Design of the Building Research in CRC prevention (BRIDGE-CRC) trial: a 6-month, parallel group Mediterranean diet and weight loss randomized controlled lifestyle intervention targeting the bile acid-gut microbiome axis to reduce colorectal cancer risk among African American/Black adults with obesit

[1]  R. Chapkin,et al.  Personalized Nutrition Using Microbial Metabolite Phenotype to Stratify Participants and Non-Invasive Host Exfoliomics Reveal the Effects of Flaxseed Lignan Supplementation in a Placebo-Controlled Crossover Trial , 2022, Nutrients.

[2]  Joshua A. Wymer.  National Diabetes Prevention Program. , 2022, Health affairs.

[3]  S. Heymsfield,et al.  Weight and body composition changes affect resting energy expenditure predictive equations during a 12‐month weight‐loss intervention , 2021, Obesity.

[4]  T. Zimmerman,et al.  Development of a Tool for Researchers to Specify New Foods to Be Included in the Automated Self-Administered 24-Hour (ASA24) Dietary Assessment Tool , 2021 .

[5]  L. Davidson,et al.  Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet , 2020, Microorganisms.

[6]  Gavin M Douglas,et al.  PICRUSt2 for prediction of metagenome functions , 2020, Nature Biotechnology.

[7]  Ribbens Neltje,et al.  Acceptability and Reliability of the Paper and Online Versions of the MEPA-III Screener , 2020, Journal of Human Nutrition.

[8]  Enrico Giampieri,et al.  Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries , 2020, Gut.

[9]  Alvaro G. Hernandez,et al.  The ‘in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice , 2020, Gut microbes.

[10]  D. Mozaffarian,et al.  Trends in Dietary Carbohydrate, Protein, and Fat Intake and Diet Quality Among US Adults, 1999-2016. , 2019, JAMA.

[11]  Eunji Kim,et al.  Colonic mucosal and exfoliome transcriptomic profiling and fecal microbiome response to a flaxseed lignan extract intervention in humans. , 2019, The American journal of clinical nutrition.

[12]  L. Vitetta,et al.  Effects of Intestinal Microbial–Elaborated Butyrate on Oncogenic Signaling Pathways , 2019, Nutrients.

[13]  Edward R. Dougherty,et al.  Quantifying the notions of canalizing and master genes in a gene regulatory network—a Boolean network modeling perspective , 2018, Bioinform..

[14]  S. Hughes,et al.  Fit & Strong! Plus Trial Outcomes for Obese Older Adults with Osteoarthritis. , 2018, The Gerontologist.

[15]  Beatriz Peñalver Bernabé,et al.  Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women , 2018, Scientific Reports.

[16]  C. Shively,et al.  Consumption of Mediterranean versus Western Diet Leads to Distinct Mammary Gland Microbiome Populations , 2018, Cell reports.

[17]  Nicholas A. Bokulich,et al.  Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women , 2018, Journal of Translational Medicine.

[18]  T. Spector,et al.  Role of the gut microbiota in nutrition and health , 2018, British Medical Journal.

[19]  S. Green,et al.  Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease , 2018, PloS one.

[20]  G. Ayala,et al.  Frequency of Intake and Type of Away-from- Home Foods Consumed Are Associated with Diet Quality in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). , 2018, The Journal of nutrition.

[21]  Sara A. Grimm,et al.  An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression , 2018, Genome Biology.

[22]  N. Ellis,et al.  Colorectal Cancer Disparity in African Americans: Risk Factors and Carcinogenic Mechanisms. , 2017, The American journal of pathology.

[23]  K. Kunstman,et al.  Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol. , 2018, Methods in molecular biology.

[24]  D. Greenwood,et al.  The Mediterranean diet and risk of colorectal cancer in the UK Women's Cohort Study. , 2017, International journal of epidemiology.

[25]  J. Wardle,et al.  The Impact of Diet‐Induced Weight Loss on Biomarkers for Colorectal Cancer: An Exploratory Study (INTERCEPT) , 2017, Obesity.

[26]  S. Klein,et al.  Effect of weight gain and weight loss on in vivo colonocyte proliferation rate in people with obesity , 2017, Obesity.

[27]  C. Haiman,et al.  High-Quality Diets Associate With Reduced Risk of Colorectal Cancer: Analyses of Diet Quality Indexes in the Multiethnic Cohort. , 2017, Gastroenterology.

[28]  M. Lamar,et al.  Building research in diet and cognition: The BRIDGE randomized controlled trial. , 2017, Contemporary clinical trials.

