Search Results - "CAREY, VINCENT"

Software for computing and annotating genomic ranges by Lawrence, Michael, Huber, Wolfgang, Pagès, Hervé, Aboyoun, Patrick, Carlson, Marc, Gentleman, Robert, Morgan, Martin T, Carey, Vincent J

“…We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing…”
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Six-Year Follow-up of a Trial of Antenatal Vitamin D for Asthma Reduction by Litonjua, Augusto A, Carey, Vincent J, Laranjo, Nancy, Stubbs, Benjamin J, Mirzakhani, Hooman, O’Connor, George T, Sandel, Megan, Beigelman, Avraham, Bacharier, Leonard B, Zeiger, Robert S, Schatz, Michael, Hollis, Bruce W, Weiss, Scott T

“…In a previously published controlled trial, maternal administration of vitamin D during pregnancy was found to protect against wheeze in the offspring at the…”
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Universality of human microbial dynamics by Bashan, Amir, Gibson, Travis E., Friedman, Jonathan, Carey, Vincent J., Weiss, Scott T., Hohmann, Elizabeth L., Liu, Yang-Yu

“…A new computational method to characterize the dynamics of human-associated microbial communities is applied to data from two large-scale metagenomic studies,…”
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RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor by Ramos, Marcel, Morgan, Martin, Geistlinger, Ludwig, Carey, Vincent J, Waldron, Levi

“…Abstract Summary The RaggedExperiment R / Bioconductor package provides lossless representation of disparate genomic ranges across multiple specimens or cells,…”
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Orchestrating high-throughput genomic analysis with Bioconductor by Huber, Wolfgang, Carey, Vincent J, Gentleman, Robert, Anders, Simon, Carlson, Marc, Carvalho, Benilton S, Bravo, Hector Corrada, Davis, Sean, Gatto, Laurent, Girke, Thomas, Gottardo, Raphael, Hahne, Florian, Hansen, Kasper D, Irizarry, Rafael A, Lawrence, Michael, Love, Michael I, MacDonald, James, Obenchain, Valerie, Oleś, Andrzej K, Pagès, Hervé, Reyes, Alejandro, Shannon, Paul, Smyth, Gordon K, Tenenbaum, Dan, Waldron, Levi, Morgan, Martin

“…A Perspective on the open-source and open-development software project Bioconductor provides an overview for prospective users and developers dealing with…”
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Trial of the MIND Diet for Prevention of Cognitive Decline in Older Persons by Barnes, Lisa L., Dhana, Klodian, Liu, Xiaoran, Carey, Vincent J., Ventrelle, Jennifer, Johnson, Kathleen, Hollings, Chiquia S., Bishop, Louise, Laranjo, Nancy, Stubbs, Benjamin J., Reilly, Xavier, Agarwal, Puja, Zhang, Shengwei, Grodstein, Francine, Tangney, Christy C., Holland, Thomas M., Aggarwal, Neelum T., Arfanakis, Konstantinos, Morris, Martha Clare, Sacks, Frank M.

“…A 3-year trial involving persons with a family history of dementia showed no differences in cognitive change or brain MRI outcomes between the MIND diet,…”
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Machine learning and its applications to biology by Tarca, Adi L, Carey, Vincent J, Chen, Xue-wen, Romero, Roberto, Drăghici, Sorin

“…[...]a section reviews methods and examples as implemented in the open source data analysis and visualization language R (http://www.r-project.org). The goal…”
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Combination lipid therapy in type 2 diabetes by Sacks, Frank M, Carey, Vincent J, Fruchart, Jean-Charles

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Vitamin D supplementation during pregnancy: Effect on the neonatal immune system in a randomized controlled trial by Hornsby, Eve, PhD, Pfeffer, Paul E., MRCP, PhD, Laranjo, Nancy, BA, Cruikshank, William, PhD, Tuzova, Marina, PhD, Litonjua, Augusto A., MD, MPH, Weiss, Scott T., MD, MS, Carey, Vincent J., PhD, O'Connor, George, MD, MS, Hawrylowicz, Catherine, PhD

“…Background Programming of the immune system during fetal development can influence asthma-related risk factors and outcomes in later life. Vitamin D is a…”
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BMI changes among U.S. Navy and Marine Corps active-duty service members during the COVID-19 pandemic, 2019-2021 by Janvrin, Miranda Lynn, Banaag, Amanda, Landry, Travis, Vincent, Carey, Koehlmoos, Tracey Pérez

“…The COVID-19 pandemic disrupted the daily life and routines of Americans across the United States (U.S.), including those of our active-duty service members…”
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The maternal prenatal and offspring early‐life gut microbiome of childhood asthma phenotypes by Lee‐Sarwar, Kathleen A., Chen, Yih‐Chieh, Chen, Yuan Yao, Kozyrskyj, Anita L., Mandhane, Piush J., Turvey, Stuart E., Subbarao, Padmaja, Bisgaard, Hans, Stokholm, Jakob, Chawes, Bo, Sørensen, Søren J., Kelly, Rachel S., Lasky‐Su, Jessica, Zeiger, Robert S., O'Connor, George T., Sandel, Megan T., Bacharier, Leonard B., Beigelman, Avraham, Carey, Vincent J., Harshfield, Benjamin J., Laranjo, Nancy, Gold, Diane R., Weiss, Scott T., Litonjua, Augusto A.

