Browsing by Subject "genomics"

Now showing 1 - 12 of 12

Open Access
1997 Delegates to the Second International Strategy Meeting on Human Genome Sequencing in Bermuda from Gert-Jan van Ommen
(2016-08-31)
Photographs from the February 1997 Bermuda meeting. Courtesy of Gert-Jan van Ommen.
Open Access
2000 NHGRI e-mail request for HGP sequencing center information, and corresponding aggregate data from NHGRI, compiled by Kris Wetterstrand
(2016-08-31)
Email exchange in 2013 between Kathryn Maxson (Duke) and Kris Wetterstrand (NHGRI), regarding country funding and other data for the HGP sequencing centers. Also includes the email request for such information, from NHGRI to the centers, in 2000, and the aggregate data collected.
Open Access
2011 18 August Mark Guyer-Jane Peterson interview
(2011-08-18)
Mark Guyer and Jane Peterson, in-person interview with Kathryn Maxson and Robert Cook-Deegan, conducted in Rockville, MD (NIH campus), 18 August 2011. Mark Guyer and Jane Peterson were grants program officers at the NIH during the HGP, and were some of the longest-standing employees in the HGP administrative structure. Both witnessed the transformation of the Office of Genome Research into the National Center for Human Genome Research and, finally, the National Human Genome Research Institute. They were close participants in the history of the Bermuda Principles within the NIH.
Open Access
2012 09 February Jean Weissenbach interview
(2016-08-31)
Jean Weissenbach, telephone interview by Kathryn Maxson and Robert Cook-Deegan, conducted from Durham, NC 09 February 2012. Jean Weissenbach, a leader in French genetic mapping, directed the French national sequencing center, Généthon, during the HGP and was instrumental in helping to build agreement to the Bermuda Principles in France.
Open Access
2017 Robert Waterston, e-mail communication to authors 4 & 9 Jan 2017
(2017-02-17)
Open Access
2017 Robert Waterston, e-mail communication to authors, 17 Feb 2017
(2017-02-17)
Open Access
A phylogenetic transform enhances analysis of compositional microbiota data.
(Elife, 2017-02-15) Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A
Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.
Open Access
Invited Commentary: Integrating Genomics and Social Epidemiology-Analysis of Late-Life Low Socioeconomic Status and the Conserved Transcriptional Response to Adversity.
(Am J Epidemiol, 2017-09-01) Belsky, Daniel W; Snyder-Mackler, Noah
Socially disadvantaged children face increased morbidity and mortality as they age. Understanding mechanisms through which social disadvantage becomes biologically embedded and devising measurements that can track this embedding are critical priorities for research to address social gradients in health. The analysis by Levine et al. (Am J Epidemiol. 2017;186(5):503-509) of genome-wide gene expression in a subsample of US Health and Retirement Study participants suggests important new directions for the field. Specifically, findings suggest promise in integrating gene expression data into population studies and provide further evidence for the conserved transcriptional response to adversity as a marker of biological embedding of social disadvantage. The study also highlights methodological issues related to the analysis of gene expression data and social gradients in health and a need to examine the conserved transcriptional response to adversity alongside other proposed measurements of biological embedding. Looking to the future, advances in genome science are opening new opportunities for sociogenomic epidemiology.
Open Access
Perceptions of Personalized Medicine in an Academic Health System: Educational Findings.
(Journal of contemporary medical education, 2015-01) Vorderstrasse, Allison; Katsanis, Sara Huston; Minear, Mollie A; Yang, Nancy; Rakhra-Burris, Tejinder; Reeves, Jason W; Cook-Deegan, Robert; Ginsburg, Geoffrey S; Ann Simmons, Leigh
Prior reports demonstrate that personalized medicine implementation in clinical care is lacking. Given the program focus at Duke University on personalized medicine, we assessed health care providers' perspectives on their preparation and educational needs to effectively integrate personalized medicine tools and applications into their clinical practices.Data from 78 health care providers who participated in a larger study of personalized and precision medicine at Duke University were analyzed using Qualtrics (descriptive statistics). Individuals age 18 years and older were recruited for the larger study through broad email contacts across the university and health system. All participants completed an online 35-question survey that was developed, pilot-tested, and administered by a team of interdisciplinary researchers and clinicians at the Center for Applied Genomics and Precision Medicine.Overall, providers reported being ill-equipped to implement personalized medicine in clinical practice. Many respondents identified educational resources as critical for strengthening personalized medicine implementation in both research and clinical practice. Responses did not differ significantly between specialists and primary providers or by years since completion of the medical degree.Survey findings support prior calls for provider and patient education in personalized medicine. Respondents identified focus areas in training, education, and research for improving personalized medicine uptake. Given respondents' emphasis on educational needs, now may be an ideal time to address these needs in clinical training and public education programs.
Open Access
Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.
(Elife, 2016-05-10) Medina, Edgar M; Turner, Jonathan J; Gordân, Raluca; Skotheim, Jan M; Buchler, Nicolas E
Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast.
Open Access
To plasticity and back again.
(Elife, 2015-03-12) Nijhout, H Frederik
Both the gain and the loss of flexibility in the development of phenotypes have led to an increased diversity of physical forms in nematode worms.
Open Access
Update on hypoxia-inducible factors and hydroxylases in oxygen regulatory pathways: from physiology to therapeutics.
(Hypoxia (Auckland, N.Z.), 2017-01) Ratcliffe, Peter; Koivunen, Peppi; Myllyharju, Johanna; Ragoussis, Jiannis; Bovée, Judith Vmg; Batinic-Haberle, Ines; Vinatier, Claire; Trichet, Valérie; Robriquet, Florence; Oliver, Lisa; Gardie, Betty
The "Hypoxia Nantes 2016" organized its second conference dedicated to the field of hypoxia research. This conference focused on "the role of hypoxia under physiological conditions as well as in cancer" and took place in Nantes, France, in October 6-7, 2016. The main objective of this conference was to bring together a large group of scientists from different spheres of hypoxia. Recent advances were presented and discussed around different topics: genomics, physiology, musculoskeletal, stem cells, microenvironment and cancer, and oxidative stress. This review summarizes the major highlights of the meeting.