Research Theme: Genomics and Genometrics
My global interest is microbial genomes evolution: understanding the underlying principles that tend to organize, model and change chromosomes of bacteria and archaea. The importance of lateral transfer, its mechanisms, and the ways one may detect such events, how one may find the origin of the horizontally transferred regions is one part of my PhD thesis. Presently, I focused my research on Streptococcus and Staphylococcus genus, and on Parachlamydia and Bifidobacterium longum. The other part is to better understand the architecture of bacterial chromosomes: how important are the position and orientation - relative to replication - of genes, how replication directs chromosome architecture, how one may see the effects of replication, transcription, translation, etc. at the level of nucleotide composition. My goal is to be able to link these two aspects of genomics.
During a semester in Boulder, Colorado, at Noboru Sueoka's lab, I had the chance to work on some aspects of forces driving G+C content in bacteria. Particularly, we could show that the distribution of the G+C content of genes in whole genomes are is very likely to be bimodal, for some yet unknown reason.
Back in Lausanne, considering that genometrics - i.e., measures of the genomes - c analysis should be available for all scientists, I maintain and develop the Comparative Genometrics website. Recently, I automated the update of the site, and, in a close future, I will add new analyses to our pages.
I use bioinformatical tools available in literature (Artemis, Glimmer, BLAST, Mega, Clustal, Phylip, etc.), and develop my own tools, mostly using R language (see http://www.cran.r-project.org/).
August - December 2003
Internship in Prof. Noboru Sueoka's lab. Subject: Effect of transcription rate on the G+C content of bacterial genes.
Colorado University, Boulder, CO, USA
Since May 2003
PhD student at the Department of Fundamental Microbiology. Subject: Analysis of the evolutive history of bacterial genomes.
Lausanne University, Switzerland
1998 - 2003
Diplôme de biologiste (equivalent to a Masters degree) in Fundamental Microbiology (Title: Nucleotide composition of RNA genes reveals universal pressures that modulate genomic architecture) Specializations in Microbiology, Neurosciences, Molecular Genetics & Signaling, Microbial Genomics, Bioinformatics
Lausanne University, Switzerland
Collyn F, Roten CA, Guy L: Solving ambiguities in contig assembly of Idiomarina loihiensis L2TR chromosome by in silico analyses. FEMS Microbiol Lett. 2007 Apr 18; [Epub ahead of print]
Guy L, Karamata D, Moreillon P, Roten C: Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705. BMC Microbiology 2005 Oct 13, 5(1):60.
Heurlier K, Dénervaud V, Haenni M, Guy L, Krishnapillai V, Haas D: Quorum-sensing-negative (lasR) mutants of Pseudomonas aeruginosa avoid cell lysis and death. J Bacteriol 2005 Jul, 187(14):4875 - 4883.
Greub G*, Collyn F*, Guy L*, Roten C-A: A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system. BMC Microbiology 2004, 4(1):48. (*equally contributed)
Guy L, and Roten CAH (2004). Genometric analysis of the organization of circular chromosomes; a universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication. Gene 2004 340(1):45-52.
Guy L, Sueoka N: Effect of directional mutation pressures, their equilibria, and extent of gene expression on diversity of G+C content in bacteria (2005). In preparation.
Panchaud A, Roten CAH, Guy L, Collyn F, Haenni M, Moreillon P: Genometric analyses reveal a pathogenicity island along chromosomes of Streptococcus species (2005). In preparation.
Guy L, Fuellemann R, Jover A, Moreillon P, Roten CAH (2006): Detecting new and ancient pathogenicity islands in the Staphylococcus aureus genome with a new fast genometric method (2006). In preparation.