Dina Sokol
Associate Professor
Computer and Information Science
Location: 3209d Ingersoll Hall
Phone: 718.951.5000 x2065
Fax: 718.951.4842
Email:
Dina Sokol's Web site
Dina Sokol's doctoral research was supported by a grant from the Israel Ministry of Trade and Industry. Her postdoc at Bar-Ilan University was funded by the Israel Science Foundation. She spent six months as a researcher at AT&T Shannon Laboratory. Sokol has published papers in both theoretical computer science venues, such as Theoretical Computer Science and ACM Transactions on Algorithms, as well as in bioinformatics journals, such as Bioinformatics and Journal of Computational Biology. Sokol is currently developing TRED - a software tool and database for tandem repeats in DNA sequences, supported by a grant from the National Science Foundation.
Education:
Ph.D., Bar Ilan University (Israel) - 2003 (Computer Science)
M.Sc., Polytechnic University - 1998 (Computer Science)
M.A., Brooklyn College - 1996 (Computer and Information Science)
B.S., Thomas Edison State College - 1995 (Computer Science)
Areas of Expertise:
Design and analysis of string algorithms. Specific areas of interest include: matching in compressed inputs, parameterized matching, two-dimensional pattern matching, and detecting repetitive sequences in strings.
Books and Publications
Liang, Y., D. Sokol, S. Zelikovitz and S.I. Levitan. "Classification of Tandem Repeats in the Human Genome." Accepted to International Journal of Knowledge Discovery in Bioinformatics. (Books and Publications: Forthcoming Publications) 2013
Marcus, S. and D. Sokol. "2d Dynamic Succinct Dictionary Matching." Submitted to IWOCA 2013. (Books and Publications: Peer Reviewed Article) 2013
Marcus, S. and D. Sokol. "2D Lyndon Words and Applications." arXiv preprint arXiv:1301.0103. (Books and Publications: Other Article) 2013
Marcus, S. and D. Sokol. "Dynamic 2D Dictionary Matching in Small Space." arXiv preprint
arXiv:1302.0072. (Books and Publications: Other Article) 2013
Marcus, S. and D. Sokol. "Engineering Small Space Dictionary Matching." arXiv preprint arXiv:1301.6428. (Books and Publications: Other Article) 2013
Marcus, S. and D. Sokol. "Engineering Small Space Dictionary Matching." Submitted to Symposium on Experimental Algorithms, SEA 2013. (Books and Publications: Peer Reviewed Article) 2013
Marcus, S. and D. Sokol. "On 2D Lyndon Words." Submitted to Workshop on Algorithms and Data Structures, WADS 2013. (Books and Publications: Peer Reviewed Article) 2013
Liang, Y., D. Sokol and S. Zelikovitz. "Clustering Tandem Repeats via Trinucleotides." Proceedings of IEEE International Conference on Data Mining, Workshop on Biological Data Mining. IEEE Computer Society. 64-71. (Books and Publications: Peer Reviewed Article) 2012
Neuburger, S. and D. Sokol. "Succinct 2D Dictionary Matching." Algorithmica, February. DOI: 10.1007/s00453-012-9615-9. (Books and Publications: Peer Reviewed Article) 2012
Sokol, D. and J. Tojeira. "Speeding Up the Detection of Tandem Repeats Over the Edit Distance.: Submitted to Theoretical Computer Science. (Books and Publications: Peer Reviewed Article) 2012
Sokol, D. and F. Atagun. "TRedD: A Database for Tandem Repeats Over the Edit Distance." Database (2010); 2010: article ID baq003, 10.1093/database/baq003. (Books and Publications: Peer Reviewed Article) 2010
Sokol, Dina, Frederick Adkins, Zhongyuan Che and Kristin Pfabe. "Finding Repeats Within Strings." DIMACS Educational Module Series, 09-2. Available at http://dimacs.rutgers.edu/Publications/Modules/Module09-2/dimacs09-2.pdf. (Books and Publications: Peer Reviewed Article) 2009
Kucherov, Gregory and Dina Sokol. "Approximate Tandem Repeats." Encyclopedia of Algorithms. Springer. (Books and Publications: Chapter) 2008
Amir, A., G.M. Landau, M. Lewenstein and D. Sokol. "Dynamic Text and Static Pattern Matching." ACM Transactions on Algorithms 3.2. (Books and Publications: Peer Reviewed Article) 2007
Harel, C., M. Lewenstein and D. Sokol. "Approximate Parameterized Matching." ACM Transactions on Algorithms 3.3. (Books and Publications: Peer Reviewed Article) 2007
Sokol, D., G. Benson and J. Tojeira. "Tandem Repeats Over the Edit Distance." Bioinformatics 23.2: e30-35. (Books and Publications: Peer Reviewed Article) 2007
Amir, A., G.M. Landau and D. Sokol. "Inplace 2D Matching in Compressed Images." Journal of Algorithms 49.2: 240-61. (Books and Publications: Peer Reviewed Article) 2003
