- Motif discovery through predictive modeling of gene regulation.
Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, and
Christina Leslie. Proceedings of RECOMB 2005. [pdf]
- An information-theoretic approach to network modularity.
Etay Ziv, Manuel Middendorf, and Chris Wiggins.
Physical Review E 71, 046117, 2005. q-bio/0411033. [pdf]
- Systematic identification of statistically significant network
measures.
Etay Ziv, Robin Koytcheff, Manuel Middendorf, and Chris Wiggins.
Physical Review E, 71, 2005. cond-mat/0306610. [pdf]
- Combining sequence and time series expression data to learn
transcriptional modules.
Anshul Kundaje, Manuel Middendorf, Chris Wiggins, and Christina Leslie.
IEEE Transactions on Computational Biology and Bioinformatics, 2005. [pdf]
- Inferring network mechanisms: The Drosophila melanogaster
protein interaction network.
Manuel Middendorf, Etay Ziv, and Chris Wiggins.
Proceedings of the National Academy of Sciences 102, 9, pp. 3192, 2004.
q-bio/0408010. [pdf] [pdf
supplement]
- Discriminative topological features reveal biological network
mechanisms.
Manuel Middendorf, Etay Ziv, Carter Adams, Jen Hom, Robin Koytcheff, Chaya
Levovitz, Gregory Woods, Linda Chen, and Chris Wiggins.
BMC Bioinformatics, 5, 2004. q-bio/0402017. [pdf]
- Predicting genetic regulatory response using classification:
Yeast stress response.
Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, and Christina
Leslie.
Proceedings of the First Annual RECOMB Regulation Workshop 2004. q-bio/0406016. [pdf]
- Predicting genetic regulatory response using classification.
Manuel
Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, and Christina Leslie.
Bioinformatics,
20, 2004, Proceedings of the Twelfth International Conference
on Intelligent Systems for Molecular Biology (ISMB 2004). q-bio/0411028.
[pdf]
