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             Evguenia (Jenya) Kopylova, Ph.D.
             jenya.kopylov AT gmail [dot] com
             Principal Research Scientist, Clarity Genomics
             Gent, Belgium and Greater San Diego Area, U.S.



About Me


I work in the fields of bioinformatics, computational biology and string algorithms. I'm currently at Clarity Genomics, developing algorithms and software for analysis of human microbiome communities.

From 2014-2016, I was a postdoc in Rob Knight's Lab at UCSD. My research focused on the development of algorithms and software for microbial data analysis and their application to microbial community datasets and genomes (see QIIME). Some projects included sequence clustering/cleaning, data analysis for the Earth Microbiome Project and the American Gut Project, genome-wide HGT (horizontal gene transfer) detection and microbiome detection in cancer tissue.

For my Ph.D. (Computer Science, 2010-2013), I was in the Bonsai bioinformatics group at LIFL, France,
under the co-supervision of Hélène Touzet and Laurent NoéThere, my research focused on developing new bioinformatic approaches for the analysis of NGS (metatranscriptomic/metagenomic) data associated with the Tara Oceans Expedition. The ANR project MAPPI was a collaboration between LIFL/Inria Lille-Nord Europe, LIAFA (University Paris-Diderot), IRISA (Rennes) and the Genoscope Laboratory (CEA, Paris).

I completed my Bachelor (Physics/Math, 2005-2009) and Master (Computer Science, 2010) degrees at McMaster University in Canada, written thesis under the supervision of W.F. SmythDuring that time, I worked on algorithms describing the trivial breakdown of repetitions for three neighboring squares.
Search and you will find.

News (job offers)
A position for a PhD grant (36 months) is available in the Bonsai group from University of Lille and Inria (France), starting January 2017 or later.

The Bonsai research group focuses on efficient algorithms and data structures for high-throughput sequencing data. This position is funded by a national collaborative project on Nanopore sequencing, that gathers groups in computational biology and web labs (ANR ASTER). The main objective is to define a general purpose local alignment algorithm that is able to handle long error-prone reads, using advanced techniques such as dimensionality reduction, seed-and-extend methods, alignment-free methods. The post requires a high level of expertise in discrete algorithms and good programming skills (C++).

For more information on the position and the application process, please contact Laurent Noé and Hélène Touzet (laurent.noe@univ-lille1.fr, helene.touzet@univ-lille1.fr).


Software






SortMeRNA: a fast & accurate rRNA filter for
metatranscriptomic reads (Illumina, Ion Torrent, PacBio)



My github page is here.

Theses


Kopylova, E., "New algorithmic and bioinformatic approaches for the analysis of data from high throughput sequencing". Bioinformatics. Université des Sciences et Technologie de Lille - Lille I, 2013. English.



Kopylova E., "Computing Repetitions in Strings: Current Algorithms & the Combinatorics of Future Ones"Open Access Dissertations and Theses, McMaster University (2010)

Publications 

For a list of publications see my profile on Google Scholar.


TALKS


Invited talk (detecting horizontal gene transfer genome-wide), Laboratory of Computational Metagenomics at University of Trento, Trento, Italy, July 2016.

Kopylova E., Noé L., Péricard P., Salson M. and Touzet H. "SortMeRNA 2: ribosomal RNA classification for taxonomic assignation". Workshop on Recent Computational Advances in Metagenomics, ECCB 2014, Sep 2014, Strasbourg, France. (Our work presented by Pierre Péricard).


Other

Languages: English (bilingual), Russian (native), French (fluent), Italian (fluent), Dutch (beginner)

Fa il tuo vero interesse e farai l'interesse di tutti - C.D.
           Tо ли дождик, то ли снег; то ли будет, то ли нет.
C'est le seul oiseau qui soutienne sa cage [l'âme]. Les Misérables. 


Last updated: 10 January 2017

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