[29]  C. Hudis,et al.  Effects of Rapid Weight Loss on Systemic and Adipose Tissue Inflammation and Metabolism in Obese Postmenopausal Women , 2017, Journal of the Endocrine Society.

[30]  N. Ellis,et al.  Race-dependent association of sulfidogenic bacteria with colorectal cancer , 2017, Gut.

[31]  J. Schneider,et al.  Serum bile acids and GLP-1 decrease following telemetric induced weight loss: results of a randomized controlled trial , 2016, Scientific Reports.

[32]  K. Flegal,et al.  Trends in Obesity Among Adults in the United States, 2005 to 2014. , 2016, JAMA.

[33]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[34]  E. Ferrannini,et al.  Increased Bile Acid Synthesis and Impaired Bile Acid Transport in Human Obesity. , 2016, The Journal of clinical endocrinology and metabolism.

[35]  H. Gaskins,et al.  Taurocholic acid metabolism by gut microbes and colon cancer , 2016, Gut microbes.

[36]  O. Sansom,et al.  Stem vs non-stem cell origin of colorectal cancer , 2015, British Journal of Cancer.

[37]  P. Aveyard,et al.  Cluster analysis of behavioural weight management strategies and associations with weight change in young women: a longitudinal analysis , 2015, International Journal of Obesity.

[38]  Mattia D'Antonio,et al.  RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application , 2015, BMC Genomics.

[39]  Leo Lahti,et al.  Fat, Fiber and Cancer Risk in African Americans and Rural Africans , 2015, Nature Communications.

[40]  Christian L. Müller,et al.  Sparse and Compositionally Robust Inference of Microbial Ecological Networks , 2014, PLoS Comput. Biol..

[41]  R. Dalle Grave,et al.  Increased Risk of Colorectal Cancer After Obesity Surgery. , 2015, Annals of surgery.

[42]  L. Davidson,et al.  Noninvasive molecular fingerprinting of host–microbiome interactions in neonates , 2014, FEBS letters.

[43]  M. Storey,et al.  Income and race/ethnicity influence dietary fiber intake and vegetable consumption. , 2014, Nutrition research.

[44]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[45]  Jiming Liu,et al.  Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range , 2014, BMC Medical Research Methodology.

[46]  J. Lara,et al.  The Effects of Bariatric Surgery on Colorectal Cancer Risk: Systematic Review and Meta-analysis , 2014, Obesity Surgery.

[47]  Jesse J Plascak,et al.  Evaluation of web-based, self-administered, graphical food frequency questionnaire. , 2014, Journal of the Academy of Nutrition and Dietetics.

[48]  Mihai Pop,et al.  Robust methods for differential abundance analysis in marker gene surveys , 2013, Nature Methods.

[49]  E. Zoetendal,et al.  Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. , 2013, The American journal of clinical nutrition.

[50]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[51]  H. Clevers,et al.  Intestinal Tumorigenesis Initiated by Dedifferentiation and Acquisition of Stem-Cell-like Properties , 2013, Cell.

[52]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[53]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[54]  Robert S Chapkin,et al.  A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response , 2012, Genome Biology.

[55]  Edward R. Dougherty,et al.  High-dimensional bolstered error estimation , 2011, Bioinform..

[56]  Mark J. Clement,et al.  Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics , 2011, Genome biology and evolution.

[57]  C. Huttenhower,et al.  Metagenomic biomarker discovery and explanation , 2011, Genome Biology.

[58]  Denis A. Evans,et al.  Adherence to a Mediterranean-type dietary pattern and cognitive decline in a community population. , 2011, The American journal of clinical nutrition.

[59]  M. Suárez-Fariñas,et al.  Diet-induced weight loss reduces colorectal inflammation: implications for colorectal carcinogenesis. , 2011, The American journal of clinical nutrition.

[60]  J. Lagergren,et al.  Risk of Obesity-Related Cancer After Obesity Surgery in a Population-Based Cohort Study , 2010, Annals of surgery.

[61]  Ivan Ivanov,et al.  Noninvasive stool-based detection of infant gastrointestinal development using gene expression profiles from exfoliated epithelial cells. , 2010, American journal of physiology. Gastrointestinal and liver physiology.

[62]  P. Lin,et al.  Effects of the DASH diet alone and in combination with exercise and weight loss on blood pressure and cardiovascular biomarkers in men and women with high blood pressure: the ENCORE study. , 2010, Archives of internal medicine.

