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Dmitri Papatsenko

Dr Papatsenko is a biologist with primary interests in developmental and regenerative biology and a background in systems biology/bioinformatics. He holds an MS degree in Biochemistry from Moscow State University (1991) and a PhD from Engelgardt Institute of Molecular Biology, Moscow (1995). He carried out postdoctoral research at Howard Hughes Medical Institute of the Rockefeller University in New York, where he introduced first systems analysis of gene control regions in Drosophila and proposed qualitative models explaining formation of spatial gene expression patterns in early embryo of Drosophila. In 2004, Dr Papatsenko was appointed as an Assistant Researcher at the University of California, Berkeley, in the laboratory of Dr Michael Levine, where he investigated developmental gene networks and proposed an integrated quantitative model for early development of Drosophila embryo. Prior to joining Skoltech, Dr Papatsenko worked at the Icahn School of Medicine at Mount Sinai, New York, as an Assistant Professor. At Mount Sinai Dr Papatsenko worked on reconstruction of gene networks maintaining pluripotency and quantitative modeling of self-renewal in embryonic and hematopoietic stem cells.


              During development and differentiation discrete information encrypted in our genomes turns into body shapes, organs and tissues, giving rise to hundreds of cell types with diverse functions and distinct fates. We are interested in uncovering general principles and molecular mechanisms, which stand behind the development of  human and model organisms.

              Major directions of our research include (i) Reconstruction and quantitative modeling of gene networks involved into stem cell renewal and differentiation. (ii) Investigation of gene expression dynamics during reprogramming and differentiation, analysis of variation of gene expression at a single cell resolution. (iii) Exploration of regulatory DNA code, analysis of structure and  function of promoters and enhancers, involved into development and differentiation.

Current activity – project description

Selected publications:

  1. Pereira, C.F., B. Chang, A. Gomes, J. Bernitz, D. Papatsenko, X. Niu, G. Swiers, E. Azzoni, M.F. de Bruijn, C. Schaniel, I.R. Lemischka, and K.A. Moore, Hematopoietic Reprogramming In Vitro Informs In Vivo Identification of Hemogenic Precursors to Definitive Hematopoietic Stem Cells. Dev Cell, 2016. 36(5): p. 525-39.
  2. Papatsenko, D. and I.R. Lemischka, Emerging Modeling Concepts and Solutions in Stem Cell Research. Curr Top Dev Biol, 2016. 116: p. 709-21.
  3. Waghray, A., N. Saiz, A.D. Jayaprakash, A.G. Freire, D. Papatsenko, C.F. Pereira, D.F. Lee, R. Brosh, B. Chang, H. Darr, J. Gingold, K. Kelley, C. Schaniel, A.K. Hadjantonakis, and I.R. Lemischka, Tbx3 Controls Dppa3 Levels and Exit from Pluripotency toward Mesoderm. Stem Cell Reports, 2015. 5(1): p. 97-110.
  4. Papatsenko, D. and I.R. Lemischka, NetExplore: a web server for modeling small network motifs. Bioinformatics, 2015. 31(11): p. 1860-2.
  5. Papatsenko, D., H. Darr, I.V. Kulakovskiy, A. Waghray, V.J. Makeev, B.D. MacArthur, and I.R. Lemischka, Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal. Stem Cell Reports, 2015. 5(2): p. 207-20.
  6. Liang, R., G. Camprecios, Y. Kou, K. McGrath, R. Nowak, S. Catherman, C.L. Bigarella, P. Rimmele, X. Zhang, M.N. Gnanapragasam, J.J. Bieker, D. Papatsenko, A. Ma’ayan, E. Bresnick, V. Fowler, J. Palis, and S. Ghaffari, A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis. PLoS Genet, 2015. 11(10): p. e1005526.
  7. Lee, D.F., J. Su, H.S. Kim, B. Chang, D. Papatsenko, R. Zhao, Y. Yuan, J. Gingold, W. Xia, H. Darr, R. Mirzayans, M.C. Hung, C. Schaniel, and I.R. Lemischka, Modeling familial cancer with induced pluripotent stem cells. Cell, 2015. 161(2): p. 240-54.
  8. Ding, J., X. Huang, N. Shao, H. Zhou, D.F. Lee, F. Faiola, M. Fidalgo, D. Guallar, A. Saunders, P.V. Shliaha, H. Wang, A. Waghray, D. Papatsenko, C. Sanchez-Priego, D. Li, Y. Yuan, I.R. Lemischka, L. Shen, K. Kelley, H. Deng, X. Shen, and J. Wang, Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming. Cell Stem Cell, 2015. 16(6): p. 653-68.
  9. Zhang, X., G. Camprecios, P. Rimmele, R. Liang, S. Yalcin, S.K. Mungamuri, J. Barminko, V. D’Escamard, M.H. Baron, C. Brugnara, D. Papatsenko, S. Rivella, and S. Ghaffari, FOXO3-mTOR metabolic cooperation in the regulation of erythroid cell maturation and homeostasis. Am J Hematol, 2014. 89(10): p. 954-63.
  10. Qiu, J., D. Papatsenko, X. Niu, C. Schaniel, and K. Moore, Divisional history and hematopoietic stem cell function during homeostasis. Stem Cell Reports, 2014. 2(4): p. 473-90.
  11. Zhang, H., J.L. Nieves, S.T. Fraser, J. Isern, P. Douvaras, D. Papatsenko, S.L. D’Souza, I.R. Lemischka, M.A. Dyer, and M.H. Baron, Expression of Podocalyxin separates the hematopoietic and vascular potentials of mouse ES cell-derived mesoderm. Stem Cells, 2013. 2013(10).
  12. Pereira, C.F., B. Chang, J. Qiu, X. Niu, D. Papatsenko, C.E. Hendry, N.R. Clark, A. Nomura-Kitabayashi, J.C. Kovacic, A. Ma’ayan, C. Schaniel, I.R. Lemischka, and K. Moore, Induction of a hemogenic program in mouse fibroblasts. Cell Stem Cell, 2013. 13(2): p. 205-18.
  13. Papatsenko, D., D. Xu, A. Ma’ayan, and I.R. Lemischka, Quantitative Approaches to Model Pluripotency and Differentiation in Stem Cells, in Stem Cell Handbook, S. Sell, Editor. 2013, Springer Science: new York. p. 59-74.
  14. Papatsenko, D., M. Levine, and Y. Goltsev, Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol, 2011. 9(1): p. e1000584.
  15. Papatsenko, D. and M. Levine, The Drosophila gap gene network is composed of two parallel toggle switches. PLoS One, 2011. 6(7): p. e21145. Epub 2011 Jul 1.


