Quantifying evolvability in small biological networks (2008)
Mugler, Andrew, Ziv, Etay, Nemenman, Ilya, Wiggins, Chris H.
We introduce a quantitative measure of the capacity of a small biological network to evolve. We apply our measure to a stochastic description of the experimental setup of Guet et al. (Science...
A non-negative expansion for small Jensen-Shannon Divergences (2008)
In this report, we derive a non-negative series expansion for the Jensen-Shannon divergence (JSD) between two probability distributions. This series expansion is shown to be useful for numerical...
Predicting Regional Classification of Levantine Ivory Sculptures: A Machine Learning Approach (2008)
Gansell, Amy Rebecca, Tamaru, Irene K., Jakulin, Aleks, Wiggins, Chris H.
Art historians and archaeologists have long grappled with the regional classification of ancient Near Eastern ivory carvings. Based on the visual similarity of sculptures, individuals within these...
Serially-regulated biological networks fully realize a constrained set of functions (2008)
Mugler, Andrew, Ziv, Etay, Nemenman, Ilya, Wiggins, Chris H.
We show that biological networks with serial regulation (each node regulated by at most one other node) are constrained to {\it direct functionality}, in which the sign of the effect of an...
A Bayesian Approach to Network Modularity (2007)
Hofman, Jake M., Wiggins, Chris H.
We present an efficient, principled, and interpretable technique for inferring module assignments and for identifying the optimal number of modules in a given network. We show how several existing...
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...
Optimal signal processing in small stochastic biochemical networks (2006)
Ziv, Etay, Nemenman, Ilya, Wiggins, Chris H.
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this...
Dynamics of Semiflexible Polymers in a Flow Field (2006)
Munk, Tobias, Hallatschek, Oskar, Wiggins, Chris H., Frey, Erwin
We present a novel method to investigate the dynamics of a single semiflexible polymer, subject to anisotropic friction in a viscous fluid. In contrast to previous approaches, we do not rely on a...
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....
The stochastic spectral dynamics of bending and tumbling (2003)
Wiggins, Chris H., Montesi, Alberto, Pasquali, Matteo
Traditional models of wormlike chains in shear flows at finite temperature approximate the equation of motion via finite difference discretization (bead and rod models). We introduce here a new...
The Viscous Nonlinear Dynamics of Twist and Writhe (1998)
Goldstein, Raymond E., Powers, Thomas R., Wiggins, Chris H.
Exploiting the "natural" frame of space curves, we formulate an intrinsic dynamics of twisted elastic filaments in viscous fluids. A pair of coupled nonlinear equations describing the temporal...
Flexive and Propulsive Dynamics of Elastica at Low Reynolds Numbers (1997)
Wiggins, Chris H., Goldstein, Raymond E.
A stiff one-armed swimmer in glycerine goes nowhere, but if its arm is elastic, exerting a restorative torque proportional to local curvature, the swimmer can go on its way. Considering this happy...
Elastohydrodynamic study of actin filaments using fluorescence microscopy (1997)
Riveline, D., Wiggins, Chris H., Ott, A., Goldstein, Raymond E.
We probed the bending of actin subject to external forcing and viscous drag. Single actin filaments were moved perpendicular to their long axis in an oscillatory way by means of an optically tweezed...
Trapping and Wiggling: Elastohydrodynamics of Driven Microfilaments (1997)
Wiggins, Chris H., Riveline, Daniel X., Ott, Albrecht, Goldstein, Raymond E.
We present a general theoretical analysis of semiflexible filaments subject to viscous drag or point forcing. These are the relevant forces in dynamic experiments designed to measure biopolymer...
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...
Multiple events on single molecules: Unbiased estimation in single-molecule biophysics
Koster, Daniel A., Wiggins, Chris H., Dekker, Nynke H.
Most analyses of single-molecule experiments consist of binning experimental outcomes into a histogram and finding the parameters that optimize the fit of this histogram to a given data model. Here...
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...
Multiple events on single molecules: Unbiased estimation in single-molecule biophysics
Koster, Daniel A., Wiggins, Chris H., Dekker, Nynke H.
Most analyses of single-molecule experiments consist of binning experimental outcomes into a histogram and finding the parameters that optimize the fit of this histogram to a given data model. Here...
A classification-based framework for predicting and analyzing gene regulatory response
Kundaje, Anshul, Middendorf, Manuel, Shah, Mihir, Wiggins, Chris H, Freund, Yoav, Leslie, Christina
Optimal Signal Processing in Small Stochastic Biochemical Networks
Ziv, Etay, Nemenman, Ilya, Wiggins, Chris H.
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we do this...
Nonmuscle Myosin IIA-Dependent Force Inhibits Cell Spreading and Drives F-Actin Flow
Cai, Yunfei, Biais, Nicolas, Giannone, Gregory, Tanase, Monica, Jiang, Guoying, Hofman, Jake M., ...
Nonmuscle myosin IIA (NMM-IIA) is involved in the formation of focal adhesions and neurite retraction. However, the role of NMM-IIA in these functions remains largely unknown. Using RNA interference...
Fast dynamics of supercoiled DNA revealed by single-molecule experiments
Crut, Aurélien, Koster, Daniel A., Seidel, Ralf, Wiggins, Chris H., Dekker, Nynke H.
The dynamics of supercoiled DNA play an important role in various cellular processes such as transcription and replication that involve DNA supercoiling. We present experiments that enhance our...
Dubin-Thaler, Benjamin J., Hofman, Jake M., Cai, Yunfei, Xenias, Harry, Spielman, Ingrid, Shneidman, Anna V., ...
Actin-based cell motility and force generation are central to immune response, tissue development, and cancer metastasis, and understanding actin cytoskeleton regulation is a major goal of cell...