Ekaterina Khrameeva

Professor: Philipp Khaitovich

Ekaterina graduated from the Department of Bioengineering and Bioinformatics, Moscow State University, in 2009. She completed her postgraduate project at the Institute for Information Transmission Problems, Russian Academy of Sciences, and defended her thesis titled “Distant interactions in eukaryotic genomes and regulation of alternative splicing” in 2015.

During her postgraduate studies, Ekaterina worked as a bioinformatician at the Justus Liebig University (Giessen), the Helmholtz Zentrum München (Munich), the Partner Institute for Computational Biology (Shanghai), and the Leiden University Medical Center (Netherlands). Ekaterina won several competitions and research grants, and published 23 papers.

Identification of biological features associated with human development and lifespan using high-throughput data analysis.

In this project, we measure gene expression, metabolite levels and genotypes in samples of human brain, as well as in other tissues and species (for comparison) using various high-throughput methods, such as DNA sequencing, RNA-seq, and mass-spectrometry. We analyze these data to study:

– molecular markers of cognitive disorders;

– human brain metabolome;

– evolution of brain metabolome, compared to other tissues;

– functions of human-specific proteins via analysis of humanized mice metabolome.

Luzhin AV, Flyamer IM, Khrameeva EE, Ulianov SV, Razin SV, Gavrilov AA. Quantitative differences in TAD border strength underly the TAD hierarchy in Drosophila chromosomes. J Cell Biochem. 2019; 120(3):4494-4503.

Khrameeva E, Kurochkin I, Bozek K, Giavalisco P, Khaitovich P. Lipidome evolution in mammalian tissues. Mol Biol Evol. 2018; 35(8):1947-1957.

Akkuratov EE, Gelfand MS, Khrameeva EE. Neanderthal and Denisovan ancestry in Papuans: A functional study. J Bioinform Comput Biol. 2018; 16(2):1840011.

Triska P, Chekanov N, Stepanov V, Khusnutdinova EK, Kumar GPA, Akhmetova V, Babalyan K, Boulygina E, Kharkov V, Gubina M, Khidiyatova I, Khitrinskaya I, Khrameeva EE, Khusainova R, Konovalova N, Litvinov S, Marusin A, Mazur AM, Puzyrev V, Ivanoshchuk D, Spiridonova M, Teslyuk A, Tsygankova S, Triska M, Trofimova N, Vajda E, Balanovsky O, Baranova A, Skryabin K, Tatarinova TV, Prokhortchouk E. Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe. BMC Genet. 2017;18(Suppl 1):110.

Ulianov SV, Galitsyna AA, Flyamer IM, Golov AK, Khrameeva EE, Imakaev MV, Abdennur NA, Gelfand MS, Gavrilov AA, Razin SV. Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure. Epigenetics&Chromatin. 2017; 10(1):35.

Bozek K, Khrameeva EE, Reznick J, Omerbašić D, Bennett NC, Lewin GR, Azpurua J, Gorbunova V, Seluanov A, Regnard P, Wanert F, Marchal J, Pifferi F, Aujard F, Liu Z, Shi P, Pääbo S, Schroeder F, Willmitzer L, Giavalisco P, Khaitovich P. Lipidome determinants of maximal lifespan in mammals. Sci Rep. 2017; 7(1):5.

Gavrilov AA, Shevelyov YY, Ulianov SV, Khrameeva EE, Kos P, Chertovich A, Razin SV. Unraveling the mechanisms of chromatin fibril packaging. Nucleus. 2016; 7(3):319-24.

Khrameeva EE, Fudenberg G, Gelfand MS, Mirny LA. History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. J Bioinform Comput Biol. 2016; 1641002.

Zhang B, Han D, Korostelev Y, Yan Z, Shao N, Khrameeva E, Velichkovsky BM, Chen YP, Gelfand MS, Khaitovich P. Changes in snoRNA and snRNA abundance in the human, chimpanzee, macaque and mouse brain. Genome Biol Evol. 2016; evw038.

Flegontov P, Changmai P, Zidkova A, Logacheva MD, Altınışık NE, Flegontova O, Gelfand MS, Gerasimov ES, Khrameeva EE, Konovalova OP, Neretina T, Nikolsky YV, Starostin G, Stepanova VV, Travinsky IV, Tříska M, Tříska P, Tatarinova TV. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Sci Rep. 2016; 6:20768.

