Bayesian sigmoid shrinkage with improper variance priors and an application to wavelet denoising. - Cajo J. F. ter Braak (Comput. Stat. Data Anal., 2006)

A Markov Chain Monte Carlo version of the genetic algorithm Differential Evolution: easy Bayesian computing for real parameter spaces. - Cajo J. F. ter Braak (Stat. Comput., 2006)

The Use of Multiple Hierarchically Independent Gene Ontology Terms in Gene Function Prediction and Genome Annotation. - Yiannis Kourmpetis; Ate van der Burgt; Marco C. A. M. Bink; Cajo J. F. ter Braak; Roeland C. H. J. van Ham (Silico Biol., 2007)

Predicting sub-Golgi localization of type II membrane proteins. - Aalt D. J. van Dijk; D. Bosch; Cajo J. F. ter Braak; A. R. van der Krol; Roeland C. H. J. van Ham (Bioinform., 2008)

Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control. - Aalt D. J. van Dijk; Cajo J. F. ter Braak; Richard G. H. Immink; Gerco C. Angenent; Roeland C. H. J. van Ham (Bioinform., 2008)

Bootstrap confidence intervals for principal response curves. - Marieke E. Timmerman; Cajo J. F. ter Braak (Comput. Stat. Data Anal., 2008)

Differential Evolution Markov Chain with snooker updater and fewer chains. - Cajo J. F. ter Braak; Jasper A. Vrugt (Stat. Comput., 2008)

Approximating a similarity matrix by a latent class model: A reappraisal of additive fuzzy clustering. - Cajo J. F. ter Braak; Yiannis Kourmpetis; Henk A. L. Kiers; Marco C. A. M. Bink (Comput. Stat. Data Anal., 2009)

Correlated mutations via regularized multinomial regression. - Janrdanan Sreekumar; Cajo J. F. ter Braak; Roeland C. H. J. van Ham; Aalt D. J. van Dijk (BMC Bioinform., 2011)

Selection properties of type II maximum likelihood (empirical Bayes) in linear models with individual variance components for predictors. - Tahira Jamil; Cajo J. F. ter Braak (Pattern Recognit. Lett., 2012)

Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes. - Yiannis Kourmpetis; Aalt D. J. van Dijk; Cajo J. F. ter Braak (Algorithms Mol. Biol., 2013)

Linking multivariate trait variation to the environment: the advantages of double constrained correspondence analysis with the R package douconca. - Cajo J. F. ter Braak; Bart-Jan van Rossum (Ecol. Informatics, 2025)