Risultati della ricerca - Theo Knijnenburg

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  1. 1
    Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes

    Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes di Joseph Zhou, Roberto Taramelli, Edoardo Pedrini, Theo Knijnenburg, Sui Huang

    Pubblicazione 2017
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  2. 2
    Fewer permutations, more accurate <i>P</i>-values

    Fewer permutations, more accurate <i>P</i>-values di Theo Knijnenburg, Lodewyk F.A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich

    Pubblicazione 2009
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  3. 3
    Combining dependent<i>P-</i>values with an empirical adaptation of Brown’s method

    Combining dependent<i>P-</i>values with an empirical adaptation of Brown’s method di William Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo Knijnenburg

    Pubblicazione 2016
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  4. 4
    Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of<i>Saccharomyces cerevisiae</i>

    Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of<i>Saccharomyces cerevisiae</i> di Derek A. Abbott, Theo Knijnenburg, Linda M. I. de Poorter, Marcel J. T. Reinders, Jack T. Pronk, Antonius J. A. van Maris

    Pubblicazione 2007
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  5. 5
    Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data

    Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptom... di Theo Knijnenburg, Jean‐Marc Daran, Marcel A. van den Broek, Pascale Daran‐Lapujade, Johannes H. de Winde, Jack T. Pronk, Marcel J. T. Reinders, Lodewyk F.A. Wessels

    Pubblicazione 2009
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  6. 6
    A deep generative model of 3D single-cell organization

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

    Pubblicazione 2022
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  7. 7
    Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes

    Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes di Marco J. L. de Groot, Pascale Daran‐Lapujade, Bas van Breukelen, Theo Knijnenburg, Erik A. F. de Hulster, Marcel J. T. Reinders, Jack T. Pronk, Albert J. R. Heck, Monique Slijper

    Pubblicazione 2007
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  8. 8
    Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

    Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites di Stephen A. Ramsey, Theo Knijnenburg, Kathleen A. Kennedy, Daniel E. Zak, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Aaron Lampano, Vladimir Litvak, Garnet Navarro, Tetyana Stolyar, Alan Aderem, Ilya Shmulevich

    Pubblicazione 2010
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  9. 9
    Physiological and Transcriptional Responses of <i>Saccharomyces cerevisiae</i> to Zinc Limitation in Chemostat Cultures

    Physiological and Transcriptional Responses of <i>Saccharomyces cerevisiae</i> to Zinc Limitation in Chemostat Cultures di Raffaele De Nicola, Lucie A. Hazelwood, Erik A. F. de Hulster, Michael C. Walsh, Theo Knijnenburg, Marcel J. T. Reinders, Graeme M. Walker, Jack T. Pronk, Jean‐Marc Daran, Pascale Daran‐Lapujade

    Pubblicazione 2007
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  10. 10
    When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation

    When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation di Made Tri Ari Penia Kresnowati, Wouter A. van Winden, Marinka J.H. Almering, Angela ten Pierick, Cor Ras, Theo Knijnenburg, Pascale Daran‐Lapujade, Jack T. Pronk, Joseph J. Heijnen, Jean‐Marc Daran

    Pubblicazione 2006
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  11. 11
    Hallmarks of Aromatase Inhibitor Drug Resistance Revealed by Epigenetic Profiling in Breast Cancer

    Hallmarks of Aromatase Inhibitor Drug Resistance Revealed by Epigenetic Profiling in Breast Cancer di Maurice P.H.M. Jansen, Theo Knijnenburg, Esther A. Reijm, Iris Simón, Ron Kerkhoven, Marjolein Droog, Arno Velds, Steven Van Laere, Luc Dirix, Xanthippi Alexi, John A. Foekens, Lodewyk F.A. Wessels, Sabine C. Linn, Els M.J.J. Berns, Wilbert Zwart

    Pubblicazione 2013
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  12. 12
    MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-β Receptor Signaling

    MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-β Receptor Signaling di Sidong Huang, Michael Hölzel, Theo Knijnenburg, Andreas Schlicker, Paul Roepman, Ultan McDermott, Mathew J. Garnett, Wipawadee Grernrum, Chong Sun, Anirudh Prahallad, Floris H. Groenendijk, Lorenza Mittempergher, Wouter Nijkamp, Jacques Neefjes, Ramón Salazar, Peter ten Dijke, Hidetaka Uramoto, Fumihiro Tanaka, Roderick L. Beijersbergen, Lodewyk F.A. Wessels, René Bernards

    Pubblicazione 2012
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  13. 13
    Epigenetic profiling for the molecular classification of metastatic brain tumors

    Epigenetic profiling for the molecular classification of metastatic brain tumors di Javier I. J. Orozco, Theo Knijnenburg, Ayla O. Manughian-Peter, Matthew P. Salomon, Garni Barkhoudarian, John R. Jalas, James S. Wilmott, Parvinder Hothi, Xiaowen Wang, Yuki Takasumi, Michael E. Buckland, John F. Thompson, Georgina V. Long, Charles Cobbs, Ilya Shmulevich, Daniel F. Kelly, Richard A. Scolyer, Dave S.�B. Hoon, Diego M. Marzese

    Pubblicazione 2018
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  14. 14
    Loss of <i>ARID1A</i> Activates <i>ANXA1</i>, which Serves as a Predictive Biomarker for Trastuzumab Resistance

    Loss of <i>ARID1A</i> Activates <i>ANXA1</i>, which Serves as a Predictive Biomarker for Trastuzumab Resistance di Katrien Berns, Amir Sonnenblick, Annemiek M.C. Gennissen, Sylvain Brohée, E. Marielle Hijmans, Bastiaan Evers, Debora Fumagalli, Christine Desmedt, Sibylle Loibl, Carsten Denkert, Patrick Neven, Wei Guo, Fan Zhang, Theo Knijnenburg, Tjalling Bosse, Michiel S. van der Heijden, Sanne Hindriksen, Wouter Nijkamp, Lodewyk F.A. Wessels, Heikki Joensuu, Gordon B. Mills, Roderick L. Beijersbergen, Christos Sotiriou, René Bernards

    Pubblicazione 2016
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  15. 15
    Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

    Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes di Kaytlyn A. Gerbin, Tanya Grancharova, Rory M. Donovan-Maiye, Melissa Hendershott, Helen G. Anderson, Jackson M. Brown, Jianxu Chen, Stephanie Dinh, Jamie L. Gehring, Gregory R. Johnson, HyeonWoo Lee, Aditya Nath, Angelique M. Nelson, M. Sluzewski, Matheus P. Viana, Calysta Yan, Rebecca J. Zaunbrecher, Kimberly R. Cordes Metzler, Nathalie Gaudreault, Theo Knijnenburg, Susanne M. Rafelski, Julie A. Theriot, Ruwanthi N. Gunawardane

    Pubblicazione 2021
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  16. 16
    Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets

    Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets di Kyle Ellrott, Christopher K. Wong, Christina Yau, Mauro A.A. Castro, Jordan Lee, Brian Karlberg, Jasleen Grewal, Vincenzo Lagani, Bahar Tercan, Verena Friedl, Toshinori Hinoue, Vladislav Uzunangelov, Lindsay Westlake, Xavier Loinaz, Ina Felau, Peggy I. Wang, Anab Kemal, Rory Johnson, Ilya Shmulevich, Alexander J. Lazar, Ioannis Tsamardinos, Katherine A. Hoadley, A. Gordon Robertson, Theo Knijnenburg, Christopher C. Benz, Joshua M. Stuart, Jean C. Zenklusen, Andrew D. Cherniack, Peter W. Laird

    Pubblicazione 2025
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  17. 17
    Genomic and molecular characterization of preterm birth