Amir, A., G.M. Landau and D. Sokol. "Inplace Run-length 2-dimensional Compressed Search." Theoretical Computer Science 290.3: 1361-83. (Books and Publications: Peer Reviewed Article) 2003
Landau, G.M., J.P. Schmidt and D. Sokol. "An Algorithm for Approximate Tandem Repeats." Journal of Computational Biology 8.1: 1-18. (Books and Publications: Peer Reviewed Article) 2001
Creative Work
Marcus, Shoshana and Dina Sokol. Software for Small Space Dictionary Matching. Available open source at http://www.sci.brooklyn.cuny.edu/~sokol/dictmatch.html. 2013
Software and Website Development: TRedD - Tandem Repeats over the edit Distance Database. Developed open source software for locating tandem repeats, TRed, and a database of tandem repeats in the human genome, TRedD, available at: http://tandem.sci.brooklyn.cuny.edu. 2009
TandemGraph: Designed, developed and maintain software for graphically depicting the tandem repeats that occur in a chromosome. 2009
Software and Website Development: Smith-Waterman Repeat Finder. Developed a Java program for finding general repeats within a sequence based on the Smith-Waterman algorithm for local sequence alignment. Developed an online interface for running the program. 2008
Awards, Honors and Fellowships
PSC-CUNY Research Award Program 43, for "Small-space Dictionary Matching Software." $3,496. (Grants and Fellowships) 2013
"Issues in Combinatorial Pattern Matching - Approximate Cycles and Repeats," submitted to BSF US-Israel Binational Science Foundation. Requested amount: $198,605. (Grants and Fellowships) 2012
"Speeding Up Tandem Repeat Detection," submitted to PSC-CUNY 44 Research Award Program TRADB-44-88. (Grants and Fellowships) 2012
NSF Computer and Communication Foundations, Program Algorithmic Foundations, submitted for "Dictionary Matching in Small Space." Requested amount: $396,334. (Grants and Fellowships) 2010
NSF Division of Biological Infrastructure, Program Advances in Biological Informatics, submitted for "Clustering and Visualizing Tandem Repeats." Requested amount: $378,759. (Grants and Fellowships) 2010
PSC-CUNY Research Award Program 41, Award # 63343-00 41, for "Small Space Dictionary Matching." $2,860. (Grants and Fellowships) 2010
PSC-CUNY Research Award # 62280-00 40, for "TandemGraph: A Graphical Tool for Modeling String Regularities." $4,298. (Grants and Fellowships) 2009
PSC-CUNY 38 Research Award Program, #69273-0038, for "TRED: A GUI Interface for Finding Tandem Repeats Over the Edit Distance." D. Sokol, S. Singh and S. Zelikovitz, co-recipients. $4,090. (Grants and Fellowships) 2008
CRA-W Computing Research Association Distributed Mentors Program. D. Sokol and N. Gurwitz, co-recipients. $8,500; July 1-Aug. 30. (Grants and Fellowships) 2006
NSF Division of Biological Infrastructure, Biological Databases and Informatics Program, for "Approximate Tandem Repeats Database, DBI-0542751." $321,308; Sept. 1, 2006-Aug. 31, 2009. (Grants and Fellowships) 2006
PSC-CUNY 37 Research Award Program, #68799-0037, for "Approximate Tandem Repeats." $3,175; Aug. 1, 2006-July 30, 2007. (Grants and Fellowships) 2006
PSC-CUNY 36 Research Award Program, #67217-0036, for "Approximate Tandem Repeats." $3,612.26; Aug. 1, 2005-July 30, 2006. (Grants and Fellowships) 2005
Israel Science Foundation Fellowship, 2002-03. (Grants and Fellowships) 2002
KITE Grant of the Israel Ministry of Trade and Industry, 2000-01. (Grants and Fellowships) 2000
National Science Foundation Fellowship, Polytechnic University, 1997-98. (Grants and Fellowships) 1997
Jack Wolfe Fellowship, Brooklyn College. (Grants and Fellowships) 1996
Research Activities
Undergraduate research: Mentored Ari Mermelstein in developing a parallel program to run on a massively parallel architecture for TRed -- finding repeats within biological sequences. 2013
Ph.D. student Shoshana Neuburger graduated. Thesis title: "Small Space 2-dimensional Dictionary Matching." 2012
Undergraduate research: Mentored an undergraduate student, P. Krauss. Developed an online interface with flexible parameter setting for the TRed program. 2012
Undergraduate research: Mentored S.I. Levitan in fall 2012. Project resulted in a classification method for the tandem repeats in the human genome based upon the trinucleotide frequencies in each repeat. 2012
