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Maxim Shatsky, Ph.D.

Contact address: 461 Koshland Hall, University of California, Berkeley, CA 94720-3102

PROFESSIONAL EXPERIENCE:

2006 – present UC Berkeley and Lawrence Berkeley National Lab:

Postdoctoral researcher

I have been involved in several diverse projects with most of my work related to 3D object reconstruction from extremely noisy 2D images produced by single-particle cryo-electron microscopy (cryo-EM).

• Developed a novel algorithm to enable an accurate registration/alignment of images produced from heterogeneous cryo-EM data. Implementation is in C++.

• Developed a novel state-of-the-art methodology for the multi-model reconstruction from heterogeneous cryo-EM data. The first general approach to solve the multi-model reconstruction problem. Implementation is in Matlab, Perl and EM software packages.

• Prioritization of bacterial genes for protein-protein interaction analysis.

• Phylogenetic analysis of GroEL protein family.

• Contributed to the development of a new alignment-free protein structure comparison approach based on Writhe decomposition.

1998 – 2006 Tel-Aviv University: Ph.D./M.Sc. researcher

I worked on various topics in structural bioinformatics which mainly involved application of geometrical approaches to solve biological problems. My work resulted in new theoretical results and several novel algorithms that set new benchmarks in the field. All algorithm implementations were done in C++ on Linux.

• Developed the following methods:

o Alignment of flexible protein structures.

o Alignment of multiple protein structures.

o Structure-based multiple sequence alignment.

o Finding a common geometrical pattern between protein binding sites.

• Proved several complexity results related to the common point set problem.

• Contributed to the development of a method for fitting multiple structures into cryo-EM density maps of intermediate resolution.

• Contributed to the GAMB++ library (a C++ library on Unix for structural bioinformatics).

1998 – 1999 Art-In Internet Technologies & Electronic Commerce Ltd:

Software Engineer (full time)

• Developed processing and billing of web application usage. Development in Java and an Oracle DB.

• Designed and implemented a module to enable secure user verification during billing transactions.

• Web server design using JSP and HTML.

TEACHING EXPERIENCE:

2001-2005 Teaching Assistant in Tel-Aviv University.

Classes: TA in Structural Bioinformatics,

Computer science workshop on structural bioinformatics,

Bioinformatics Laboratory.

EDUCATION:

2001-2006 Ph.D. in Computer Science, Tel-Aviv University

Thesis: The Common Point Set Problem with Applications to

Protein Structure Analysis

Supervisors: Prof. Haim Wolfson and Prof. Ruth Nussinov.

1998-2001 M.Sc. in Computer Science, magna cum laude, Tel-Aviv University.

Thesis: Alignment of flexible protein structures.

Supervisors: Prof. Haim Wolfson and Prof. Ruth Nussinov.

1995-1998 B.Sc. in Computer Science and Mathematics, Tel-Aviv University.

INTERSHIPS AND SUMMER SCHOOLS:

2000 CIME "Mathematical Methods for Protein Structure Analysis and Design"

summer school, Martina Franca, Italy.

1998 Internship at Weizmann Institute of Science, department of Particle Physics.

Project subject: Applying artificial Neural Networks in high energy physics.

AWARDS AND SCHOLARSHIPS:

2006 The Jorge Deutsch Prize for excellence in PhD studies.

2003-2006 Complexity Science Center PhD scholarship.

2005 Award for excellence in Ph.D. studies.

2005 Best Structural Poster award at RECOMB 2005.

2003 Wolf scholarship for excellence in PhD studies.

2000 Award for excellence in M.Sc. studies.

TALKS AT CONFERENCES AND WORKSHOPS:

2007 3rd Workshop on Single Particle Reconstruction and Visualization, Houston, TX

2005 9th Annual International Conference on Research in Computational Molecular

Biology (RECOMB 2005) Cambridge, MA

2005 The 1st International Symposium on Computational Life Science, Konstanz, Germany (CompLife '05)

2005 Fourth Workshop on Geometric Computing, Nachsholim, Israel

2003 Weizmann Institute of Science, Bioinformatics Workshop Series 2002-2003

2002 2nd Workshop on Algorithms in Bioinformatics, Rome, Italy (WABI'02)

2001 Annual Israeli Bioinformatics Symposium, Tel Aviv Univ. (AIBS'01)

2000 8th International Conference on Intelligent Systems for Molecular Biology,

San Diego, CA (ISMB'00)

REFEREEING:

Journal of the Association for Computing Machinery, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Computers & Operations Research, Proteins: Structure, Function, and Bioinformatics, Nucleic Acids Research, BMC Bioinformatics, ECCB, WABI, RECOMB.

PUBLICATIONS:

• D. Zhi, M. Shatsky, SE Brenner. 2010. Alignment-free local structural search by writhe decomposition. Bioinformatics. in press.

• M. Shatsky, R.J. Hall, E. Nogales, J. Malik, S.E. Brenner. Automated Multi-model Reconstruction from Single-Particle Electron Microscopy Data. J Struct Bio. 170:98-108, 2010.

