A5081015175- Gene expression and cancer classification
- Asthma and respiratory diseases
- Bioinformatics and Genomic Networks
- Neonatal Respiratory Health Research
- Diet and metabolism studies
- Nutritional Studies and Diet
- Genetic Associations and Epidemiology
- Chronic Obstructive Pulmonary Disease (COPD) Research
- HIV Research and Treatment
- Epigenetics and DNA Methylation
- HIV/AIDS drug development and treatment
- Statistical Methods and Bayesian Inference
- Vitamin D Research Studies
- Genomics and Phylogenetic Studies
- Statistical Methods and Inference
- Gut microbiota and health
- HIV/AIDS Research and Interventions
- Breastfeeding Practices and Influences
- Scientific Computing and Data Management
- Streptococcal Infections and Treatments
- Pediatric health and respiratory diseases
- Single-cell and spatial transcriptomics
- Diabetes, Cardiovascular Risks, and Lipoproteins
- Genetics, Bioinformatics, and Biomedical Research
- Molecular Biology Techniques and Applications
Brigham and Women's Hospital
2016-2025
Harvard University
2016-2025
Mass General Brigham
2022-2025
Columbia University
2023
New York Proton Center
2023
Rush University Medical Center
2021
Beth Israel Deaconess Medical Center
2017-2021
Université du Québec à Montréal
2020
Broad Institute
2020
RELX Group (United States)
2020
Abstract The Bioconductor project is an initiative for the collaborative creation of extensible software computational biology and bioinformatics. goals include: fostering development widespread use innovative software, reducing barriers to entry into interdisciplinary scientific research, promoting achievement remote reproducibility research results. We describe details our aims methods, identify current challenges, compare other open bioinformatics projects, provide working examples.
We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges integrating data with the statistical features of R its extensions. At core are three packages: IRanges, GenomicRanges, GenomicFeatures. These packages provide scalable structures genome, special support transcript structures, read alignments coverage vectors. Computational facilities include efficient algorithms overlap nearest neighbor detection, calculation other range operations. This...
The possible advantage for weight loss of a diet that emphasizes protein, fat, or carbohydrates has not been established, and there are few studies extend beyond 1 year.We randomly assigned 811 overweight adults to one four diets; the targeted percentages energy derived from in diets were 20, 15, 65%; 25, 55%; 40, 45%; 35%. consisted similar foods met guidelines cardiovascular health. participants offered group individual instructional sessions 2 years. primary outcome was change body after...
Context.—Obesity is a well-established risk factor for coronary heart disease (CHD), but whether regional fat distribution contributes independently to remains unclear.Objective.—To compare waist-hip ratio (WHR) and waist circumference in determining of CHD women.Design Setting.—Prospective cohort study among US female registered nurses participating the Nurses' Health Study conducted between 1986, when completed questionnaire, follow-up June 1994.Participants.—A total 44,702 women aged 40...
Reduced intake of saturated fat is widely recommended for prevention cardiovascular disease. The type macronutrient that should replace remains uncertain.To compare the effects 3 healthful diets, each with reduced intake, on blood pressure and serum lipids.Randomized, 3-period, crossover feeding study (April 2003 to June 2005) conducted in Baltimore, Md, Boston, Mass. Participants were 164 adults prehypertension or stage 1 hypertension. Each period lasted 6 weeks body weight was kept...
Obesity is an established risk factor for non-insulin-dependent diabetes mellitus (NIDDM). Anthropometric measures of overall and central obesity as predictors NIDDM have not been well studied, especially in women. Among 43,581 women enrolled the Nurses' Health Study who 1986 provided waist, hip, weight information were initially free from other major chronic diseases, incidence was followed to 1994. After adjustment age, family history diabetes, smoking, exercise, several dietary factors,...