Mentored a master's student in developing software for suffix tree construction. Developed software in Java for constructing a suffix tree and a generalized suffix tree for dictionary matching based on Ukkonen's algorithm. 2010
Conferences, Seminars and Symposiums
"Small Space Dictionary Matching." Research at CUNY. CUNY Graduate Center. New York. (Conferences, Seminars and Symposiums: Invited Talk) 2011
Neuburger, S. and D. Sokol. "Succinct 2D Dictionary Matching With No Slowdown." Proceedings of the Algorithms and Data Structures Symposium (WADS 2011, New York). LNCS. (Conferences, Seminars and Symposiums: Conference Presentation) 2011
Neuburger, S. and D. Sokol. "Small-space 2D Dictionary Matching." Combinatorial Pattern Matching Proceedings, 21st Annual Symposium, CPM 2010, New York. Lecture Notes in Computer Science 6129. Springer. 27-39. (Conferences, Seminars and Symposiums: Conference Presentation) 2010
"TRedD: A Database for Tandem Repeats Over the Edit Distance." Computer Science Departmental Colloquium. CUNY Graduate Center. New York, October. (Conferences, Seminars and Symposiums: Invited Talk) 2009
Sokol, D. and R. Rakhamimov. "TandemGraph: A Graphical Tool for Modeling String Regularities." Proceedings of BIOCOMP '09: International Conference on Bioinformatics & Computational Biology, Las Vegas. 536-40. (Conferences, Seminars and Symposiums: Conference Presentation) 2009
"TRED: Tandem Repeats Over the Edit Distance." The SCORE Retreat of Brooklyn College. New York Academy of Sciences. January. (Conferences, Seminars and Symposiums: Contributed Talk) 2007
Sokol, D., G. Benson and J. Tojeira. "Tandem Repeats Over the Edit Distance." European Conference of Computational Biology. January. (Conferences, Seminars and Symposiums: Conference Presentation) 2007
"Tandem Repeats Over the Edit Distance." Third Annual International Stringology Research Workshop. University of Haifa, Israel, May. (Conferences, Seminars and Symposiums: Invited Talk) 2006
Sokol, D. and J. Tojeira. "Filtering Tandem Repeats in DNA Sequences." Proceedings of BIOCOMP '06: International Conference on Bioinformatics & Computational Biology, Las Vegas.: 161-67. (Conferences, Seminars and Symposiums: Conference Presentation) 2006
Harel, C., M. Lewenstein and D. Sokol. "Approximate Parameterized Matching." Proceedings of the 12th Annual European Symposium on Algorithms: Lecture Notes in Computer Science 3221: 414-25. (Conferences, Seminars and Symposiums: Conference Presentation) 2004
Amir, A., G.M. Landau and D. Sokol. "2-D Matching in Compressed Images." Proceedings of the 14th Annual ACM-SIAM Symposium on Discrete Algorithms: 853-62. (Conferences, Seminars and Symposiums: Conference Presentation) 2003
Amir, A., G.M. Landau, M. Lewenstein and D. Sokol. "Dynamic Text and Static Pattern Matching." Proceedings of the 8th International Workshop on Algorithms and Data Structures (WADS): Lecture Notes in Computer Science 2748. Springer-Verlag. 340-64. (Conferences, Seminars and Symposiums: Conference Presentation) 2003
Amir, A., G.M. Landau and D. Sokol. "Inplace Run-length 2-dimensional Compressed Search." Proceedings of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms: 817-18. (Conferences, Seminars and Symposiums: Conference Presentation) 2000
Professional Leadership
Faculty adviser to WICS (Women in Computer Science) student club. (Professional Leadership: Organizational Leadership Position) 2013
Chair, Undergraduate Curriculum Committee. (Professional Leadership: Committee Service) 2011
Member, Program Committee for SPIRE'11 - 18th Annual Symposium on String Processing and Information Retrieval. (Professional Leadership: Organizational Leadership Position) 2011
Composed a set of syllabi for most of the courses offered by the Computer and Information Science Department at Brooklyn College. (Professional Leadership: Committee Service) 2010
Member, Program Committee, Conference on Combinatorial Pattern Matching - CPM 2010. (Professional Leadership: Organizational Leadership Position) 2010
Member, review committee for Brooklyn College undergraduate research course CISC 5000. (Professional Leadership: Committee Service) 2010
Session chairwoman, CPM 2010 -- 21st Annual Symposium on Combinatorial Pattern Matching. (Professional Leadership: Organizational Leadership Position) 2010
Member, Program Committee for SPIRE'08, Symposium on String Processing and Information Retrieval. (Professional Leadership: Organizational Leadership Position) 2008
