effect of chronic peripheral…”
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Immune-profiling of ZIKV-infected patients identifies a distinct function of plasmacytoid dendritic cells for immune cross-regulation by Sun, Xiaoming, Hua, Stephane, Gao, Ce, Blackmer, Jane E., Ouyang, Zhengyu, Ard, Kevin, Ciaranello, Andrea, Yawetz, Sigal, Sax, Paul E., Rosenberg, Eric S., Lichterfeld, Mathias, Yu, Xu G.

“…Zika virus (ZIKV) is a mosquito-borne pathogen with increasing public health significance. To characterize immune responses to ZIKV, here we examine…”
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Transcriptional Changes during Naturally Acquired Zika Virus Infection Render Dendritic Cells Highly Conducive to Viral Replication by Sun, Xiaoming, Hua, Stephane, Chen, Hsiao-Rong, Ouyang, Zhengyu, Einkauf, Kevin, Tse, Samantha, Ard, Kevin, Ciaranello, Andrea, Yawetz, Sigal, Sax, Paul, Rosenberg, Eric S., Lichterfeld, Mathias, Yu, Xu G.

“…Although dendritic cells are among the human cell population best equipped for cell-intrinsic antiviral immune defense, they seem highly susceptible to…”
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MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function by Shen, Zeyang, Hoeksema, Marten A, Ouyang, Zhengyu, Benner, Christopher, Glass, Christopher K

“…Genetic variation in regulatory elements can alter transcription factor (TF) binding by mutating a TF binding motif, which in turn may affect the activity of…”
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Pegylated Interferon-α-Induced Natural Killer Cell Activation Is Associated With Human Immunodeficiency Virus-1 DNA Decline in Antiretroviral Therapy-Treated HIV-1/Hepatitis C Virus-Coinfected Patients by Hua, Stéphane, Vigano, Selena, Tse, Samantha, Zhengyu, Ouyang, Harrington, Sean, Negron, Jordi, Garcia-Broncano, Pilar, Marchetti, Giulia, Genebat, Miguel, Leal, Manuel, Resino, Salvador, Ruiz-Mateos, Ezequiel, Lichterfeld, Mathias, Yu, Xu G

“…Interferon alpha (IFN-α) can potently reduce human immunodeficiency virus type 1 (HIV-1) replication in tissue culture and animal models, but may also modulate…”
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Potent Cell-Intrinsic Immune Responses in Dendritic Cells Facilitate HIV-1-Specific T Cell Immunity in HIV-1 Elite Controllers by Martin-Gayo, Enrique, Buzon, Maria Jose, Ouyang, Zhengyu, Hickman, Taylor, Cronin, Jacqueline, Pimenova, Dina, Walker, Bruce D, Lichterfeld, Mathias, Yu, Xu G

“…The majority of HIV-1 elite controllers (EC) restrict HIV-1 replication through highly functional HIV-1-specific T cell responses, but mechanisms supporting…”
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Cooperation between cGAS and RIG-I sensing pathways enables improved innate recognition of HIV-1 by myeloid dendritic cells in elite controllers by Martin-Gayo, Enrique, Gao, Ce, Calvet-Mirabent, Marta, Ouyang, Zhengyu, Lichterfeld, Mathias, Yu, Xu G

“…Spontaneous control of HIV-1 replication in the absence of anti-retroviral therapy (ART) naturally occurs in a small proportion of HIV-1-infected individuals…”
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A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers by Martin-Gayo, Enrique, Cole, Michael B, Kolb, Kellie E, Ouyang, Zhengyu, Cronin, Jacqueline, Kazer, Samuel W, Ordovas-Montanes, Jose, Lichterfeld, Mathias, Walker, Bruce D, Yosef, Nir, Shalek, Alex K, Yu, Xu G

“…Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and…”
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Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies by Martin-Gayo, Enrique, Gao, Ce, Chen, Hsiao Rong, Ouyang, Zhengyu, Kim, Dhohyung, Kolb, Kellie E., Shalek, Alex K., Walker, Bruce D., Lichterfeld, Mathias, Yu, Xu G.