    Genomic and molecular characterization of preterm birth di Theo Knijnenburg, Joseph G. Vockley, Nyasha Chambwe, David L. Gibbs, Crystal Humphries, Kathi Huddleston, Elisabeth Klein, Prachi Kothiyal, Ryan Tasseff, Varsha Dhankani, Dale L. Bodian, Wendy S.W. Wong, Gustavo Glusman, Denise E. Mauldin, Michael Miller, Joseph Slagel, Summer Elasady, Jared C. Roach, Roger Kramer, Kalle Leinonen, Jasper Linthorst, Rajiv Baveja, Robin Baker, Benjamin D. Solomon, Greg Eley, Ramaswamy K. Iyer, G. Larry Maxwell, Brady Bernard, Ilya Shmulevich, Leroy Hood, John E. Niederhuber

    Pubblicazione 2019
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  18. 18
    A Landscape of Pharmacogenomic Interactions in Cancer

    A Landscape of Pharmacogenomic Interactions in Cancer di Francesco Iorio, Theo Knijnenburg, Daniël J. Vis, Graham R. Bignell, Michael P. Menden, Michaël Schubert, Nanne Aben, Emanuel Gonçalves, Syd Barthorpe, Howard Lightfoot, Thomas Cokelaer, Patricia Greninger, Ewald van Dyk, Han Chang, Heshani de Silva, Holger Heyn, Xianming Deng, Regina K. Egan, Qingsong Liu, Tatiana Mironenko, Xeni Mitropoulos, Laura Richardson, Jinhua Wang, Tinghu Zhang, Sebastián Morán, Sergi Sayols, Maryam Soleimani, David Tamborero, Núria López-Bigas, Petra Ross‐Macdonald, Manel Esteller, Nathanael S. Gray, Daniel A. Haber, Michael R. Stratton, Cyril H. Benes, Lodewyk F.A. Wessels, Julio Sáez-Rodríguez, Ultan McDermott, Mathew J. Garnett

    Pubblicazione 2016
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  19. 19
    Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data

    Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data di Galen F. Gao, Joel S. Parker, Sheila M. Reynolds, Tiago C. Silva, Liang-Bo Wang, Wanding Zhou, Rehan Akbani, Matthew H. Bailey, Saianand Balu, Benjamin P. Berman, Denise Brooks, Hu Chen, Andrew D. Cherniack, John A. Demchok, Li Ding, Ina Felau, Sharon Gaheen, Daniela S. Gerhard, David I. Heiman, Kyle M. Hernandez, Katherine A. Hoadley, Reyka G. Jayasinghe, Anab Kemal, Theo Knijnenburg, Peter W. Laird, Michael K.A. Mensah, Andrew J. Mungall, A. Gordon Robertson, Hui Shen, Roy Tarnuzzer, Zhining Wang, Matthew A. Wyczalkowski, Liming Yang, Jean C. Zenklusen, Zhenyu Zhang, Han Liang, Michael S. Noble

    Pubblicazione 2019
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  20. 20
    Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer

    Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer di Jian Carrot‐Zhang, Nyasha Chambwe, Jeffrey S. Damrauer, Theo Knijnenburg, A. Gordon Robertson, Christina Yau, Wanding Zhou, Ashton C. Berger, Kuan‐lin Huang, Justin Y. Newberg, R. Jay Mashl, Alessandro Romanel, Rosalyn W. Sayaman, Francesca Demichelis, Ina Felau, Garrett M. Frampton, Seunghun Han, Katherine A. Hoadley, Anab Kemal, Peter W. Laird, Alexander J. Lazar, Xiuning Le, Ninad Oak, Hui Shen, Christopher K. Wong, Jean C. Zenklusen, Elad Ziv, Andrew D. Cherniack, Rameen Beroukhim, François Aguet, Li Ding, John A. Demchok, Michael K.A. Mensah, Rory Johnson, Roy Tarnuzzer, Linghua Wang, Liming Yang, Jessica Alföldi, Konrad J. Karczewski, Daniel G. MacArthur, Matthew Meyerson, Christopher C. Benz, Joshua M. Stuart

    Pubblicazione 2020
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