Manuel Middendorf

Inferring network mechanisms: the Drosophila melanogaster protein interaction network.

E. Ziv, C. Wiggins, M. Middendorf, 2004, Proceedings of the National Academy of Sciences of the United States of America.

A classification-based framework for predicting and analyzing gene regulatory response

Yoav Freund, Chris Wiggins, Anshul Kundaje, 2006, BMC Bioinformatics.

Information-theoretic approach to network modularity.

E. Ziv, C. Wiggins, M. Middendorf, 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

Predicting genetic regulatory response using classification

Yoav Freund, Chris Wiggins, Anshul Kundaje, 2004, ISMB/ECCB.

Discriminative topological features reveal biological network mechanisms

E. Ziv, C. Wiggins, C. Levovitz, 2004, BMC Bioinformatics.

Systematic identification of statistically significant network measures.

Manuel Middendorf, Etay Ziv, Robin Koytcheff, 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

Discriminative topological features reveal biological network mechanisms

Manuel Middendorf, Etay Ziv, Carter Adams, 2004, BMC Bioinformatics.

Combining sequence and time series expression data to learn transcriptional modules

Anshul Kundaje, Feng Gao, Manuel Middendorf, 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Motif Discovery Through Predictive Modeling of Gene Regulation

Yoav Freund, Chris Wiggins, Anshul Kundaje, 2005, RECOMB.

Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response

Yoav Freund, Chris Wiggins, Anshul Kundaje, 2004, Regulatory Genomics.