Search Results - "Knijnenburg, Theo A."

A deep generative model of 3D single-cell organization by Donovan-Maiye, Rory M, Brown, Jackson M, Chan, Caleb K, Ding, Liya, Yan, Calysta, Gaudreault, Nathalie, Theriot, Julie A, Maleckar, Mary M, Knijnenburg, Theo A, Johnson, Gregory R

“…We introduce a framework for end-to-end integrative modeling of 3D single-cell multi-channel fluorescent image data of diverse subcellular structures. We…”
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Epigenetic profiling for the molecular classification of metastatic brain tumors by Orozco, Javier I. J., Knijnenburg, Theo A., Manughian-Peter, Ayla O., Salomon, Matthew P., Barkhoudarian, Garni, Jalas, John R., Wilmott, James S., Hothi, Parvinder, Wang, Xiaowen, Takasumi, Yuki, Buckland, Michael E., Thompson, John F., Long, Georgina V., Cobbs, Charles S., Shmulevich, Ilya, Kelly, Daniel F., Scolyer, Richard A., Hoon, Dave S. B., Marzese, Diego M.

“…Optimal treatment of brain metastases is often hindered by limitations in diagnostic capabilities. To meet this challenge, here we profile DNA methylomes of…”
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Fewer permutations, more accurate P-values by Knijnenburg, Theo A., Wessels, Lodewyk F. A., Reinders, Marcel J. T., Shmulevich, Ilya

“…Motivation: Permutation tests have become a standard tool to assess the statistical significance of an event under investigation. The statistical significance,…”
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Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression by Poole, William, Leinonen, Kalle, Shmulevich, Ilya, Knijnenburg, Theo A, Bernard, Brady

“…Cancer researchers have long recognized that somatic mutations are not uniformly distributed within genes. However, most approaches for identifying cancer…”
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Loss of ARID1A Activates ANXA1, which Serves as a Predictive Biomarker for Trastuzumab Resistance by Berns, Katrien, Sonnenblick, Amir, Gennissen, Annemiek, Brohée, Sylvain, Hijmans, E Marielle, Evers, Bastiaan, Fumagalli, Debora, Desmedt, Christine, Loibl, Sibylle, Denkert, Carsten, Neven, Patrick, Guo, Wei, Zhang, Fan, Knijnenburg, Theo A, Bosse, Tjalling, van der Heijden, Michiel S, Hindriksen, Sanne, Nijkamp, Wouter, Wessels, Lodewyk F A, Joensuu, Heikki, Mills, Gordon B, Beijersbergen, Roderick L, Sotiriou, Christos, Bernards, René

“…Despite the substantial progress in the development of targeted anticancer drugs, treatment failure due to primary or acquired resistance is still a major…”
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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

“…Recurrent inactivating mutations in components of SWI/SNF chromatin-remodeling complexes have been identified across cancer types, supporting their roles as…”
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Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation by Askovich, Peter S, Ramsey, Stephen A, Diercks, Alan H, Kennedy, Kathleen A, Knijnenburg, Theo A, Aderem, Alan

“…The innate immune response to pathogenic challenge is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that…”
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Identifying Personalized Metabolic Signatures in Breast Cancer by Baloni, Priyanka, Dinalankara, Wikum, Earls, John C, Knijnenburg, Theo A, Geman, Donald, Marchionni, Luigi, Price, Nathan D

“…Cancer cells are adept at reprogramming energy metabolism, and the precise manifestation of this metabolic reprogramming exhibits heterogeneity across…”
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Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins by Mirzaei, Hamid, Knijnenburg, Theo A., Kim, Bong, Robinson, Max, Picotti, Paola, Carter, Gregory W., Li, Song, Dilworth, David J., Eng, Jimmy K., Aitchison, John D., Shmulevich, Ilya, Galitski, Timothy, Aebersold, Ruedi, Ranish, Jeffrey

“…Regulation of gene expression involves the orchestrated interaction of a large number of proteins with transcriptional regulatory elements in the context of…”
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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

“…Random Forest has become a standard data analysis tool in computational biology. However, extensions to existing implementations are often necessary to handle…”
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Combining dependent P-values with an empirical adaptation of Brown's method by Poole, William, Gibbs, David L, Shmulevich, Ilya, Bernard, Brady, Knijnenburg, Theo A

