Publications (by topic)
Computational Biology (current research)
- Sean Simmons, Cenk Sahinalp, Bonnie Berger. Enabling Privacy-Preserving GWAS in Heterogenous Human Populations. (Presented at RECOMB, accepted for publication to Cell Systems)
Preprint (Warning: very different from final version)
- Sean Simmons, Bonnie Berger. Realizing Privacy Preserving Genome-wide Association Studies. (Bioinformatics)
Paper
- Sean Simmons, Bonnie Berger. One Size Doesn't Fit All: Measuring Individual Privacy in Aggregate Genomic Data. (Presented, IEEE Symposium on Security and Privacy, GenoPri workshop)
PrivMAF Website, Paper
- Sean Simmons, Jian Peng, Jadwiga Bienkowska, Bonnie Berger. Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. (Journal of Computational Biology 2015)
CSUMI Website
- F. Blanchet-Sadri, Sean Simmons. Counting minimal semi-Sturmian words. Discrete Applied Mathematics. 161, 2851-2861 (2013)
- Francine Blanchet-Sadri, Sean Simmons, Amelia Tebbe, Amy Veprauskas. Abelian periods, partial words, and an extension of a theorem of Fine and Wilf. RAIRO - Theoretical Informatics and Applications. 47, (2013)
Website
- F. Blanchet-Sadri, Sean Simmons. Deciding representability of sets of words of equal length. Theoretical Computer Science. 475, 34-46 (2012)
Website
- F. Blanchet-Sadri, Sean Simmons, Dimin Xu. Abelian repetitions in partial words. Advances in Applied Mathematics. 48, 194-214 (2012).
Website
- F. Blanchet-Sadri, Jane I. Kim, Robert Mercas, William Severa, Sean Simmons, Dimin Xu. Avoiding abelian squares in partial words. Journal of Combinatorial Theory Series A. 119, 257-270 (2012)
Website
- Francine Blanchet-Sadri, Robert Mercas, Sean Simmons, Eric Weissenstein. Avoidable binary patterns in partial words.. Acta Inf. 48, 25-41 (2011)
Website
- F. Blanchet-Sadri, B. Blakeley, J. Gunter, S. Simmons and E. Weissenstein. Classifying all avoidable sets of partial words of size two. In C. Martin-Vide (Ed.), Scientific Applications of Language Methods, Ch. 2, Imperial College Press, London, 59-101 (2010)
Website
- Sean Simmons. Algebraic Cryptanalysis of Simplified AES. Cryptologia. 33, 305-314 (2009)
- April 18, 2016. RECOMB 2016. Santa Monica, CA, USA.
- March 15, 2016. Simons Institute. Berkeley, CA, USA.
- February 24, 2016. MIT Bioinformatics Seminar. Cambridge, MA, USA.
- November 19, 2015. Indiana University School of Informatics and Computing Center for Bioinformatics Research Seminar. Bloomington, IN, USA.
- October 20, 2015. Dagstuhl Seminar on Genomic Privacy. Dagstuhl, Germany.
- May 21, 2015. GenoPri workshop (at IEEE S and P). San Jose, CA, USA.
- March 13, 2015. SFU Seminar Talk on Genomic Data Privacy. Burnaby, BC, Canada.