Search Results - "Sheffield, C"

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor by Sheffield, Nathan C, Bock, Christoph

“…Genomic datasets are often interpreted in the context of large-scale reference databases. One approach is to identify significantly overlapping gene sets,…”
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Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics by Farlik, Matthias, Sheffield, Nathan C., Nuzzo, Angelo, Datlinger, Paul, Schönegger, Andreas, Klughammer, Johanna, Bock, Christoph

“…Methods for single-cell genome and transcriptome sequencing have contributed to our understanding of cellular heterogeneity, whereas methods for single-cell…”
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ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors by Schmidl, Christian, Rendeiro, André F, Sheffield, Nathan C, Bock, Christoph

“…ChIPmentation combines chromatin immunoprecipitation with on-bead tagmentation for rapid and highly robust ChIP-seq library preparation. Chromatin…”
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Retinal ciliopathies through the lens of Bardet-Biedl Syndrome: Past, present and future by Chandra, Bharatendu, Tung, Moon Ley, Hsu, Ying, Scheetz, Todd, Sheffield, Val C.

“…The primary cilium is a highly specialized and evolutionary conserved organelle in eukaryotes that plays a significant role in cell signaling and trafficking…”
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Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1 by Tomazou, Eleni M., Sheffield, Nathan C., Schmidl, Christian, Schuster, Michael, Schönegger, Andreas, Datlinger, Paul, Kubicek, Stefan, Bock, Christoph, Kovar, Heinrich

“…Transcription factor fusion proteins can transform cells by inducing global changes of the transcriptome, often creating a state of oncogene addiction. Here,…”
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The BBSome Controls Energy Homeostasis by Mediating the Transport of the Leptin Receptor to the Plasma Membrane by Guo, Deng-Fu, Cui, Huxing, Zhang, Qihong, Morgan, Donald A, Thedens, Daniel R, Nishimura, Darryl, Grobe, Justin L, Sheffield, Val C, Rahmouni, Kamal

“…Bardet-Biedl syndrome (BBS) is a highly pleiotropic autosomal recessive disorder associated with a wide range of phenotypes including obesity. However, the…”
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Predicting cell-type-specific gene expression from regions of open chromatin by Natarajan, Anirudh, Yardimci, Galip Gürkan, Sheffield, Nathan C, Crawford, Gregory E, Ohler, Uwe

“…Complex patterns of cell-type-specific gene expression are thought to be achieved by combinatorial binding of transcription factors (TFs) to sequence elements…”
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Bedshift: perturbation of genomic interval sets by Gu, Aaron, Cho, Hyun Jae, Sheffield, Nathan C

“…Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. There is no way to objectively evaluate the…”
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Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease by Stone, Edwin M., MD, PhD, Andorf, Jeaneen L., BA, Whitmore, S. Scott, PhD, DeLuca, Adam P., PhD, Giacalone, Joseph C., BS, Streb, Luan M., BA, Braun, Terry A., PhD, Mullins, Robert F., PhD, Scheetz, Todd E., PhD, Sheffield, Val C., MD, PhD, Tucker, Budd A., PhD

“…Purpose To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive…”
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ARL13B, PDE6D, and CEP164 form a functional network for INPP5E ciliary targeting by Humbert, Melissa C, Weihbrecht, Katie, Searby, Charles C, Li, Yalan, Pope, Robert M, Sheffield, Val C, Seo, Seongjin

“…Mutations affecting ciliary components cause a series of related genetic disorders in humans, including nephronophthisis (NPHP), Joubert syndrome (JBTS),…”
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Transplantation of iPSC-derived TM cells rescues glaucoma phenotypes in vivo by Zhu, Wei, Gramlich, Oliver W., Laboissonniere, Lauren, Jain, Ankur, Sheffield, Val C., Trimarchi, Jeffrey M., Tucker, Budd A., Kuehn, Markus H.

