Homepage of Michael Tolstorukov

Michael Y. Tolstorukov

e-mail: [email protected]; [email protected]  –  tel: + 1 (617) 643-6152

Updated: 10 Feb 2013

Professional resume

EDUCATION

1995-1999

Ph.D. in Physics and Mathematics with specialty in Biophysics, 1999

School of Radiophysics, V. Karazin Kharkov National University, Kharkov, Ukraine

Ph.D. Thesis:  “Influence of hydration on dynamical properties of nucleic acids,” Supervisor: Prof. V.Y. Maleev

1998

Workshop on the Structure of Biological Macromolecules, March, 1998

Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy

1990-1995

Combined B.S.&M.S. in Physics of Biological Systems (with honors), 1995

School of Radiophysics, V. Karazin Kharkov National University, Kharkov, Ukraine

M.S. Thesis:  “Study of hysteresis phenomenon in the nucleic acid-water system,” Supervisors: Prof. V.Y. Maleev, Dr. A.I. Gasan, and Dr. S.V. Gatash

B.S. Thesis:  “Influence of hydration on conformational changes in biopolymers,” Supervisor: Dr. A.I. Gasan

AREAS OF PROFESSIONAL INTERESTS AND EXPERTISE

Bioinformatics and computational biology

Genomics and genome biology

 Chromatin structure, nucleosome positioning

 Epigenetic gene regulation, development

 Methodology for analysis of next generation sequencing data

Structural biology

 Protein-DNA interactions

 Nucleic acid structure and conformational dynamics, hydration

 PROFESSIONAL EXPERIENCE AND EMPLOYMENT HISTORY

Department of Molecular Biology, Massachusetts General Hospital
Division of Genetics, DOM, Brigham and Women’s Hospital, Boston, MA, USA

Sept 2012 – present

Titles:

Departmental Fellow / Assistant in Molecular Biology (Department of Molecular Biology, MGH); Associate Geneticist (Brigham and Woman’s Hospital); Instructor in Medicine (Harvard Medical School)

Research:

Leading a computational group that works in the fields of epigenomics and genome biology.

July 2007 – Sept 2012

Department of Medicine, Brigham and Women’s Hospital; Center for Biomedical Informatics, Harvard Med School, Boston, MA, USA (since 2008)

Titles:

Instructor in Medicine (since 09/2011); Postdoctoral Fellow (2007-2011, advisor Dr. P.J. Park)

Research:

Next generation sequencing data analysis: methodology and application to chromatin structure studies, Epigenetic pathways, Nucleosome positioning: genome-wide profiling and prediction, Histone variants, Gene expression analysis, model organism Encode (part of Drosophila Chromosomal Proteins group)

1995 – June 2007

Department of Molecular and Applied Biophysics, V. Karazin Kharkov National University, Kharkov, Ukraine

Titles:

Assistant Professor (1999-2007), Junior Research Scientist (1997-1999)

Research:

Structural genomics: Nucleosome positioning; CpG islands; Comparative analysis of pro- and eukaryotic transcription pathways; Bacterial chromosome packaging; Bioinformatic analysis and modeling protein-DNA interaction; Conformational transitions in DNA.

Teaching:

Lecturing for undergraduate and graduate students: Undergraduate course: Structure and function of biopolymers. Graduate course: Numerical Analysis of Biological Macromolecules with Computer Practicum.  Supervision of student projects.

March 2000 – 2005

Laboratory of Experimental and Computational Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD

Titles:

Post-doctoral Visiting Fellow

Research:

Sequence-dependence of the DNA structure and gene regulation in pro- and eukaryotic genomes; DNA packing in bacterial nucleoid; Bioinformatic analysis of DNA sequence-dependent deformability in the protein-DNA complexes; Sequence-dependence of B/A transition in DNA.

 COMPUTATIONAL EXPERTISE

Scientific programming in R, FORTRAN (extensive experience); C/C++, Perl (some experience)

Linux/Windows environment

Bioinformatics resources and web services for sequence and structure analysis: GEO, ClustalW, TRANSFAC, USCS Genome browser, PDB/NDB, EASE

Molecular modeling in NAMD, VMD; Chimera

 GRANTS, AWARDS, ACHIEVEMENTS

2000 – 2005

Postdoctoral Visiting Fellow Award, NIH Visiting Program

1999

Travel Fellowship to attend XIII Biophysical Congress in New Delhi under IUPAB / UNESCO / ICSU Programme

1998

Grant from ICTP, Italy to attend the Workshop on “Structure of biological macromolecules”

1997

CRDF Travel Grant #97093 to attend the International Conference ANDM’97

1996 -1997

Post-graduate Soros Student Fellowship, IRF (Switzerland-Ukraine)

1995 -1998

Full Merit Post-graduate Scholarship, School of Radio Physics, Kharkov National University

1994

1st prize in the Young Scientist Paper Contest, School of Radio Physics, Kharkov National University

1990 -1995

Full Merit Scholarship, School of Radio Physics, Kharkov National University

 PROFESSIONAL SERVICE

·         Secretary of the School Scientific Council, School of Radiophysics, V. Karazin Kharkov National University, 1999-2000

·         Local Organizing Committee Member, II Ukrainian Biophysical Society Congress, Kharkov, Ukraine, 1999

·         Local Organizing Committee Member, International Conference on Mathematical Methods in the Electromagnetic Theory, Kharkov, Ukraine, 1998

·         Paper reviewing for scientific journals (Biopolymers; Bioinformatics; Proteins: Structure, Function, and Bioinformatics; FEBS Letters)

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