Publications



Highlights


@article{Canisius:2016bb,
author = {Canisius, Sander and Martens, John W M and Wessels, Lodewyk F A},
title = {{A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence.}},
journal = {Genome biology},
year = {2016},
volume = {17},
number = {1},
pages = {261},
month = dec
}

@article{Thijssen:2016gp,
author = {Thijssen, Bram and Dijkstra, Tjeerd M H and Heskes, Tom and Wessels, Lodewyk F A},
title = {{BCM: toolkit for Bayesian analysis of Computational Models using samplers.}},
journal = {BMC systems biology},
year = {2016},
volume = {10},
number = {1},
pages = {100},
month = oct
}


@article{Aben:2016,
author = {Aben, Nanne and Vis, Daniel and Michaut, Magali and Wessels, Lodewyk},
title = {{TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.}},
journal = {Bioinformatics (ECCB 2016)},
year = {2016},
month = sep
}

@article{Iorio:2016ds,
author = {Iorio, Francesco and Knijnenburg, Theo A and Vis, Daniel J and Bignell, Graham R and Menden, Michael P and Schubert, Michael and Aben, Nanne and Goncalves, Emanuel and Barthorpe, Syd and Lightfoot, Howard and Cokelaer, Thomas and Greninger, Patricia and van Dyk, Ewald and Chang, Han and de Silva, Heshani and Heyn, Holger and Deng, Xianming and Egan, Regina K and Liu, Qingsong and Mironenko, Tatiana and Mitropoulos, Xeni and Richardson, Laura and Wang, Jinhua and Zhang, Tinghu and Moran, Sebastian and Sayols, Sergi and Soleimani, Maryam and Tamborero, David and Lopez-Bigas, Nuria and Ross-Macdonald, Petra and Esteller, Manel and Gray, Nathanael S and Haber, Daniel A and Stratton, Michael R and Benes, Cyril H and Wessels, Lodewyk F A and Saez-Rodriguez, Julio and McDermott, Ultan and Garnett, Mathew J},
title = {{A Landscape of Pharmacogenomic Interactions in Cancer.}},
journal = {Cell},
year = {2016},
url = {http://www.cell.com/fulltext/S0092-8674(16)30746-2},
month = jul
}

@article{vanDyk:2016ez,
author = {van Dyk, Ewald and Hoogstraat, Marlous and Ten Hoeve, Jelle and Reinders, Marcel J T and Wessels, Lodewyk F A},
title = {{RUBIC identifies driver genes by detecting recurrent DNA copy number breaks.}},
journal = {Nature communications},
year = {2016},
volume = {7},
url = {http://www.readcube.com/articles/10.1038/ncomms12159},
pages = {12159}
}



@article{Schlicker:2016fq,
author = {Schlicker, Andreas and Michaut, Magali and Rahman, Rubayte and Wessels, Lodewyk F A},
title = {{OncoScape: Exploring the cancer aberration landscape by genomic data fusion}},
journal = {Scientific reports},
year = {2016},
volume = {6},
pages = {28103},
url = {http://www.nature.com/articles/srep28103},
month = jun
}


@article{Guinney:2015dm,
author = {Guinney, Justin and Dienstmann, Rodrigo and Wang, Xin and de Reynies, Aurélien and Schlicker, Andreas and Soneson, Charlotte and Marisa, Laetitia and Roepman, Paul and Nyamundanda, Gift and Angelino, Paolo and Bot, Brian M and Morris, Jeffrey S and Simon, Iris M and Gerster, Sarah and Fessler, Evelyn and De Sousa E Melo, Felipe and Missiaglia, Edoardo and Ramay, Hena and Barras, David and Homicsko, Krisztian and Maru, Dipen and Manyam, Ganiraju C and Broom, Bradley and Boige, Val{\'e}rie and Perez Villamil, Beatriz and Laderas, Ted and Salazar, Ramon and Gray, Joe W and Hanahan, Douglas and Tabernero, Josep and Bernards, Rene and Friend, Stephen H and Laurent-Puig, Pierre and Medema, Jan Paul and Sadanandam, Anguraj and Wessels, Lodewyk and Delorenzi, Mauro and Kopetz, Scott and Vermeulen, Louis and Tejpar, Sabine},
title = {{The consensus molecular subtypes of colorectal cancer}},
journal = {Nature medicine},
year = {2015},
url = {http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3967.html},
month = oct
}




By Year


%%%%%%%% 2017 %%%%%%%%

@article{Droog:2017bm,
author = {Droog, Marjolein and Nevedomskaya, Ekaterina and Dackus, Gwen M and Fles, Renske and Kim, Yongsoo and Hollema, Harry and Mourits, Marian and Nederlof, Petra M and Van Boven, Hester H and Linn, Sabine C and van Leeuwen, Flora E and Wessels, Lodewyk F A and Zwart, Wilbert},
title = {{Estrogen receptor alpha wields treatment-specific enhancers between morphologically similar endometrial tumors.}},
journal = {PNAS},
year = {2017},
month = feb
}



%%%%%%%% 2016 %%%%%%%%




@article{Canisius:2016bb,
author = {Canisius, Sander and Martens, John W M and Wessels, Lodewyk F A},
title = {{A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence.}},
journal = {Genome biology},
year = {2016},
volume = {17},
number = {1},
pages = {261},
month = dec
}



@article{Knijnenburg:2016ib,
author = {Knijnenburg, Theo A and Klau, Gunnar W and Iorio, Francesco and Garnett, Mathew J and McDermott, Ultan and Shmulevich, Ilya and Wessels, Lodewyk F A},
title = {{Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.}},
journal = {Scientific reports},
year = {2016},
volume = {6},
pages = {36812},
month = nov
}



@article{Koppens:2016hl,
author = {Koppens, Martijn Aj and Bounova, Gergana and Cornelissen-Steijger, Paulien and de Vries, Nienke and Sansom, Owen J and Wessels, Lodewyk Fa and van Lohuizen, Maarten},
title = {{Large variety in a panel of human colon cancer organoids in response to EZH2 inhibition.}},
journal = {Oncotarget},
year = {2016},
month = sep
}



@article{Thijssen:2016gp,
author = {Thijssen, Bram and Dijkstra, Tjeerd M H and Heskes, Tom and Wessels, Lodewyk F A},
title = {{BCM: toolkit for Bayesian analysis of Computational Models using samplers.}},
journal = {BMC systems biology},
year = {2016},
volume = {10},
number = {1},
pages = {100},
month = oct
}


@article{Aben:2016,
author = {Aben, Nanne and Vis, Daniel and Michaut, Magali and Wessels, Lodewyk},
title = {{TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.}},
journal = {Bioinformatics (ECCB 2016)},
year = {2016},
month = sep
}



@article{Boelens:2016ga,
author = {Boelens, Mirjam C and Nethe, Micha and Klarenbeek, Sjoerd and de Ruiter, Julian R and Schut, Eva and Bonzanni, Nicola and Zeeman, Amber L and Wientjens, Ellen and van der Burg, Eline and Wessels, Lodewyk and van Amerongen, Renee and Jonkers, Jos},
title = {{PTEN Loss in E-Cadherin-Deficient Mouse Mammary Epithelial Cells Rescues Apoptosis and Results in Development of Classical Invasive Lobular Carcinoma.}},
journal = {Cell reports},
year = {2016},
month = aug
}



@article{Iorio:2016ds,
author = {Iorio, Francesco and Knijnenburg, Theo A and Vis, Daniel J and Bignell, Graham R and Menden, Michael P and Schubert, Michael and Aben, Nanne and Goncalves, Emanuel and Barthorpe, Syd and Lightfoot, Howard and Cokelaer, Thomas and Greninger, Patricia and van Dyk, Ewald and Chang, Han and de Silva, Heshani and Heyn, Holger and Deng, Xianming and Egan, Regina K and Liu, Qingsong and Mironenko, Tatiana and Mitropoulos, Xeni and Richardson, Laura and Wang, Jinhua and Zhang, Tinghu and Moran, Sebastian and Sayols, Sergi and Soleimani, Maryam and Tamborero, David and Lopez-Bigas, Nuria and Ross-Macdonald, Petra and Esteller, Manel and Gray, Nathanael S and Haber, Daniel A and Stratton, Michael R and Benes, Cyril H and Wessels, Lodewyk F A and Saez-Rodriguez, Julio and McDermott, Ultan and Garnett, Mathew J},
title = {{A Landscape of Pharmacogenomic Interactions in Cancer.}},
journal = {Cell},
year = {2016},
url = {http://www.cell.com/fulltext/S0092-8674(16)30746-2},
month = jul
}

@article{vanDyk:2016ez,
author = {van Dyk, Ewald and Hoogstraat, Marlous and Ten Hoeve, Jelle and Reinders, Marcel J T and Wessels, Lodewyk F A},
title = {{RUBIC identifies driver genes by detecting recurrent DNA copy number breaks.}},
journal = {Nature communications},
year = {2016},
volume = {7},
url = {http://www.readcube.com/articles/10.1038/ncomms12159},
pages = {12159}
}



@article{Hogenbirk:2016kc,
author = {Hogenbirk, Marc A and Heideman, Marinus R and de Rink, Iris and Velds, Arno and Kerkhoven, Ron M and Wessels, Lodewyk F A and Jacobs, Heinz},
title = {{Defining chromosomal translocation risks in cancer.}},
journal = {Proceedings of the National Academy of Sciences},
year = {2016},
volume = {113},
number = {26},
pages = {E3649--56},
month = jun
}

@article{Koppens:2016ky,
author = {Koppens, Martijn Aj and Bounova, Gergana and Gargiulo, Gaetano and Tanger, Ellen and Janssen, Hans and Cornelissen-Steijger, Paulien and Blom, Marleen and Song, Ji-Ying and Wessels, Lodewyk F and van Lohuizen, Maarten},
title = {{Deletion of Polycomb Repressive Complex 2 From Mouse Intestine Causes Loss of Stem Cells.}},
journal = {Gastroenterology},
year = {2016},
month = jun
}



@article{Schlicker:2016fq,
author = {Schlicker, Andreas and Michaut, Magali and Rahman, Rubayte and Wessels, Lodewyk F A},
title = {{OncoScape: Exploring the cancer aberration landscape by genomic data fusion}},
journal = {Scientific reports},
year = {2016},
volume = {6},
pages = {28103},
url = {http://www.nature.com/articles/srep28103},
month = jun
}



@article{deLint:2016js,
author = {de Lint, Klaas and Poell, Jos B and Soueidan, Hayssam and Jastrzebski, Katarzyna and Vidal Rodriguez, Jordi and Lieftink, Cor and Wessels, Lodewyk F A and Beijersbergen, Roderick L},
title = {{Sensitizing triple-negative breast cancer to PI3K inhibition by co-targeting IGF1R.}},
journal = {Molecular Cancer Therapeutics},
year = {2016},
month = may
}



@article{Droog:2016dy,
author = {Droog, Marjolein and Nevedomskaya, Ekaterina and Kim, Yongsoo and Severson, Tesa and Flach, Koen D and Opdam, Mark and Schuurman, Karianne and Gradowska, Patrycja and Hauptmann, Michael and Dackus, Gwen and Hollema, Harry and Mourits, Marian and Nederlof, Petra M and Van Boven, Hester H and Linn, Sabine C and Wessels, Lodewyk F A and van Leeuwen, Flora E and Zwart, Wilbert},
title = {{Comparative cistromics reveals genomic crosstalk between FOXA1 and ER alpha in tamoxifen-associated endometrial carcinomas.}},
journal = {Cancer research},
year = {2016},
month = may
}



@article{Vis:2016ca,
author = {Vis, Daniel J and Bombardelli, Lorenzo and Lightfoot, Howard and Iorio, Francesco and Garnett, Mathew J and Wessels, Lodewyk Fa},
title = {{Multilevel models improve precision and speed of IC50 estimates.}},
journal = {Pharmacogenomics},
year = {2016},
volume = {17},
number = {7},
pages = {691--700},
month = may
}

@article{Severson:2016kl,
author = {Severson, Tesa M and Nevedomskaya, Ekaterina and Peeters, Justine and Kuilman, Thomas and Krijgsman, Oscar and van Rossum, Annelot and Droog, Marjolein and Kim, Yongsoo and Koornstra, Rutger and Beumer, In{\`e}s and Glas, Annuska M and Peeper, Daniel and Wesseling, Jelle and Simon, Iris M and Wessels, Lodewyk and Linn, Sabine C and Zwart, Wilbert},
title = {{Neoadjuvant tamoxifen synchronizes ERa binding and gene expression profiles related to outcome and proliferation.}},
journal = {Oncotarget},
year = {2016},
month = apr
}


@article{Berns:2016cr,
author = {Berns, Katrien and Sonnenblick, Amir and Gennissen, Annemiek and Brohée, Sylvain and Hijmans, Marielle E and Evers, Bastiaan and Fumagalli, Debora and Desmedt, Christine and Loibl, Sibylle and Denkert, Carsten and Neven, Patrick and Guo, Wei and Zhang, Fan and Knijnenburg, Theo A and Bosse, Tjalling and van der Heijden, Michiel S and Hindriksen, Sanne and Nijkamp, Wouter and Wessels, Lodewyk F A and Joensuu, Heikki and Mills, Gordon B and Beijersbergen, Roderick L and Sotiriou, Christos and Bernards, René},
title = {{Loss of ARID1A activates ANXA1, which serves as a predictive biomarker for trastuzumab resistance.}},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
year = {2016},
month = may
}


@article{Siu:2016dt,
author = {Siu, Lillian L and Lawler, Mark and Haussler, David and Knoppers, Bartha Maria and Lewin, Jeremy and Vis, Daniel J and Liao, Rachel G and Andr{\'e}, Fabrice and Banks, Ian and Barrett, J Carl and Caldas, Carlos and Camargo, Anamaria Aranha and Fitzgerald, Rebecca C and Mao, Mao and Mattison, John E and Pao, William and Sellers, William R and Sullivan, Patrick and Teh, Bin Tean and Ward, Robyn L and ZenKlusen, Jean Claude and Sawyers, Charles L and Voest, Emile E},
title = {{Facilitating a culture of responsible and effective sharing of cancer genome data.}},
journal = {Nature medicine},
year = {2016},
volume = {22},
number = {5},
pages = {464--471},
month = may
}


