Search Results - "Jensen, Mark A."

The NCI Genomic Data Commons as an engine for precision medicine by Jensen, Mark A., Ferretti, Vincent, Grossman, Robert L., Staudt, Louis M.

“…The National Cancer Institute Genomic Data Commons (GDC) is an information system for storing, analyzing, and sharing genomic and clinical data from patients…”
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Kidney-resident macrophages promote a proangiogenic environment in the normal and chronically ischemic mouse kidney by Puranik, Amrutesh S., Leaf, Irina A., Jensen, Mark A., Hedayat, Ahmad F., Saad, Ahmad, Kim, Ki-Wook, Saadalla, Abdulrahman M., Woollard, John R., Kashyap, Sonu, Textor, Stephen C., Grande, Joseph P., Lerman, Amir, Simari, Robert D., Randolph, Gwendalyn J., Duffield, Jeremy S., Lerman, Lilach O.

“…Renal artery stenosis (RAS) caused by narrowing of arteries is characterized by microvascular damage. Macrophages are implicated in repair and injury, but the…”
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The Evolutionary Divergence of Shiga Toxin-Producing Escherichia coli Is Reflected in Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Spacer Composition by Yin, Shuang, Jensen, Mark A, Bai, Jiawei, Debroy, Chitrita, Barrangou, Rodolphe, Dudley, Edward G

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Single-cell expression quantitative trait loci (eQTL) analysis of SLE-risk loci in lupus patient monocytes by Ghodke-Puranik, Yogita, Jin, Zhongbo, Zimmerman, Kip D, Ainsworth, Hannah C, Fan, Wei, Jensen, Mark A, Dorschner, Jessica M, Vsetecka, Danielle M, Amin, Shreyasee, Makol, Ashima, Ernste, Floranne, Osborn, Thomas, Moder, Kevin, Chowdhary, Vaidehi, Langefeld, Carl D, Niewold, Timothy B

“…Abstract Background We performed expression quantitative trait locus (eQTL) analysis in single classical (CL) and non-classical (NCL) monocytes from patients…”
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Autoantibody repertoire characterization provides insight into the pathogenesis of monogenic and polygenic autoimmune diseases by Clarke, Thomas, Du, Pan, Kumar, Satyendra, Okitsu, Shinji L, Schuette, Mark, An, Qi, Zhang, Jinyang, Tzvetkov, Evgeni, Jensen, Mark A, Niewold, Timothy B, Ferre, Elise M N, Nardone, Julie, Lionakis, Michail S, Vlach, Jaromir, DeMartino, Julie, Bender, Andrew T

“…Autoimmune diseases vary in the magnitude and diversity of autoantibody profiles, and these differences may be a consequence of different types of breaks in…”
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A Practical Guide to The Cancer Genome Atlas (TCGA) by Wang, Zhining, Jensen, Mark A, Zenklusen, Jean Claude

“…The Cancer Genome Atlas (TCGA) is one of the most ambitious and successful cancer genomics programs to date. The TCGA program has generated, analyzed, and made…”
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Distinct Single Cell Gene Expression in Peripheral Blood Monocytes Correlates With Tumor Necrosis Factor Inhibitor Treatment Response Groups Defined by Type I Interferon in Rheumatoid Arthritis by Wampler Muskardin, Theresa L, Fan, Wei, Jin, Zhongbo, Jensen, Mark A, Dorschner, Jessica M, Ghodke-Puranik, Yogita, Dicke, Betty, Vsetecka, Danielle, Wright, Kerry, Mason, Thomas, Persellin, Scott, Michet, Clement J, Davis, 3rd, John M, Matteson, Eric, Niewold, Timothy B

“…Previously, we demonstrated in test and validation cohorts that type I IFN (T1IFN) activity can predict non-response to tumor necrosis factor inhibitors (TNFi)…”
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Modeling the Role of Bacteriophage in the Control of Cholera Outbreaks by Jensen, Mark A., Faruque, Shah M., Mekalanos, John J., Levin, Bruce R.

