Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae. - Theo A. Knijnenburg; Marcel J. T. Reinders; Jean-Marc Daran; Pascale A. S. Daran-Lapujade; Lodewyk F. A. Wessels (CSB Workshops, 2005)

Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in Yeast. - Theo A. Knijnenburg; Lodewyk F. A. Wessels; Marcel J. T. Reinders (CMSB, 2006)

Artifacts of Markov blanket filtering based on discretized features in small sample size applications. - Theo A. Knijnenburg; Marcel J. T. Reinders; Lodewyk F. A. Wessels (Pattern Recognit. Lett., 2006)

Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation. - Maarten Clements; Eugene P. van Someren; Theo A. Knijnenburg; Marcel J. T. Reinders (Genom. Proteom. Bioinform., 2007)

Combinatorial influence of environmental parameters on transcription factor activity. - Theo A. Knijnenburg; Lodewyk F. A. Wessels; Marcel J. T. Reinders (ISMB, 2008)

Creating gene set activity profiles with time-series expression data. - Theo A. Knijnenburg; Lodewyk F. A. Wessels; Marcel J. T. Reinders (Int. J. Bioinform. Res. Appl., 2008)

Fewer permutations, more accurate P-values. - Theo A. Knijnenburg; Lodewyk F. A. Wessels; Marcel J. T. Reinders; Ilya Shmulevich (Bioinform., 2009)

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. - Stephen A. Ramsey; Theo A. Knijnenburg; Kathleen A. Kennedy; Daniel E. Zak; Mark Gilchrist; Elizabeth S. Gold; Carrie D. Johnson; Aaron E. Lampano; Vladimir Litvak; Garnet Navarro; Tetyana Stolyar; Alan Aderem; et al. (Bioinform., 2010)

EPEPT: A web service for enhanced P-value estimation in permutation tests. - Theo A. Knijnenburg; Jake Lin; Hector Rovira; John Boyle; Ilya Shmulevich (BMC Bioinform., 2011)

Fastbreak: a tool for analysis and visualization of structural variations in genomic data. - Ryan Bressler; Jake Lin; Andrea Eakin; Thomas Robinson; Richard Kreisberg; Hector Rovira; Theo A. Knijnenburg; John Boyle; Ilya Shmulevich (EURASIP J. Bioinform. Syst. Biol., 2012)

Combining dependent P-values with an empirical adaptation of Brown's method. - William Poole; David L. Gibbs; Ilya Shmulevich; Brady Bernard; Theo A. Knijnenburg (Bioinform., 2016)

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression. - William Poole; Kalle Leinonen; Ilya Shmulevich; Theo A. Knijnenburg; Brady Bernard (PLoS Comput. Biol., 2017)

A deep generative model of 3D single-cell organization. - Rory M. Donovan-Maiye; Eva Maxfield Brown; K. Caleb Chan; Liya Ding 001; Calysta Yan; Nathalie Gaudreault; Julie A. Theriot; Mary M. Maleckar; Theo A. Knijnenburg; Gregory R. Johnson (PLoS Comput. Biol., 2022)