@article{Vecchione:2016hn,
author = {Vecchione, Loredana and Gambino, Valentina and Raaijmakers, Jonne and Schlicker, Andreas and Fumagalli, Arianna and Russo, Mariangela and Villanueva, Alberto and Beerling, Evelyne and Bartolini, Alice and Mollevi, David G and El-Murr, Nizar and Chiron, Marielle and Calvet, Loreley and Nicolazzi, C{\'e}line and Combeau, C{\'e}cile and Henry, Christophe and Simon, Iris M and Tian, Sun and In 't Veld, Sjors and D'Ario, Giovanni and Mainardi, Sara and Beijersbergen, Roderick L and Lieftink, Cor and Linn, Sabine and Rumpf-Kienzl, Cornelia and Delorenzi, Mauro and Wessels, Lodewyk and Salazar, Ramon and Di Nicolantonio, Federica and Bardelli, Alberto and van Rheenen, Jacco and Medema, Ren{\'e} H and Tejpar, Sabine and Bernards, Ren{\'e}},
title = {{A Vulnerability of a Subset of Colon Cancers with Potential Clinical Utility.}},
journal = {Cell},
year = {2016},
volume = {165},
number = {2},
pages = {317--330},
month = apr
}



@article{Johnson:2016df,
author = {Johnson, J and Thijssen, B and McDermott, U and Garnett, M and Wessels, L F A and Bernards, R},
title = {{Targeting the RB-E2F pathway in breast cancer.}},
journal = {Oncogene},
year = {2016},
month = feb
}

@article{Nevedomskaya:2016bf,
author = {Nevedomskaya, Ekaterina and Stelloo, Suzan and van der Poel, Henk G and de Jong, Jeroen and Wessels, Lodewyk F A and Bergman, Andries M and Zwart, Wilbert},
title = {{Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer.}},
journal = {Genomics Data},
year = {2016},
volume = {7},
pages = {124--126},
month = mar
}


@article{Michaut:2016fe,
author = {Michaut, Magali and Chin, Suet-Feung and Majewski, Ian and Severson, Tesa M and Bismeijer, Tycho and de Koning, Leanne and Peeters, Justine K and Schouten, Philip C and Rueda, Oscar M and Bosma, Astrid J and Tarrant, Finbarr and Fan, Yue and He, Beilei and Xue, Zheng and Mittempergher, Lorenza and Kluin, Roelof J C and Heijmans, Jeroen and Snel, Mireille and Pereira, Bernard and Schlicker, Andreas and Provenzano, Elena and Ali, Hamid Raza and Gaber, Alexander and O'Hurley, Gillian and Lehn, Sophie and Muris, Jettie J F and Wesseling, Jelle and Kay, Elaine and Sammut, Stephen John and Bardwell, Helen A and Barbet, Aurélie S and Bard, Floriane and Lecerf, Caroline and O'Connor, Darran P and Vis, Daniel J and Benes, Cyril H and McDermott, Ultan and Garnett, Mathew J and Simon, Iris M and Jirstrom, Karin and Dubois, Thierry and Linn, Sabine C and Gallagher, William M and Wessels, Lodewyk F A and Caldas, Carlos and Bernards, René},
title = {{Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer.}},
journal = {Scientific reports},
year = {2016},
volume = {6},
pages = {18517},
url = {http://www.nature.com/articles/srep18517}
}



%%%%%%%% 2015 %%%%%%%%

@article{Iskit:2015bl,
author = {Iskit, Sedef and Schlicker, Andreas and Wessels, Lodewyk and Peeper, Daniel S},
title = {{Fra-1 is a key driver of colon cancer metastasis and a Fra-1 classifier predicts disease-free survival.}},
journal = {Oncotarget},
year = {2015},
month = dec
}



@article{PlanellsCases:2015em,
author = {Planells-Cases, Rosa and Lutter, Darius and Guyader, Charlotte and Gerhards, Nora M and Ullrich, Florian and Elger, Deborah A and Kucukosmanoglu, Asli and Xu, Guotai and Voss, Felizia K and Reincke, S Momsen and Stauber, Tobias and Blomen, Vincent A and Vis, Daniel J and Wessels, Lodewyk F and Brummelkamp, Thijn R and Borst, Piet and Rottenberg, Sven and Jentsch, Thomas J},
title = {{Subunit composition of VRAC channels determines substrate specificity and cellular resistance to Pt-based anti-cancer drugs.}},
journal = {The EMBO journal},
year = {2015},
month = nov
}



@article{Nevedomskaya:2014kg,
author = {Nevedomskaya, Ekaterina and Wessels, Lodewyk and Zwart, Wilbert},
title = {{Genome-wide epigenetic profiling of breast cancer tumors treated with aromatase inhibitors}},
journal = {Genomics Data},
year = {2014},
volume = {2},
pages = {195--198},
month = dec
}



@article{Guinney:2015dm,
author = {Guinney, Justin and Dienstmann, Rodrigo and Wang, Xin and de Reynies, Aurélien and Schlicker, Andreas and Soneson, Charlotte and Marisa, Laetitia and Roepman, Paul and Nyamundanda, Gift and Angelino, Paolo and Bot, Brian M and Morris, Jeffrey S and Simon, Iris M and Gerster, Sarah and Fessler, Evelyn and De Sousa E Melo, Felipe and Missiaglia, Edoardo and Ramay, Hena and Barras, David and Homicsko, Krisztian and Maru, Dipen and Manyam, Ganiraju C and Broom, Bradley and Boige, Val{\'e}rie and Perez Villamil, Beatriz and Laderas, Ted and Salazar, Ramon and Gray, Joe W and Hanahan, Douglas and Tabernero, Josep and Bernards, Rene and Friend, Stephen H and Laurent-Puig, Pierre and Medema, Jan Paul and Sadanandam, Anguraj and Wessels, Lodewyk and Delorenzi, Mauro and Kopetz, Scott and Vermeulen, Louis and Tejpar, Sabine},
title = {{The consensus molecular subtypes of colorectal cancer}},
journal = {Nature medicine},
year = {2015},
url = {http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3967.html},
month = oct
}



@article{Periyasamy:2015dg,
author = {Periyasamy, Manikandan and Patel, Hetal and Lai, Chun-Fui and Nguyen, Van T M and Nevedomskaya, Ekaterina and Harrod, Alison and Russell, Roslin and Remenyi, Judit and Ochocka, Anna Maria and Thomas, Ross S and Fuller-Pace, Frances and Gyorffy, Balazs and Caldas, Carlos and Navaratnam, Naveenan and Carroll, Jason S and Zwart, Wilbert and Coombes, R Charles and Magnani, Luca and Buluwela, Laki and Ali, Simak},
title = {{APOBEC3B-Mediated Cytidine Deamination Is Required for Estrogen Receptor Action in Breast Cancer.}},
journal = {Cell reports},
year = {2015},
volume = {13},
number = {1},
pages = {108--121},
month = oct
}



@article{deJong:2014be,
author = {de Jong, Johann and Wessels, Lodewyk F A and van Lohuizen, Maarten and de Ridder, Jeroen and Akhtar, Waseem},
title = {{Applications of DNA integrating elements: Facing the bias bully.}},
journal = {Mobile genetic elements},
year = {2014},
volume = {4},
number = {6},
pages = {1--6},
month = nov
}



@article{Knijnenburg:2015cx,
author = {Knijnenburg, Theo A and Bismeijer, Tycho and Wessels, Lodewyk F A and Shmulevich, Ilya},
title = {{A multilevel pan-cancer map links gene mutations to cancer hallmarks.}},
journal = {Chinese journal of cancer},
year = {2015},
volume = {34},
number = {3},
pages = {48},
month = mar
}


@article{OnbehalfoftheCenterforPersonalizedCancerTreatment:2015hq,
author = {Lips*, Esther H and Michaut*, Magali and Hoogstraat, Marlous and Mulder, Lennart and Besselink, Nicolle JM and Koudijs, Marco J and Cuppen, Edwin and Voest, Emile E and Bernards, Rene and Nederlof, Petra M and Wesseling, Jelle and Rodenhuis, Sjoerd and Wessels, Lodewyk Fa},
title = {{Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response}},
journal = {Breast cancer research : BCR},
year = {2015},
volume = {17},
number = {1},
pages = {1037},
month = oct
}



@article{Stelloo:2015ef,
author = {Stelloo, Suzan and Nevedomskaya, Ekaterina and van der Poel, Henk G and de Jong, Jeroen and van Leenders, Geert Jlh and Jenster, Guido and Wessels, Lodewyk Fa and Bergman, Andries M and Zwart, Wilbert},
title = {{Androgen receptor profiling predicts prostate cancer outcome.}},
journal = {EMBO molecular medicine},
year = {2015},
month = sep
}

@article{deJong:2015hl,
author = {de Jong, Monique C and Ten Hoeve, Jelle and Grenman, Reidar and Wessels, Lodewyk and Kerkhoven, Ron and Te Riele, Hein and van den Brekel, Michiel Wm and Verheij, Marcel and Begg, Adrian C},
title = {{Pretreatment microRNA expression impacting on epithelial to mesenchymal transition predicts intrinsic radiosensitivity in head and neck cancer celllines and patients.}},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
year = {2015},
month = aug
}

@article{Wijdeven:2015cy,
author = {Wijdeven, R H and Pang, B and van der Zanden, S Y and Qiao, X and Blomen, V and Hoogstraat, M and Lips, E H and Janssen, L and Wessels, L and Brummelkamp, T R and Neefjes, J},
title = {{Genome-Wide Identification and Characterization of Novel Factors Conferring Resistance to Topoisomerase II Poisons in Cancer}},
journal = {Cancer research},
year = {2015},
month = aug
}



@article{Kemper:2015cz,
author = {Kemper, Kristel and Krijgsman, Oscar and Cornelissen-Steijger, Paulien and Shahrabi, Aida and Weeber, Fleur and Song, Ji-Ying and Kuilman, Thomas and Vis, Daniel J and Wessels, Lodewyk F and Voest, Emile E and Schumacher, Ton Nm and Blank, Christian U and Adams, David J and Haanen, John B and Peeper, Daniel S},
title = {{Intra- and inter-tumor heterogeneity in a vemurafenib-resistant melanoma patient and derived xenografts.}},
journal = {EMBO molecular medicine},
year = {2015},
month = jun
}



@article{ElKebir:um,
author = {El-Kebir, Mohammed and Soueidan, Hayssam and Hume, Thomas and Beisser, Daniela and Dittrich, Marcus and M{\"u}ller, Tobias and Blin, Guillaume and Heringa, Jaap and Nikolski, Macha and Wessels, Lodewyk F A and Klau, Gunnar W},
title = {{xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model}},
journal = {Bioinformatics},
year = {2015}
}



@article{Anonymous:Z28XTRNo,
title = {{BRCA1-like signature in triple negative breast cancer: molecular and clinical characterization reveals subgroups with therapeutic potential}},
year = {2015},
journal = {Molecular Oncology},
author = {Tesa M. Severson, Justine Peeters, Ian Majewski, Magali Michaut, Astrid Bosma, Philip C. Schouten, Suet-Feung Chin, Bernard Pereira, Mae A. Goldgraben, Tycho Bismeijer, Roelof J.C. Kluin, Jettie J.F. Muris, Karin Jirström, Ron M. Kerkhoven, Lodewyk Wessels, Carlos Caldas, René Bernards, Iris M. Simon, Sabine Linn},
url = {http://www.sciencedirect.com/science/article/pii/S157478911500099X}
}



@article{Pang:2015gg,
author = {Pang, Baoxu and de Jong, Johann and Qiao, Xiaohang and Wessels, Lodewyk F A and Neefjes, Jacques},
title = {{Chemical profiling of the genome with anti-cancer drugs defines target specificities.}},
journal = {Nature Chemical Biology},
year = {2015},
month = may
}



@article{vandeWetering:2015is,
author = {van de Wetering, Marc and Francies, Hayley E and Francis, Joshua M and Bounova, Gergana and Iorio, Francesco and Pronk, Apollo and van Houdt, Winan and van Gorp, Joost and Taylor-Weiner, Amaro and Kester, Lennart and McLaren-Douglas, Anne and Blokker, Joyce and Jaksani, Sridevi and Bartfeld, Sina and Volckman, Richard and van Sluis, Peter and Li, Vivian S W and Seepo, Sara and Sekhar Pedamallu, Chandra and Cibulskis, Kristian and Carter, Scott L and McKenna, Aaron and Lawrence, Michael S and Lichtenstein, Lee and Stewart, Chip and Koster, Jan and Versteeg, Rogier and van Oudenaarden, Alexander and Saez-Rodriguez, Julio and Vries, Robert G J and Getz, Gad and Wessels, Lodewyk and Stratton, Michael R and McDermott, Ultan and Meyerson, Matthew and Garnett, Mathew J and Clevers, Hans},
title = {{Prospective derivation of a living organoid biobank of colorectal cancer patients.}},
journal = {Cell},
year = {2015},
volume = {161},
number = {4},
pages = {933--945},
month = may
}




@article{Schouten:2015im,
author = {Schouten, Philip C and Grigoriadis, Anita and Kuilman, Thomas and Mirza, Hasan and Watkins, Johnathan A and Cooke, Saskia A and van Dyk, Ewald and Severson, Tesa M and Rueda, Oscar M and Hoogstraat, Marlous and Verhagen, Caroline and Natrajan, Rachael and Chin, Suet-Feung and Lips, Esther H and Kruizinga, Janneke and Velds, Arno and Nieuwland, Marja and Kerkhoven, Ron M and Krijgsman, Oscar and Vens, Conchita and Peeper, Daniel and Nederlof, Petra M and Caldas, Carlos and Tutt, Andrew N and Wessels, Lodewyk F and Linn, Sabine C},
title = {{Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms.}},
journal = {Molecular oncology},
year = {2015},
month = mar
}



