Epistasis Blog

From the Computational Genetics Laboratory at Dartmouth Medical School (www.epistasis.org)

Tuesday, March 17, 2009

Second Annual Dartmouth Integrative Biology Symposium

When: April 28 & 29, 2009

Where: Alumni Hall, Dartmouth College, Hanover, NH

Schedule: Click here

Speakers: Click here

For more information click here

Summary:

The invited speakers to the Second Annual Dartmouth Integrative Biology Symposium are the intellectual and innovative leaders in their respective fields of genomics, proteomics, biostatistics, bioinformatics, and systems biology. The purpose of the symposium is to make the research and medical communities aware of the latest cutting-edge ideas and progress in systems biology, and to raise awareness of the exciting advances in integrative biology at Dartmouth.

High-throughput approaches are being employed in broad and diverse areas of research, including the probing of basic cell biology questions as to how genes differ and are differentially expressed at the RNA and protein levels, how cells and tissues interact to work as an integrated whole, the diagnosis and prognosis of disease, evolution of genes and gene expression, pathology and forensic applications, drug discovery and development, identification of drug targets in pharmacogenomics, and many other areas. The biostatistical and bioinformatics methods to analyze and integrate the huge volumes of data that are generated by these kind of studies are being developed at an phenomenal pace. Thus the theme of this year's Symposium: Emerging Technologies.

Saturday, March 14, 2009

Is Genetic Evolution Predictable?

Here is an interesting paper from Science by Stern and Orgogozo that suggests epistasis and pleiotropy may be features of short-term rather than long-term evolution. This is important for human genetics because it suggests that phenotypic variation within species (e.g. humans) may result from mutations that have epistatic effects.

Stern DL, Orgogozo V. Is genetic evolution predictable? Science. 2009 Feb 6;323(5915):746-51. [PubMed]

Abstract

Ever since the integration of Mendelian genetics into evolutionary biology in the early 20th century, evolutionary geneticists have for the most part treated genes and mutations as generic entities. However, recent observations indicate that all genes are not equal in the eyes of evolution. Evolutionarily relevant mutations tend to accumulate in hotspot genes and at specific positions within genes. Genetic evolution is constrained by gene function, the structure of genetic networks, and population biology. The genetic basis of evolution may be predictable to some extent, and further understanding of this predictability requires incorporation of the specific functions and characteristics of genes into evolutionary theory.

Tuesday, March 10, 2009

A Fundamental Theorem of Biomedical Informatics

What is biomedical informatics? What is it not? See the new paper by Friedman.

Friedman CP. A "fundamental theorem" of biomedical informatics. J Am Med Inform Assoc. 2009 Mar-Apr;16(2):169-70. [PubMed]

Abstract

This paper proposes, in words and pictures, a "fundamental theorem" to help clarify what informatics is and what it is not. In words, the theorem stipulates that a person working in partnership with an information resource is "better" than that same person unassisted. The theorem is applicable to health care, research, education, and administrative activities. Three corollaries to the theorem illustrate that informatics is more about people than technology; that in order for the theorem to hold, resources must be informative in addition to being correct; and that the theorem can fail to hold for reasons explained by understanding the interaction between the person and the resource.

Monday, March 09, 2009

pubget - A New Search Tool

Ran across this new search tool. Try it with epistasis. Try it with multifactor dimensionality reduction.

Saturday, March 07, 2009

Epigenetic Epidemiology

This is a nice review on a hot new area. It will be interesting to know how much genetic information interacts with epigenetic information. This seems like an obvious layer of complexity in the genotype to phenotype map. This would be a good area for graduate students, postdocs or junior faculty to get into.

Foley DL, Craig JM, Morley R, Olsson CJ, Dwyer T, Smith K, Saffery R. Prospects for epigenetic epidemiology. Am J Epidemiol. 2009 Feb 15;169(4):389-400. [PubMed]

Abstract

Epigenetic modification can mediate environmental influences on gene expression and can modulate the disease risk associated with genetic variation. Epigenetic analysis therefore holds substantial promise for identifying mechanisms through which genetic and environmental factors jointly contribute to disease risk. The spatial and temporal variance in epigenetic profile is of particular relevance for developmental epidemiology and the study of aging, including the variable age at onset for many common diseases. This review serves as a general introduction to the topic by describing epigenetic mechanisms, with a focus on DNA methylation; genetic and environmental factors that influence DNA methylation; epigenetic influences on development, aging, and disease; and current methodology for measuring epigenetic profile. Methodological considerations for epidemiologic studies that seek to include epigenetic analysis are also discussed.

Tuesday, March 03, 2009

Jim Yong Kim, M.D., Ph.D., has been elected the 17th President of Dartmouth by the College's Board of Trustees

For more information about our new president click here. Find the press release here.

Jim Yong Kim, M.D., Ph.D., Chair of the Department of Global Health and Social Medicine at Harvard Medical School, has been elected the 17th President of Dartmouth by the College’s Board of Trustees. Ed Haldeman, Chair of Dartmouth’s Board of Trustees, announced the appointment today at a meeting of students, faculty and staff.

I hope this is good news for the Dartmouth Medical School that often plays second fiddle to the undergraduate mission of Dartmouth College. We are very excited to have a president that understands the medical school mission. Further, having someone from outside Dartmouth will bring fresh new ideas to a college that has a long history of hiring from within.

Sunday, March 01, 2009

MDR Download Record

We set a record in February for the most downloads of our open-source MDR software package in one month. There were more than 1000 downloads of MDR from Sourceforge.net last month. This beats the previous record by more than 300. Version 2.0 of MDR is now in beta testing. Be sure and send us your comments, suggestions and bug reports.

Visit the MDR web page here for more information.

Download the latest version from here.

See the November and December MDR 101 posts from 2006 for tips and advice on performing an MDR analysis. Start here.

Thanks for your interest! We hope you find MDR useful for your studies.