“…Background The infant fecal microbiome is known to impact subsequent asthma risk, but the environmental exposures impacting this association, the role of the…”
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Effect of Prenatal Supplementation With Vitamin D on Asthma or Recurrent Wheezing in Offspring by Age 3 Years: The VDAART Randomized Clinical Trial by Litonjua, Augusto A, Carey, Vincent J, Laranjo, Nancy, Harshfield, Benjamin J, McElrath, Thomas F, O’Connor, George T, Sandel, Megan, Iverson, Ronald E, Lee-Paritz, Aviva, Strunk, Robert C, Bacharier, Leonard B, Macones, George A, Zeiger, Robert S, Schatz, Michael, Hollis, Bruce W, Hornsby, Eve, Hawrylowicz, Catherine, Wu, Ann Chen, Weiss, Scott T

“…IMPORTANCE: Asthma and wheezing begin early in life, and prenatal vitamin D deficiency has been variably associated with these disorders in offspring…”
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Subtyping COPD by Using Visual and Quantitative CT Imaging Features by Park, Jinkyeong, Hobbs, Brian D., Crapo, James D., Make, Barry J., Regan, Elizabeth A., Humphries, Stephen, Carey, Vincent J., Lynch, David A., Silverman, Edwin K.

“…Multiple studies have identified COPD subtypes by using visual or quantitative evaluation of CT images. However, there has been no systematic assessment of a…”
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Vitamin D supplementation in pregnancy, prenatal 25(OH)D levels, race, and subsequent asthma or recurrent wheeze in offspring: Secondary analyses from the Vitamin D Antenatal Asthma Reduction Trial by Wolsk, Helene M., MD, Harshfield, Benjamin J., BA, Laranjo, Nancy, BA, Carey, Vincent J., PhD, O'Connor, George, MD, Sandel, Megan, MD, Strunk, Robert C., MD, Bacharier, Leonard B., MD, Zeiger, Robert S., MD, Schatz, Michael, MD, Hollis, Bruce W., PhD, Weiss, Scott T., MD, Litonjua, Augusto A., MD, MPH

“…Background Nutrient trials differ from drug trials because participants have varying circulating levels at entry into the trial. Objective We sought to study…”
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Democratizing knowledge representation with BioCypher by Lobentanzer, Sebastian, Aloy, Patrick, Baumbach, Jan, Bohar, Balazs, Carey, Vincent J., Charoentong, Pornpimol, Danhauser, Katharina, Doğan, Tunca, Dreo, Johann, Dunham, Ian, Farr, Elias, Fernandez-Torras, Adrià, Gyori, Benjamin M., Hartung, Michael, Hoyt, Charles Tapley, Klein, Christoph, Korcsmaros, Tamas, Maier, Andreas, Mann, Matthias, Ochoa, David, Pareja-Lorente, Elena, Popp, Ferdinand, Preusse, Martin, Probul, Niklas, Schwikowski, Benno, Sen, Bünyamin, Strauss, Maximilian T., Turei, Denes, Ulusoy, Erva, Waltemath, Dagmar, Wodke, Judith A. H., Saez-Rodriguez, Julio

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Bioconductor: an open source framework for bioinformatics and computational biology by Reimers, Mark, Carey, Vincent J

“…This chapter describes the Bioconductor project and details of its open source facilities for analysis of microarray and other high-throughput biological…”
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Effects of High vs Low Glycemic Index of Dietary Carbohydrate on Cardiovascular Disease Risk Factors and Insulin Sensitivity: The OmniCarb Randomized Clinical Trial by Sacks, Frank M, Carey, Vincent J, Anderson, Cheryl A. M, Miller, Edgar R, Copeland, Trisha, Charleston, Jeanne, Harshfield, Benjamin J, Laranjo, Nancy, McCarron, Phyllis, Swain, Janis, White, Karen, Yee, Karen, Appel, Lawrence J

“…IMPORTANCE: Foods that have similar carbohydrate content can differ in the amount they raise blood glucose. The effects of this property, called the glycemic…”
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Graphs in molecular biology by Huber, Wolfgang, Carey, Vincent J, Long, Li, Falcon, Seth, Gentleman, Robert

“…Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction…”
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Factors influencing the infant gut microbiome at age 3-6 months: Findings from the ethnically diverse Vitamin D Antenatal Asthma Reduction Trial (VDAART) by Sordillo, Joanne E., ScD, Zhou, Yanjiao, MD, PhD, McGeachie, Michael J., PhD, Ziniti, John, BA, Lange, Nancy, MD, MPH, Laranjo, Nancy, BA, Savage, Jessica R., MD, Carey, Vincent, PhD, O'Connor, George, MD, MS, Sandel, Megan, MD, MPH, Strunk, Robert, MD, PhD, Bacharier, Leonard, MD, Zeiger, Robert, MD, PhD, Weiss, Scott T., MD, MS, Weinstock, George, PhD, Gold, Diane R., MD, MPH, Litonjua, Augusto A., MD, MPH

“…Background The gut microbiome in infancy influences immune system maturation, and may have an important impact on allergic disease risk. Objective We sought to…”
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The Role of Vitamin D in the Transcriptional Program of Human Pregnancy by Al-Garawi, Amal, Carey, Vincent J, Chhabra, Divya, Mirzakhani, Hooman, Morrow, Jarrett, Lasky-Su, Jessica, Qiu, Weiliang, Laranjo, Nancy, Litonjua, Augusto A, Weiss, Scott T

“…Patterns of gene expression of human pregnancy are poorly understood. In a trial of vitamin D supplementation in pregnant women, peripheral blood…”
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