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Charles Chapus

Ph.D. University of Paris 7 - Denis Diderot

Department of Organismic and Evolutionary Biology
Museum of Comparative Zoology
Harvard University
26 Oxford Street
Cambridge, MA 02138

phone: (617)-496-8387
fax: (617)-495-5667

email: cchapus (at) oeb.harvard.edu

 

Education:

1995-1997 : Degree in Chemistry and Physics : University of Paris 11 - Orsay


1997-2001 : Engineer and Master Degree in Chemistry and Physics (Emphasis: Biology) at the ESPCI

2001 : Master Degree in BioInformatics at the University of Paris 7 - Denis Diderot

2001 - April 2005 : Ph. D. in Biology at the University of Paris 7 - Denis Diderot. Advisor: Dr. Patrick Deschavanne (http://www.ebgm.jussieu.fr/)

Research Interests:

With my multi-field background, I like to bring together different fields. I'm a computionnal biologist with a strong informatic background. My principal interest is comparing species using the huge amount of molecular data that are available.
During my Ph. D., I have use the sequence analysis tool (the genomic signature) to asset phylogenetic relationships between species. The first part of this work was to evaluate the possibility to use the genomic signature, the whole set of oligonucleotid frequencies in DNA sequence, as a phylogenetic tools. Afterwards I use the genomic signature to compare a large amount of species (more particulary the bacteria) with the help of homologous (genes) or non-homologous (whole genome, random DNA sequences) sequences.
My postdoctoral work in the laboratory of Pr. Scott Edwards is focused on comparative genomics. My work consists in evaluating the relationship inside the sauropsids and the structural changes of their genomes. I'm using two BAC libraries that are available in our lab (Alligator Mississipiensis and Chrysemys picta) and compare the BAC-end sequences to the Chicken (Gallus Gallus) genome. The BAC-end sequences are a efficient tool to detect structural changes between species. The Crocodilians and the Turtles (represented here respectively by the American Alligator and the Painted Turtle) are at the root of the birds. The number of structural changes between these species should be relatively low. We expected too to find new genes in the American Alligator and the Painted Turtle with the mapping. I'm planning to use the script and database that I have developed to study some bird species like the Emu (Dromaius novaehollandia).

In the Scott Edwards' lab, I have developped some scripts to asset bioinformatics questions from my co-workers. My scripts are written in Python and some of them can be downloaded on this page.

 

Recent Publications:

In Progress

 

My Script:

Most of the concerns of my co-workers were about PHASE. I have developed some scripts that allows formatting of PHYLIP or NEXUS to a PHASE-friendly format. I have also written a script to translate the output of PHASE in Nexus. My scripts are written in Python and are so multi-plateform

  • Phylip2Phase: read a PHYLIP file (Unix line break) and output a PHASE input file.

Phylip2Phase.py phylip_file outfile

  • Nexus2Phase: read a Nexus file (Unix line break) and output a PHASE input file.

Nexus2Phase.py nexus_file outfile

  • Phase2Nexus: look at the output file of PHASE and report a Nexus file. It is possible to have an optionnal output : the table of the allelles.

Phase2Nexus.py output_from_phase outfile_nexus <optionnal_allelle_table>


 

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