@article{Kuilman:2015ca,
author = {Kuilman, Thomas and Velds, Arno and Kemper, Kristel and Ranzani, Marco and Bombardelli, Lorenzo and Hoogstraat, Marlous and Nevedomskaya, Ekaterina and Xu, Guotai and de Ruiter, Julian and Lolkema, Martijn P and Ylstra, Bauke and Jonkers, Jos and Rottenberg, Sven and Wessels, Lodewyk F and Adams, David J and Peeper, Daniel S and Krijgsman, Oscar},
title = {{CopywriteR: DNA copy number detection from off-target sequence data.}},
journal = {Genome biology},
year = {2015},
volume = {16},
pages = {49}
}


@article{Rad:2015eg,
author = {Rad, Roland and Rad, Lena and Wang, Wei and Strong, Alexander and Ponstingl, Hannes and Bronner, Iraad F and Mayho, Matthew and Steiger, Katja and Weber, Julia and Hieber, Maren and Veltkamp, Christian and Eser, Stefan and Geumann, Ulf and {\"O}llinger, Rupert and Zukowska, Magdalena and Barenboim, Maxim and Maresch, Roman and Cadinanos, Juan and Friedrich, Mathias and Varela, Ignacio and Constantino-Casas, Fernando and Sarver, Aaron and Ten Hoeve, Jelle and Prosser, Haydn and Seidler, Barbara and Bauer, Judith and Heikenw{\"a}lder, Mathias and Metzakopian, Emmanouil and Krug, Anne and Ehmer, Ursula and Schneider, G{\"u}nter and Kn{\"o}sel, Thomas and R{\"u}mmele, Petra and Aust, Daniela and Gr{\"u}tzmann, Robert and Pilarsky, Christian and Ning, Zemin and Wessels, Lodewyk and Schmid, Roland M and Quail, Michael A and Vassiliou, George and Esposito, Irene and Liu, Pentao and Saur, Dieter and Bradley, Allan},
title = {{A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer.}},
journal = {Nature genetics},
year = {2015},
volume = {47},
number = {1},
pages = {47--56},
month = jan
}

@article{Michailidou:2015ds,
author = {Michailidou, Kyriaki and Beesley, Jonathan and Lindstrom, Sara and Canisius, Sander and Dennis, Joe and Lush, Michael J and Maranian, Mel J and Bolla, Manjeet K and ...},
title = {{Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer}},
journal = {Nature genetics},
year = {2015},
volume = {47},
number = {4},
pages = {373--380},
month = mar
}

@article{Groenendijk:2015ig,
author = {Groenendijk, Floris H and de Jong, Jeroen and van de Putte, Elisabeth E Fransen and Michaut, Magali and Schlicker, Andreas and Peters, Dennis and Velds, Arno and Nieuwland, Marja and van den Heuvel, Michel M and Kerkhoven, Ron M and Wessels, Lodewijk F and Broeks, Annegien and van Rhijn, Bas W G and Bernards, Rene and van der Heijden, Michiel S},
title = {{ERBB2 Mutations Characterize a Subgroup of Muscle-invasive Bladder Cancers with Excellent Response to Neoadjuvant Chemotherapy}},
journal = {European Urology},
year = {2015},
pages = {1--5},
month = jan
}



%%%%%%%% 2014 %%%%%%%%

@article{Jaspers:2014bf,
author = {Jaspers, Janneke E and Sol, Wendy and Kersbergen, Ariena and Schlicker, Andreas and Guyader, Charlotte and Xu, Guotai and Wessels, Lodewyk and Borst, Piet and Jonkers, Jos and Rottenberg, Sven},
title = {{BRCA2-deficient sarcomatoid mammary tumors exhibit multi-drug resistance.}},
journal = {Cancer research},
year = {2014},
month = dec
}

@article{Spanjaard:2014eu,
author = {Spanjaard, Emma and Smal, Ihor and Angelopoulos, Nicos and Verlaan, Ingrid and Matov, Alexandre and Meijering, Erik and Wessels, Lodewyk and Bos, Hans and de Rooij, Johan},
title = {{Quantitative imaging of focal adhesion dynamics and their regulation by HGF and Rap1 signaling.}},
journal = {Experimental cell research},
year = {2014},
month = oct
}

@article{Possik:2014iw,
author = {Possik, Patricia A and M{\"u}ller, Judith and Gerlach, Carmen and Kenski, Juliana C N and Huang, Xinyao and Shahrabi, Aida and Krijgsman, Oscar and Song, Ji-Ying and Smit, Marjon A and Gerritsen, Bram and Lieftink, Cor and Kemper, Kristel and Michaut, Magali and Beijersbergen, Roderick L and Wessels, Lodewyk and Schumacher, Ton N and Peeper, Daniel S},
title = {{Parallel In Vivo and In Vitro Melanoma RNAi Dropout Screens Reveal Synthetic Lethality between Hypoxia and DNA Damage Response Inhibition.}},
journal = {Cell reports},
year = {2014},
volume = {9},
number = {4},
pages = {1375--1386},
month = nov
}

@article{Oosterkamp:2014ii,
author = {Oosterkamp, Hendrika M and Hijmans, E Marielle and Brummelkamp, Thijn R and Canisius, Sander and Wessels, Lodewyk F A and Zwart, Wilbert and Bernards, René},
title = {{USP9X downregulation renders breast cancer cells resistant to tamoxifen.}},
journal = {Cancer research},
year = {2014},
volume = {74},
number = {14},
pages = {3810--3820},
month = jul
}

@article{Rosell:2014hc,
author = {Rosell, Meritxell and Nevedomskaya, Ekaterina and Stelloo, Suzan and Nautiyal, Jaya and Poliandri, Ariel and Steel, Jennifer H and Wessels, Lodewyk F A and Carroll, Jason S and Parker, Malcolm G and Zwart, Wilbert},
title = {{Complex Formation and Function of Estrogen Receptor alpha in Transcription Requires RIP140.}},
journal = {Cancer research},
year = {2014},
volume = {74},
number = {19},
pages = {5469--5479},
month = oct
}

@article{Sieuwerts:2014dp,
author = {Sieuwerts, Anieta M and Willis, Scooter and Burns, Michael B and Look, Maxime P and Gelder, Marion E Meijer-Van and Schlicker, Andreas and Heideman, Marinus R and Jacobs, Heinz and Wessels, Lodewyk and Leyland-Jones, Brian and Gray, Kathryn P and Foekens, John A and Harris, Reuben S and Martens, John W M},
title = {{Elevated APOBEC3B Correlates with Poor Outcomes for Estrogen-Receptor-Positive Breast Cancers.}},
journal = {Hormones & cancer},
year = {2014},
month = aug
}


@article{Knijnenburg:2014ke,
author = {Knijnenburg, Theo A and Ramsey, Stephen A and Berman, Benjamin P and Kennedy, Kathleen A and Smit, Arian F A and Wessels, Lodewyk F A and Laird, Peter W and Aderem, Alan and Shmulevich, Ilya},
title = {{Multiscale representation of genomic signals}},
journal = {Nature methods},
year = {2014},
volume = {11},
number = {6},
pages = {689--694},
month = apr
}


@article{Lee:wb,
author = {Lee, Eunjee and de Ridder, Jeroen and Kool, Jaap and Wessels, Lodewyk F A and Bussemaker, Harmen J},
title = {{Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis.}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2014},
volume = {111},
number = {15},
pages = {5747--5752},
month = apr
}

@article{Vollebergh:2014jj,
author = {Vollebergh, Marieke A and Lips, Esther H and Nederlof, Petra M and Wessels, Lodewyk F A and Wesseling, Jelle and vander Vijver, Marc J and de Vries, Elisabeth G E and van Tinteren, Harm and Jonkers, Jos and Hauptmann, Michael and Rodenhuis, Sjoerd and Linn, Sabine C},
title = {{Genomic patterns resembling BRCA1- and BRCA2-mutated breast cancers predict benefit of intensified carboplatin-based chemotherapy.}},
journal = {Breast cancer research : BCR},
year = {2014},
volume = {16},
number = {3},
pages = {R47}
}

@article{deRonde:2014bf,
author = {de Ronde, Jorma J and Bonder, Marc Jan and Lips, Esther H and Rodenhuis, Sjoerd and Wessels, Lodewyk F A},
title = {{Breast cancer subtype specific classifiers of response to neoadjuvant chemotherapy do not outperform classifiers trained on all subtypes.}},
journal = {PloS one},
year = {2014},
volume = {9},
number = {2},
pages = {e88551}
}

@article{Aguilar:2014ew,
author = {Aguilar, Helena and Urruticoechea, Ander and Halonen, Pasi and Kiyotani, Kazuma and Mushiroda, Taisei and Barril, Xavier and Serra-Musach, Jordi and Islam, Abul and Caizzi, Livia and Di Croce, Luciano and Nevedomskaya, Ekaterina and Zwart, Wilbert and Bostner, Josefine and Karlsson, Elin and Tenorio, Gizeh Pérez and Fornander, Tommy and Sgroi, Dennis C and Garcia-Mata, Rafael and Jansen, Maurice Phm and Garcia, Nadia and Bonifaci, Nuria and Climent, Fina and Soler, Maria Teresa and Rodriguez-Vida, Alejo and Gil, Miguel and Brunet, Joan and Martrat, Griselda and Gomez-Baldo, Laia and Extremera, Ana I and Figueras, Agnes and Balart, Josep and Clarke, Robert and Burnstein, Kerry L and Carlson, Kathryn E and Katzenellenbogen, John A and Vizoso, Miguel and Esteller, Manel and Villanueva, Alberto and Rodriguez-Pena, Ana B and Bustelo, Xosé R and Nakamura, Yusuke and Zembutsu, Hitoshi and Staal, Olle and Beijersbergen, Roderick L and Pujana, Miguel Angel},
title = {{VAV3 mediates resistance to breast cancer endocrine therapy.}},
journal = {Breast cancer research : BCR},
year = {2014},
volume = {16},
number = {3},
pages = {R53},
month = may
}




@article{bonzannipetri,
 title={Petri Nets are a Biologist’s Best Friend},
 year={2014},
 author={Bonzanni, Nicola and Feenstra, Anton and Fokkink, Wan and Heringa, Jaap},
 journal={Lecture Notes in Bioinformatics}
}


%%%%%%%% 2013 %%%%%%%%

@article{deRonde:2013iz,
author = {de Ronde, J J and Rigaill, G and Rottenberg, S and Rodenhuis, S and Wessels, L F A},
title = {{Identifying subgroup markers in heterogeneous populations}},
journal = {Nucleic acids research},
year = {2013},
month = sep
}

@article{vanDyk:2013jv,
author = {van Dyk, Ewald and Reinders, Marcel J T and Wessels, Lodewyk F A},
title = {{A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control.}},
journal = {Nucleic acids research},
year = {2013},
volume = {41},
number = {9},
pages = {e100},
month = may
}


@article{bonzanni2013hard,
 title={Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model},
 author={Bonzanni, Nicola and Garg, Abhishek and Feenstra, K Anton and Sch{\"u}tte, Judith and Kinston, Sarah and Miranda-Saavedra, Diego and Heringa, Jaap and Xenarios, Ioannis and G{\"o}ttgens, Berthold},
 journal={Bioinformatics},
 volume={29},
 number={13},
 pages={i80--i88},
 year={2013},
 publisher={Oxford University Press}
}



%%%%%%%%% Sander %%%%%%%%

@article{pmid23910573,
 title = {{A gene signature for late distant metastasis in breast cancer identifies a potential mechanism of late recurrences.}},
 author = {Lorenza Mittempergher and Mahasti Saghatchian and Denise M Wolf and Stefan Michiels and Sander Canisius and Philippe Dessen and Suzette Delaloge and Vladimir Lazar and Stephen C Benz and Thomas Tursz and René Bernards and Laura J van't Veer},
 journal = {{Mol Oncol}},
 volume = {7},
 number = {5},
 year = {2013},
 month = oct,
 pages = {987-99},
 abstract = {Breast cancer risk of recurrence is known to span 20 years, yet existing prognostic signatures are best at predicting early recurrences (≤ 5 years). There is a critical need to identify those patients at risk of late-relapse (>5 years), in order to select potential candidates for further treatment and to identify molecular targets for such treatment.},
 pubmed = {23910573},
 pii = {S1574-7891(13)00091-4},
 doi = {10.1016/j.molonc.2013.07.006},
 nlmuniqueid = {101308230}
}

@article{pmid22907427,
 title = {{PKA phosphorylation redirects ERα to promoters of a unique gene set to induce tamoxifen resistance.}},
 author = {R de Leeuw and K Flach and C Bentin Toaldo and X Alexi and S Canisius and J Neefjes and R Michalides and W Zwart},
 journal = {{Oncogene}},
 volume = {32},
 number = {30},
 year = {2013},
 month = jul,
 pages = {3543-51},
 pii = {onc2012361},
 doi = {10.1038/onc.2012.361},
 pubmed = {22907427},
 nlmuniqueid = {8711562}
}

@article{pmid23535729,
 title = {{Large-scale genotyping identifies 41 new loci associated with breast cancer risk.}},
 author = {Kyriaki Michailidou and Per Hall and Anna Gonzalez-Neira and Maya Ghoussaini and Joe Dennis and Roger L Milne and Marjanka K Schmidt and Jenny Chang-Claude and Stig E Bojesen and Manjeet K Bolla et al.},
 journal = {{Nat. Genet.}},
 volume = {45},
 number = {4},
 year = {2013},
 month = apr,
 pages = {353-61, 361e1-2},
 abstract = {Breast cancer is the most common cancer among women. Common variants at 27 loci have been identified as associated with susceptibility to breast cancer, and these account for ∼9% of the familial risk of the disease. We report here a meta-analysis of 9 genome-wide association studies, including 10,052 breast cancer cases and 12,575 controls of European ancestry, from which we selected 29,807 SNPs for further genotyping. These SNPs were genotyped in 45,290 cases and 41,880 controls of European ancestry from 41 studies in the Breast Cancer Association Consortium (BCAC). The SNPs were genotyped as part of a collaborative genotyping experiment involving four consortia (Collaborative Oncological Gene-environment Study, COGS) and used a custom Illumina iSelect genotyping array, iCOGS, comprising more than 200,000 SNPs. We identified SNPs at 41 new breast cancer susceptibility loci at genome-wide significance (P < 5 × 10(-8)). Further analyses suggest that more than 1,000 additional loci are involved in breast cancer susceptibility.},
 pii = {ng.2563},
 doi = {10.1038/ng.2563},
 pubmed = {23535729},
 pmc = {PMC3771688},
 mid = {NIHMS498947},
 nlmuniqueid = {9216904}
}

