Students Advised: Andre R. O. Cavalcanti

Fall 2008:
Lydia dePillis (High School) Modeling the evolution of ciliate’s nuclear dimorphism
Thomas Dixon (’11) Detecting fusion genes in Eukaryotic Genomes.
Amanda Koire (’11) Detecting fusion genes in Eukaryotic Genomes.
Chalotte Chang (’10) Amino Acid Usage in Genomes and the Origin of the Genetic Code.
Allison Dubner (’09) Ciliates as model systems for the study of pathogenic alveolates.
Marie Adachi (’09) Modeling the evolution of ciliate’s nuclear dimorphism.
Hannah Salim (’09) Automatic detecting fusion genes in Eukaryotic Genomes.

Summer 2008:
Marie Adachi (’09) Modeling the evolution of ciliate’s nuclear dimorphism.
Hannah Salim (’09) Automatic detecting fusion genes in Eukaryotic Genomes.
Scott Zimmerman (’09) Mathematical analysis of the two-locus, two-allele problem.

Spring 2008:
Charlotte Chang (’10) Amino Acid Usage in Genomes and the Origin of the Genetic Code.
Marie Adachi (’09) Modeling the evolution of ciliate’s nuclear dimorphism.
Joshua Lippai (’09) Modeling translation incorporating codon bias.

Fall 2007:
Chalotte Chang (’10) Amino Acid Usage in Genomes and the Origin of the Genetic Code.
Hannah Salim (’09) Automatic detecting fusion genes in EST databases.
Marie Adachi (’09) Modeling the evolution of ciliate’s nuclear dimorphism.
Allison Dubner (’09) Amino Acid Usage in Genomes and the Origin of the Genetic Code.
Joshua Lippai (’09) Modeling translation incorporating codon bias.

Summer 2007:
Charlotte Chang (’10) Amino Acid Usage in Genomes and the Origin of the Genetic Code.
Hannah Salim (’09) Codon Usage Bias in Single Gene and Whole Genomes.
Marie Adachi (’09) Analysis of Tandem Stop Codons in Yeast.

Spring 2007:
Marie Adachi (’09) Analysis of Tandem Stop Codons in Yeast.
Christopher Marsh (’09) A New Model for Genetic Code Evolution.
Jessica Lee (’09) Spatial Correlations of Seabird and Prey in Artic Waters.
Hannah Salim (’09) Codon Usage Bias in Single Gene and Whole Genomes.
Derek Young (’09) Development of an Automated System for Comparison of Bird Songs.
Scott Zimmerman (’09) Development of an Automated System for Comparison of Bird Songs.
Michael Lawson (’09) Detection of Fusion Genes in EST Databases.
David Dorsey (’07) Polyphenolic Damage and Repair in Yeast DNA.
Michelle Kaye (’07) Investigating Nested Genes in the Caenorhabditis elegans.
Karen Ring (’07) Consequences of Stop Codon Reassignment in Ciliate Genomes.

Fall 2006:
Marie Adachi (’09) Analysis of Tandem Stop Codons in Yeast.
Christopher Marsh (’09) A New Model for Genetic Code Evolution.
Jessica Lee (’09) Spatial Correlations of Seabird and Prey in Artic Waters.
Michael Lawson (’09) BioinformaticsAnalysis of Proteins Related to the Rab GTPase Cycle.
David Dorsey (’07) Polyphenolic Damage and Repair in Yeast and Mammalian DNA.
Michelle Kaye (’07) Investigating Nested Genes in the Caenorhabditis elegans.
Karen Ring (’07) Consequences of Stop Codon Reassignment in Ciliate Genomes.

Summer 2006:
Allison Dubner (’09) Amino Acid Usage in Genomes and the Origin of the Genetic Code.
Derek Young (’09) Amino Acid Usage in Genomes and the Origin of the Genetic Code.
Jessica Lee (’09) Spatial Correlations of Seabird and Prey in Artic Waters.
Michelle Kaye (’07) Conservation of Intron Location in C. elegans Paralogous Genes.
Alejandra McCord (’07) Computational Screen for Axon Guidance Genes in Drosophila

Spring 2006:
Allison Dubner (’09) Amino Acid Usage in Genomes and the Origin of the Genetic Code.
Michelle Kaye (’07) Conservation of Intron Location in C. elegans Paralogous Genes.
Alejandra McCord (’07) Computational Screen for Axon Guidance Genes in Drosophila.
Amelia Huck (’06) Study of Long Range Expressional Correlation in the Yeast Genome.
Peter Elingboe (’06) Application of Chaos Game Representation to DNA Alignment
Stephen Ou (’06) Polyphenolic Damage and Repair in Yeast and Mammalian DNA

Fall 2005:
Michelle Kaye (’07) Conservation of Intron Location in C. elegans Paralogous Genes.
Alejandra McCord (’07) Computational Screen for Axon Guidance Genes in Drosophila.
Dana Mohamed (’06) Genomic analyses of Stop codon reassignment in two ciliate lineages.
Peter Elingboe (’06) Application of Chaos Game Representation to DNA Alignment
Shiri Azenkot (’05) Multiple Sequence Alignment by Genetic Algorithm.

• Elisa Soares Leite – Universidade Federal de Pernambuco – Dept. of Fundamental Chemistry, Junior Student, 1999 – 2000.
       Paper: Cavalcanti, Leite, Neto, Ferreira (2004).
  
• Kaveri Rajamaran – Princeton University – Dept. of Molecular Biology Summer Program, Junior Student, Mount Holyoke College, 2003.
       Research Project: Evolution of the genetic code.
  
• Lorenzo Orecchia – Princeton University – Dept. of Computer Science – Junior Student, 2003.
       Paper: Cavalcanti, Stover, Orecchia, Doak, Landweber (2004).
  
• Thomas H. Clarke – Princeton University – Dept. of Molecular Biology – Junior/Senior Student (co-supervised Junior Paper and Senior Thesis), 2003– 2004.
       Paper: Cavalcanti, Clarke, Landweber (2004).
  
• Craig McFarland – Princeton University – Dept. of Molecular Biology – Junior Student, 2004.
  Research Project: Study of two-gene chromosomes in Oxytricha trifallax.