Our Projects, formally speaking
1. Genotype - Phenotype relationships in humans.We are developing novel methods for linking human whole genome variation with human disease and trait variation. We apply these methods to multiple datasets in the contexts of prematurity, autism, heart disease and more [20, 29, 32, 34, 36, 38, 39, 43].
2. Genotype - Phenotype relationships between mammals.We develop novel methods to link trait evolution in the mammalian tree to whole genome evolution in over a hundred species. Application of these methods allow us to shed new light on human genome function, on human disease and on human evolution [29, 34, 35]. See our "Forward Genomics" web server.
3. Extracting genetic knowledge from high throughput genomic assays.High throughput genomic assays are most often used to make biochemical discoveries. We develop methods to extract genetic and developmental knowledge from these assays [27, 28, 31]. Through joint work with Sue McConnell we take special interest in the developing neocortex [29, 41]. Also see our popular GREAT web server for the cis-regulatory interpretation of high throughput genomic datasets.
4. Vertebrate transcription regulation.Much of our work relies on our strong foundations in the study of vertebrate gene regulation [9-11, 14, 15, 18, 22, 25, 27, 29-33, 35, 38-42, 44]. See our PRISM resource of predicted transcription factor functions and COMPLEX resource for predicted transcription factor dimers and complexes. Also see our zCNE resource of conserved non-coding (likely gene regulatory) sequences in the zebrafish genome.
5. Vertebrate genome evolution.We are extremely well versed in human and vertebrate genome evolution [9-11, 14, 17, 18, 22, 23, 25, 26, 29, 33-35, 37, 39, 40]. Notably, we discovered ultraconservation and correctly postulated that many of these elements are developmental enhancers. We also showed that mammalian ultraconserved elements evolve under extreme purifying selection, and that they are almost never lost during mammalian evolution [9, 23, 25]. We also discovered the first developmental enhancers conserved between human and protostomes , attempted to group human conserved non-coding DNA into paralog families , and studied the co-option of mobile elements into cis-regulatory roles [18, 22, 26, 41].
6. Evolutionary Developmental Biology ("evo devo").We have done work in the field of evolutionary developmental biology [29, 33-35, 43], including a first survey of developmental enhancers (including a penile spine/vibrissae enhancer) uniquely lost in humans , fueled by our deep interest in phenotype - genotype relationships.