Gina M. Cannarozzi, Ph. D.
Tel: +41 1 311 5805
URL http://www.cannarozzi.com/
American, Swiss, two children.

translational regulation, codon-based models of evolution and statistical analyses, selection on synonymous codons, phylogenetic tree reconstruction, mammalian evolution

Senior Research Associate (Oberassistent) (3/11 - present): group of Zerihun Tadele and Cris Kuhlemeier, Institute of Plant Sciences, University of Bern, Bern Switzerland

• Assembly and annotation of a plant (Eragrostis tef) genome and transcriptome

Senior Research Associate (Oberassistent) (7/00 - 6/10):
group of Professor G. H. Gonnet, Department Informatik, ETH Zurich, Switzerland.

• Advised Masters and bachlors students in their thesis works- specific topics: Framework for simulation and evaluation of algorithmic trading in a distributed environment, Codon Mutation Matrices, Synonymous Codon Mutation Matrices and their use as a Molecular Clock, Use of Codon Mutation Matrices to Detect Periods of Rapid Evolution, Construction of Phylogenetic Trees from Indels in Multiple Sequence Alignments, Codon Usage Bias in Secondary Structure and at Domain Boundaries, Phylogenetic Tree Construction using Genetic Algorithms
  
• Developed libraries for the Darwin software system (Darwin is an interpreted programming language tailored to solving problems in bioinformatics)
  
• Developed algorithms for phylogenetic tree construction
  
• Developed tools for evolutionary analysis (detecting periods of rapid evolution and displaying them on a phylogenetic tree)

Postdoctoral Associate (10/96 - 12/99):
Laboratory of Professor S. A. Benner,
Biochemistry Division, Chemistry Department. University of Florida, Gainesville, Florida.

• Used evolutionary information to predict protein secondary and tertiary structure
  
• Refined heuristics used for protein secondary structure prediction
  
• Developed tools for the automatic evalutation of protein secondary structure prediction
  
• Maintained internet prediction server
  

Consultant (12/95 - 12/99):
PERL programming and system administration for international Internet service provider
Zytek Communications Corporation, Paris, France.
Stephen Melvin, Ph.D.

• Administered system users
  
• Used PERL for programming of internet server analysis tools
  

Postdoctoral Associate (4/95 - 10/96):
Study of Asymmetry in Artificial Membranes with 31P and 2H NMR
Laboratoire de Professeur Philippe Devaux (33 1) 44 27 60 98
Institut de Biologie Physico-Chimique, Paris, France

Graduate Studies: Ph.D. in Chemistry (April 1995):
University of California, San Diego, San Diego, California, USA. April 1995
Thesis: Deuterium NMR Study of the Conformation and Motion of n-Alkanes in Urea Inclusion Compounds by Nuclear Spin Relaxation
Thesis Advisor: Professor Regitze R. Vold in the Department of Chemistry and Biochemistry at the University of California, San Diego.

• Extensively used 2H NMR techniques (relaxation, lineshapes) to study molecular motion in solids and ordered systems
  
• Used solid state 13C and 31P NMR under CP/MAS conditions to measure interatomic distances
  
• Programmed in FORTRAN and C, used UNIX, DOS, Windows and Macintosh
  
• Assisted general, physical and analytical chemistry laboratory and lecture courses
  
• Used molecular dynamics calculation for analysis of alkane motion
  
• Administered UNIX systems
  
• Used and maintained Chemagnetics, Tecmag, and Nicolet, and Bruker Spectrometers
  

M.S. in Chemistry, University of California, San Diego, March 1990

B.S. in Chemistry, University of Central Florida , Orlando, Florida, USA, June 1988
Research Assistant (1/87 - 5/88):
University of Central Florida , Orlando (Professor Seth Elsheimer) Synthesis of isoxazolidines

Computational Biology, Computer Science Department, ETH Zurich, yearly, Fall 2000 - 2009
Bioinformatics II, Computer Science Department, ETH Zurich, yearly, Spring 2005 to 2010
Computational Biology, Computer Science Dept., University of Basel, yearly from 2005-2006
Post-genomic Science, Chemistry Department, University of Florida, 1998
Assisted many General, Physical and Analytical Chemistry lectures and labs, 1990-1995

European Science Foundation Travel Award, February 2010, 1478 Euros SIB Poster award, SIB Days, Montreux, February, 2010 Intelligent Systems in Molecular Biology Highlights talk "A phylogenetic study of human, dog and mouseâ", July 2008 American Society for Engineering Education Postdoctoral Fellowship 1995
National Institute of Health Postdoctoral Fellowship 1995
Outstanding Teaching Award 1993-1994
Dow Chemical Scholarship 1984-1988
Florida Undergraduate Scholarship 1985 - 1988

Gina M. Cannarozzi, Mahmadou Faty, Nicol N. Schraudolph, Alexander Roth, Peter von Rohr, Markus Friberg, Pedro Gonnet, Gaston. H. Gonnet, Yves Barral, A role for codon in translation dynamics, Cell, Volume 141, Issue 2, 355-367, 16 April 2010. link