@article{pmid22871386,
 title = {{TRPM7 is required for breast tumor cell metastasis.}},
 author = {Jeroen Middelbeek and Arthur J Kuipers and Linda Henneman and Daan Visser and Ilse Eidhof and Remco van Horssen and Bé Wieringa and Sander V Canisius and Wilbert Zwart and Lodewyk F Wessels and Fred C G J Sweep and Peter Bult and Paul N Span and Frank N van Leeuwen and Kees Jalink},
 journal = {{Cancer Res.}},
 volume = {72},
 number = {16},
 year = {2012},
 month = aug,
 pages = {4250-61},
 abstract = {TRPM7 encodes a Ca2+-permeable nonselective cation channel with kinase activity. TRPM7 has been implicated in control of cell adhesion and migration, but whether TRPM7 activity contributes to cancer progression has not been established. Here we report that high levels of TRPM7 expression independently predict poor outcome in breast cancer patients and that it is functionally required for metastasis formation in a mouse xenograft model of human breast cancer. Mechanistic investigation revealed that TRPM7 regulated myosin II-based cellular tension, thereby modifying focal adhesion number, cell-cell adhesion and polarized cell movement. Our findings therefore suggest that TRPM7 is part of a mechanosensory complex adopted by cancer cells to drive metastasis formation.},
 pii = {0008-5472.CAN-11-3863},
 doi = {10.1158/0008-5472.CAN-11-3863},
 pubmed = {22871386},
 nlmuniqueid = {2984705R}
}

@article{pmid21667122,
 title = {{Association of the germline TP53 R72P and MDM2 SNP309 variants with breast cancer survival in specific breast tumor subgroups.}},
 author = {Alexandra J van den Broek and Annegien Broeks and Hugo M Horlings and Sander V M Canisius and Linde M Braaf and Anita Langerød and Laura J Van't Veer and Marjanka K Schmidt},
 journal = {{Breast Cancer Res. Treat.}},
 volume = {130},
 number = {2},
 year = {2011},
 month = nov,
 pages = {599-608},
 abstract = {The tumor suppressor gene TP53 and its regulator MDM2 are both important players in the DNA-damage repair "TP53 response pathway". Common germline polymorphisms in these genes may affect outcome in patients with tumors characterized by additional somatic changes in the same or a related pathway. To evaluate this hypothesis, we determined the effect of the common germline TP53 R72P and MDM2 SNP309 polymorphisms on breast cancer survival in a consecutive cohort of breast cancer patients (age at diagnosis <53 years, n = 295) with gene expression data available. Patients were classified in subgroups according to their tumor TP53 mutation status and three gene expression profiles; a TP53 mutation status expression signature, a PTEN/PI3K pathway signature and the 70-gene prognosis profile. Survival analyses were performed using Cox regression models adjusting for clinico-pathological characteristics and treatment. An increase in breast cancer-specific mortality was observed for carriers of the germline MDM2 SNP309 rare GG-genotype (range hazard ratios: 2-3) or TP53 R72P heterozygous GC-genotype (range hazard ratios: 1-2) compared to those having the common genotypes within subgroups of tumors displaying a "more aggressive phenotype" gene expression profile. There was no evidence of such an effect on survival within the TP53-mutated tumor group for TP53 R72P carriers but a suggestion of an effect for MDM2 SNP309 carriers (GG vs. TT-genotype HR 2.99, P = 0.06). These results indicate that common polymorphisms in specific pathways may add to the worse prognosis of patients with tumors in which these pathways are affected by somatic alterations.},
 doi = {10.1007/s10549-011-1615-y},
 pubmed = {21667122},
 nlmuniqueid = {8111104}
}

@article{pmid22002538,
 title = {{Oestrogen receptor-co-factor-chromatin specificity in the transcriptional regulation of breast cancer.}},
 author = {Wilbert Zwart and Vasiliki Theodorou and Marleen Kok and Sander Canisius and Sabine Linn and Jason S Carroll},
 journal = {{EMBO J.}},
 volume = {30},
 number = {23},
 year = {2011},
 month = nov,
 pages = {4764-76},
 abstract = {The complexity of oestrogen receptor α (ERα)-mediated transcription is becoming apparent, but global insight into the co-regulatory proteins that assist ERα transcription is incomplete. Here, we present the most comprehensive chromatin-binding landscape of ERα co-regulatory proteins to date. We map by ChIP-seq the essential p160 co-regulators (SRC1, SRC2 and SRC3), and the histone acetyl transferases p300 and CBP in MCF-7 breast cancer cells. We find a complex network of co-regulator binding, with preferential binding sites for each co-regulator. Unlike previous suggestions, we find SRC recruitment almost exclusively following ligand treatment. Interestingly, we find specific subsets of genes regulated by ligand-dependent and -independent co-regulator recruitment. Co-factor-binding profiles were integrated with expression data from cell lines and primary tumour cohorts, to reveal specific transcriptional networks that influence clinical outcome. Genes that are bound by SRC3, but not other p160 proteins, have predictive value in cohorts of breast cancer patients. By generating a robust and global view of co-factor-binding properties, we discover new levels of co-regulator complexity, but also reveal specific gene networks that may influence endocrine response.},
 pii = {emboj2011368},
 doi = {10.1038/emboj.2011.368},
 pubmed = {22002538},
 pmc = {PMC3243612},
 nlmuniqueid = {8208664}
}




@article{Tian:2012bk,
author = {Tian, Sun and Roepman, Paul and Popovici, Vlad and Michaut, Magali and Majewski, Ian and Salazar, Ramon and Santos, Cristina and Rosenberg, Robert and Nitsche, Ulrich and Mesker, Wilma E and Bruin, Sjoerd and Tejpar, Sabine and Delorenzi, Mauro and Bernards, Ren{\'e} and Simon, Iris},
title = {{A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency}},
journal = {The Journal of pathology},
year = {2012},
pages = {n/a--n/a},
month = oct
}





@article{Jong14,
 author = {de Jong, Johann and Akhtar, Waseem and Badhai, Jitendra and Rust, Alistair G. and Rad, Roland and Hilkens, John and Berns, Anton and van Lohuizen, Maarten and Wessels, Lodewyk F. A. and de Ridder, Jeroen},
 day = {10},
 doi = {10.1371/journal.pgen.1004250},
 journal = {PLoS Genet},
 month = apr,
 number = {4},
 pages = {e1004250+},
 posted-at = {2014-04-11 20:18:22},
 publisher = {Public Library of Science},
 title = {Chromatin Landscapes of Retroviral and Transposon Integration Profiles},
 url = {http://dx.doi.org/10.1371/journal.pgen.1004250},
 volume = {10},
 year = {2014}
}

@Article{Akhtar13,
AUTHOR = {Akhtar, Waseem and de Jong, Johann and Pindyurin, Alexey V. and Pagie, Ludo and Meuleman, Wouter and de Ridder, Jeroen and Berns, Anton and Wessels, Lodewyk F. A. and van Lohuizen, Maarten and van Steensel, Bas},
TITLE = {Chromatin position effects assayed by thousands of reporters integrated in parallel.},
JOURNAL = {Cell},
VOLUME = {154},
YEAR = {2013},
NUMBER = {4},
PAGES = {914-27},
URL = {http://www.biomedsearch.com/nih/Chromatin-position-effects-assayed-by/23953119.html},
PubMedID = {23953119},
ISSN = {1097-4172},
}

@article{Jong11,
 author = {de Jong, Johann and de Ridder, Jeroen and van der Weyden, Louise and Sun, Ning and van Uitert, Miranda and Berns, Anton and van Lohuizen, Maarten and Jonkers, Jos and Adams, David J. and Wessels, Lodewyk F. A.},
 day = {1},
 doi = {10.1093/nar/gkr447},
 issn = {1362-4962},
 journal = {Nucleic Acids Res},
 keywords = {bioinformatics, staffpaper},
 month = aug,
 number = {15},
 pages = {e105},
 pmid = {21652642},
 posted-at = {2011-06-10 17:15:11},
 priority = {2},
 title = {Computational identification of insertional mutagenesis targets for cancer gene discovery},
 url = {http://dx.doi.org/10.1093/nar/gkr447},
 volume = {39},
 year = {2011}
}

@proceedings {4555,
 title = {Mutational Genomics for Cancer Pathway Discovery},
 journal = {8th IAPR International Conference, PRIB 2013, Nice, France, June 17-20, 2013. Proceedings},
 volume = {7986},
 year = {2013},
 pages = {pp 35-46},
 publisher = {Springer Berlin Heidelberg},
 isbn = {978-3-642-39158-3},
 doi = {10.1007/978-3-642-39159-0_4},
 author = {Jeroen de Ridder and Jaap Kool and Anthony G Uren and Jan J. Bot and Johann de Jong and Alistair G. Rust and Anton Berns and Maarten van Lohuizen and Adams, David J and Lodewyk F. A. Wessels and Marcel J.T. Reinders}
}

@article{citeulike:13203265,
 author = {Akhtar, Waseem and Pindyurin, Alexey V. and de Jong, Johann and Pagie, Ludo and Ten Hoeve, Jelle and Berns, Anton and Wessels, Lodewyk F. and van Steensel, Bas and van Lohuizen, Maarten},
 issn = {1750-2799},
 journal = {Nature protocols},
 keywords = {cell-biology, gwas, tools},
 month = jun,
 number = {6},
 pages = {1255--1281},
 pmid = {24810036},
 posted-at = {2014-05-28 14:28:00},
 priority = {2},
 title = {Using {TRIP} for genome-wide position effect analysis in cultured cells.},
 url = {http://view.ncbi.nlm.nih.gov/pubmed/24810036},
 volume = {9},
 year = {2014}
}

@article{citeulike:12856709,
 author = {Bard-Chapeau, Emilie A. and Nguyen, Anh-Tuan and Rust, Alistair G. and Sayadi, Ahmed and Lee, Philip and Chua, Belinda Q. and New, Lee-Sun and de Jong, Johann and Ward, Jerrold M. and Chin, Christopher K. Y. and Chew, Valerie and Toh, Han C. and Abastado, Jean-Pierre and Benoukraf, Touati and Soong, Richie and Bard, Frederic A. and Dupuy, Adam J. and Johnson, Randy L. and Radda, George K. and Chan, Eric C. and Wessels, Lodewyk F. A. and Adams, David J. and Jenkins, Nancy A. and Copeland, Neal G.},
 day = {8},
 doi = {10.1038/ng.2847},
 issn = {1061-4036},
 journal = {Nat Genet},
 keywords = {cancer, informatics},
 month = jan,
 number = {1},
 pages = {24--32},
 posted-at = {2013-12-19 11:49:25},
 priority = {2},
 publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
 title = {Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model},
 url = {http://dx.doi.org/10.1038/ng.2847},
 volume = {46},
 year = {2014}
}

@article{citeulike:12249981,
 author = {Heideman, Marinus R. and Wilting, Roel H. and Yanover, Eva and Velds, Arno and de Jong, Johann and Kerkhoven, Ron M. and Jacobs, Heinz and Wessels, Lodewyk F. and Dannenberg, Jan-Hermen},
 day = {14},
 doi = {10.1182/blood-2012-08-450916},
 journal = {Blood},
 keywords = {c-myc, project\_hdac},
 month = mar,
 number = {11},
 pages = {2038--2050},
 pmid = {23327920},
 posted-at = {2013-04-08 17:23:11},
 priority = {2},
 title = {Dosage-dependent tumor suppression by histone deacetylases 1 and 2 through regulation of {c-Myc} collaborating genes and p53 function},
 url = {http://dx.doi.org/10.1182/blood-2012-08-450916},
 volume = {121},
 year = {2013}
}

@article{citeulike:8136180,
 author = {Tamulonis, Carlos and Postma, Marten and Marlow, Heather Q. and Magie, Craig R. and de Jong, Johann and Kaandorp, Jaap},
 day = {23},
 doi = {10.1016/j.ydbio.2010.10.017},
 issn = {00121606},
 journal = {Developmental Biology},
 keywords = {modeling, morphogenesis},
 month = mar,
 number = {1},
 pages = {217--228},
 posted-at = {2012-09-12 13:56:26},
 priority = {2},
 title = {A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering},
 url = {http://dx.doi.org/10.1016/j.ydbio.2010.10.017},
 volume = {351},
 year = {2011}
}



