EPEPT: A web service for enhanced P-value estimation in permutation tests

by Knijnenburg, Theo A, Lin, Jake, Rovira, Hector, Boyle, John, Shmulevich, Ilya
Published 2011

A regression model approach to enable cell morphology correction in high-throughput flow cytometry

by Knijnenburg, Theo A, Roda, Oriol, Wan, Yakun, Nolan, Garry P, Aitchison, John D, Shmulevich, Ilya
Published 2011

Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation

by Clements, Maarten, van Someren, Eugene P., Knijnenburg, Theo A., Reinders, Marcel J.T.
Published 2007

A multilevel pan-cancer map links gene mutations to cancer hallmarks

by Knijnenburg, Theo A., Bismeijer, Tycho, Wessels, Lodewyk F. A., Shmulevich, Ilya
Published 2015

Fastbreak: a tool for analysis and visualization of structural variations in genomic data

by Bressler, Ryan, Lin, Jake, Eakin, Andrea, Robinson, Thomas, Kreisberg, Richard, Rovira, Hector, Knijnenburg, Theo, Boyle, John, Shmulevich, Ilya
Published 2012

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

by Knijnenburg, Theo A., Klau, Gunnar W., Iorio, Francesco, Garnett, Mathew J., McDermott, Ultan, Shmulevich, Ilya, Wessels, Lodewyk F. A.
Published 2016

CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data

by Bressler, Ryan, Kreisberg, Richard B., Bernard, Brady, Niederhuber, John E., Vockley, Joseph G., Shmulevich, Ilya, Knijnenburg, Theo A.
Published 2015

Using Incomplete Trios to Boost Confidence in Family Based Association Studies

by Dhankani, Varsha, Gibbs, David L., Knijnenburg, Theo, Kramer, Roger, Vockley, Joseph, Niederhuber, John, Shmulevich, Ilya, Bernard, Brady
Published 2016

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

by Knijnenburg, Theo A, de Winde, Johannes H, Daran, Jean-Marc, Daran-Lapujade, Pascale, Pronk, Jack T, Reinders, Marcel JT, Wessels, Lodewyk FA
Published 2007

Multiscale Representation of Genomic Signals

by Knijnenburg, Theo A., Ramsey, Stephen A., Berman, Benjamin P., Kennedy, Kathleen A., Smit, Arian F.A., Wessels, Lodewyk F.A., Laird, Peter W., Aderem, Alan, Shmulevich, Ilya
Published 2014

SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer

by Papadakis, Andreas I, Sun, Chong, Knijnenburg, Theo A, Xue, Yibo, Grernrum, Wipawadee, Hölzel, Michael, Nijkamp, Wouter, Wessels, Lodewyk FA, Beijersbergen, Roderick L, Bernards, Rene, Huang, Sidong
Published 2015

A Landscape of Pharmacogenomic Interactions in Cancer

by Iorio, Francesco, Knijnenburg, Theo A., Vis, Daniel J., Bignell, Graham R., Menden, Michael P., Schubert, Michael, Aben, Nanne, Gonçalves, Emanuel, Barthorpe, Syd, Lightfoot, Howard, Cokelaer, Thomas, Greninger, Patricia, van Dyk, Ewald, Chang, Han, de Silva, Heshani, Heyn, Holger, Deng, Xianming, Egan, Regina K., Liu, Qingsong, Mironenko, Tatiana, Mitropoulos, Xeni, Richardson, Laura, Wang, Jinhua, Zhang, Tinghu, Moran, Sebastian, Sayols, Sergi, Soleimani, Maryam, Tamborero, David, Lopez-Bigas, Nuria, Ross-Macdonald, Petra, Esteller, Manel, Gray, Nathanael S., Haber, Daniel A., Stratton, Michael R., Benes, Cyril H., Wessels, Lodewyk F.A., Saez-Rodriguez, Julio, McDermott, Ultan, Garnett, Mathew J.
Published 2016