Our Lab

We are broadly interested in the evolution of development (Evo-Devo), evolutionary genomics and molecular evolution. We integrate developmental, genomic and computational approaches to understand the evolution of genes and gene functions. Please explore the projects pursued by individual members of the lab. You are welcome to contact us if you are interested in joining the lab or have any questions.

*A POSTDOCTORAL POSITION IS CURRENTLY AVAILABLE TO STUDY GENETICS AND GENOMICS OF STRESS RESPONSE*

Lab News

November 15, 2011

A paper by Rob Arthur and Ilya was published in Genetics. We tested whether functionally important sites in bacterial, yeast, and animal promoters are more conserved than their neighbors. We found that substitutions are predominantly seen in less important sites and that those that occurred tended to have less impact on gene expression than possible alternatives. These results suggest that purifying selection operates on promoter sequences. See the paper for more details.

August 1, 2011

A project carried out by Zhengying and Kelsie was published in PLoS ONE. We demonstrated that cis-regulatory elements of fly and human heat-shock genes are upregulated in C. elegans upon exposure to heat. Because enhancers of tissue-specific Drosophila genes are not appropriately recognized in nematodes, our results suggest that different aspects of regulatory logic may evolve at different rates. See the paper for more details.

July 1, 2011

A project carried out by Antoine and Kacy was published in PLoS Genetics. We demonstrated that promoter of C. elegans unc-47 consists of two distinct domains. The proximal is conserved and sufficient to direct appropriate spatial expression. The distal is not conserved, but confers robustness of expression, arguing that this function does not require sequence conservation. Robustness-promoting sequences are AT-enriched consistent with nucleosome depletion. Because general sequence composition can be maintained despite sequence turnover, our results explain how different functional constraints can lead to vastly disparate rates of sequence divergence within a promoter. See the paper for more details.

July 5, 2010

We welcomed Kelsie Eichel to the lab.

April 15, 2010

Congratulations to Kacy Gordon who was awarded an NSF Graduate Research Fellowship!

February 15, 2010

Our paper reporting a new method for predicting a class of small non-protein-coding RNAs (H/ACA snoRNAs) was published in RNA. Short RNAs are notoriously difficult to discover using genome sequences alone. We developed an algorithm that relies on empirically discovered sequences motifs and the notions of "genome neighborhoods" where snoRNAs genes are most likely to be found. We showed that by combining diverse data types into a single prediction engine and by entraining it on features restricted to particular phylogenetic groups, we can substantially improve the quality of computational predictions. See the paper for more details.

July 15, 2009

We welcomed Erin Zucker Aprison to the lab.

April 3, 2009

We welcomed two people in the lab − Zhengying He (a new postdoc) and Kacy Gordon (a graduate student).

March 2009

Our study on "Detecting heterozygosity in shotgun genome assemblies" was published in Genome Research. We demonstrated that despite intense inbreeding, the heterozygous fraction of the whole genome shotgun assemblies of three gonochoristic Caenorhabditis species, C. brenneri, C. remanei, and C. japonica, is considerable (up to 30%). We developed approaches for recognizing heterozygous regions of genome assemblies. Because of this extensive retained heterozygosity, allele frequencies within sequenced "strains" are continuing to change, and phenotypes are continuing to evolve. See the paper for more details.