Short Bio

I am currently a PostDoc in the SchatzLab at Cold Spring Harbor Laboratory. We are developing new models and recommendations for genome sequencing by simulating the sequencing and assembly of several dozen model genomes using current and emerging third generation sequencing technologies to map out how well we can expect those genomes to assemble. We are also developing and deploying new methods for assessing repeat content and assembly quality of genomes. We are also enhancing the Iplant Discovery Environment with additional state of the art assembly algorithms.

I completed my PhD at the Graduate Center of CUNY, under the guidance of Professor Dina Sokol. My thesis research focused on pattern matching algorithms. Specifically, we developed new techniques for 2D dictionary matching in small-space. During my graduate studies, I taught in the CIS department of Brooklyn College.

My CV can be found here.

My old home page at Brooklyn College was primarily intended for my students. It includes my graduate work as well.

Selected Publications:

  • S. Marcus and D. Sokol. Engineering Small Space Dictionary Matching. CorR abs/1301.6428, 2013.

  • S. Marcus and D. Sokol. Dynamic 2D Dictionary Matching in Small Space. CoRR abs/1302.0072, 2013.

  • S. Marcus and D. Sokol. 2D Lyndon Words and Applications. CoRR abs/1301.0103, 2013.

  • S. Marcus and D. Sokol. On 2D Lyndon Words. accepted to String Processing and Information Retrieval Symposium (SPIRE), 2013.

  • S. Neuburger and D. Sokol. Succinct 2D Dictionary Matching. Algorithmica, 65(3): 662-684, DOI: 10.1007/s00453-012-9615-9, March 2013.
    [URL to article]

  • S. Neuburger and D. Sokol. Succinct 2D Dictionary Matching With No Slowdown. Proceedings of the 12th Algorithms and Data Structures Symposium (WADS), 2011.
    [paper] [slides] The original publication is available at

  • S. Neuburger and D. Sokol. Small-space 2D Compressed Dictionary Matching. Proceedings of the 21st Annual Symposium on Combinatorial Pattern Matching (CPM), 2010.
    [paper] [slides] The original publication is available at

  • Doctoral Dissertation: 2D Dictionary Matching in Small-Space
    [thesis] [slides]

Shoshana Marcus, Ph.D.
Cold Spring Harbor Laboratory
One Bungtown Road
Koch Building 1121
Cold Spring Harbor, NY 11724

E-mail: smarcus <at>
Phone: (516) 367-8393