Interactions and Biological Complexity

How do the linear instructions of the genome come to define the breath-taking complexity of animal bodies? Genes and proteins interact to control the expression phenotypes of cells, cells interact to specify tissue phenotypes, and tissues interact to form organs, which themselves interact to make bodies. And all these processes vary through the lifetime of an individual and through evolutionary time as species evolve.

Rates of evolution

How fast can evolution go? Why, if bacteria evolve 'faster' than humans, do they not 'win the race'? What determines rates of evolution: mutation, selection, genetic system, biological interactions?

High Throughput Data Analysis

If tissue X has 500 reads in 4000bp and tissue Y has 700 reads in 5000bp, are these the same?


R package:mlgt
Processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.

R package:mlPhaser
Phase haplotypes from genotypes based on a list of known haplotypes. Suited to highly diverse loci such as HLA.
CRAN page

Rowe, C., D. T. Gerrard, R. Jenkins, A. Berry, K. Durkin, L. Sundstrom, C. E. Goldring, B. K. Park, N. R. Kitteringham, K. P. Hanley, and N. A. Hanley
Proteome-wide analyses of human hepatocytes during differentiation and de-differentiation.
Hepatology doi:10.1002/hep.26414 Abstract / Full Text
Gerrard DT, Fricke C, Edward DA, Edwards DR, Chapman T
Genome-Wide Responses of Female Fruit Flies Subjected to Divergent Mating Regimes.
PLoS ONE 8(6): e68136. doi:10.1371/journal.pone.0068136 Abstract / Full Text
Kayserili, M. A., D. T. Gerrard, P. Tomancak, and A. T. Kalinka
An excess of gene expression divergence on the x chromosome in drosophila embryos: Implications for the Faster-X hypothesis.
PLoS Genet 8 (12), e1003200+. Abstract / Full Text
Edward, DA, Fricke, C, Gerrard, DT and Chapman T
Quantifying the life history response to increased male exposure in female Drosophila melanogaster.
Evolution 65(2), 564-573 Abstract / Full Text
Gallo, SM, Gerrard, DT, Miner, D, Simich, M, Des Soye, B, Bergman, CM, and Halfon, MS.
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila.
Nucleic Acids Research 39(suppl 1), D118-D123 Abstract / Full Text
Kalinka, A. T., Varga, K. M., Gerrard, D. T., Preibisch, S., Corcoran, D. L., Jarrells, J., Ohler, U., Bergman, C. M., Tomancak, P.
Gene expression divergence recapitulates the developmental hourglass model.
Nature 468 (7325), 811-814 Abstract / Full Text
Pils, S, Gerrard, DT, Meyer, A and Hauck, C
CEACAM3: an innate immune receptor directed against human-restricted bacterial pathogens.
International Journal of Medical Microbiology 298 (7-8), 553-560. Abstract / Full Text
Gerrard, DT and Meyer, A
Positive selection and gene conversion in SPP120, a fertilization-related gene, during the East African Cichlid fish radiation.
Molecular Biology and Evolution 24 (10), 2286-2297 Abstract / Full Text
Gerrard, DT and Filatov, DA
Adaptive evolution on the mammalian Y chromosome.
Molecular Biology and Evolution 22(6), 1423-32 Abstract / Full Text
Filatov, DA and Gerrard, DT
High mutation rates in human and ape pseudoautosomal genes.
Gene 317, 67-77 Abstract / Full Text
Gerrard, DT and Bornberg-Bauer, E
doMosaic - Analysis of the mosaic-like domain arrangements in proteins.
Informatica 27(1), 15-20 Abstract / Full Text