Publications

1. ReproZip: Computational Reproducibility With Ease Fernando Chirigati (New York University); Remi Rampin (New York University); Dennis Shasha (New York University); Juliana Freire (New York University) ACM Sigmod 2016

2. Conjugate conformal prediction for online binary classification. M. A. Kocak, D. Shasha, and E. Erkip. Conference on Uncertainty in Artificial Intelligence, UAI 2016, July 2016
3. Negative Example Selection for Protein Function Prediction: The NoGO Database Noah Youngs, Duncan Penfold-Brown, Richard Bonneau, Dennis Shasha PLOS Computational Biology, June 12, 2014 DOI: 10.1371/journal.pcbi.1003644 http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003644
4. Gene regulatory networks in plants: learning causality from time and perturbation Gabriel Krouk, Jesse Lingeman, Amy Marshall Colon, Gloria Coruzzi and Dennis Shasha Genome Biology, June 2013
5. Computational reproducibility: state-of-the-art, challenges, and database research opportunities. J. Freire, P. Bonnet, D. Shasha. In Proceedings of ACM SIGMOD 2012, pp. 593-596, 2012.
6. Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate, Gabriel Krouk, Piotr Mirowski, Yann LeCun, Dennis E Shasha and Gloria M Coruzzi Genome Biology 2010, 11:R123 doi:10.1186/gb-2010-11-12-r123 Published: 23 December 2010

Stored Clocked Programs Inside DNA: a simplifying framework for Nanocomputing Jessie Chang and Dennis Shasha, Morgan and Claypool, 2011, 66 pages