Abstract Summary: The rtracklayer package supports the integration of existing genome browsers with experimental data analyses performed in R. user may (i) transfer annotation tracks to and from a browser (ii) create manipulate views focus on particular set annotations specific genomic region. Currently, UCSC is supported. Availability: freely available http://www.bioconductor.org/. A quick-start vignette included package. Contact: mflawren@fhcrc.org
<h3>Context.</h3> —Gestational diabetes mellitus (GDM) affects 3% to 5% of pregnancies. Knowledge risk factors for GDM is needed identify possible preventive strategies. <h3>Objective.</h3> —To assess whether recognized determinants non-insulindependent also may be markers increased GDM. <h3>Design.</h3> —Prospective cohort study. <h3>Setting.</h3> —The Nurses' Health Study II, which involves female US nurses aged 25 42 years at entry. <h3>Participants.</h3> analyses included 14613 women...
Journal Article Modelling multivariate binary data with alternating logistic regressions Get access VINCENT CAREY, CAREY 1Department of Biostatistics, Johns Hopkins School Hygiene and Public Health615 N. Wolfe Street, Baltimore, Maryland 21205, U.S.A. Search for other works by this author on: Oxford Academic Google Scholar SCOTT L. ZEGER, ZEGER PETER DIGGLE 2School Engineering, Computing, Mathematical Sciences, Lancaster UniversityLancaster, U.K. Biometrika, Volume 80, Issue 3, September...
"Mixed-Effects Models in S and S-Plus." Journal of the American Statistical Association, 96(455), pp. 1135–1136
<h3>Importance</h3> Asthma and wheezing begin early in life, prenatal vitamin D deficiency has been variably associated with these disorders offspring. <h3>Objective</h3> To determine whether (cholecalciferol) supplementation can prevent asthma or recurrent wheeze childhood. <h3>Design, Setting, Participants</h3> The Vitamin Antenatal Reduction Trial was a randomized, double-blind, placebo-controlled trial conducted 3 centers across the United States. Enrollment began October 2009 completed...
Abstract Summary: VariantAnnotation is an R / Bioconductor package for the exploration and annotation of genetic variants. Capabilities exist reading, writing filtering variant call format (VCF) files. allows ready access to additional facilities advanced statistical analysis, data transformation, visualization integration with diverse genomic resources. Availability implementation: This implemented in available download at Web site ( http://bioconductor.org/packages/2.13/bioc/html/ .html )....
The impact of cigarette smoking can persist for extended periods following cessation and may involve epigenetic reprogramming. Changes in DNA methylation associated with help to identify molecular pathways that contribute the latency between exposure disease onset. Cross-sectional cohort data from subjects International COPD Genetics Network (n = 1085) Boston Early-Onset study 369) were analyzed as discovery replication cohorts, respectively. Genome-wide on 27 578 CpG sites 14 475 genes...
Background— Microvascular renal and retinal diseases are common major complications of type 2 diabetes mellitus. The relation between plasma lipids microvascular disease is not well established. Methods Results— case subjects were 2535 patients with mellitus an average duration 14 years, 1891 whom had kidney 1218 retinopathy. matched for duration, age, sex, low-density lipoprotein cholesterol to 3683 control who did have or study was conducted in 24 sites 13 countries. primary analysis...
<h3>Importance</h3> Foods that have similar carbohydrate content can differ in the amount they raise blood glucose. The effects of this property, called glycemic index, on risk factors for cardiovascular disease and diabetes are not well understood. <h3>Objective</h3> To determine effect index total dietary diabetes. <h3>Design, Setting, Participants</h3> Randomized crossover-controlled feeding trial conducted research units academic medical centers, which 163 overweight adults (systolic...
Low vitamin D status in pregnancy was proposed as a risk factor of preeclampsia.We assessed the effect supplementation (4,400 vs. 400 IU/day), initiated early (10-18 weeks), on development preeclampsia. The effects serum (25-hydroxyvitamin [25OHD]) levels preeclampsia incidence at trial entry and third trimester (32-38 weeks) were studied. We also conducted nested case-control study 157 women to investigate peripheral blood D-associated gene expression profiles 10 18 weeks 47 participants...