Theo Knijnenburg

Theo Knijnenburg

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Theo Knijnenburg

Theo Knijnenburg

Publications by authors named "Theo Knijnenburg"

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37Publications

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Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways.

Nucleic Acids Res 2018 10;46(18):9496-9509

Department of Biochemistry, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/nar/gky727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182128PMC
October 2018

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

Sci Rep 2016 11 23;6:36812. Epub 2016 Nov 23.

Netherlands Cancer Institute, Amsterdam, and The Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1038/srep36812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120272PMC
November 2016

Combining dependent P-values with an empirical adaptation of Brown's method.

Bioinformatics 2016 09;32(17):i430-i436

Institute for Systems Biology, Seattle, WA 98109-5263, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013915PMC
September 2016

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

Chin J Cancer 2015 Sep 14;34(10):439-49. Epub 2015 Sep 14.

Institute for Systems Biology, Seattle, WA, 98109, USA.

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http://dx.doi.org/10.1186/s40880-015-0050-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593384PMC
September 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

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

Cell Res 2015 Apr 6;25(4):445-58. Epub 2015 Feb 6.

Department of Biochemistry, The Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada.

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http://dx.doi.org/10.1038/cr.2015.16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387553PMC
April 2015

Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose.

Yeast 2015 Jan 13;32(1):29-45. Epub 2014 May 13.

Department of Biotechnology, Delft University of Technology, Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands.

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http://dx.doi.org/10.1002/yea.3015DOI Listing
January 2015

Hallmarks of aromatase inhibitor drug resistance revealed by epigenetic profiling in breast cancer.

Cancer Res 2013 Nov;73(22):6632-41

Authors' Affiliations: Department of Medical Oncology, Erasmus University Medical Center, Cancer Institute, Rotterdam; Departments of Molecular Carcinogenesis and Molecular Pathology, Central Genomic Facility, the Netherlands Cancer Institute; Agendia NV, Amsterdam, the Netherlands; and Translational Cancer Research Unit, Laboratory of Pathology, Antwerp University/Oncology Centre, GZA Hospitals St-Augustinus, Antwerp, Belgium.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-0704DOI Listing
November 2013

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

Mol Syst Biol 2011 Sep 27;7:531. Epub 2011 Sep 27.

Institute for Systems Biology, 401 Terry Avenue North, 1441 North 34th Street, Seattle, WA 98109-5234, USA.

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http://msb.embopress.org/cgi/doi/10.1038/msb.2011.64
Publisher Site
http://dx.doi.org/10.1038/msb.2011.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202802PMC
September 2011

Fewer permutations, more accurate P-values.

Bioinformatics 2009 Jun;25(12):i161-8

Institute for Systems Biology, Seattle, WA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687965PMC
June 2009

Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures.

Appl Environ Microbiol 2007 Dec 12;73(23):7680-92. Epub 2007 Oct 12.

Yeast Research Group, Division of Molecular and Life Sciences, University of Abertay, Dundee DD1 1HG, Scotland.

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http://dx.doi.org/10.1128/AEM.01445-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168061PMC
December 2007

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

Microbiology 2007 Nov;153(Pt 11):3864-78

Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.

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http://dx.doi.org/10.1099/mic.0.2007/009969-0DOI Listing
November 2007

Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae.

FEMS Yeast Res 2007 Sep 30;7(6):819-33. Epub 2007 Apr 30.

Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1111/j.1567-1364.2007.00242.xDOI Listing
September 2007

Integration of known transcription factor binding site information and gene expression data to advance from co-expression to co-regulation.

Genomics Proteomics Bioinformatics 2007 May;5(2):86-101

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2600 GA Delft, the Netherlands.

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http://linkinghub.elsevier.com/retrieve/pii/S167202290760019
Publisher Site
http://dx.doi.org/10.1016/S1672-0229(07)60019-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054099PMC
May 2007

Exploiting combinatorial cultivation conditions to infer transcriptional regulation.

BMC Genomics 2007 Jan 22;8:25. Epub 2007 Jan 22.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-8-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797021PMC
January 2007