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Vlad Cojocaru

Max Planck Institute for Molecular Biomedicine, Muenster, Germany

Institution web page: http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru/index.html
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Born: 1976

Interests: Computational Structural Biology, Stem Cell Biology

Details:
*1995-1999: I obtained a BSc degree in Physics and Chemistry at the West University Timisoara, graduated with a average grade of 9.57 (on a scale from 1.00 to 10.00)

*1999-2000: I started the MSc program at the Faculty of Chemistry, West University Timisoara. During this time I had the pleasure to meet Tudor Oprea who played a great role in the future development of my career.

*2000: I was accepted in the International MSc/PhD Program Molecular Biology - International Max Planck Research School, Goettingen, Germany in June 2000. For details about the program please consult http://www.gpmolbio.uni-goettingen.de/

*2000-2001: I completed the Master in Molecular Biology at the Georg-August Univ. Goettingen, Germany, August 2001 - graduated with a grade of 2.0 (on a scale from 5.0 to 1.0) meaning B=very good. According to this grade and the rules of the program, I was directly accepted for the PhD program without the requirement to write a master thesis.

*2001-2005: I obtained a PhD degree in Molecular Biology at the Georg August University, Geottingen, Germany, graduated in July 2005 with "magna cum laude"(the date of doctoral thesis defense was: 28.06.2005). My PhD work (project started 01.01.2002) has been performed in the Department of Thomas M. Jovin at the Max Planck Institute for Biophysical Chemistry, Goettingen, Germany (www.mpibpc.mpg.de). Two publications as first author (one in "RNA" and one in "Nucliec Acids Research") and other two articles as co-authors (one in "Developmental Biology" and one in "Mechanisms of Development") resulted from my work at the MPI in Goettingen.

*2005-2010: I completed a period of postdoctoral research in the group of Rebecca Wade at EML Research Heidelberg (now named "Heidelberg Institute for Theoretical Studies (HITS) gGmbH) (www.h-its.org) located in the beautiful and historical Villa-Bosch (www.villa-bosch.de) and now in a brand new building. I was awarded a postdoc fellowship by the Klaus Tschira Foundation from 01.10.2005 until 30.09.2008. Two articles (with me first and co-corresponding author) describing my research on the dynamics of cytochromes P450 (enzymes essential for drug metabolism) during my stay at HITS have been now (as of June 2011) accepted for publication in PLoS Computational Biology and Current Drug Metabolism.

*2010-Present: I am a research associate (as of June 2011 project leader) in the Department of Cellular and Developmental Biology at the Max Planck Institute for Molecular Biomedicine in Muenster, Germany, working on applying Computational Structural Biology tools for stem cell research. Recently, I was awarded a DFG grant under the DFG priority program SPP1356 "Pluripotency and Cellular Reprogramming".

** I am proud that 3 journal covers were selected from illustrations I used to present my work (Nucleic Acids Research 2005, Biophysica et Biochimica Acta 2007, PloS Computational Biology 2011)

Selected publications:
• Merino F, Bouvier B, Cojocaru V. Cooperative DNA recognition modulated by an interplay between protein-protein interactions and DNA-mediated allostery. PLoS Computational Biology, in press, 2015.
• Yu X, Cojocaru V, Mustafa G, Salo-Ahen OM, Lepesheva GI, Wade RC. Dynamics of CYP51: implications for function and inhibitor design. . Journal of Molecular Recognition, 28(2), pp. 59-73, 2015.
• Narasimhan K, Pillay S, Huang YH, Jayabal S, Udayasuryan B, Veerapandian V, Kolatkar P, Cojocaru V, Pervushin K, Jauch R. DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors. . Nucleic Acids Research, 43 (3), pp. 1513-1528, 2015.
• Merino F., Ng C. K. L., Veerapandian V., Schöler H. R., Jauch R., Cojocaru V. . Structural basis for the SOX-dependent genomic redistribution of OCT4 in stem cell differentiation. Structure, 22(9), pp. 1274-86, 2014.
• Jerabek S., Merino F., Schöler H. R., Cojocaru V. . OCT4: Dynamic DNA binding pioneers stem cell pluripotency. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1839(3), pp. 138-54, 2014.
• Feldman-Salit A, Hering S, Messiha HL, Veith N, Cojocaru V, Sieg A, Westerhoff HV, Kreikemeyer B, Wade RC, Fiedler T. Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria. Journal of Biological Chemistry, 288(29):21295-306, 2013.
• Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. PLoS Computational Biology , 9(7):e1003159, 2013.
• Daniel Esch, Juha Vahokoski, Matthew R. Groves, Vivian Pogenberg, Vlad Cojocaru, Hermann vom Bruch, Dong Han, Hannes C. A. Drexler, Marcos J. Araúzo-Bravo, Calista K. L. Ng, Ralf Jauch, Matthias Wilmanns and Hans R. Schöler. A unique Oct4 interface is crucial for reprogramming to pluripotency. Nature Cell Biology, 15(3):295-301, 2013.
• Xiaofeng Yu, Vlad Cojocaru, Rebecca C. Wade. Conformational Diversity and Ligand Tunnels of Mammalian Cytochrome P450s. Biotechnology and Applied Biochemistry, 60(1):134-45, 2013.
• Tapia N, Reinhardt P, Duemmler A, Wu G, Araúzo-Bravo MJ, Esch D, Greber B, Cojocaru V, Rascon CA, Tazaki A, Kump K, Voss R, Tanaka EM, Schöler HR. Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteins. . Nature Communications, 3, p. 1279, 2012.
• Cojocaru V., Balali-Mood K., Sansom M. S. P., Wade R. C. . Structure and dynamics of the membrane-bound cytochrome P450 2C9. PLoS Computational Biology, 7(8):e1002152, 2011.
• Cojocaru V., Winn P. J., Wade R. C. . Multiple, ligand-dependent routes from the active site of cytochrome P450 2C9. Current Drug Metabolism, 13(2):143-154, 2011.
• Slanchev K, Stebler J, Goudarzi M, Cojocaru V, Weidinger G, Raz E. Control of Dead end localization and activity--implications for the function of the protein in antagonizing miRNA function. . Mechanism of Development, 126(3-4), pp. 270-7, 2009.
• Vlad Cojocaru, Peter J. Winn, Rebecca C. Wade. The Ins and Outs of Cytochrome P450s. Biochimica et Biophysica Acta, 1770(3), pp. 390-401, 2007.
• Vlad Cojocaru, Reinhard Klement, Thomas M. Jovin. Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif. Nucleic Acids Research, 33, pp. 3435-3446, 2005.
• Vlad Cojocaru, Stephanie Nottrott, Reinhard Klement and Thomas M. Jovin. The snRNP 15. 5K protein folds its cognate K-turn RNA. A combined theoretical and biochemical study. RNA, 11, pp. 197-209, 2005.
• Stebler J, Spieler D, Slanchev K, Molyneaux KA, Richter U, Cojocaru V, Tarabykin V, Wylie C, Kessel M, Raz E. . Primordial germ cell migration in the chick and mouse embryo: the role of the chemokine SDF-1/CXCL12. Developmental Biology, 272, pp. 351-361, 2004.

Theses and dissertations:
• Vlad Cojocaru. Molecular motions at the 5' stem-loop of U4 snRNA: Implications for U4/U6 snRNP assembly. 2005.


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