Bibliography on CarthaGène and mapping with CarthaGène

Papers using CarthaGène for actual mapping are invited to cite the following paper:

• CARTHAGENE: multipopulation integrated genetic and radiated hybrid mapping
  S. de Givry, M. Bouchez, P. Chabrier, D. Milan, et T. Schiex.
  Bioinformatics, 21(8): 1703-1704 (2005).

Other papers on CarthaGène:

• A. Prasad , T. Schiex , S. McKay , B. Murdoch , Z. Wang , J.E Womack , P. Stothard and S.S Moore.
  High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly.
  
  BMC Genomics, 2007, 8:310 doi:10.1186/1471-2164-8-310.
• Marques E, de Givry S, Stothard P, Murdoch B, Wang Z, Womack J, Moore SS.
  A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly.
  
  BMC Genomics 2007, 8:254 (26 July 2007)
• T. Faraut, S. de Givry, P. Chabrier, T. Derrien, F. Galibert, C. Hitte and T. Schiex.
  A comparative genome approach to marker ordering.
  Proc. ECCB'2006 (Eilat, Israel).
• Thomas Schiex, Patrick Chabrier, Martin Bouchez and Denis Milan
  Boosting EM for Radiation Hybrid and Genetic Mapping
  In the proceedings of WABI'2001 (First Workshop on Algorithms in Bioinformatics), LNCS 2149. Aug. 2001.
• T. Schiex and C. Gaspin.
  Cartagene: Constructing and joining maximum likelihood genetic maps.
  In Proc. of ISMB'97, Halkidiki, Greece, June 1997.
• T. Schiex and C. Gaspin.
  Genetic algorithms for genetic mapping.
  In Proc. of EA'97, Nïmes, France, 1997.
• T. Schiex, C. Gaspin, V. Laurent, and B. Mangin.
  Constructing and joining maximum likelihood genetic maps.
  In Proc. of EUCARPIA'97, Poznan, Poland, 1997.
• V. Laurent, E. Wajnberg, B. Mangin, T. Schiex, C. Gaspin, and F. Vanlerberghe-Masutti.
  A composite genetic map of the parasitoid wasp trichogramma brassicae based on rapd markers.
  Genetics, 150, Sep 1998.
• P. Chabrier, C. Gaspin, and T. Schiex.
  Demonstration of carthagene, a genetic/radiated hybric mapping software.
  Plant & Animal Genome VIII Conference, San Diego, CA, Computer Demonstration, C11, jan 2000.
• P. Chabrier, C. Gaspin, and T. Schiex.
  Carthagene: A maximum likelihood multiple population genetic/radiated hybrid mapping software.
  Plant & Animal Genome VIII Conference, San Diego, CA, Poster, P19, jan 2000.
• Integration of Genetic and Radiation Hybrid Maps of the Pig : the Second Generation IMpRH Maps.
  Denis Milan , Thomas Schiex , Martine Yerle , Anette Rink , Craig Beattie , Rachel Hawken , Larry Schook , Hiroshi Yasue , Merete Fredholm , Gary Rohrer
  Plant, Animal & Microbe Genomes X Conference, January 12-16, 2002. San Diego, CA
• O. Demeure, C. Renard, M. Yerle, T. Faraut, J. Riquet, A. Robic, T. Schiex, A. Rink, D. Milan.
  Rearranged gene order between pig and human in A QTL region on SSC 7.
  Mammalian Genome, 2003.
  

References to web sites, papers and mapping projects that relied on CarthaGène. Please contact us if you have links to insert here.

• INRA-University of Minnesota porcine Radiation Hybrid (IMpRH) panel
• A Microsatellite-Based Linkage Map of the Honeybee, Apis mellifera L.
• Integrating linkage and radiation hybrid mapping data for bovine chromosome 15
• A radiation hybrid map of chicken chromosome 4
• A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes
• A radiation hybrid map of chicken chromosome 15
• Radiation hybrid mapping of three skeletal muscle genes (CKM, ECH1 and TNNT1) to porcine chromosome 6
• The First Comprehensive Genetic Linkage Map of a Marsupial: The Tammar Wallaby (Macropus eugenii)
• Assignment1 of monoglyceride lipase (MGLL) gene to bovine chromosome 22q24 by in situ hybridization and confirmation by radiation hybrid mapping
• Computers programs for RH mapping
• Construction of a dense comparative map between human chromosome 1p36p35 and swine chromosome 6 by using human sequence-tagged sites
• Integration of genetic and radiation hybrid maps of the Pig : the second generation IMpRH maps.
• A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1
• Radiation Hybrid Mapping project - IMpRH7000rad
• Rearranged gene order between pig and human in a QTL region on SSC 7
• Linkage software
• Mappaggio fisico del genoma bovino con un pannello di ibridi di radiazione
• Bases genetiques de l'apyrenie chez la baie de raisin
• A Composite Genetic Map of the Parasitoid Wasp Trichogramma brassicae Based on RAPD Markers

References to software tools used inside CarthaGène:

• Keld Helsgaun Lin-Kernighan implementation used in the multiple two-points ordering strategies of CarthaGène (The code is distributed for research use. The author reserves all rights to the code and you must contact him if you want to use this code for other purposes).

Last modified: Wed Dec 19 15:45:30 CET 2007