comparative genomics, insect genomics, molecular evolution, computational biology, comparative analysis, genomics
Waterhouse Robert M, Tegenfeldt Fredrik, Li Jia, Zdobnov Evgeny M, Kriventseva Evgenia V (2013), OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs., in Nucleic acids research
, 41(Database i), 1-65.
Waterhouse Robert M, Zdobnov Evgeny M, Kriventseva Evgenia V (2011), Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi., in Genome biology and evolution
, 3, 75-86.
Li Jia, Waterhouse Robert M, Zdobnov Evgeny M (2011), A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits., in BMC evolutionary biology
, 11, 337-337.
Colbourne John K, Pfrender Michael E, Gilbert Donald, Thomas W Kelley, Tucker Abraham, Oakley Todd H, Tokishita Shinichi, Aerts Andrea, Arnold Georg J, Basu Malay Kumar, Bauer Darren J, Cáceres Carla E, Carmel Liran, Casola Claudio, Choi Jeong-Hyeon, Detter John C, Dong Qunfeng, Dusheyko Serge, Eads Brian D, Fröhlich Thomas, Geiler-Samerotte Kerry A, Gerlach Daniel, Hatcher Phil, Jogdeo Sanjuro, Krijgsveld Jeroen (2011), The ecoresponsive genome of Daphnia pulex., in Science (New York, N.Y.)
, 331(6017), 555-61.
Waterhouse Robert M, Zdobnov Evgeny M, Tegenfeldt Fredrik, Li Jia, Kriventseva Evgenia V (2011), OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011., in Nucleic acids research
, 39(Database i), 283-8.
Bartholomay Lyric C, Waterhouse Robert M, Mayhew George F, Campbell Corey L, Michel Kristin, Zou Zhen, Ramirez Jose L, Das Suchismita, Alvarez Kanwal, Arensburger Peter, Bryant Bart, Chapman Sinead B, Dong Yuemei, Erickson Sara M, Karunaratne S H P Parakrama, Kokoza Vladimir, Kodira Chinnappa D, Pignatelli Patricia, Shin Sang Woon, Vanlandingham Dana L, Atkinson Peter W, Birren Bruce, Christophides George K, Clem Rollie J, Hemingway Janet (2010), Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens., in Science (New York, N.Y.)
, 330(6000), 88-90.
Arensburger Peter, Megy Karine, Waterhouse Robert M, Abrudan Jenica, Amedeo Paolo, Antelo Beatriz, Bartholomay Lyric, Bidwell Shelby, Caler Elisabet, Camara Francisco, Campbell Corey L, Campbell Kathryn S, Casola Claudio, Castro Marta T, Chandramouliswaran Ishwar, Chapman Sinéad B, Christley Scott, Costas Javier, Eisenstadt Eric, Feschotte Cedric, Fraser-Liggett Claire, Guigo Roderic, Haas Brian, Hammond Martin, Hansson Bill S (2010), Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics., in Science (New York, N.Y.)
, 330(6000), 86-8.
Kirkness Ewen F, Haas Brian J, Sun Weilin, Braig Henk R, Perotti M Alejandra, Clark John M, Lee Si Hyeock, Robertson Hugh M, Kennedy Ryan C, Elhaik Eran, Gerlach Daniel, Kriventseva Evgenia V, Elsik Christine G, Graur Dan, Hill Catherine A, Veenstra Jan A, Walenz Brian, Tubío José Manuel C, Ribeiro José M C, Rozas Julio, Johnston J Spencer, Reese Justin T, Popadic Aleksandar, Tojo Marta, Raoult Didier (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.
Hunt Brendan G, Wyder Stefan, Elango Navin, Werren John H, Zdobnov Evgeny M, Yi Soojin V, Goodisman Michael A D (2010), Sociality is linked to rates of protein evolution in a highly social insect., in Molecular biology and evolution
, 27(3), 497-500.
Kim Jaebum, Cunningham Ryan, James Brian, Wyder Stefan, Gibson Joshua D, Niehuis Oliver, Zdobnov Evgeny M, Robertson Hugh M, Robinson Gene E, Werren John H, Sinha Saurabh (2010), Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances., in PLoS computational biology
, 6(1), 1000652-1000652.
Werren John H, Richards Stephen, Desjardins Christopher A, Niehuis Oliver, Gadau Jürgen, Colbourne John K, Nasonia Genome Working Group, Werren John H, Richards Stephen, Desjardins Christopher A, Niehuis Oliver, Gadau Jürgen, Colbourne John K, Beukeboom Leo W, Desplan Claude, Elsik Christine G, Grimmelikhuijzen Cornelis J P, Kitts Paul, Lynch Jeremy A, Murphy Terence, Oliveira Deodoro C S G, Smith Christopher D, van de Zande Louis, Worley Kim C, Zdobnov Evgeny M (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.