Theo A. Knijnenburg

13 papers A 1Journal 10Unranked 2
YearRankTypeTitle / Venue / Authors
2022 J jnl
A deep generative model of 3D single-cell organization.
PLoS Comput. Biol.
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
2017 J jnl
Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.
PLoS Comput. Biol.
William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard
2016 J jnl
Combining dependent
Bioinform.
William Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo A. Knijnenburg
2012 J jnl
Fastbreak: a tool for analysis and visualization of structural variations in genomic data.
EURASIP J. Bioinform. Syst. Biol.
Ryan Bressler, Jake Lin, Andrea Eakin, Thomas Robinson, Richard Kreisberg, Hector Rovira, Theo A. Knijnenburg, John Boyle, Ilya Shmulevich
2011 J jnl
EPEPT: A web service for enhanced P-value estimation in permutation tests.
BMC Bioinform.
Theo A. Knijnenburg, Jake Lin, Hector Rovira, John Boyle, Ilya Shmulevich
2010 J jnl
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.
Bioinform.
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
2009 J jnl
Fewer permutations, more accurate
Bioinform.
Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich
2008 A conf
Combinatorial influence of environmental parameters on transcription factor activity.
ISMB
Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2008 J jnl
Creating gene set activity profiles with time-series expression data.
Int. J. Bioinform. Res. Appl.
Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2007 J jnl
Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation.
Genom. Proteom. Bioinform.
Maarten Clements, Eugene P. van Someren, Theo A. Knijnenburg, Marcel J. T. Reinders
2006 J jnl
Artifacts of Markov blanket filtering based on discretized features in small sample size applications.
Pattern Recognit. Lett.
Theo A. Knijnenburg, Marcel J. T. Reinders, Lodewyk F. A. Wessels
2006 — conf
Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in Yeast.
CMSB
Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2005 — conf
Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae.
CSB Workshops
Theo A. Knijnenburg, Marcel J. T. Reinders, Jean-Marc Daran, Pascale A. S. Daran-Lapujade, Lodewyk F. A. Wessels