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Pathway-Based Genomics Prediction using Generalized Elastic Net. PDF available through Get Fulltext Research

Sokolov, Artem Carlin, Daniel E Paull, Evan O Baertsch, Robert Stuart, Joshua M

Published in PLoS computational biology

We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection. The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions is desired. The method naturally steers sol...

Compact modeling of allosteric multisite proteins: application to a cell size checkpoint. PDF available through Get Fulltext Research

Enciso, Germán Kellogg, Douglas R Vargas, Arturo

Published in PLoS computational biology

We explore a framework to model the dose response of allosteric multisite phosphorylation proteins using a single auxiliary variable. This reduction can closely replicate the steady state behavior of detailed multisite systems such as the Monod-Wyman-Changeux allosteric model or rule-based models. Optimal ultrasensitivity is obtained when the activ...

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