Anna Faddieva-Vakhrusheva

Curriculum vitae

Research interest

I would like to improve human life quality, so to make sure we do not contaminate the Earth we inhabit. Therefore I am interested in ecology, especially in soil quality assessment.

My background isin Bioinformatics. Previous years I was involved in studies ofevolution of bacterial genomes by shift of stop-codonsand in development of an evolutionary based approach to identify sequence errors in genomes of RNA viruses. I have had a great deal of experience in scripting programming on Perl with BioPerl modules, working with viral and bacterial genomes alignments, analyzing sequence data, making phylogenetic analysis and statistical data analysis (maximum likelihood estimation, Bayesian statistics).

Nowadays I apply bioinformatics analysis to next-generation sequence data for answering ecological research questions in the context of environmental quality.

Selected publications

Vakhrusheva, A.A., Kazanov, M.D., Mironoy, A.A., Bazykin, G.A. (2011). Evolution of procarvotic genes by shift of stop codons. J. Mol. Evol. 72: 138-146.

Research project

Assembly and annotation of the genomes ofFolsomia candida and Orchesella cincta and comparative genomics of stress defense systems

My PhD project is a part of larger consortium BE-Basic (Bio-based Ecologically Balanced Sustainable Industrial Chemistry) aiming at development, application and validation of genomics-based monitoring tools for soil quality control. In Animal Ecology Department at the Vrije University Amsterdam we develop classifiers based on the Folsomiacandida (F. candida) and Orchesellacincta (O.cincta) gene expression for ecotoxicological testing on specific soil polluters. F. candida was chosen as a model organism for soil quality control and O.cincta as a model organism for studying long term pollution of the soil.

Combination of  Illumina and 454 next-generation sequencing (NGS) technologies will be implemented to obtain complete genome and transcriptome of F.candida and O.cincta.
In this context we collaborate with Leiden Genome Technology Center (Prof. Dr. J. den Dunnen).
During the project we are going to assemble the complete genome and transcriptome of F.candida and O. cincta by using several available assembly platforms (CLC, Velvet, AbySS, SOAPdeNovo). Subsequently, gene annotation and phylogenetic analysis will allow us to further characterize the genome content.

We hypothesize, that occupation of different niches influenced the evolution of stress defence systems. Not only evolution of genes families will be investigated, but also cis-regulatory motives among stress-response gene networks will be analyzed to study plasticity of stress response pathways.

Duration: Four years (November 2011- November 2015) 

Participants: Faddieva (Vakhrusheva) Anna, Dr. Dick Roelofs, Prof. Dr. Nico van Straalen

Partners:

• Bio-based Ecologically Balanced Sustainable Industrial Chemistry  (BE-Basic)
• Leiden Genome Technology Center (LGTC)