comparative genomics; insect genomics; molecular evolution; computational biology; comparative analysis; genomics
(2013), OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs., in Nucleic acids research
, 41(Database i), 1-65.
(2011), A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits., in BMC evolutionary biology
, 11, 337-337.
(2011), Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi., in Genome biology and evolution
, 3, 75-86.
(2011), The ecoresponsive genome of Daphnia pulex., in Science (New York, N.Y.)
, 331(6017), 555-61.
(2011), OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011., in Nucleic acids research
, 39(Database i), 283-8.
(2010), Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens., in Science (New York, N.Y.)
, 330(6000), 88-90.
(2010), Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics., in Science (New York, N.Y.)
, 330(6000), 86-8.
(2010), Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle., in Proceedings of the National Academy of Sciences of the United States of America
, 107(27), 12168-73.
(2010), Sociality is linked to rates of protein evolution in a highly social insect., in Molecular biology and evolution
, 27(3), 497-500.
(2010), Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances., in PLoS computational biology
, 6(1), 1000652-1000652.
(2010), Functional and evolutionary insights from the genomes of three parasitoid Nasonia species., in Science (New York, N.Y.)
, 327(5963), 343-8.
The availability of genomic data facilitates a fascinating range of studies of cellular
processes at the molecular level. It is also clear that analysis of such tremendous
amounts of data is impossible without computational approaches, particularly in the
forthcoming era of ultra-high-throughput sequencing.
The objective of this proposal is to develop and employ computational strategies to
interrogate the sequencing data for patterns of natural selection that shape the
repertoire of functional genomic elements.
From our and others recent studies we have learned a lot about the repertoire and
evolution of protein-coding genes, yet further questions arise that we will approach:
- What is the origin of apparently species-unique genes?
- Does neofunctionalization explain “runaway” gene duplications?
Beyond protein-coding genes, we are getting closer to uncovering the full
complements of microRNA genes and of conserved non-coding sequences (CNC).
The profound impact of microRNAs on cellular regulation is commonly appreciated
- What are the global trends of microRNA’ome evolution?
The repertoire of CNCs might be as large as that of protein-coding genes, yet:
- What is the functional spectrum of conserved non-coding sequences?
Furthermore, once our understanding of microRNAs and CNCs matures, we will be
able to approach questions similar to what we ask regarding protein-coding genes.
The vision: a comparative, phylogenetically informed analysis of all genomic
components and their relationships to observed functional diversity; especially
promising in the light of the phenomenal adaptive radiations of arthropods. Each
sequenced genome tells a story, yet we are still to assemble this puzzle into a
coherent evolutionary picture through the analysis of all of them together.
I have contributed to the initial analyses of many animal genomes (mouse, rat,
malaria mosquito, chicken, honey bee, 12 Drosophilids, beetle, Dengue mosquito)
focusing on gene families, orthology, gene prediction, microRNA genes, and
conserved genomic gene clusters. This experience and established collaborations
with the leading researchers in the field (see provided letters of support) present
unique settings for the proposed project.