@article{Sun2014,
abstract = {Treatment of BRAF(V600E) mutant melanoma by small molecule drugs that target the BRAF or MEK kinases can be effective, but resistance develops invariably. In contrast, colon cancers that harbour the same BRAF(V600E) mutation are intrinsically resistant to BRAF inhibitors, due to feedback activation of the epidermal growth factor receptor (EGFR). Here we show that 6 out of 16 melanoma tumours analysed acquired EGFR expression after the development of resistance to BRAF or MEK inhibitors. Using a chromatin-regulator-focused short hairpin RNA (shRNA) library, we find that suppression of sex determining region Y-box 10 (SOX10) in melanoma causes activation of TGF-$\beta$ signalling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-$\beta$ (PDGFRB), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-$\beta$ results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-$\beta$ becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells having varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug, but this is reversed when the drug treatment is discontinued. We find evidence for SOX10 loss and/or activation of TGF-$\beta$ signalling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Our findings provide a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a 'drug holiday' and identify patients with EGFR-positive melanoma as a group that may benefit from re-treatment after a drug holiday.},
author = {Sun, Chong and Wang, Liqin and Huang, Sidong and Heynen, Guus J J E and Prahallad, Anirudh and Robert, Caroline and Haanen, John and Blank, Christian and Wesseling, Jelle and Willems, Stefan M and Zecchin, Davide and Hobor, Sebastijan and Bajpe, Prashanth K and Lieftink, Cor and Mateus, Christina and Vagner, Stephan and Grernrum, Wipawadee and Hofland, Ingrid and Schlicker, Andreas and Wessels, Lodewyk F a and Beijersbergen, Roderick L and Bardelli, Alberto and {Di Nicolantonio}, Federica and Eggermont, Alexander M M and Bernards, Rene},
doi = {10.1038/nature13121},
file = {:C$\backslash$:/Users/schlandi/work/literature/papers/Sun\_Nature\_2014.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Animals,Antineoplastic Agents,Antineoplastic Agents: administration \& dosage,Antineoplastic Agents: pharmacology,Cell Aging,Cell Aging: drug effects,Cell Proliferation,Cell Proliferation: drug effects,Drug Resistance,Epidermal Growth Factor,Epidermal Growth Factor: biosynthesis,Epidermal Growth Factor: genetics,Epidermal Growth Factor: metabolism,Female,Flow Cytometry,Gene Expression Regulation,Gene Library,Humans,Indoles,Indoles: administration \& dosage,Indoles: pharmacology,Melanoma,Melanoma: drug therapy,Melanoma: enzymology,Melanoma: genetics,Melanoma: pathology,Mice,Mitogen-Activated Protein Kinase Kinases,Mitogen-Activated Protein Kinase Kinases: antagoni,Mitogen-Activated Protein Kinase Kinases: metaboli,Neoplasm,Neoplasm: drug effects,Neoplasm: genetics,Neoplastic,Neoplastic: drug effects,Platelet-Derived Growth Factor beta,Platelet-Derived Growth Factor beta: biosynthesis,Platelet-Derived Growth Factor beta: genetics,Platelet-Derived Growth Factor beta: metabolism,Protein Kinase Inhibitors,Protein Kinase Inhibitors: administration \& dosage,Protein Kinase Inhibitors: pharmacology,Proto-Oncogene Proteins B-raf,Proto-Oncogene Proteins B-raf: antagonists \& inhib,Proto-Oncogene Proteins B-raf: genetics,Proto-Oncogene Proteins B-raf: metabolism,RNA,Receptor,Receptor Protein-Tyrosine Kinases,Receptor Protein-Tyrosine Kinases: biosynthesis,Receptor Protein-Tyrosine Kinases: genetics,Receptor Protein-Tyrosine Kinases: metabolism,SOXE Transcription Factors,SOXE Transcription Factors: deficiency,SOXE Transcription Factors: genetics,Signal Transduction,Signal Transduction: drug effects,Small Interfering,Sulfonamides,Sulfonamides: administration \& dosage,Sulfonamides: pharmacology,Transforming Growth Factor beta,Transforming Growth Factor beta: metabolism,Transforming Growth Factor beta: pharmacology,cancer},
mendeley-tags = {cancer},
month = apr,
number = {7494},
pages = {118--22},
pmid = {24670642},
publisher = {Nature Publishing Group},
title = {{Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24670642},
volume = {508},
year = {2014}
}
@article{Sun2014a,
abstract = {There are no effective therapies for the \~{}30\% of human malignancies with mutant RAS oncogenes. Using a kinome-centered synthetic lethality screen, we find that suppression of the ERBB3 receptor tyrosine kinase sensitizes KRAS mutant lung and colon cancer cells to MEK inhibitors. We show that MEK inhibition results in MYC-dependent transcriptional upregulation of ERBB3, which is responsible for intrinsic drug resistance. Drugs targeting both EGFR and ERBB2, each capable of forming heterodimers with ERBB3, can reverse unresponsiveness to MEK inhibition by decreasing inhibitory phosphorylation of the proapoptotic proteins BAD and BIM. Moreover, ERBB3 protein level is a biomarker of response to combinatorial treatment. These data suggest a combination strategy for treating KRAS mutant colon and lung cancers and a way to identify the tumors that are most likely to benefit from such combinatorial treatment.},
author = {Sun, Chong and Hobor, Sebastijan and Bertotti, Andrea and Zecchin, Davide and Huang, Sidong and Galimi, Francesco and Cottino, Francesca and Prahallad, Anirudh and Grernrum, Wipawadee and Tzani, Anna and Schlicker, Andreas and Wessels, Lodewyk F A and Smit, Egbert F and Thunnissen, Erik and Halonen, Pasi and Lieftink, Cor and Beijersbergen, Roderick L and {Di Nicolantonio}, Federica and Bardelli, Alberto and Trusolino, Livio and Bernards, Rene},
doi = {10.1016/j.celrep.2014.02.045},
issn = {2211-1247},
journal = {Cell reports},
month = apr,
number = {1},
pages = {86--93},
pmid = {24685132},
title = {{Intrinsic resistance to MEK inhibition in KRAS mutant lung and colon cancer through transcriptional induction of ERBB3.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24685132},
volume = {7},
year = {2014}
}
@article{Roepman2013,
abstract = {In most colorectal cancer (CRC) patients, outcome cannot be predicted because tumors with similar clinicopathological features can have differences in disease progression and treatment response. Therefore, a better understanding of the CRC biology is required to identify those patients who will benefit from chemotherapy and to find a more tailored therapy plan for other patients. Based on unsupervised classification of whole genome data from 188 stages I-IV CRC patients, a molecular classification was developed that consist of at least three major intrinsic subtypes (A-, B- and C-type). The subtypes were validated in 543 stages II and III patients and were associated with prognosis and benefit from chemotherapy. The heterogeneity of the intrinsic subtypes is largely based on three biological hallmarks of the tumor: epithelial-to-mesenchymal transition, deficiency in mismatch repair genes that result in high mutation frequency associated with microsatellite instability and cellular proliferation. A-type tumors, observed in 22\% of the patients, have the best prognosis, have frequent BRAF mutations and a deficient DNA mismatch repair system. C-type patients (16 have the worst outcome, a mesenchymal gene expression phenotype and show no benefit from adjuvant chemotherapy treatment. Both A-type and B-type tumors have a more proliferative and epithelial phenotype and B-types benefit from adjuvant chemotherapy. B-type tumors (62 show a low overall mutation frequency consistent with the absence of DNA mismatch repair deficiency. Classification based on molecular subtypes made it possible to expand and improve CRC classification beyond standard molecular and immunohistochemical assessment and might help in the future to guide treatment in CRC patients.},
annote = {Owner: schlandi
 
Added to JabRef: 2013.10.15},
author = {Roepman, Paul and Schlicker, Andreas and Tabernero, Josep and Majewski, Ian and Tian, Sun and Moreno, Victor and Snel, Mireille H and Chresta, Christine M and Rosenberg, Robert and Nitsche, Ulrich and Macarulla, Teresa and Capella, Gabriel and Salazar, Ramon and Orphanides, George and Wessels, Lodewyk Fa and Bernards, Rene and Simon, Iris M},
file = {:C$\backslash$:/Users/schlandi/work/literature/papers/Roepman\_IntJCancer\_2013.pdf:pdf},
journal = {Int J Cancer},
month = jul,
title = {{Colorectal cancer intrinsic subtypes predict chemotherapy benefit, deficient mismatch repair and epithelial-to-mesenchymal transition.}},
url = {http://dx.doi.org/10.1002/ijc.28387 C:$\backslash$Users$\backslash$schlandi$\backslash$work$\backslash$literature$\backslash$papers$\backslash$Roepman\_IntJCancer\_2013.pdf},
year = {2013}
}
@article{Huang2012,
abstract = {Inhibitors of the ALK and EGF receptor tyrosine kinases provoke dramatic but short-lived responses in lung cancers harboring EML4-ALK translocations or activating mutations of EGFR, respectively. We used a large-scale RNAi screen to identify MED12, a component of the transcriptional MEDIATOR complex that is mutated in cancers, as a determinant of response to ALK and EGFR inhibitors. MED12 is in part cytoplasmic where it negatively regulates TGF-$\beta$R2 through physical interaction. MED12 suppression therefore results in activation of TGF-$\beta$R signaling, which is both necessary and sufficient for drug resistance. TGF-$\beta$ signaling causes MEK/ERK activation, and consequently MED12 suppression also confers resistance to MEK and BRAF inhibitors in other cancers. MED12 loss induces an EMT-like phenotype, which is associated with chemotherapy resistance in colon cancer patients and to gefitinib in lung cancer. Inhibition of TGF-$\beta$R signaling restores drug responsiveness in MED12(KD) cells, suggesting a strategy to treat drug-resistant tumors that have lost MED12.},
annote = {Owner: schlandi
 
Added to JabRef: 2012.12.03},
author = {Huang, Sidong and H\"{o}lzel, Michael and Knijnenburg, Theo and Schlicker, Andreas and Roepman, Paul and McDermott, Ultan and Garnett, Mathew and Grernrum, Wipawadee and Sun, Chong and Prahallad, Anirudh and Groenendijk, Floris H and Mittempergher, Lorenza and Nijkamp, Wouter and Neefjes, Jacques and Salazar, Ramon and {Ten Dijke}, Peter and Uramoto, Hidetaka and Tanaka, Fumihiro and Beijersbergen, Roderick L and Wessels, Lodewyk F A and Bernards, Ren\'{e}},
file = {:C$\backslash$:/Users/schlandi/work/literature/papers/Huang\_Cell\_2012.pdf:pdf},
journal = {Cell},
keywords = {cancer,expression signature,therapy outcome},
mendeley-tags = {cancer,expression signature,therapy outcome},
number = {5},
pages = {937--950},
title = {{MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-$\beta$ Receptor Signaling.}},
url = {http://dx.doi.org/10.1016/j.cell.2012.10.035 C:$\backslash$Users$\backslash$schlandi$\backslash$work$\backslash$literature$\backslash$papers$\backslash$Huang\_Cell\_2012.pdf},
volume = {151},
year = {2012}
}
@article{Schlicker2012,
abstract = {ABSTRACT:Colorectal cancer (CRC) is a heterogeneous and biologically poorly understood disease. To tailor CRC treatment, it is essential to first model this heterogeneity by defining subtypes of patients with homogeneous biological and clinical characteristics and second match these subtypes to cell lines for which extensive pharmacological data is available, thus linking targeted therapies to patients most likely to respond to treatment.We applied a new unsupervised, iterative approach to stratify CRC tumor samples into subtypes based on genome-wide mRNA expression data. By applying this stratification to several CRC cell line panels and integrating pharmacological response data, we generated hypotheses regarding the targeted treatment of different subtypes.In agreement with earlier studies, the two dominant CRC subtypes are highly correlated with a gene expression signature of epithelial-mesenchymal-transition (EMT). Notably, further dividing these two subtypes using iNMF (iterative Non-negative Matrix Factorization) revealed five subtypes that exhibit activation of specific signaling pathways, and show significant differences in clinical and molecular characteristics. Importantly, we were able to validate the stratification on independent, published datasets comprising over 1600 samples. Application of this stratification to four CRC cell line panels comprising 74 different cell lines, showed that the tumor subtypes are well represented in available CRC cell line panels. Pharmacological response data for targeted inhibitors of SRC, WNT, GSK3b, aurora kinase, PI3 kinase, and mTOR, showed significant differences in sensitivity across cell lines assigned to different subtypes. Importantly, some of these differences in sensitivity were in concordance with high expression of the targets or activation of the corresponding pathways in primary tumor samples of the same subtype.The stratification presented here is robust, captures important features of CRC, and offers valuable insight into functional differences between CRC subtypes. By matching the identified subtypes to cell line panels that have been pharmacologically characterized, it opens up new possibilities for the development and application of targeted therapies for defined CRC patient sub-populations.},
annote = {Owner: schlandi
 
Added to JabRef: 2013.02.12},
author = {Schlicker, Andreas and Beran, Garry and Chresta, Christine M and McWalter, Gael and Pritchard, Alison and Weston, Susie and Runswick, Sarah and Davenport, Sara and Heathcote, Kerry and Castro, Denis Alferez and Orphanides, George and French, Tim and Wessels, Lodewyk Fa},
file = {:C$\backslash$:/Users/schlandi/work/literature/papers/Schlicker\_BMCMedGenomics\_2012.pdf:pdf},
journal = {BMC Med Genomics},
keywords = {cell line,cluster analysis,colorectal cancer,therapy outcome},
mendeley-tags = {cell line,cluster analysis,colorectal cancer,therapy outcome},
pages = {66},
title = {{Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines.}},
url = {http://dx.doi.org/10.1186/1755-8794-5-66},
volume = {5},
year = {2012}
}






@ARTICLE{Staiger2012,
 author = {Staiger C and Cadot S and Kooter R and Dittrich M and Müller T
 and Klau GW and Wessels LF},
 title = {A critical evaluation of network and pathway based classifiers for
 outcome
 prediction in breast cancer},
 journal = {Plos One},
 year = {2012},
 volume = {7},
 month = {April},
 URL = {http://dx.doi.org/10.1371/journal.pone.0034796}}





@ARTICLE{vollebergh:2011b,
 AUTHOR = {Vollebergh MA AND Nederlof PM AND Wessels LF AND Joosse SA AND Van Beers E AND Froklage F AND
 Holtkamp M AND Schrama JG AND Wesseling J AND Hauptmann M AND De Bruin M AND Rodenhuis M AND
 Linn SC},
 TITLE = {A clinical test for {BRCA}ness: using array comparative genomic hybridization to predict benefit
 of high dose, platinum containing, chemotherapy in {ER}-low/{HER}2-negative breast cancer patients},
 JOURNAL = {Ann Oncol},
 YEAR = 2011,
 NOTE = {In press}
}


%%%%%%%%%%%%%%%%%%%% 2011 complete %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



@ARTICLE{jong:2011,
 AUTHOR = {De Jong J AND De Ridder J AND Van der Weyden L AND Sun N AND Van Uitert M
 AND Berns A AND Van Lohuizen M AND Jonkers J AND Adams DJ AND Wessels LF},
 TITLE = {Computational identification of insertional mutagenesis targets for cancer gene discovery},
 JOURNAL = {Nucl Acids Res},
 YEAR = 2011,
 VOLUME = {39 (15)},
 PAGES = {e105},
 URL = {http://dx.doi.org/10.1093/nar/gkr447}
}



@ARTICLE{vollebergh:2011a,
 AUTHOR = {Vollebergh MA AND Lips EH AND Nederlof PM AND Wessels LF AND Schmidt MK AND Van Beers EH
 AND Cornelissen S AND Holtkamp M AND Froklage FE AND De Vries EG AND Schrama JG AND Wesseling J
 Van de Vijver MJ AND Van Tinteren H AND De Bruin M AND Hauptmann M AND Rodenhuis S AND Linn SC},
 TITLE = {An {aCGH} classifier derived from {BRCA1}-mutated breast cancer and benefit of high-dose platinum-based
 chemotherapy in {HER2}-negative breast cancer patients},
 JOURNAL = {\it Ann Oncol},
 YEAR = 2011,
 VOLUME = 22,
 NUMBER = 7,
 PAGES = {1561--1570},
 URL = {http://dx.doi.org/10.1093/annonc/mdq624}
}




