Ekaterina E. Khrameeva
Engineer Researcher

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Scientific interests:

• alternative splicing regulation by secondary structures
• chromatin organization and its functional implications
• high-throughput sequencing data analysis
• trans-splicing
• genomic rearrangements

Education:

2009 – present time: Moscow State University, Faculty of Bioengineering and Bioinformatics, postgraduate student
2004 – 2009: Moscow State University, Faculty of Bioengineering and Bioinformatics, graduated cumlaudae

Research experience:

2011.11 – present time: Partner Institute for Computational Biology (Shanghai, China)
• P. Khaitovich's research group
• Scholarship
• Novel snoRNAs in primate brains
• Neanderthal CNVs and gene flow (joint work with Michael Lachmann)
• Perl and R programming
2012.03 – 2012.04: Justus Liebig University (Giessen, Germany)
• A. Bindereif's research group
• Scholarship
• RNA-protein binding and splicing regulation (CLIP technology)
• Perl and R programming
2011.01 – 2011.04: Helmholtz Zentrum Munchen (Munich, Germany)
• Institute for Bioinformatics
• Scholarship
• RNA secondary structure modeling
• Java programming
2007.09 – present time: Institute for Information Transmission Problems of the Russian Academy of Sciences
• Bioinformatics Research and Training Center
• Junior researcher
• Computational analysis of RNA secondary structures
• JAVA, PERL programming
2007.06 – 2007.07: Leiden University Medical Center (Leiden, Netherlands)
• enter for Human and Clinical Genetics
• Internship
• integrated analysis of gene expression and genome copy number data
• R programming

Awards & Grants:

• Chinese Academy of Sciences, 2011-2012. Fellowship for young international scientists.
• Dynasty Foundation, 2010-2011 (Dmitry Zimin's Russian Charitable Foundation). Young scientist fellowship (molecular and cellular biology).
• Severin Prize, 2008. Winner, the first prize.
• International Competition of Scientific Papers in Nanotechnology for Young Researchers «Rusnanotech '08». Winner, the second prize.
• XV International Conference “Lomonosov-2008”. Prize for the best report.

Publications:

Khrameeva EE, Bozek K, He L, Yan Z, Jiang X, Wei Y, Tang K, Gelfand MS, Prufer K, Kelso J, Paabo S, Giavalisco P, Lachmann M, Khaitovich P. Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nature Communications, 2014 Apr 1. PubMed PDF

Rossbach O, Hung LH, Khrameeva E, Schreiner S, Konig J, Curk T, Zupan B, Ule J, Gelfand MS, Bindereif A. Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. RNA Biology, 2014 Feb 7. PubMed PDF

Khrameeva E.E., Gelfand M.S. Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. BMC Bioinformatics 2012 13 Suppl 6:S4. doi: 10.1186/1471-2105-13-S6-S4. PubMed  PDF

Khrameeva E.E., Mironov A.A., Fedonin G.G., Khaitovich P., Gelfand M.S. Spatial proximity and similarity of the epigenetic state of genome domains. PLoS One 2012 7(4): e33947. PubMed  PDF

Pervouchine D.D., Khrameeva E.E., Pichugina M.Y., Nikolaienko O.V., Gelfand M.S., Rubtsov P.M., Mironov A.A. Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. Rna 2012 18(1): 1-15. PubMed  PDF

Khrameeva E.E., Drutsa V.L., Vrzheshch E.P., Dmitrienko D.V., Vrzheshch P.V. Mutants of monomeric red fluorescent protein mRFP1 at residue 66: structure modeling by molecular dynamics and search for correlations with spectral properties. Biochemistry (Mosc) 2008 73(10): 1085-1095. PubMed  PDF


Conferences:

The 8th Winter Symposium on Chemometrcs “Modern Methods on Data Analysis”. Drakino, Russia, 27.02-02.03.2012
• E.E.Khrameeva, G.G.Fedonin, M.S.Gelfand. The impact of interchromosomal associations on the functional state of the human genome (talk)

RECOMB-Seq 2012 Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. E.E. Khrameeva, M.S. Gelfand

Cold Spring Harbor Asia (CSHA '11) Spatial proximity and similarity of the epigenetic state of genome domains E.E. Khrameeva, A.A. Mironov, P. Khaitovich, and M.S. Gelfand

Information Technologies and Systems (ITaS '11) Comparison of 117 mRNA and genome sequencing experiments between laboratories and platforms E.E. Khrameeva, M.S. Gelfand

Moscow Conference on Computational Molecular Biology (MCCMB 2011) Interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments E.E. Khrameeva, M.S. Gelfand

Albany 2011: The 17th Conversation The Impact of Interchromosomal Associations on the Functional State of the Human Genome J. Biomol. Struct. Dynam. 2011, 28: 112. (talk) E.E. Khrameeva, A.A. Mironov, M.S. Gelfand

24th International Mammalian Genome Conference Association between spatial proximity and functional similarity in human genome E.E. Khrameeva, A.A. Mironov, M.S. Gelfand

Information Technologies and Systems (ITaS '10) Functional similarity and chimeric transcripts in spatially close genome domains. E.E. Khrameeva, A.A. Mironov, M.S. Gelfand

18th annual international conference on Intelligent Systems for Molecular Biology (ISMB2010) Spatial proximity and similarity of functional states of genome domains. E.E. Khrameeva, A.A. Mironov, Ph. Khaitovich, and M.S. Gelfand

Bioinformatics after Next Generation Sequencing, Zvenigorod 2010 Long range correlations in the genome and chromatin E.E. Khrameeva, A.A. Mironov, M.S. Gelfand

XVII International Conference “Lomonosov-2010” Long-range interactions in eukaryotic chromatin and their possible imprint on function and evolution E.E. Khrameeva

Information Technologies and Systems (ITaS '09) Transcription of chromosomal translocations in the human genome E.E. Khrameeva, P.V. Mazin

Moscow Conference on Computational Molecular Biology (MCCMB'09) Regulation of splicing by small non-coding RNAs E.E. Khrameeva, A.A. Mironov, M.S. Gelfand, D.D. Pervouchine

First International Competition of Scientific Papers in Nanotechnology for Young Researchers «Rusnanotech '08» Regulation of splicing by conserved RNA structures E.E. Khrameeva

Information Technologies and Systems (ITaS '08) Secondary structures in Drosophila introns E.E. Khrameeva, A.A. Mironov, M.S. Gelfand, D.D. Pervushin

XV International Conference “Lomonosov-2008” Secondary structures in Drosophila introns E.E. Khrameeva, A.A. Mironov, M.S. Gelfand, D.D. Pervushin

Moscow Conference on Computational Molecular Biology (MCCMB'07) Molecular Modeling of mRFP1 mutant structures and correlations with their properties Ekaterina E. Khrameeva

XIV International Conference “Lomonosov-2007” Molecular modeling of mRFP1 mutant structures and correlations with their properties E.E. Khrameeva