Adrian Schneider, Gina M. Cannarozzi A Schneider and GM Cannarozzi, Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal, Molecular Biology and Evolution 26(6): 1259-1272, 2009. link

Gina M. Cannarozzi, Adrian Schneider, Gaston. H. Gonnet, (2007) A Phylogenomic Study of Human, Dog, and Mouse. PLoS Comput Biol 3(1): e2 link
This article in the popular press:
Süddeutsche Zeitung, November 28, 2006: Hundsverwandschaft - Saeuger-Stammbaum neu geordnet. pdf
ETH Life, December 22, 2006: Auf den Hund gekommen. ETH Life. link
Mittelland Zeitung, January 11, 2007: Die lieben Verwandten. pdf

Adrian Schneider, Gaston H. Gonnet, Gina M. Cannarozzi, (2007): SynPAM - a Distance Measure Based on Synonymous Codon Substitutions, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(4): 553-560. link

Tal Pupko, Adi Doron-Faigenboim, David A. Liberles and Gina M. Cannarozzi, book chapter in Ancestral Sequence Reconstruction, Oxford University Press, 2007. link

Gina M. Cannarozzi, Adrian Schneider, Gaston. H. Gonnet, Probabilistic Ancestral Sequences Based on the Markovian Model of Evolution- Algorithms and Applications, book chapter in Ancestral Sequence Reconstruction, Oxford University Press, 2007. link

Victor Goetsch, Gaston Gonnet, Gina M. Cannarozzi, Phylogenetic Tree Construction using Gap Information of Multiple Sequence Alignments, in preparation.

Adrian Schneider Gaston Gonnet, Gina M. Cannarozzi, Synonymous Codon Substitution Matrices, V. N. Alexandrov et al. (Eds): ICCS 2006, Part II, LNCS 3992, p630-637, 2006. link

Christophe Dessimoz, Gina M. Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider, and Gaston Gonnet, OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements, A. McLysaght et al. (Eds): RECOMB 2005 Workshop on Comparative Genomics, LNBI 3687, pp. 61-72, 2005. link

Adrian Schneider, Gina M. Cannarozzi, Gaston Gonnet, Empirical codon substitution matrix. BMC Bioinformatics 2005, 6:134 link

Peter von Rohr, Markus Friberg, Gina Cannarozzi, Gaston Gonnet, Dept. Computer Science, February - March Research Focus, 2004

Gina M. Cannarozzi, Michael T. Hallett, Jan Norberg, Xianghong Zhu, A cross-comparison of a large dataset of genes, Bioinformatics, 16 (7): 654-655 JUL 2000.

Dietlind Gerloff, Gina M. Cannarozzi, Marcin Joachimiak, Fred E. Cohen, David Schreiber, and Steven A. Benner, Evolutionary, Mechanistic and Predictive Analyses of the Hydroxymethyldihydropterin Pyrophosphokinase Family of Proteins. Biochemical and Biophysical Research Communications 254, 70-76 (1999).

Dietlind Gerloff, Marcin Joachimiak, Fred E. Cohen, Gina M. Cannarozzi, S. G. Chamberlin and Steven A. Benner, (1998). Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family Biochem. Biophys. Res. Comm. 251, 173-181.

Steven A. Benner, Gina M. Cannarozzi, Marcel Turcotte, Dietlind Gerloff, Gareth Chelvanayagam, Bona Fide Predictions of Protein Secondary Structure using Transparent Analyses of Multiple Sequence Alignments, Chemical Reviews, 97 (8): 2725-2843 DEC 1997.

M. Traikia, D. B. Langlais, Gina M. Cannarozzi, and P. F. Devaux, High resolution spectra of liposomes using MAS NMR: the case of intermediate size vesicles, Journal of Magnetic Resonance Vol. 125, No. 1, p140-144.

Gina M. Cannarozzi, G. H. Meresi R. L. Vold, and R. R. Vold , Conformation and Stability of Alkane/Urea Inclusion Compounds: Evidence from 2H NMR spectroscopy, J. Phys. Chem. 95, 1525 (1991).

ISMB 2007, Highlights Track, A Phylogenomic Study of Human, Dog and Mouse. July, 2008. Toronto, Canada.

SynPAM- a new measure of synonymous change, at the International Symposium on the Evolution of Vertebrates Lund, Sweden 1-3 June, 2006

Empirical Codon mutation matrices and their uses in molecular evolution including ancestral reconstruction, invited talk at "Using Ancestral Sequence Reconstruction to Understand Protein Function", March 30-31 Kristineberg, Sweden.

Two day Darwin Short course at the University of Bergen, Norway, September 2004.

32nd Speedup Workshop and 14th Orap Forum on Life Science Applications September 27, 2002. talk entitled "Darwin: a language for heavy-duty computations in bioinformatics" !!>