@ARTICLE{kok:2011,
 AUTHOR = {Kok M AND Zwart W AND Holm C AND Fles R AND Hauptmann M AND Van't Veer LJ AND
 Wessels LF AND Neefjes J AND Stal O AND Linn SC AND Landberg G AND Michalides R},
 TITLE = {{PKA}-induced phosphorylation of {ER}alpha at serine 305 and high {PAK1} levels is associated
 with sensitivity to tamoxifen in {ER}-positive breast cancer},
 JOURNAL = {Breast Cancer Res Treat},
 YEAR = 2011,
 VOLUME = 125,
 NUMBER = 1,
 PAGES = {1-12},
 URL = {http://dx.doi.org/10.1007/s10549-010-0798-y}
}




%%%%%%%%%%%%%%%%%%%% 2010 complete %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



@ARTICLE{Ramsey2010,
 AUTHOR = {Ramsey SA AND Knijnenburg TA AND Kennedy KA AND Zak DE
 AND Gilchrist M AND Gold ES AND Johnson CD AND Lampano AE
 AND Litvak V AND Navarro G AND Stolyar T AND Aderem A AND Shmulevich I},
 title = {Genome-wide histone acetylation data improve prediction of mammalian
 transcription factor binding sites.},
 journal = {Bioinformatics},
 year = 2010,
 volume = 26,
 number = 17,
 pages = {2071--2075},
 url = {http://dx.doi.org/10.1093/bioinformatics/btq405},
 pdf = {/~knijnenburg/publications/Ramsey_2010_TFBinding.pdf}
}

@ARTICLE{Saleem2010,
 author = {Saleem RA AND Long-O'Donnell R AND Dilworth DJ AND Armstrong AM
 AND Jamakhandi AP AND Wan Y AND Knijnenburg TA AND Niemisto A AND Boyle J
 AND Rachubinski RA AND Shmulevich I AND Aitchison JD},
 title = {Genome-wide analysis of effectors of peroxisome biogenesis},
 journal = {PLoS One},
 year = 2010,
 volume = 5,
 number = 8,
 pages = {e11953},
 url = {http://dx.doi.org/10.1371/journal.pone.0011953}
}



@Article{21126340,
 AUTHOR = {Bruin S AND Klijn C AND Liefers GJ AND Braaf LM AND Joosse SA AND Van Beers EH AND Verwaal VJ
 AND Morreau H AND Wessels LF AND Van Velthuysen ML AND Tollenaar RA AND Van 't Veer LJ},
 TITLE = {Specific genomic aberrations in primary colorectal cancer are associated with liver metastases},
 JOURNAL = {BMC Cancer},
 VOLUME = 10,
 YEAR = 2010,
 NUMBER = 1,
 PAGES = 662,
 URL = {http://dx.doi.org/10.1186/1471-2407-10-662}
}



@ARTICLE{ridder:2010,
 AUTHOR = {De Ridder J AND Gerrits A AND Bot J AND De Haan G AND Reinders M AND Wessels LF},
 TITLE = {Inferring Combinatorial Association Logic Networks in Multimodal Genome-Wide Screens},
 JOURNAL = {Bioinformatics},
 YEAR = 2010,
 VOLUME = {26(12)},
 PAGES = {i149-157},
 URL = {http://dx.doi.org/10.1093/bioinformatics/btq211}
}

@ARTICLE{bemmel:2010,
 AUTHOR = {Van Bemmel JG AND Pagie L AND Braunschweig U AND Brugman W AND Meuleman W
 AND Kerkhoven RM AND Van Steensel B},
 TITLE = {The insulator protein {SU(HW)} fine-tunes nuclear lamina interactions of the \emph{Drosophila} genome},
 JOURNAL = {PLoS One},
 YEAR = 2010,
 VOLUME = {5(11)},
 PAGES = {e15013},
 URL = {http://dx.doi.org/10.1371/journal.pone.0015013}
}

@Article{20735817,
 AUTHOR = {Holstege H AND Van Beers E AND Velds A AND Liu X AND Joosse S AND Klarenbeek S AND Schut E
 AND Kerkhoven R AND Klijn C AND Wessels L AND Nederlof P AND Jonkers J},
 TITLE = {Cross-species comparison of {aCGH} data from mouse and human {BRCA1}- and {BRCA2}-mutated breast cancers},
 JOURNAL = {BMC Cancer},
 VOLUME = {10},
 YEAR = 2010,
 NUMBER = {1},
 PAGES = {455},
 URL = {http://dx.doi.org/10.1186/1471-2407-10-455}
}

@article{de2010kc,
 author={De Ronde JJ AND Klijn C AND Velds A AND Holstege H AND Reinders MJ AND Jonkers J
 AND Wessels LF},
 title={{KC-SMARTR}: An {R} package for detection of statistically significant aberrations in multi-experiment {aCGH} data},
 journal={BMC Res Notes},
 year={2010},
 volume={3},
 number={1},
 pages={298},
 URL = {http://dx.doi.org/10.1186/1756-0500-3-298}
}

@Article{2010Klijn2,
 AUTHOR = {Varela I* AND \textbf{Klijn C*} AND Stephens P AND Mudie L AND Stebbings L AND Galappaththige D
 AND Van der Gulden H AND Schut E AND Klarenbeek S AND Campbell P AND Wessels L AND Stratton
 M AND Jonkers J AND Futreal PA AND Adams D},
 NOTE ={(*Varela and Klijn contributed equally)},
 TITLE = {Somatic structural rearrangements in genetically engineered mouse mammary tumors},
 JOURNAL = {Genome Biol},
 VOLUME = {11},
 YEAR = {2010},
 NUMBER = {10},
 PAGES = {R100},
 URL = {http://dx.doi.org/10.1186/gb-2010-11-10-r100}
}

@article{taskesen2010hat,
 title={{HAT}: {H}ypergeometric Analysis of Tiling-arrays with application to promoter-{GeneChip} data},
 author={Taskesen E AND Beekman R AND De Ridder J AND Wouters BJ AND Peeters JK AND Touw IP AND Reinders MJ AND Delwel R},
 journal={BMC Bioinformatics},
 year={2010},
 volume={11},
 number={1},
 pages={275},
 URL = {http://dx.doi.org/10.1186/1471-2105-11-275}
}


@ARTICLE{meuleman:2010,
 AUTHOR = {Peric-Hupkes D AND Meuleman W AND Pagie L AND Bruggeman SW AND Solovei I AND Brugman W AND Graf S AND Flicek P AND
 Kerkhoven RM AND van Lohuizen M AND Reinders M AND Wessels L AND van Steensel B},
 TITLE = {Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation.},
 JOURNAL = {Mol Cell},
 YEAR = 2010,
 VOLUME = {38(4)},
 PAGES = {603--613},
 URL = {http://dx.doi.org/10.1016/j.molcel.2010.03.016}
}


@ARTICLE{ronde:10,
 AUTHOR = {De Ronde JJ AND Hannemann J AND Halfwerk H AND Mulder L AND Straver ME AND Vrancken Peeters MJ AND Wesseling J AND Van de Vijver M
 AND Wessels LF AND Rodenhuis S},
 TITLE = {Concordance of clinical and molecular breast cancer subtyping in the context of preoperative chemotherapy response.},
 JOURNAL = {Breast Cancer Res Treat},
 YEAR = 2010,
 VOLUME = 119,
 PAGES = {119--126},
 URL = {http://dx.doi.org/10.1007/s10549-009-0499-6}
}


@ARTICLE{jong:2010,
 AUTHOR = {De Jong MC AND Pramana J AND Knegjens JL AND Balm AJ AND Van den Brekel MW AND
 Hauptmann M AND Begg AC AND Rasch CR},
 TITLE = {{HPV} and high risk gene expression profiles predict response to chemoradiotherapy in head
 and neck cancer independent of clinical factors},
 JOURNAL = {Radiother Oncol},
 YEAR = 2010,
 VOLUME = {95(3)},
 PAGES = {365--370},
 URL = {http://dx.doi.org/10.1016/j.radonc.2010.02.001}
}




@ARTICLE{ronde:2010,
 AUTHOR = {De Ronde J AND Wessels LF AND Wesseling J},
 TITLE = {Molecular subtyping of breast cancer: ready to use?},
 JOURNAL = {Lancet Oncol},
 YEAR = 2010,
 VOLUME = 11,
 PAGES = {306--307},
 URL = {http://dx.doi.org/10.1016/S1470-2045(10)70036-X}
}

@ARTICLE{broeks:2010,
 AUTHOR = {Broeks A AND Braaf LM AND Wessels LF AND Van de Vijver M AND De Bruin ML AND Stovall M
 AND Russell NS AND Van Leeuwen FE AND Van 't Veer LJ},
 TITLE = {Radiation-associated breast tumors display a distinct gene expression profile},
 JOURNAL = {Int J Radiat Oncol Biol Phys},
 YEAR = 2010,
 VOLUME = 76,
 PAGES = {540--547},
 URL = {http://dx.doi.org/10.1016/j.ijrobp.2009.09.004}
}

@ARTICLE{mattison:2010,
 AUTHOR = {Mattison J AND Kool J AND Uren AG AND De Ridder J AND Wessels L AND Jonkers J
 AND Bignell GR AND Butler A AND Rust AG AND Brosch M AND Wilson CH AND Van der Weyden L AND
 Largaespada DA AND Stratton MR AND Futreal PA AND Van Lohuizen M AND Berns A AND Collier LS
 AND Hubbard T AND Adams DJ},
 TITLE = {Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach},
 JOURNAL = {Cancer Res},
 YEAR = 2010,
 VOLUME = 70,
 PAGES = {883--895},
 URL = {http://dx.doi.org/10.1158/0008-5472.CAN-09-1737}
}

@ARTICLE{kool:2010,
 AUTHOR = {Kool J AND Uren AG AND Martins CP AND Sie D AND De Ridder J AND Turner G AND
 Van Uitert M AND Matentzoglu K AND Lagcher W AND Krimpenfort P AND Gadiot J AND
 Pritchard C AND Lenz J AND Lund AH AND Jonkers J AND Rogers J AND Adams DJ AND
 Wessels L AND Berns A AND Van Lohuizen M},
 TITLE = {Insertional mutagenesis in mice deficient for {p15Ink4b}, {p16Ink4a}, {p21Cip1}, and {p27Kip1}
 reveals cancer gene interactions and correlations with tumor phenotypes},
 JOURNAL = {Cancer Res},
 YEAR = 2010,
 VOLUME = 70,
 PAGES = {520--531},
 URL = {http://dx.doi.org/10.1158/0008-5472.CAN-09-2736}
}

@ARTICLE{klijn:2010,
 AUTHOR = {Klijn C AND Bot J AND Adams DJ AND Reinders M AND Wessels L AND Jonkers J},
 TITLE = {Identification of networks of co-occurring, tumor-related {DNA} copy number changes using a
 genome-wide scoring approach},
 JOURNAL = {PLoS Comput Biol},
 YEAR = 2010,
 VOLUME = 6,
 PAGES = {e1000631},
 URL = {http://dx.doi.org/10.1371/journal.pcbi.1000631}
}

@ARTICLE{horlings:2010,
 AUTHOR = {Horlings HM AND Lai C AND Nuyten DS AND Halfwerk H AND Kristel P AND Van Beers E
 AND Joosse SA AND Klijn C AND Nederlof PM AND Reinders MJ AND Wessels LF
 AND Van de Vijver MJ},
 TITLE = {Integration of {DNA} copy number alterations and prognostic gene expression signatures in breast
 cancer patients},
 JOURNAL = {Clin Cancer Res},
 YEAR = 2010,
 VOLUME = 16,
 PAGES = {651--663},
 URL = {http://dx.doi.org/10.1158/1078-0432.CCR-09-0709}
}


%%%%%%%%%%%%%%%%%%%% 2009 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%




@ARTICLE{knijnenburg:2009a,
 AUTHOR = {Knijnenburg TA AND Daran JM AND Van den Broek MA AND Daran-Lapujade PA AND De Winde JH AND
 Pronk JT AND Reinders MJ AND Wessels LF},
 TITLE = {Combinatorial effects of environmental parameters on transcriptional regulation in {S}accharomyces
 cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data},
 JOURNAL = {BMC Genomics},
 YEAR = 2009,
 VOLUME = 10,
 PAGES = 53,
 URL = {http://dx.doi.org/10.1186/1471-2164-10-53},
 pdf = {/~knijnenburg/publications/Knijnenburg_2009_Compendium.pdf}
}

@ARTICLE{knijnenburg:2009b,
 AUTHOR = {Knijnenburg TA AND Wessels LF AND Reinders MJ AND Shmulevich I},
 TITLE = {Fewer permutations, more accurate {P}-values},
 JOURNAL = {Bioinformatics},
 YEAR = 2009,
 VOLUME = 25,
 NUMBER = 12,
 PAGES = {i161--i168},
 URL = {http://dx.doi.org/10.1093/bioinformatics/btp211},
 PDF = {/~knijnenburg/publications/Knijnenburg_2009_Permutations.pdf}
}




@ARTICLE{gast:2009a,
 AUTHOR = {Gast MC AND Van Dulken EJ AND Van Loenen TK AND Kingma-Vegter F AND Westerga J AND Flohil CC
 AND Knol JC AND Jimenez CR AND Van Gils CH AND Wessels LF AND Schellens JH AND Beijnen JH},
 TITLE = {Detection of breast cancer by surface-enhanced laser desorption/ionization time-of-flight
 mass spectrometry tissue and serum protein profiling},
 JOURNAL = {Int J Biol Markers},
 YEAR = 2009,
 VOLUME = 24,
 PAGES = {130--141}
}

