Quantification of Cell Movement Reveals Distinct Edge Motility Types During Cell Spreading (2007)
Benjamin J. Dubin-Thaler, Jake M. Hofman, Harry V. Xenias, Ingrid A. Spielman, Anna H. Shneidman, Lawrence David, ...
Actin-based motility is central to cellular processes such as migration, bacterial engulfment, and cancer metastasis, and requires precise spatial and temporal regulation of the cytoskeleton. We...
Margolin, Adam A, Nemenman, Ilya, Basso, Katia, Wiggins, Chris, Stolovitzky, Gustavo, Favera, Riccardo, ...
Abstract Background Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide...
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,...
On The Reconstruction of Interaction Networks with Applications to Transcriptional Regulation (2004)
Margolin, Adam A., Nemenman, Ilya, Wiggins, Chris, Stolovitzky, Gustavo, Califano, Andrea
A novel information-theoretic method for reconstruction of interaction networks is introduced. We prove that the method is exact for some class of networks. Performance tests on large synthetic...
Margolin, Adam A., Nemenman, Ilya, Basso, Katia, Klein, Ulf, Wiggins, Chris, Stolovitzky, Gustavo, ...
Background: Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide ``reverse...
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...
Process Pathway Inference via Time Series Analysis (2002)
Wiggins, Chris, Nemenman, Ilya
Motivated by recent experimental developments in functional genomics, we construct and test a numerical technique for inferring it process pathways, in which one process calls another process, from...
Optical Trapping Interferometry Study of Molecular Motor Kinetics (1996)
Chris Wiggins, Advisor Professor, Steve Block
Using optical trapping interferometry, the position as a function of time of silica beads pulled by the molecular motor kinesin was measured in an in vitro motility assay. Kinesin motility occurs...
Discriminative topological features reveal biological network mechanisms
Middendorf, Manuel, Ziv, Etay, Adams, Carter, Hom, Jen, Koytcheff, Robin, Levovitz, Chaya, ...