Theo A. Knijnenburg

Publication Activity (10 Years)

Years Active: 2005-2022
Publications (10 Years): 3

Top Topics

Gene Expression Data Sets

Generative Model

Survival Prediction

Clustering Algorithm

Top Venues

PLoS Comput. Biol.

Publications

Rory M. Donovan-Maiye, Jackson M. Brown, K. Caleb Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg, Gregory R. Johnson
A deep generative model of 3D single-cell organization. PLoS Comput. Biol. 18 (1) (2022)
William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard
Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression. PLoS Comput. Biol. 13 (2) (2017)
William Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo A. Knijnenburg
values with an empirical adaptation of Brown's method. Bioinform. 32 (17) (2016)
Ryan Bressler, Jake Lin, Andrea Eakin, Thomas Robinson, Richard Kreisberg, Hector Rovira, Theo A. Knijnenburg, John Boyle, Ilya Shmulevich
Fastbreak: a tool for analysis and visualization of structural variations in genomic data. EURASIP J. Bioinform. Syst. Biol. 2012 (2012)
Theo A. Knijnenburg, Jake Lin, Hector Rovira, John Boyle, Ilya Shmulevich
EPEPT: A web service for enhanced P-value estimation in permutation tests. BMC Bioinform. 12 (2011)
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
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinform. 26 (17) (2010)
Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich
-values. Bioinform. 25 (12) (2009)
Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders
Creating gene set activity profiles with time-series expression data. Int. J. Bioinform. Res. Appl. 4 (3) (2008)
Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders
Combinatorial influence of environmental parameters on transcription factor activity. ISMB (2008)
Maarten Clements, Eugene P. van Someren, Theo A. Knijnenburg, Marcel J. T. Reinders
Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation. Genom. Proteom. Bioinform. 5 (2) (2007)
Theo A. Knijnenburg, Marcel J. T. Reinders, Lodewyk F. A. Wessels
Artifacts of Markov blanket filtering based on discretized features in small sample size applications. Pattern Recognit. Lett. 27 (7) (2006)
Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders
Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in Yeast. CMSB (2006)
Theo A. Knijnenburg, Marcel J. T. Reinders, Jean-Marc Daran, Pascale A. S. Daran-Lapujade, Lodewyk F. A. Wessels
Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae. CSB Workshops (2005)