Ulianov SV*, Khrameeva EE*, Gavrilov AA, Flyamer IM, Kos P, Mikhaleva EA, Penin AA, Logacheva MD, Imakaev MV, Chertovich A, Gelfand MS, Shevelyov YY, Razin SV. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Genome Res. 2016; 26(1):70-84.

Torkova A, Koroleva O, Khrameeva E, Fedorova T, Tsentalovich M. Structure-Functional Study of Tyrosine and Methionine Dipeptides: An Approach to Antioxidant Activity Prediction. Int J Mol Sci. 2015; 16(10):25353-76.

Kaufmann S, Fuchs C, Gonik M, Khrameeva EE, Mironov AA, Frishman D. Inter-chromosomal contact networks provide insights into Mammalian chromatin organization. PLoS One. 2015; 10(5):e0126125.

Zhenilo S, Khrameeva E, Tsygankova S, Zhigalova N, Mazur A, Prokhortchouk E. Individual genome sequencing identified a novel enhancer element in exon 7 of the CSFR1 gene by shift of expressed allele ratios. Gene. 2015; 566(2):223-8.

Yang J, Hung LH, Licht T, Kostin S, Looso M, Khrameeva E, Bindereif A, Schneider A, Braun T. RBM24 is a major regulator of muscle-specific alternative splicing. Dev Cell. 2014; 31(1):87-99.

Koroleva O, Torkova A, Nikolaev I, Khrameeva E, Fedorova T, Tsentalovich M, Amarowicz R. Evaluation of the antiradical properties of phenolic acids. Int J Mol Sci. 2014; 15(9):16351-80.

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. Nat Commun. 2014; 5:3584.

Rossbach O, Hung LH, Khrameeva E, Schreiner S, König J, Curk T, Zupan B, Ule J, Gelfand MS, Bindereif A. Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. RNA Biol. 2014; 11(2):146-55.

Rösel-Hillgärtner TD, Hung LH, Khrameeva E, Le Querrec P, Gelfand MS, Bindereif A. A novel intra-U1 snRNP cross-regulation mechanism: alternative splicing switch links U1C and U1-70K expression. PLoS Genet. 2013; 9(10):e1003856.

Khrameeva EE, Gelfand MS. Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. BMC Bioinformatics. 2012; 13 Suppl 6:S4.

Khrameeva EE, Mironov AA, Fedonin GG, Khaitovich P, Gelfand MS. Spatial proximity and similarity of the epigenetic state of genome domains. PLoS One. 2012; 7(4):e33947.

Pervouchine DD, Khrameeva EE, Pichugina MY, Nikolaienko OV, Gelfand MS, Rubtsov PM, Mironov AA. Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. RNA. 2012; 18(1):1-15.

Khrameeva EE, Drutsa VL, Vrzheshch EP, Dmitrienko DV, Vrzheshch PV. 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):1085-95.

2015: Institute for Information Transmission Problems

Candidate of biological sciences degree

2009 – 2012: Moscow State University

Faculty of Bioengineering and Bioinformatics

PhD student

Thesis “Distant interactions in eukaryotic genomes and regulation of splicing”

Supervisors Prof. Andrey Mironov, Prof. Mikhail Gelfand

2004 – 2009:  Moscow State University

Faculty of Bioengineering and Bioinformatics

Specialist degree, graduated cumlaudae

Thesis “Search for RNA secondary structures participating in regulation of splicing”

Supervisors Dr. Dmitry Pervouchine, Prof. Mikhail Gelfand

  • Evolution and molecular biology
  • Neanderthal ancestry in modern humans
  • Chromatin 3D structure
  • Regulation of alternative splicing
  • RNA secondary structure

Systems Biology Fellowship Program, 2016-2019.

Winner, for the project ‘Molecular signatures of normal and aberrant development, aging and longevity in human brain’.

Academia Europaea, 2014.

Prize for Young Russian Scientists.

Russian Foundation for Basic Research, 2012-2013.

Grant for young scientists.

Natural Science Foundation of China, 2012-2013.

The Research Fellowship for International Young Scientists.

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).

International Competition of Scientific Papers in Nanotechnology for Young Researchers «Rusnanotech ’08».

Winner, the second prize.

Severin Prize, 2008.

Winner, the first prize.

XV International Conference “Lomonosov-2008”.

Prize for the best report.