@ARTICLE{gast:2009b,
 AUTHOR = {Gast MC AND Van Gils CH AND Wessels LF AND Harris N AND Bonfrer JM AND Rutgers EJ
 AND Schellens JH AND Beijnen JH},
 TITLE = {Serum protein profiling for diagnosis of breast cancer using {SELDI-TOF MS}},
 JOURNAL = {Oncol Rep},
 YEAR = 2009,
 VOLUME = 22,
 PAGES = {205--213}
}

@ARTICLE{gast:2009c,
 AUTHOR = {Gast MC AND Van Gils CH AND Wessels LF AND Harris N AND Bonfrer JM AND Rutgers EJ AND Schellens
 JH AND Beijnen JH},
 TITLE = {Influence of sample storage duration on serum protein profiles assessed by surface-enhanced laser
 desorption/ionisation time-of-flight mass spectrometry ({SELDI-TOF MS})},
 JOURNAL = {Clin Chem Lab Med},
 YEAR = 2009,
 VOLUME = 47,
 PAGES = {694--705},
 URL = {http://dx.doi.org/10.1515/CCLM.2009.151}
}

@ARTICLE{joose:2009,
 AUTHOR = {Joosse SA AND Van Beers EH AND Tielen IH AND Horlings H AND Peterse JL AND Hoogerbrugge N AND
 Ligtenberg MJ AND Wessels LF AND Axwijk P AND Verhoef S AND Hogervorst FB AND Nederlof PM},
 TITLE = {Prediction of {BRCA1}-association in hereditary non-{BRCA1/2} breast carcinomas with array-{CGH}},
 JOURNAL = {Breast Cancer Res Treat},
 YEAR = 2009,
 VOLUME = 116,
 PAGES = {479--489},
 URL = {http://dx.doi.org/10.1007/s10549-008-0117-z}
}


@ARTICLE{Meuleman2009,
 AUTHOR = {Meuleman W AND Engwegen JY AND Gast MC AND Wessels LF AND Reinders MJ},
 TITLE = {Analysis of mass spectrometry data using sub-spectra},
 JOURNAL = {BMC Bioinformatics},
 YEAR = 2009,
 VOLUME = {10 Suppl 1},
 NUMBER = {S51},
 URL = {http://www.biomedcentral.com/1471-2105/10/S1/S51}
}




@ARTICLE{Vliet2009,
 author = {Van Vliet MH and Wessels LF AND Reinders MJ},
 title = {Knowledge driven decomposition of tumor expression profiles},
 year = 2009,
 journal = {BMC Bioinformatics},
 volume = 10,
 pages = {S20},
 number = {Suppl 1},
 url = {http://www.biomedcentral.com/1471-2105/10/S1/S20}
}



@ARTICLE{Kok2009,
 AUTHOR = {Kok M AND Linn SC AND Van Laar RK AND Jansen MP AND Van den Berg TM AND Delahaye LJ AND Glas AM AND Peterse JL AND
 Hauptmann M AND Foekens JA AND Klijn JG AND Wessels LF AND Van't Veer LJ AND Berns EM},
 TITLE = {Comparison of gene expression profiles predicting progression in breast cancer patients treated with tamoxifen},
 JOURNAL = {Breast Cancer Res Treat},
 YEAR = 2009,
 VOLUME = 113,
 PAGES = {275--283},
 URL = {http://dx.doi.org/10.1007/s10549-008-9939-y}
}




%%%%%%%%%%%%%%%%%%%% 2008 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@ARTICLE{knijnenburg:2008a,
 AUTHOR = {Knijnenburg TA AND Wessels LF AND Reinders MJ},
 TITLE = {Combinatorial influence of environmental parameters on transcription factor activity},
 JOURNAL = {Bioinformatics},
 YEAR = 2008,
 VOLUME = 24,
 NUMBER = 13,
 PAGES = {i172--i181},
 URL = {http://dx.doi.org/10.1093/bioinformatics/btn155},
 PDF = {/~knijnenburg/publications/Knijnenburg_2008_InfluenceOnTFActivity.pdf}
}

@ARTICLE{Knijnenburg2008b,
 AUTHOR = {Knijnenburg TA AND Wessels LF AND Reinders MJ},
 TITLE = {Creating gene set activity profiles with time-series expression data},
 JOURNAL = {Int J Bioinform Res Appl},
 YEAR = 2008,
 VOLUME = 4,
 NUMBER = 3,
 PAGES = {306--323},
 PDF = {/~knijnenburg/publications/Knijnenburg_2008_GSAP.pdf}
}



@ARTICLE{Reyal2008,
 author = {Reyal F AND Van Vliet MH AND Armstrong N AND Horlings H AND
 De Visser KE AND Kok M AND Teschendorff AE AND Mook S AND
 Salmon R AND Van de Vijver MJ AND Wessels LF},
 title = {A comprehensive analysis of nine prognostic signatures reveals the
 high predictive capacity of proliferation, immune response and {RNA}
 splicing modules in breast cancer},
 JOURNAL = {Breast Cancer Res},
 YEAR = 2008,
 VOLUME = 10,
 pages = {R93},
 URL = {http://dx.doi.org/10.1186/bcr2192}
}

@ARTICLE{Meuleman2008,
 AUTHOR = {Meuleman W AND Engwegen JY AND Gast MC AND Beijnen JH AND Reinders MJ AND Wessels LF},
 TITLE = {Comparison of normalisation methods for surface-enhanced laser desorption and ionisation ({SELDI}) time-of-flight ({TOF}) mass spectrometry data},
 JOURNAL = {BMC Bioinformatics},
 YEAR = 2008,
 VOLUME = 9,
 NUMBER = {88},
 URL = {http://www.biomedcentral.com/1471-2105/9/88}
}

@ARTICLE{Vliet2008,
 author = {Van Vliet M AND Reyal F AND Horlings H AND Van de Vijver MJ AND Reinders M AND Wessels L},
 title = {Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability},
 journal = {BMC Genomics},
 year = 2008,
 volume = 9,
 pages = {375},
 url = {http://dx.doi.org/10.1186/1471-2164-9-375}
}

@ARTICLE{Uitert2008,
 author = {Van Uitert M AND Meuleman W AND Wessels L},
 title = {Biclustering Sparse Binary Genomic Data},
 journal = {J Comput Biol},
 year = 2008,
 volume = 15,
 pages = {1329--1345},
 url = {http://dx.doi.org/10.1089/cmb.2008.0066}
}

@ARTICLE{Guelen2008,
 AUTHOR = {Guelen L AND Pagie L AND Brasset E AND Meuleman W AND Faza MB AND Talhout W AND Eussen BH AND De Klein A AND Wessels L AND De Laat W AND Van Steensel B},
 TITLE = {Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions},
 JOURNAL = {Nature},
 YEAR = 2008,
 VOLUME = 453,
 PAGES = {948--951},
 URL = {http://dx.doi.org/10.1038/nature06947}
}


@ARTICLE{engwegen,
 author = {Engwegen JY AND Depla AC AND Smits ME AND Snel P AND Tuynman H AND Cats A AND Van Heukelem HA AND Meuleman W AND Wessels LF AND Schellens JH AND Beijnen JH},
 title = {Detection of colorectal cancer by serum and tissue protein profiling: a prospective study in a population at risk},
 journal = {Biomark Insights},
 year = {2008},
 volume = {3},
 pages = {375--385},
 URL = {http://www.la-press.com/article.php?article_id=891}
}



@ARTICLE{weigelt:08,
 AUTHOR = {Weigelt B AND Horlings HM AND Kreike B AND Hayes MM AND Hauptmann M AND Wessels LF AND De Jong D AND Van de Vijver MJ AND Van 't Veer LJ AND Peterse JL},
 YEAR = 2008,
 TITLE = {Refinement of breast cancer classification by molecular characterisation of histological special types},
 JOURNAL = {J Pathol},
 VOLUME = 216,
 PAGES = {141-150},
 URL = {http://dx.doi.org/10.1002/path.2407}
}


@ARTICLE{Foijer2008,
 AUTHOR = {Foijer F AND Simonis M AND Van Vliet M AND Wessels LF AND Kerkhoven R AND Sorger PK AND te Riele H},
 TITLE = {Oncogenic pathways impinging on the {G2}-restriction point},
 JOURNAL = {Oncogene},
 YEAR = {2008},
 VOLUME = {27},
 PAGES = {1142--1154},
 URL = {http://dx.doi.org/10.1038/sj.onc.1210724}
}

@ARTICLE{Klijn2008,
 AUTHOR = {Klijn C AND Holstege H AND De Ridder J AND Liu X AND Reinders M AND Jonkers J AND Wessels L},
 TITLE = {Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array {CGH} data},
 JOURNAL = {Nucleic Acids Res},
 YEAR = {2008},
 VOLUME = {36},
 PAGES = {e13},
 URL = {http://dx.doi.org/10.1093/nar/gkm1143}
}

@ARTICLE{Stoop2008,
 AUTHOR = {Van der Stoop P AND Boutsma EA AND Hulsman D AND Noback S AND Heimerikx M AND Kerkhoven RM AND Voncken JW AND Wessels LF AND Van Lohuizen M},
 TITLE = {Ubiquitin {E3} ligase {R}ing1b/{R}nf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells},
 JOURNAL = {PLoS ONE},
 YEAR = {2008},
 VOLUME = {3},
 PAGES = {e2235},
 URL = {http://dx.doi.org/10.1371/journal.pone.0002235}
}

@ARTICLE{Uren2008,
 AUTHOR = {Uren AG AND Kool J AND Matentzoglu K AND De Ridder J AND Mattison J AND Van Uitert M AND Lagcher W AND Sie D AND Tanger E AND Cox T AND Reinders M AND Hubbard TJ AND Rogers J AND Jonkers J AND Wessels L AND Adams DJ AND Van Lohuizen M AND Berns A},
 TITLE = {Large-scale mutagenesis in p19({ARF})- and p53-deficient mice identifies cancer genes and their collaborative networks},
 JOURNAL = {Cell},
 YEAR = {2008},
 VOLUME = {133},
 PAGES = {727--741},
 URL = {http://dx.doi.org/10.1016/j.cell.2008.03.021}
}


%%%%%%%%%%%%%%%%%%%% 2007 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@ARTICLE{Abbott2007,
 author = {Abbott DA AND Knijnenburg TA AND De Poorter LM AND Reinders MJ AND Pronk JT
 AND Van Maris AJ},
 title = {Generic and specific transcriptional responses to different weak
 organic acids in anaerobic chemostat cultures of {S}accharomyces cerevisiae},
 journal = {FEMS Yeast Res},
 year = 2007,
 volume = 7,
 number = 6,
 pages = {819--833},
 url = {http://dx.doi.org/10.1111/j.1567-1364.2007.00242.x},
 pdf = {/~knijnenburg/publications/Abbott_2007_Acids.pdf}
}

@ARTICLE{Clements2007,
 author = {Clements M AND Van Someren EP AND Knijnenburg TA AND Reinders MJ},
 title = {Integration of known transcription factor binding site information
 and gene expression data to advance from co-expression to co-regulation},
 journal = {Genomics Proteomics Bioinformatics},
 year = 2007,
 volume = 5,
 number = 2,
 pages = {86--101},
 url = {http://dx.doi.org/10.1016/S1672-0229(07)60019-9},
 pdf = {/~knijnenburg/publications/Clements_2007_IntegratingTFInfo.pdf}
}

@ARTICLE{Groot2007,
 author = {De Groot MJ AND Daran-Lapujade PA AND Van Breukelen B AND Knijnenburg TA
 AND De Hulster EA AND Reinders MJ AND Pronk JT AND Heck AJ AND Slijper M},
 title = {Quantitative proteomics and transcriptomics of anaerobic and aerobic
 yeast cultures reveals post-transcriptional regulation of key cellular
 processes},
 journal = {Microbiology},
 year = 2007,
 volume = 153,
 number = 11,
 pages = {3864--3878},
 url = {http://dx.doi.org/10.1099/mic.0.2007/009969-0},
 pdf = {/~knijnenburg/publications/Groot_2007_Aerobic.pdf},
}

@ARTICLE{Nicola2007,
 author = {De Nicola R AND Hazelwood LA AND De Hulster EA AND Walsh MC AND Knijnenburg TA
 AND Reinders MJ AND Walker GM AND Pronk JT AND Daran JG AND Daran-Lapujade PA},
 title = {Physiological and transcriptional responses of {S}accharomyces cerevisiae
 to zinc limitation in chemostat cultures.},
 journal = {Appl Environ Microbiol},
 year = 2007,
 volume = 73,
 number = 23,
 pages = {7680--7692},
 url = {http://dx.doi.org/10.1128/AEM.01445-07},
 pdf = {/~knijnenburg/publications/Nicola_2007_Zinc.pdf}
}

@ARTICLE{Knijnenburg2007a,
 AUTHOR = {Knijnenburg TA AND De Winde JH AND Daran JM AND Daran-Lapujade P AND Pronk JT AND Reinders MJ AND Wessels LF},
 TITLE = {Exploiting combinatorial cultivation conditions to infer transcriptional regulation},
 JOURNAL = {BMC Genomics},
 YEAR = 2007,
 VOLUME = 8,
 PAGES = 25,
 URL = {http://dx.doi.org/10.1186/1471-2164-8-25},
 PDF = {/~knijnenburg/publications/Knijnenburg_2007_Combinatorial.pdf}
}


@ARTICLE{Liu2007a,
 author = {Liu X AND Holstege H AND Van der Gulden H AND Treur-Mulder M AND Zevenhoven J AND Velds A AND Kerkhoven RM AND Van Vliet MH AND Wessels LF AND Peterse JL AND Berns A AND Jonkers J},
 title = {Somatic loss of {BRCA1} and p53 in mice induces mammary tumors with features of human {BRCA1}-mutated basal-like breast cancer},
 journal = {Proc Natl Acad Sci USA},
 year = {2007},
 volume = {104},
 pages = {12111--12116},
 url = {http://dx.doi.org/10.1073/pnas.0702969104}
}


@ARTICLE{Ridder2007a,
 AUTHOR = {De Ridder J AND Kool J AND Uren J AND Bot J AND Wessels L AND Reinders MJ},
 TITLE = {Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes},
 JOURNAL = {Bioinformatics},
 YEAR = {2007},
 VOLUME = {23},
 PAGES = {i133--i141},
 URL = {http://dx.doi.org/10.1093/bioinformatics/btm202}
}

