Theo A. Knijnenburg

According to our database, Theo A. Knijnenburg authored at least 13 papers between 2005 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

A deep generative model of 3D single-cell organization.

Rory M. Donovan-Maiye, Eva Maxfield Brown, K. Caleb Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg, Gregory R. Johnson

PLoS Comput. Biol., 2022

2017

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

2016

Combining dependent <i>P-</i>values with an empirical adaptation of Brown's method.

William Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo A. Knijnenburg

Bioinform., 2016

2012

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

2011

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

2010

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, Ilya Shmulevich

Bioinform., 2010

2009

Fewer permutations, more accurate <i>P</i>-values.

Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich

Bioinform., 2009

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

Combinatorial influence of environmental parameters on transcription factor activity.

Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

2007

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

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

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

Proceedings of the Computational Methods in Systems Biology, International Conference, 2006

2005

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

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005