“…Combining P-values from multiple statistical tests is a common exercise in bioinformatics. However, this procedure is non-trivial for dependent P-values. Here,…”
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Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes by de Groot, Marco J. L, Daran-Lapujade, Pascale, van Breukelen, Bas, Knijnenburg, Theo A, de Hulster, Erik A. F, Reinders, Marcel J. T, Pronk, Jack T, Heck, Albert J. R, Slijper, Monique

“…1 Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University,…”
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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

“…Cells exposed to stimuli exhibit a wide range of responses ensuring phenotypic variability across the population. Such single cell behavior is often examined…”
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Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer by Robertson, A. Gordon, Yau, Christina, Carrot-Zhang, Jian, Damrauer, Jeffrey S., Knijnenburg, Theo A., Chambwe, Nyasha, Hoadley, Katherine A., Kemal, Anab, Zenklusen, Jean C., Cherniack, Andrew D., Beroukhim, Rameen, Zhou, Wanding

“…Cellular and molecular aberrations contribute to the disparity of human cancer incidence and etiology between ancestry groups. Multiomics profiling in The…”
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EPEPT: a web service for enhanced P-value estimation in permutation tests by Knijnenburg, Theo A, Lin, Jake, Rovira, Hector, Boyle, John, Shmulevich, Ilya

“…In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the…”
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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.

“…Systematic studies of cancer genomes have provided unprecedented insights into the molecular nature of cancer. Using this information to guide the development…”
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Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer by Carrot-Zhang, Jian, Chambwe, Nyasha, Damrauer, Jeffrey S., Knijnenburg, Theo A., Robertson, A. Gordon, Yau, Christina, Zhou, Wanding, Berger, Ashton C., Huang, Kuan-lin, Newberg, Justin Y., Mashl, R. Jay, Romanel, Alessandro, Sayaman, Rosalyn W., Demichelis, Francesca, Felau, Ina, Frampton, Garrett M., Han, Seunghun, Hoadley, Katherine A., Kemal, Anab, Laird, Peter W., Lazar, Alexander J., Le, Xiuning, Oak, Ninad, Shen, Hui, Wong, Christopher K., Zenklusen, Jean C., Ziv, Elad, Aguet, Francois, Ding, Li, Demchok, John A., Mensah, Michael K.A., Caesar-Johnson, Samantha, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Alfoldi, Jessica, Karczewski, Konrad J., MacArthur, Daniel G., Meyerson, Matthew, Benz, Christopher, Stuart, Joshua M., Cherniack, Andrew D., Beroukhim, Rameen

“…We evaluated ancestry effects on mutation rates, DNA methylation, and mRNA and miRNA expression among 10,678 patients across 33 cancer types from The Cancer…”
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Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data by Knijnenburg, Theo A, Daran, Jean-Marc G, van den Broek, Marcel A, Daran-Lapujade, Pascale As, de Winde, Johannes H, Pronk, Jack T, Reinders, Marcel J T, Wessels, Lodewyk F A

“…Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow…”
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Physiological and Transcriptional Responses of Saccharomyces cerevisiae to Zinc Limitation in Chemostat Cultures by De Nicola, Raffaele, Hazelwood, Lucie A, De Hulster, Erik A.F, Walsh, Michael C, Knijnenburg, Theo A, Reinders, Marcel J.T, Walker, Graeme M, Pronk, Jack T, Daran, Jean-Marc, Daran-Lapujade, Pascale

“…Transcriptional responses of the yeast Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under limiting and…”
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Genome-wide analysis of effectors of peroxisome biogenesis by Saleem, Ramsey A, Long-O'Donnell, Rose, Dilworth, David J, Armstrong, Abraham M, Jamakhandi, Arvind P, Wan, Yakun, Knijnenburg, Theo A, Niemistö, Antti, Boyle, John, Rachubinski, Richard A, Shmulevich, Ilya, Aitchison, John D

“…Peroxisomes are intracellular organelles that house a number of diverse metabolic processes, notably those required for beta-oxidation of fatty acids…”
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