@ARTICLE{Berlo2007,
 AUTHOR = {Van Berlo R AND Wessels LF AND De Ridder D AND Reinders MJ},
 TITLE = {Protein complex prediction using an integrative bioinformatics approach},
 JOURNAL = {J Bioinform Comput Biol},
 YEAR = {2007},
 VOLUME = {5},
 PAGES = {839--864},
 URL = {http://www.worldscinet.com/cgi-bin/details.cgi?id=pii:S0219720007002953&type=html}
}

@ARTICLE{Lai2007,
 AUTHOR = {Lai C AND Horlings HH AND Van de Vijver MJ AND Van Beers EH AND Nederlof PM AND Wessels LF AND Reinders MJ},
 TITLE = {{SIRAC}: {S}upervised {I}dentification of {R}egions of {A}berration in {aCGH} datasets},
 JOURNAL = {BMC Bioinformatics},
 YEAR = {2007},
 VOLUME = {8},
 PAGES = {422},
 URL = {http://dx.doi.org/10.1186/1471-2105-8-422}
}

@ARTICLE{Theodorou2007,
 AUTHOR = {Theodorou V AND Kimm M AND Boer M AND Wessels LF AND Theelen W AND Jonkers J AND Hilkens J},
 TITLE = {Identification of novel genes, gene families and pathways involved in mammary cancer by {MMTV} insertional mutagenesis},
 JOURNAL = {Nat Genet},
 YEAR = {2007},
 VOLUME = {39},
 PAGES = {759--69},
 URL = {http://www.nature.com/ng/journal/v39/n6/abs/ng2034.html}
}

@ARTICLE{Vliet2007,
 AUTHOR = {Van Vliet MH AND Klijn CN AND Wessels LF AND Reinders MJ},
 TITLE = {Module-based outcome prediction using breast cancer compendia},
 JOURNAL = {PLoS ONE},
 YEAR = {2007},
 VOLUME = {2},
 PAGES = {e1047},
 URL = {http://dx.doi.org/10.1371/journal.pone.0001047}
}


%%%%%%%%%%%%%%%%%%%% 2006 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@ARTICLE{Knijnenburg2006b,
 author = {Knijnenburg TA AND Reinders MJ AND Wessels LF},
 title = {Artifacts of {M}arkov blanket filtering based on discretized features
 in small sample size applications},
 journal = {Pattern Recognition Letters},
 year = 2006,
 volume = 27,
 pages = {709-714},
 pdf = {/~knijnenburg/publications/Knijnenburg_2006_MarkovBlankets.pdf}
}

@ARTICLE{Knijnenburg2006a,
 author = {Knijnenburg TA AND Wessels LF AND Reinders MJ},
 title = {Condition transition analysis reveals {TF} activity related to nutrient-limitation-specific
 effects of oxygen presence in yeast},
 journal = {International Conference on Computational Methods in Systems Biology},
 year = 2006,
 pages = {271-284},
 pdf = {/~knijnenburg/publications/Knijnenburg_2006_ConditionTransitionAnalysis.pdf}
}

@ARTICLE{Kresnowati2006,
 author = {Kresnowati MT AND Van Winden WA AND Almering MJ AND Ten Pierick A AND Ras C
 AND Knijnenburg TA AND Daran-Lapujade PA AND Pronk JT AND Heijnen JJ AND Daran JG},
 title = {When transcriptome meets metabolome: fast cellular responses of yeast
 to sudden relief of glucose limitation},
 journal = {Mol Syst Biol},
 year = 2006,
 volume = 2,
 pages = 49,
 url = {http://dx.doi.org/10.1038/msb4100083},
 pdf = {/~knijnenburg/publications/Kresnowati_2006_Glucosepulse.pdf}
}



@ARTICLE{Ridder2006,
 AUTHOR = {De Ridder J AND Uren A AND Kool J AND Reinders M AND Wessels L},
 TITLE = {Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens},
 JOURNAL = {PLoS Comput Biol},
 YEAR = {2006},
 VOLUME = {2},
 PAGES = {e166},
 URL = {http://dx.doi.org/10.1371/journal.pcbi.0020166}
}


@ARTICLE{Lai2006,
 AUTHOR = {Lai C AND Reinders MJ AND Van't Veer LJ AND Wessels LF},
 TITLE = {A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets},
 JOURNAL = {BMC Bioinformatics},
 YEAR = {2006},
 VOLUME = {7},
 PAGES = {235},
 URL = {http://dx.doi.org/10.1186/1471-2105-7-235}
}

@ARTICLE{Fan2006,
 AUTHOR = {Fan C AND Oh DS AND Wessels L AND Weigelt B AND Nuyten DS AND Nobel AB AND Van't Veer LJ AND Perou CM},
 TITLE = {Concordance among gene-expression-based predictors for breast cancer},
 JOURNAL = {N Engl J Med},
 YEAR = {2006},
 VOLUME = {355},
 PAGES = {560--569},
 URL = {http://dx.doi.org/10.1056/NEJMoa052933}
}

@ARTICLE{Glas2006,
 AUTHOR = {Glas AM AND Floore A AND Delahaye LJ AND Witteveen AT AND Pover RC AND Bakx N AND Lahti-Domenici JS AND Bruinsma TJ AND Warmoes MO AND Bernards R AND Wessels LF AND Van't Veer LJ},
 TITLE = {Converting a breast cancer microarray signature into a high-throughput diagnostic test},
 JOURNAL = {BMC Genomics},
 YEAR = {2006},
 VOLUME = {7},
 PAGES = {278},
 URL = {http://dx.doi.org/10.1186/1471-2164-7-278}
}

@ARTICLE{Houwelingen2006,
 AUTHOR = {Van Houwelingen HC AND Bruinsma T AND Hart AA AND Van't Veer LJ AND Wessels LF},
 TITLE = {Cross-validated {C}ox regression on microarray gene expression data},
 JOURNAL = {Stat Med},
 YEAR = {2006},
 VOLUME = {25},
 PAGES = {3201--3216},
 URL = {http://dx.doi.org/10.1002/sim.2353}
}

@ARTICLE{Nuyten2006,
 AUTHOR = {Nuyten D AND Kreike B AND Hart A AND Chi JT AND Sneddon J AND Wessels L AND Peterse H AND Bartelink H AND Brown H AND Chang H AND Van de Vijver MJ},
 TITLE = {Predicting a local recurrence after breast-conserving therapy by gene expression profiling},
 JOURNAL = {Breast Cancer Res},
 YEAR = {2006},
 VOLUME = {8},
 PAGES = {R62},
 URL = {http://dx.doi.org/10.1186/bcr1614}
}

@ARTICLE{Roepman2006,
 AUTHOR = {Roepman P AND Kemmeren P AND Wessels LF AND Slootweg PJ AND Holstege FC},
 TITLE = {Multiple robust signatures for detecting lymph node metastasis in head and neck cancer},
 JOURNAL = {Cancer Res},
 YEAR = {2006},
 VOLUME = {66},
 PAGES = {2361--2366},
 URL = {http://dx.doi.org/10.1158/0008-5472.CAN-05-3960}
}


%%%%%%%%%%%%%%%%%%%% 2005 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

@ARTICLE{Knijnenburg2005,
 author = {Knijnenburg TA AND Reinders MJ AND Wessels LF},
 title = {The selection of relevant and non-redundant features to improve classification
 performance of microarray gene expression data},
 journal = {Eleventh Annual Conference of the Advanced School for Computing and Imaging},
 year = {2005},
 pdf = {/~knijnenburg/publications/Knijnenburg_2005_RelevantNonRedundantFeatures.pdf},
}




@ARTICLE{Vliet2005,
 AUTHOR = {Van Vliet MH AND Van Kempen GM AND Reinders MJ AND De Ridder D},
 TITLE = {Computational estimation of the composition of fat/oil mixtures containing interesterifications from gas and liquid chromatography data},
 JOURNAL = {J Am Oil Chem Soc},
 YEAR = {2005},
 VOLUME = {82},
 PAGES = {707--716},
 URL = {http://www.aocs.org/press/jabs.asp?abs_id=3820&issue=10&yr=2005}
}

@ARTICLE{Wessels2005,
 AUTHOR = {Wessels LF AND Reinders MJ AND Hart AA AND Veenman CJ AND Dai H AND He YD AND Van't Veer LJ},
 TITLE = {A protocol for building and evaluating predictors of disease state based on microarray data},
 JOURNAL = {Bioinformatics},
 YEAR = {2005},
 VOLUME = {21},
 PAGES = {3755--3762},
 URL = {http://dx.doi.org/10.1093/bioinformatics/bti429}
}

@ARTICLE{Beers2005,
 AUTHOR = {Van Beers EH AND Van Welsem T AND Wessels LF AND Li LF AND Oldenburg RA AND Devilee P AND Cornelisse CJ AND Verhoef S AND Hogervorst FB AND Van't Veer LJ AND Nederlof PM},
 TITLE = {Comparative genomic hybridization profiles in human {BRCA1} and {BRCA2} breast tumors highlight differential sets of genomic aberrations},
 JOURNAL = {Cancer Res},
 YEAR = {2005},
 VOLUME = {65},
 PAGES = {822--827},
 URL = {http://cancerres.aacrjournals.org/cgi/content/full/65/3/822}
}

@ARTICLE{Glas2005,
 AUTHOR = {Glas AM AND Kersten MJ AND Delahaye LJ AND Witteveen AT AND Kibbelaar RE AND Velds A AND Wessels LF AND Joosten P AND Kerkhoven RM AND Bernards R AND Van Krieken JH AND Kluin PM AND Van't Veer LJ AND De Jong D},
 TITLE = {Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment},
 JOURNAL = {Blood},
 YEAR = {2005},
 VOLUME = {105},
 PAGES = {301--307},
 URL = {http://dx.doi.org/10.1182/blood-2004-06-2298}
}

@ARTICLE{Hannemann2005,
 AUTHOR = {Hannemann J AND Oosterkamp HM AND Bosch CA AND Velds A AND WesselsLF AND Loo C AND Rutgers EJ AND Rodenhuis S AND Van de Vijver MJ},
 TITLE = {Changes in gene expression associated with response to neoadjuvant chemotherapy in breast cancer},
 JOURNAL = {J Clin Oncol},
 YEAR = {2005},
 VOLUME = {23},
 PAGES = {3331--3342},
 URL = {http://dx.doi.org/10.1200/JCO.2005.09.077}
}

@ARTICLE{Roepman2005,
 AUTHOR = {Roepman P AND Wessels LF AND Kettelarij N AND Kemmeren P AND Miles AJ AND Lijnzaad P AND Tilanus MG AND Koole R AND Hordijk GJ AND Van der Vliet PC AND Reinders MJ AND Slootweg PJ AND Holstege FC},
 TITLE = {An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas},
 JOURNAL = {Nat Genet},
 YEAR = {2005},
 VOLUME = {37},
 PAGES = {182--186},
 URL = {http://dx.doi.org/10.1038/ng1502}
}

@ARTICLE{Weigelt2005,
 AUTHOR = {Weigelt B AND Wessels LF AND Bosma AJ AND Glas AM AND Nuyten DS AND He YD AND Dai H AND Peterse JL AND Van't Veer LJ},
 TITLE = {No common denominator for breast cancer lymph node metastasis},
 JOURNAL = {Br J Cancer},
 YEAR = {2005},
 VOLUME = {93},
 PAGES = {924--932},
 URL = {http://dx.doi.org/10.1038/sj.bjc.6602794}
}


%%%%%%%%%%%%%%%%%%%% 2004 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



%%%%%%%%%%%%%%%%%%%% 2003 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



@ARTICLE{Staal2003,
 AUTHOR = {Staal FJ AND Van der Burg M AND Wessels LF AND Barendregt BH AND Baert MR AND Van den Burg CM AND Van Huffel C
 AND Langerak AW AND Van der Velden VH AND Reinders MJ AND Van Dongen JJ},
 TITLE = {{DNA} microarrays for comparison of gene expression profiles between diagnosis and relapse in precursor-{B} acute
 lymphoblastic leukemia: choice of technique and purification influence the identification of potential diagnostic markers},
 JOURNAL = {Leukemia},
 YEAR = {2003},
 VOLUME = {17},
 PAGES = {1324--1332},
 URL = {http://dx.doi.org/10.1038/sj.leu.2402974}
}

@ARTICLE{Weigelt2003,
 AUTHOR = {Weigelt B AND Glas AM AND Wessels LF AND Witteveen AT AND Peterse JL AND Van't Veer LJ},
 TITLE = {Gene expression profiles of primary breast tumors maintained in distant metastases},
 JOURNAL = {P Natl Acad Sci USA},
 YEAR = {2003},
 VOLUME = {100},
 PAGES = {15901--15905},
 URL = {http://dx.doi.org/10.1073/pnas.2634067100}
}


%%%%%%%%%%%%%%%%%%%% 2002 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%




@ARTICLE{Wessels2002,
 AUTHOR = {Wessels LF AND Van Welsem T AND Hart AA AND Van't Veer LJ AND Reinders MJ AND Nederlof PM},
 TITLE = {Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for {BRCA1} tumors},
 JOURNAL = {Cancer Res},
 YEAR = {2002},
 VOLUME = {62},
 PAGES = {7110--7117},
 URL = {http://cancerres.aacrjournals.org/cgi/content/full/62/23/7110}
}

@ARTICLE{Someren2002,
 AUTHOR = {Van Someren EP AND Wessels LF AND Backer E AND Reinders MJ},
 TITLE = {Genetic network modeling},
 JOURNAL = {Pharmacogenomics},
 YEAR = {2002},
 VOLUME = {3},
 PAGES = {507--525},
 URL = {http://dx.doi.org/10.1517/14622416.3.4.507}
}


%%%%%%%%%%%%%%%%%%%% 2001 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



@ARTICLE{Wessels2001,
 AUTHOR = {Wessels LF AND Van Someren EP AND Reinders MJ},
 TITLE = {A comparison of genetic network models},
 JOURNAL = {Pac Symp Biocomput},
 YEAR = {2001},
 PAGES = {508--519},
 URL = {http://psb.stanford.edu/psb-online/proceedings/psb01/abstracts/p508.html}
}


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