“…The induction of broadly neutralizing antibodies (bnAbs) is highly desired for an effective vaccine against HIV-1. Typically, bnAbs develop in patients with…”
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scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing by Li, Kejie, Sun, Yu H, Ouyang, Zhengyu, Negi, Soumya, Gao, Zhen, Zhu, Jing, Wang, Wanli, Chen, Yirui, Piya, Sarbottam, Hu, Wenxing, Zavodszky, Maria I, Yalamanchili, Hima, Cao, Shaolong, Gehrke, Andrew, Sheehan, Mark, Huh, Dann, Casey, Fergal, Zhang, Xinmin, Zhang, Baohong

“…Single-cell RNA sequencing is a state-of-the-art technology to understand gene expression in complex tissues. With the growing amount of data being generated,…”
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Characterizing the composition of iPSC derived cells from bulk transcriptomics data with CellMap by Ouyang, Zhengyu, Bourgeois-Tchir, Nathanael, Lyashenko, Eugenia, Cundiff, Paige E., Cullen, Patrick F., Challa, Ravi, Li, Kejie, Zhang, Xinmin, Casey, Fergal, Engle, Sandra J., Zhang, Baohong, Zavodszky, Maria I.

“…Induced pluripotent stem cell (iPSC) derived cell types are increasingly employed as in vitro model systems for drug discovery. For these studies to be…”
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Recommendations of scRNA-seq Differential Gene Expression Analysis Based on Comprehensive Benchmarking by Gagnon, Jake, Pi, Lira, Ryals, Matthew, Wan, Qingwen, Hu, Wenxing, Ouyang, Zhengyu, Zhang, Baohong, Li, Kejie

“…To guide analysts to select the right tool and parameters in differential gene expression analyses of single-cell RNA sequencing (scRNA-seq) data, we developed…”
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Integrated single-cell transcriptomics of cerebrospinal fluid cells in treatment-naïve multiple sclerosis by Straeten, Frederike, Zhu, Jing, Börsch, Anna-Lena, Zhang, Baohong, Li, Kejie, Lu, I-Na, Gross, Catharina, Heming, Michael, Li, Xiaolin, Rubin, Rebekah, Ouyang, Zhengyu, Wiendl, Heinz, Mingueneau, Michael, Meyer Zu Hörste, Gerd

“…Multiple sclerosis (MS) is a chronic and often disabling autoimmune disease of the central nervous system (CNS). Cerebrospinal fluid (CSF) surrounds and…”
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Cx3cr1- deficient microglia exhibit a premature aging transcriptome by Gyoneva, Stefka, Hosur, Raghavendra, Gosselin, David, Zhang, Baohong, Ouyang, Zhengyu, Cotleur, Anne C, Peterson, Michael, Allaire, Norm, Challa, Ravi, Cullen, Patrick, Roberts, Chris, Miao, Kelly, Reynolds, Taylor L, Glass, Christopher K, Burkly, Linda, Ransohoff, Richard M

“…CX3CR1, one of the highest expressed genes in microglia in mice and humans, is implicated in numerous microglial functions. However, the molecular mechanisms…”
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Conserved and differential gene interactions in dynamical biological systems by Ouyang, Zhengyu, Song, Mingzhou, Güth, Robert, Ha, Thomas J., Larouche, Matt, Goldowitz, Dan

“…Motivation: While biological systems operated from a common genome can be conserved in various ways, they can also manifest highly diverse dynamics and…”
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Treatment of HIV-Infected Individuals with the Histone Deacetylase Inhibitor Panobinostat Results in Increased Numbers of Regulatory T Cells and Limits Ex Vivo Lipopolysaccharide-Induced Inflammatory Responses by Brinkmann, Christel Rothe, Højen, Jesper Falkesgaard, Rasmussen, Thomas Aagaard, Kjær, Anne Sofie, Olesen, Rikke, Denton, Paul W, Østergaard, Lars, Ouyang, Zhengyu, Lichterfeld, Mathias, Yu, Xu, Søgaard, Ole Schmeltz, Dinarello, Charles, Tolstrup, Martin

“…Histone deacetylase inhibitors (HDACi) modulate the transcriptional activity of all cells, including innate and adaptive immune cells. Therefore, we aimed to…”
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CellDepot: A Unified Repository for scRNA-seq Data and Visual Exploration by Lin, Dongdong, Chen, Yirui, Negi, Soumya, Cheng, Derrick, Ouyang, Zhengyu, Sexton, David, Li, Kejie, Zhang, Baohong

“…[Display omitted] •CellDepot contains over 270 processed scRNA-seq datasets from 8 species.•CellDepot provides advanced searching and filtering of datasets…”
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