“…Glaucoma is a common cause of vision loss or blindness and reduction of intraocular pressure (IOP) has been proven beneficial in a large fraction of glaucoma…”
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Primary Ciliary Dyskinesia Caused by Homozygous Mutation in DNAL1, Encoding Dynein Light Chain 1 by Mazor, Masha, Alkrinawi, Soliman, Chalifa-Caspi, Vered, Manor, Esther, Sheffield, Val C., Aviram, Micha, Parvari, Ruti

“…In primary ciliary dyskinesia (PCD), genetic defects affecting motility of cilia and flagella cause chronic destructive airway disease, randomization of…”
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Accumulation of non-outer segment proteins in the outer segment underlies photoreceptor degeneration in Bardet–Biedl syndrome by Datta, Poppy, Allamargot, Chantal, Hudson, Joseph S., Andersen, Emily K., Bhattarai, Sajag, Drack, Arlene V., Sheffield, Val C., Seo, Seongjin

“…Compartmentalization and polarized protein trafficking are essential for many cellular functions. The photoreceptor outer segment (OS) is a sensory compartment…”
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Regulation of Insulin Receptor Trafficking by Bardet Biedl Syndrome Proteins by Starks, Rachel D, Beyer, Andreas M, Guo, Deng Fu, Boland, Lauren, Zhang, Qihong, Sheffield, Val C, Rahmouni, Kamal

“…Insulin and its receptor are critical for the regulation of metabolic functions, but the mechanisms underlying insulin receptor (IR) trafficking to the plasma…”
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Intrinsic Protein-Protein Interaction-mediated and Chaperonin-assisted Sequential Assembly of Stable Bardet-Biedl Syndrome Protein Complex, the BBSome by Zhang, Qihong, Yu, Dahai, Seo, Seongjin, Stone, Edwin M., Sheffield, Val C.

“…The pleiotropic features of obesity, retinal degeneration, polydactyly, kidney abnormalities, cognitive impairment, hypertension, and diabetes found in…”
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Restoration of Aqueous Humor Outflow Following Transplantation of iPSC-Derived Trabecular Meshwork Cells in a Transgenic Mouse Model of Glaucoma by Zhu, Wei, Jain, Ankur, Gramlich, Oliver W, Tucker, Budd A, Sheffield, Val C, Kuehn, Markus H

“…Primary open-angle glaucoma (POAG) is particularly common in older individuals and associated with pathologic degeneration of the trabecular meshwork (TM). We…”
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Methods for constructing and evaluating consensus genomic interval sets by Rymuza, Julia, Sun, Yuchen, Zheng, Guangtao, LeRoy, Nathan J, Murach, Maria, Phan, Neil, Zhang, Aidong, Sheffield, Nathan C

“…The amount of genomic region data continues to increase. Integrating across diverse genomic region sets requires consensus regions, which enable comparing…”
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ATF4 leads to glaucoma by promoting protein synthesis and ER client protein load by Kasetti, Ramesh B., Patel, Pinkal D., Maddineni, Prabhavathi, Patil, Shruti, Kiehlbauch, Charles, Millar, J. Cameron, Searby, Charles C., Raghunathan, VijayKrishna, Sheffield, Val C., Zode, Gulab S.

“…The underlying pathological mechanisms of glaucomatous trabecular meshwork (TM) damage and elevation of intraocular pressure (IOP) are poorly understood. Here,…”
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Primary cilia membrane assembly is initiated by Rab11 and transport protein particle II (TRAPPII) complex-dependent trafficking of Rabin8 to the centrosome by Westlake, Christopher J, Baye, Lisa M, Nachury, Maxence V, Wright, Kevin J, Ervin, Karen E, Phu, Lilian, Chalouni, Cecile, Beck, John S, Kirkpatrick, Donald S, Slusarski, Diane C, Sheffield, Val C, Scheller, Richard H, Jackson, Peter K

“…Sensory and signaling pathways are exquisitely organized in primary cilia. Bardet-Biedl syndrome (BBS) patients have compromised cilia and signaling. BBS…”
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Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development by Duvall, Eliza, Benitez, Cecil M, Tellez, Krissie, Enge, Martin, Pauerstein, Philip T, Li, Lingyu, Baek, Songjoon, Quake, Stephen R, Smith, Jason P, Sheffield, Nathan C, Kim, Seung K, Arda, H Efsun

“…Delineating gene regulatory networks that orchestrate cell-type specification is a continuing challenge for developmental biologists. Single-cell analyses…”
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