“…Cholera is a waterborne diarrheal disease that continues to plague the developing world. Individuals become infected by consuming water from reservoirs…”
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HIV-specific probabilistic models of protein evolution by Nickle, David C, Heath, Laura, Jensen, Mark A, Gilbert, Peter B, Mullins, James I, Kosakovsky Pond, Sergei L

“…Comparative sequence analyses, including such fundamental bioinformatics techniques as similarity searching, sequence alignment and phylogenetic inference,…”
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BIO::Phylo-phyloinformatic analysis using perl by Vos, Rutger A, Caravas, Jason, Hartmann, Klaas, Jensen, Mark A, Miller, Chase

“…Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these…”
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Improved Coreceptor Usage Prediction and Genotypic Monitoring of R5-to-X4 Transition by Motif Analysis of Human Immunodeficiency Virus Type 1 env V3 Loop Sequences by Jensen, Mark A, Li, Fu-Sheng, van 't Wout, Angélique B, Nickle, David C, Shriner, Daniel, He, Hong-Xia, McLaughlin, Sherry, Shankarappa, Raj, Margolick, Joseph B, Mullins, James I

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Improved Detection of CXCR4-Using HIV by V3 Genotyping: Application of Population-Based and “Deep” Sequencing to Plasma RNA and Proviral DNA by Swenson, Luke C, Moores, Andrew, Low, Andrew J, Thielen, Alexander, Dong, Winnie, Woods, Conan, Jensen, Mark A, Wynhoven, Brian, Chan, Dennison, Glascock, Christopher, Harrigan, P Richard

“…BACKGROUND:Tropism testing should rule out CXCR4-using HIV before treatment with CCR5 antagonists. Currently, the recombinant phenotypic Trofile assay…”
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A Reliable Phenotype Predictor for Human Immunodeficiency Virus Type 1 Subtype C Based on Envelope V3 Sequences by Jensen, Mark A, Coetzer, Mia, van 't Wout, Angélique B, Morris, Lynn, Mullins, James I

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Changes in Human Immunodeficiency Virus Type 1 Fitness and Genetic Diversity during Disease Progression by TROYER, Ryan M, COLLINS, Kalonji R, VANHAM, Guido, ARTS, Eric J, ABRAHA, Awet, FRAUNDORF, Erika, MOORE, Dawn M, KRIZAN, Randall W, TOOSSI, Zahra, COLEBUNDERS, Robert L, JENSEN, Mark A, MULLINS, James I

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Targeting of Myelin Protein Zero in a Spontaneous Autoimmune Polyneuropathy by Kim, Hye-Jung, Jung, Cha-Gyun, Jensen, Mark A, Dukala, Danuta, Soliven, Betty

“…Elimination of the costimulatory molecule B7-2 prevents autoimmune diabetes in NOD mice, but leads to the development of a spontaneous autoimmune…”
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Coping with viral diversity in HIV vaccine design by Nickle, David C, Rolland, Morgane, Jensen, Mark A, Pond, Sergei L Kosakovsky, Deng, Wenjie, Seligman, Mark, Heckerman, David, Mullins, James I, Jojic, Nebojsa

“…The ability of human immunodeficiency virus type 1 (HIV-1) to develop high levels of genetic diversity, and thereby acquire mutations to escape immune…”
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Intelligence Authorization Acts: Their Impact on the Intelligence Community by Jensen, Mark A.

“…Intelligence Authorization Acts (IAAs), generally passed annually since the late 1970s, are an important tool for Congress to influence the direction of the…”
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Type I Interferon Predicts an Alternate Immune System Phenotype in Systemic Lupus Erythematosus by Thanarajasingam, Uma, Muppirala, Anoohya N., Jensen, Mark A., Ghodke‐Puranik, Yogita, Dorschner, Jessica M., Vsetecka, Danielle M., Amin, Shreyasee, Makol, Ashima, Ernste, Floranne, Osborn, Thomas, Moder, Kevin, Chowdhary, Vaidehi, Niewold, Timothy B.

“…Objective Type I interferon (IFN) is important to systemic lupus erythematosus (SLE) pathogenesis, but it is not clear how chronic elevations in IFN alter…”
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Single-cell gene expression patterns in lupus monocytes independently indicate disease activity, interferon and therapy by Jin, Zhongbo, Fan, Wei, Jensen, Mark A, Dorschner, Jessica M, Bonadurer, George F, Vsetecka, Danielle M, Amin, Shreyasee, Makol, Ashima, Ernste, Floranne, Osborn, Thomas, Moder, Kevin, Chowdhary, Vaidehi, Niewold, Timothy B

“…ObjectivesImportant findings can be masked in gene expression studies of mixed cell populations. We examined single-cell gene expression in SLE patient…”
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Reconstruction and Function of Ancestral Center-of-Tree Human Immunodeficiency Virus Type 1 Proteins by ROLLAND, Morgane, JENSEN, Mark A, NICKLE, David C, JIAN YAN, LEARN, Gerald H, HEATH, Laura, WEINER, David, MULLINS, James I

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