All publications



The following publications were elected by Faculty of 1000:

2015 Familial cancer paper evaluation

2013 Reprogramming paper evaluation

2011 Time warping paper evaluation

2005 Bicoid paper evaluation

2003 Eve stripe 2 Nature paper evaluation

2003 Fly vision paper evaluation

Editorial evaluations of publications and comments:

Comment to 2013 reprogramming paper in Cell Stem Cell

Evaluation of 2011 time warping paper by Nature Review Genetics

Dispatch for 2007 fly gradients modeling paper by Current Biology


Member of International Society for Computational Biology (ISCB).

Reviewer for: Nature Publishing Group journals, Bioinformatics journals, journals on developmental biology, PloS journals, BMC journals, National Science Foundation





Maria Poliakova
Research Scientist
Dmitry Shcherbinin
Research Scientist

SkolTech course: Developmental Biology

            In the past decades the area of developmental biology has exploded with many new findings explaining how unfertilized eggs give rise to complex organisms with diverse spatial complexity. Certain mechanisms and principles driving development of living things became clear at the molecular level. Nowadays, solid theories, supported by experimental findings, explain how gradients of signaling molecules set future body axes and how discrete genome information unfolds into spatial organization of tissues and organs.

            Major goal of the course is to bring the attention of students to the most prominent problems in the area of developmental molecular biology and ignite their interest to this very important field of biological sciences.

            According to the goals, the course combined a series of most studied and most essential examples of model systems and principles, which allow to explain major features of development, such as formation of spatial gene expression patterns, morphogenesis and cell differentiation.


SkolTech course: Stem Cell Biology

            The Stem Cells course includes a spectrum of biological and medical perspectives from fundamental basic biology of stem cells and mechanisms of regeneration through reprogramming of somatic cells and evaluation of pluripotent stem cells for therapeutic purposes.

            The course offers a broad overview in research strategies and state-of-the-art cellular, molecular and genetic approaches for advancing stem cell research. The course covers the following topics: Pluripotency, self-renewal and differentiation. Signal transduction in stem cells and stem cell niches. Embryonic stem cells in model organisms. Hematopoietic and other adult stem cells. Mechanisms of reprogramming and regeneration.

ФИО: Папаценко Дмитрий Александрович

Занимаемая должность: Старший преподаватель

Ученая степень: Кандидат биологических наук,
Институт молекулярной биологии им. В.А. Энгельгардта РАН, 1995

Наименование направления подготовки и/или специальности: Молекулярная биология

Общий стаж работы: 25 лет

Педагогический стаж: 2 лет