Motif Discovery through Predictive Modeling of Gene Regulation (2007)
Middendorf, Manuel, Kundaje, Anshul, Shah, Mihir, Freund, Yoav, Wiggins, Chris H., Leslie, Christina
We present MEDUSA, an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data. We use a modern large-margin...
A classification-based framework for predicting and analyzing gene regulatory response (2006)
Kundaje, Anshul, Middendorf, Manuel, Shah, Mihir, Wiggins, Chris H, Freund, Yoav, Leslie, Christina
Abstract Background We have recently introduced a predictive framework for studying gene transcriptional regulation in simpler organisms using a novel supervised learning algorithm called GeneClass....
Discriminative topological features reveal biological network mechanisms (2004)
Middendorf, Manuel, Ziv, Etay, Adams, Carter, Hom, Jen, Koytcheff, Robin, Levovitz, Chaya, ...
Abstract Background Recent genomic and bioinformatic advances have motivated the development of numerous network models intending to describe graphs of biological, technological, and sociological...
An Information-Theoretic Approach to Network Modularity (2004)
Ziv, Etay, Middendorf, Manuel, Wiggins, Chris
Exploiting recent developments in information theory, we propose, illustrate, and validate a principled information-theoretic algorithm for module discovery and resulting measure of network...
Predicting Genetic Regulatory Response Using Classification (2004)
Middendorf, Manuel, Kundaje, Anshul, Wiggins, Chris, Freund, Yoav, Leslie, Christina
We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae,...
Inferring Network Mechanisms: The Drosophila melanogaster Protein Interaction Network (2004)
Middendorf, Manuel, Ziv, Etay, Wiggins, Chris
Naturally occurring networks exhibit quantitative features revealing underlying growth mechanisms. Numerous network mechanisms have recently been proposed to reproduce specific properties such as...
Predicting Genetic Regulatory Response using Classification: Yeast Stress Response (2004)
Middendorf, Manuel, Kundaje, Anshul, Wiggins, Chris, Freund, Yoav, Leslie, Christina
We present a novel classification-based algorithm called GeneClass for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as...
Discriminative Topological Features Reveal Biological Network Mechanisms (2004)
Middendorf, Manuel, Ziv, Etay, Adams, Carter, Hom, Jen, Koytcheff, Robin, Levovitz, Chaya, ...
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The...
Systematic identification of statistically significant network measures (2003)
Ziv, Etay, Koytcheff, Robin, Middendorf, Manuel, Wiggins, Chris
We present a novel graph embedding space (i.e., a set of measures on graphs) for performing statistical analyses of networks. Key improvements over existing approaches include discovery of...
Discriminative topological features reveal biological network mechanisms
Middendorf, Manuel, Ziv, Etay, Adams, Carter, Hom, Jen, Koytcheff, Robin, Levovitz, Chaya, ...
Inferring network mechanisms: The Drosophila melanogaster protein interaction network
Middendorf, Manuel, Ziv, Etay, Wiggins, Chris H.
Naturally occurring networks exhibit quantitative features revealing underlying growth mechanisms. Numerous network mechanisms have recently been proposed to reproduce specific properties such as...
Discriminative topological features reveal biological network mechanisms
Middendorf, Manuel, Ziv, Etay, Adams, Carter, Hom, Jen, Koytcheff, Robin, Levovitz, Chaya, ...
Inferring network mechanisms: The Drosophila melanogaster protein interaction network
Middendorf, Manuel, Ziv, Etay, Wiggins, Chris H.
Naturally occurring networks exhibit quantitative features revealing underlying growth mechanisms. Numerous network mechanisms have recently been proposed to reproduce specific properties such as...