Theo A. Knijnenburg - researchr alias

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Viewing Publication 1 - 13 from 13

2022

A deep generative model of 3D single-cell organizationRory 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. ploscb, 18(1), 2022. [doi]

2017

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expressionWilliam Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard. ploscb, 13(2), 2017. [doi]

2016

P-values with an empirical adaptation of Brown's methodWilliam Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo A. Knijnenburg. bioinformatics, 32(17):430-436, 2016. [doi]

2012

Fastbreak: a tool for analysis and visualization of structural variations in genomic dataRyan Bressler, Jake Lin, Andrea Eakin, Thomas Robinson, Richard Kreisberg, Hector Rovira, Theo A. Knijnenburg, John Boyle, Ilya Shmulevich. ejbsb, 2012:15, 2012. [doi]

2011

EPEPT: A web service for enhanced P-value estimation in permutation testsTheo A. Knijnenburg, Jake Lin, Hector Rovira, John Boyle, Ilya Shmulevich. bmcbi, 12:411, 2011. [doi]

2010

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sitesStephen 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. bioinformatics, 26(17):2071-2075, 2010. [doi]

2009

Fewer permutations, more accurate ::::P::::-valuesTheo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich. bioinformatics, 25(12), 2009. [doi]

2008

Combinatorial influence of environmental parameters on transcription factor activityTheo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders. ismb 2008: 172-181 [doi]

Creating gene set activity profiles with time-series expression dataTheo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders. ijbra, 4(3):306-323, 2008. [doi]

2007

Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-RegulationMaarten Clements, Eugene P. van Someren, Theo A. Knijnenburg, Marcel J. T. Reinders. gpb, 5(2):86-101, 2007. [doi]

2006

Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in YeastTheo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders. cmsb 2006: 271-284 [doi]

Artifacts of Markov blanket filtering based on discretized features in small sample size applicationsTheo A. Knijnenburg, Marcel J. T. Reinders, Lodewyk F. A. Wessels. prl, 27(7):709-714, 2006. [doi]

2005

Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiaeTheo A. Knijnenburg, Marcel J. T. Reinders, J. M. Daran, P. Daran-Lapujade, Lodewyk F. A. Wessels. csb 2005: 71-72 [doi]

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