Learning and inference in computational systems biology

Online version:

Introduction / Neil D. Lawrence

Reverse engineering of gene regulatory networks / Johannes Jaeger and Nicholas A.M. Monk

Framework for comparative assessment of parameter estimation and inference methods in systems biology / Pedro Mendes

Estimation of parametric nonlinear ODEs for biological networks identification / Florence d'Alché-Buc, Nicholas Brunel

A brief introduction to Bayesian inference / Neil D. Lawrence, Magnus Rattray

Inferring transcriptional networks using prior biological knowledge and constrained state-space models / John Angus [and others]

Mixtures of factor analyzers for modeling transcriptional regulation / Kuang Lin, and Dirk Husmeier

System identification and model ranking: the Bayesian perspective / Mark Girolami, Ben Calderhead and Vladislav Vyshemirsky

Gaussian processes for missing species in biochemical systems / Neil D. Lawrence [and others]

Markov chain Monte Carlo algorithms for SDE parameter estimation / Darren J. Wilkinson and Andrew Golightly

Approximate inference for stochastic reaction processes / Andreas Ruttor, Guido Sanguinetti, and Manfred Opper

Toward the inference of stochastic biochemical network and parameterized grammar models / Guy Yosiphon and Eric Mjolsness