• B.G. Han, M. Dong, H. Liu, L. Camp, J. Geller, M. Singer, T.C. Hazen, M. Choi, H.E. Witkowska, D.A. Ball, D. Typke, K.H. Downing, M. Shatsky, S.E. Brenner, J.M. Chandonia, M.D. Biggin, R.M. Glaeser. Survey of large protein complexes in D. vulgaris reveals great structural diversity. PNAS. 106:16580-16585, 2009.

• M. Shatsky, R.J. Hall, S.E. Brenner, and R.M. Glaeser. A method for the alignment of heterogeneous macromolecules from electron microscopy. J Struct Bio. 166:67-78, 2009.

• A. Shulman-Peleg, M.Shatsky, R.Nussinov and H.J.Wolfson. Prediction of Interacting Single-Stranded RNA Bases by Protein-Binding Patterns. Journal of Molecular Biology, 379(2):299-316, 2008.

• A. Shulman-Peleg, M.Shatsky, R.Nussinov and H.J.Wolfson. Spatial chemical conservation of hot spot interactions in protein-protein complexes, BMC Biology, 5(1):43, 2007.

• D. Zhi, M. Shatsky, S. Brenner. Alignment-Free Local Structural Search by Writhe Decomposition. (abstract) Workshop on Algorithms in Bioinformatics, Springer Verlag, Lecture Notes in Computer Science, 2007.

• K. Lasker, O. Dror, M.Shatsky, R.Nussinov, H.Wolfson. EMatch: Discovery of High Resolution Structural Homologues of Protein Domains In Intermediate Resolution Cryo-EM. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(1):28-39, 2007.

• M. Shatsky, A. Shulman-Peleg, R. Nussinov, H. Wolfson. The Multiple Common Point Set Problem and its Application to Molecule Binding Pattern Detection. Journal of Computational Biology, 13(2):407-28, 2006.

• M. Shatsky, R. Nussinov, and H.J. Wolfson. Optimization of Multiple Sequence Alignment Based on Multiple Structure Alignment. Proteins: Structure, Function, and Bioinformatics, 62(1):209-17, 2006.

• A. Shulman-Peleg, M. Shatsky, R. Nussinov, H. Wolfson. MAPPIS: Multiple 3D Alignment of Protein-Protein Interfaces. M.R. Berthold et al. (Eds.): CompLife 2005, Lecture Notes in Computer Science, Volume 3695, pp. 91-103, 2005.

• M. Shatsky, A. Shulman-Peleg, R. Nussinov, H. Wolfson. Recognition of Binding Patterns Common to a Set of Protein Structures. RECOMB 2005, Lecture Notes in Computer Science, Springer, vol. 3500, pp. 440-455, 2005.

• M. Shatsky, R. Nussinov, H. Wolfson. A Method for Simultaneous Alignment of Multiple Protein Structures. Proteins: Structure, Function, and Genetics, 56(1), 143-156, 2004.

• M. Shatsky, R. Nussinov, H. Wolfson. FlexProt: Alignment of Flexible Protein Structures Without a Pre-definition of Hinge Regions. Journal of Computational Biology, 11(1), 83-106, 2004.

• D. Schneidman-Duhovny, Y. Inbar, V. Polak, M. Shatsky, I. Halperin, H. Benyamini, A. Barzilay, O. Shem-Tov, N. Haspel, R. Nussinov, H. J. Wolfson. Taking Geometry to its Edge: Fast Unbound Rigid (and Hinge-bent) Docking. Proteins: Structure, Function, and Genetics, 52(1), 107-112, 2003.

• M. Shatsky, H.J. Wolfson, R.Nussinov. MultiProt - a Multiple Protein Structural Alignment Algorithm. Workshop on Algorithms in Bioinformatics, Springer Verlag, Lecture Notes in Computer Science 2452: 235-250, 2002.

• M. Shatsky, R. Nussinov, H. Wolfson. Flexible protein alignment and hinge detection. Proteins: Structure, Function, and Genetics,48:242-256, 2002.

• B. Ma, M. Shatsky, H.J. Wolfson, R.Nussinov. Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations. Protein Science, 11, 184-197, 2002.

• M. Shatsky, Z. Fligelman, R. Nussinov, H.J. Wolfson. Alignment of Flexible Protein Structures. Proc. 8th International Conference on Intelligent Systems for Molecular Biology (ISMB'00), 329-343, The AAAI press, 2000.

Book Chapters and Reviews:

• M. Shatsky, R. Nussinov, and H.J. Wolfson. Algorithms for Multiple Protein Structure Alignment and Structure-Derived Multiple Sequence Alignment. Protein Structure Prediction Series: Methods in Molecular Biology , Vol. 413. Zaki, Mohammed; Bystroff, Chris (Eds.), 2nd ed., 2007. Springer, Humana Press.

• H. Wolfson, M. Shatsky, D. Duhovny, O. Dror, A. Shulman, B.Ma, R. Nussinov. From structure to function: methods and applications. Curr Protein Pept Sci., 6(2):171-83, 2005.

Software/Web-servers:

• Shulman-Peleg, M.Shatsky, R.Nussinov and H.J.Wolfson. MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Research. 36(Web Server issue):W260-4, 2008.

• M. Shatsky, O. Dror, D. Duhovny, A. Shulman, R. Nussinov, H. Wolfson. BioInfo3D: A Suite of Tools for Structural Bioinformatics. Nucleic Acid Research 32, 503-507, 2004.

References are available upon request.

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