[63]  S. Hunt,et al.  Cancer and Obesity: Effect of Bariatric Surgery , 2009, World Journal of Surgery.

[64]  P. Harris,et al.  Research electronic data capture (REDCap) - A metadata-driven methodology and workflow process for providing translational research informatics support , 2009, J. Biomed. Informatics.

[65]  T. Strine,et al.  The PHQ-8 as a measure of current depression in the general population. , 2009, Journal of affective disorders.

[66]  M. Brun,et al.  Conditioning-Based Modeling of Contextual Genomic Regulation , 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[67]  Daniela M Witten,et al.  Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data , 2009, Statistical applications in genetics and molecular biology.

[68]  D. Glueck.  Sample Size Calculations in Clinical Research 2nd edition by CHOW, S.‐C., SHAO, J., and WANG, H. , 2008 .

[69]  Ananda Sen,et al.  Design of a Mediterranean exchange list diet implemented by telephone counseling. , 2008, Journal of the American Dietetic Association.

[70]  Yahong Peng,et al.  Recommendations for the Primary Analysis of Continuous Endpoints in Longitudinal Clinical Trials , 2008 .

[71]  William Caplan,et al.  Weight-loss outcomes: a systematic review and meta-analysis of weight-loss clinical trials with a minimum 1-year follow-up. , 2007, Journal of the American Dietetic Association.

[72]  D. Panagiotakos,et al.  Adherence to the Mediterranean food pattern predicts the prevalence of hypertension, hypercholesterolemia, diabetes and obesity, among healthy adults; the accuracy of the MedDietScore. , 2007, Preventive medicine.

[73]  Edward R. Dougherty,et al.  What should be expected from feature selection in small-sample settings , 2006, Bioinform..

[74]  B. Löwe,et al.  A brief measure for assessing generalized anxiety disorder: the GAD-7. , 2006, Archives of internal medicine.

[75]  R. Knight,et al.  UniFrac: a New Phylogenetic Method for Comparing Microbial Communities , 2005, Applied and Environmental Microbiology.

[76]  M. Feinleib.  National Center for Health Statistics (NCHS) , 2005 .

[77]  Steven A. Julious,et al.  Sample sizes for estimation in clinical research , 2004 .

[78]  W. Babidge,et al.  Sulfides impair short chain fatty acid β-oxidation at acyl-CoA dehydrogenase level in colonocytes: Implications for ulcerative colitis , 1998, Molecular and Cellular Biochemistry.

[79]  R. Turner,et al.  Homeostasis model assessment: insulin resistance and β-cell function from fasting plasma glucose and insulin concentrations in man , 1985, Diabetologia.

[80]  J. Lupton,et al.  Quantification of human intestinal gene expression profiles using exfoliated colonocytes: a pilot study , 2003, Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals.

[81]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[82]  E. Dougherty,et al.  Identification of combination gene sets for glioma classification. , 2002, Molecular cancer therapeutics.

[83]  K. Kinzler,et al.  Top-down morphogenesis of colorectal tumors , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Helen Brown,et al.  Applied Mixed Models in Medicine , 2000, Technometrics.

[85]  Edward R. Dougherty,et al.  Coefficient of determination in nonlinear signal processing , 2000, Signal Process..

[86]  E. Deci,et al.  Self-determination theory and the facilitation of intrinsic motivation, social development, and well-being. , 2000, The American psychologist.

[87]  P. Mitchell,et al.  Estimates of animal and plant protein intake in US adults: results from the Third National Health and Nutrition Examination Survey, 1988-1991. , 1999, Journal of the American Dietetic Association.

[88]  R C Littell,et al.  Statistical analysis of repeated measures data using SAS procedures. , 1998, Journal of animal science.

[89]  David R. Williams,et al.  Racial Differences in Physical and Mental Health , 1997, Journal of health psychology.

[90]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[91]  A. Bandura.  Human agency in social cognitive theory. , 1989, The American psychologist.

[92]  Daniel J Buysse,et al.  The Pittsburgh sleep quality index: A new instrument for psychiatric practice and research , 1989, Psychiatry Research.

[93]  A. Fornace,et al.  DNA damage-inducible transcripts in mammalian cells. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[94]  Sheldon Cohen.  Perceived stress in a probability sample of the United States , 1988 .

[95]  J. Pennebaker,et al.  Disclosure of traumas and psychosomatic processes. , 1988, Social science & medicine.

[96]  B. Reddy.  Diet and excretion of bile acids. , 1981, Cancer research.