Epistasis Blog

From the Artificial Intelligence Innovation Lab at Cedars-Sinai Medical Center (www.epistasis.org)

Sunday, February 25, 2007


I first went to see Dr. Edward Tufte when I was a graduate student. His workshop and books on visualizing information are superb. Attending his course will significantly change how you look at the world. I just sent my entire lab to his recent Boston course. I recommend you do the same! His web page can be found here.

Saturday, February 10, 2007

The Evolution of Sex

A new paper in Nature Reviews Genetics looks at the interplay between sex and genetic architecture. In particular, the role of epistasis is explored.

de Visser JA, Elena SF. The evolution of sex: empirical insights into the roles of epistasis and drift. Nat Rev Genet. 2007 Feb;8(2):139-49. [PubMed]

Despite many years of theoretical and experimental work, the explanation for why sex is so common as a reproductive strategy continues to resist understanding. Recent empirical work has addressed key questions in this field, especially regarding rates of mutation accumulation in sexual and asexual organisms, and the roles of negative epistasis and drift as sources of adaptive constraint in asexually reproducing organisms. At the same time, new ideas about the evolution of sexual recombination are being tested, including intriguing suggestions of an important interplay between sex and genetic architecture, which indicate that sex and recombination could have affected their own evolution.

Wednesday, February 07, 2007

Journal of Artificial Evolution and Applications

I have been appointed Associate Editor of the new Journal of Artificial Evolution and Applications.

Aims and Scope

Journal of Artificial Evolution and Applications aims at being a reference for all researchers and practitioners who study the theory and application of methodologies pertaining to Evolutionary Computation and related fields. Original contributions are sought describing recent achievements in Evolutionary Computation research, with particular, but not exclusive, regard to:

Genetic Algorithms
Genetic Programming
Evolutionary Programming
Evolution Strategies
Swarm Intelligence
Learning Classifier Systems
Artificial Immune Systems
Interactive Evolution
Evolvable Hardware
Hybrid approaches relying on the joint use of Evolutionary Computation methods and other Computational Intelligence and optimization methods

Previously unpublished reports on applications of Evolutionary Computation techniques to problems of industrial, technological and social relevance are particularly solicited, including, but not limited to:

Combinatorial and Stochastic Optimization of Industrial Processes
Bioinformatics and Biomedical Engineering
Computer Vision and Pattern Recognition
Communication and Networking Technologies
Transportation and Logistics

In-depth reviews of the state of the art in any of the theoretical or application fields listed above are also accepted.

The journal publishes two types of issues: regular issues and special issues. The regular issues publish collections of papers without special solicitation. The special issues are specifically aimed at targeted topics of current interest; they consist of manuscripts contributed by authors responding to a particular Call-for-Papers. Regular papers can be submitted at any time, while special issue papers can only be submitted according to a planned schedule and submission guidelines as stated in the relevant Call-for-Papers. Proposals for special issues should be submitted directly to the Editor-in-Chief of the journal.

Tuesday, February 06, 2007

Epistasis Conferences

There are two upcoming conferences that focus on gene-gene and gene-environment interactions. The first one has more of a human genetics and epidemiology focus while the second has more of an evolutionary biology and animal breeding focus. They both look very interesting. I will be attending and speaking at the first one.

Approaches to Complex Pathways in Molecular Epidemiology
May 30 - June 2, 2007
Hyatt Regency Tamaya
Santa Ana Pueblo (Albuquerque area), New Mexico

Symposium on Epistasis: Predicting Phenotypes and Evolutionary Trajectories
May 31 – June 3, 2007
Scheman Education Building
Iowa State University

Monday, February 05, 2007

GECCO Tutorial and Workshop Schedule

The schedule for workshops and tutorials at the Genetic and Evolutionary Computation Conference (GECCO) in London has been posted here.

My workshop on Open-Source Software for Applied Genetic and Evolutionary Computation (SoftGEC) will be held the morning of July 7th (time TBA). More information can be found here.

My tutorial on Bioinformatics will be held on the morning of July 8th (time TBA). More information can be found here.

The Biological Applications sessions that I am chairing with Dr. Clare Bates Congdon will be held July 9-11. Details about the GECCO program can be found here.

Friday, February 02, 2007

Symbolic Modeling of Epistasis

Our paper on "Symbolic Modeling of Epistasis" has been published in a special issue of Human Heredity on gene-gene and gene-environment interactions. You can find it here. There are a number of nice papers in this issue. The PubMed entry for this paper is here.

The Symbolic Modeler (SyMod) software package that was used in this paper is available for testing. Email me for an alpha version to evaluate.