Gina Cannarozzi

Last Name

Cannarozzi

First Name

Gina

ORCID

0000-0002-0704-663X

Organisational unit

02021 - Inf.zentrum Chemie Biologie Pharmazie

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Publications 1 - 10 of 15

Measuring codon usage bias
Roth, Alexander; Anisimova, Maria; Cannarozzi, Gina (2012)
Codon evolution : mechanisms and models
OMA, a comprehensive, automated project for the identification of orthologs from complete genome data
Dessimoz, Christophe; Cannarozzi, Gina; Gil, Manuel; et al. (2005)
Comparative genomics : proceedings / RECOMB 2005 International Workshop, RCG 2005, Dublin, Ireland, September 18-20-2005
Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences
Pupko, Tal; Doron-Faigenboim, Adi; Liberles, David A.; et al. (2007)
Ancestral sequence reconstruction
SynPAM - A Distance Measure Based on Synonymous Codon Substitutions
Schneider, Adrian; Gonnet, Gaston H.; Cannarozzi, Gina (2007)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Empirical codon substitution matrix
Schneider, Adrian; Cannarozzi, Gina; Gonnet, Gaston (2005)
BMC Bioinformatics
Background Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution. Results A set of 17,502 alignments of orthologous sequences from five vertebrate genomes yielded 8.3 million aligned codons from which the number of substitutions between codons were counted. From this data, both a probability matrix and a matrix of similarity scores were computed. They are 64 × 64 matrices describing the substitutions between all codons. Substitutions from sense codons to stop codons are not considered, resulting in block diagonal matrices consisting of 61 × 61 entries for the sense codons and 3 × 3 entries for the stop codons. Conclusion The amount of genomic data currently available allowed for the construction of an empirical codon substitution matrix. However, more sequence data is still needed to construct matrices from different subsets of DNA, specific to kingdoms, evolutionary distance or different amount of synonymous change. Codon mutation matrices have advantages for alignments up to medium evolutionary distances and for usages that require DNA such as ancestral reconstruction of DNA sequences and the calculation of Ka/Ks ratios.
Technology generation to dissemination: lessons learned from the tef improvement project
Cannarozzi, Gina; Chanyalew, Solomon; Assefa, Kebebew; et al. (2018)
Euphytica
Indigenous crops also known as orphan crops are key contributors to food security, which is becoming increasingly vulnerable with the current trend of population growth and climate change. They have the major advantage that they fit well into the general socio-economic and ecological context of developing world agriculture. However, most indigenous crops did not benefit from the Green Revolution, which dramatically increased the yield of major crops such as wheat and rice. Here, we describe the Tef Improvement Project, which employs both conventional- and molecular-breeding techniques to improve tef—an orphan crop important to the food security in the Horn of Africa, a region of the world with recurring devastating famines. We have established an efficient pipeline to bring improved tef lines from the laboratory to the farmers of Ethiopia. Of critical importance to the long-term success of this project is the cooperation among participants in Ethiopia and Switzerland, including donors, policy makers, research institutions, and farmers. Together, European and African scientists have developed a pipeline using breeding and genomic tools to improve the orphan crop tef and bring new cultivars to the farmers in Ethiopia. We highlight a new variety, Tesfa, developed in this pipeline and possessing a novel and desirable combination of traits. Tesfa’s recent approval for release illustrates the success of the project and marks a milestone as it is the first variety (of many in the pipeline) to be released.
Synonymous Codon Substitution Matrices
Schneider, Adrian; Gonnet, Gaston H.; Cannarozzi, Gina (2006)
Lecture Notes in Computer Science ~ Computational science - ICCS 2006 : 6th international conference, Reading, UK, May 28 - 31, 2006; proceedings
Probabilistic ancestral sequences based on the Markovian model of evolution
Cannarozzi, Gina; Schneider, Adrian; Gonnet, Gaston H. (2007)
Ancestral sequence reconstruction
Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal
Schneider, Adrian; Cannarozzi, Gina (2009)
Molecular Biology and Evolution
The role of omics in improving the orphan crop tef
Gonzales, Lorena Y. Ramírez; Cannarozzi, Gina; Jäggi, Lea; et al. (2024)
Trends in Genetics
Tef or teff [Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef's diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research.

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Gina Cannarozzi

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