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51

Insertional mutagenesis in a HER2-positive breast cancer model reveals ERAS as a driver of cancer and therapy resistance

Ikink, Gerjon J., Boer, Mandy, Bakker, Elvira R. M., Vendel-Zwaagstra, Annabel, Klijn, Chris, ten Hoeve, Jelle, Jonkers, Jos, Wessels, Lodewyk F., Hilkens, John

Journal:

Year:

2018

Language:

english

File:

PDF, 5.40 MB

english, 2018

52

Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis

Staiger, Christine, Cadot, Sidney, Györffy, Balázs, Wessels, Lodewyk F. A., Klau, Gunnar W.

Journal:

Frontiers in Genetics

Year:

2013

Language:

english

File:

PDF, 2.57 MB

english, 2013

53

PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors

Mourragui, Soufiane, Loog, Marco, van de Wiel, Mark A, Reinders, Marcel J T, Wessels, Lodewyk F A

Journal:

Year:

2019

Language:

english

File:

PDF, 751 KB

english, 2019

54

Radiation-Associated Breast Tumors Display a Distinct Gene Expression Profile

Annegien Broeks, Linde M. Braaf, Lodewyk F.A. Wessels, Marc van de Vijver, Marie L. De Bruin, Marilyn Stovall, Nicola S. Russell, Flora E. van Leeuwen, Laura J. Van 't Veer

Journal:

International Journal of Radiation Oncology*Biology*Physics

Year:

2010

Language:

english

File:

PDF, 382 KB

english, 2010

55

[Lecture Notes in Computer Science] Pattern Recognition in Bioinformatics Volume 7036 || A New Gene Selection Method Based on Random Subspace Ensemble for Microarray Cancer Classification

Loog, Marco, Wessels, Lodewyk, Reinders, Marcel J. T., de Ridder, Dick

Year:

2011

Language:

english

File:

PDF, 183 KB

english, 2011

56

SPIE Proceedings [SPIE International Symposium on Biomedical Optics - San Jose, CA (Saturday 19 January 2002)] Biomedical Nanotechnology Architectures and Applications - Computer-based optimization of high-throughput peptide screening

van der Veen, Peter J., Wessels, Lodewyk F. A., Slootstra, Jerry W., Meloen, Rob H., Reinders, Marcel J. T., Hellendoorn, J., Bornhop, Darryl J., Dunn, David A., Mariella, Jr., Raymond P., Murphy, Cat

Year:

2002

Language:

english

File:

PDF, 332 KB

english, 2002

57

Identification of a Druggable Pathway Controlling Glioblastoma Invasiveness

Pencheva, Nora, de Gooijer, Mark C., Vis, Daniel J., Wessels, Lodewyk F.A., Würdinger, Tom, van Tellingen, Olaf, Bernards, René

Journal:

Year:

2017

Language:

english

File:

PDF, 7.79 MB

english, 2017

58

Comparative genomic analysis of oral versus laryngeal and pharyngeal cancer

Vossen, David M., Verhagen, Caroline V.M., Verheij, Marcel, Wessels, Lodewyk F.A., Vens, Conchita, van den Brekel, Michiel W.M.

Journal:

Year:

2018

Language:

english

File:

PDF, 887 KB

english, 2018

59

Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis

Bismeijer, Tycho, Canisius, Sander, Wessels, Lodewyk F. A., Leslie, Christina S.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.04 MB

english, 2018

60

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

Wouter Meuleman, Judith YMN Engwegen, Marie-Christine W Gast, Jos H Beijnen, Marcel JT Reinders, Lodewyk FA Wessels

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 378 KB

english, 2008

61

O20: Discovering genetic profiles by array-CGH in familial breast tumors

Erik H. van Beers, Simon A. Joosse, Frans B. Hogervorst, Lodewyk F. Wessels, Rogier A. Oldenburg, Peter Devilee, Cees J. Cornelisse, Senno Verhoef, Laura J. van t Veer, Petra M. Nederlof

Journal:

European Journal of Medical Genetics

Year:

2005

Language:

english

File:

PDF, 52 KB

english, 2005

62

Applications of DNA integrating elements: Facing the bias bully

de Jong, Johann, Wessels, Lodewyk F A, van Lohuizen, Maarten, de Ridder, Jeroen, Akhtar, Waseem

Journal:

Mobile Genetic Elements

Year:

2014

Language:

english

File:

PDF, 523 KB

english, 2014

63

Are contralateral parenchymal enhancement on dynamic contrast-enhanced MRI and genomic ER-pathway activity in ER-positive/HER2-negative breast cancer related?

van der Velden, Bas H.M., Bismeijer, Tycho, Canisius, Sander, Loo, Claudette E., Lips, Esther H., Wesseling, Jelle, Viergever, Max A., Wessels, Lodewyk F.A., Gilhuijs, Kenneth G.A.

Journal:

European Journal of Radiology

Year:

2019

Language:

english

File:

PDF, 490 KB

english, 2019

64

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

Theo A Knijnenburg, Jean-Marc G Daran, Marcel A van den Broek, Pascale AS Daran-Lapujade, Johannes H de Winde, Jack T Pronk, Marcel JT Reinders, Lodewyk FA Wessels

Journal:

Year:

2009

Language:

english

File:

PDF, 1.20 MB

english, 2009

65

Biclustering Sparse Binary Genomic Data

Uitert, Miranda van, Meuleman, Wouter, Wessels, Lodewyk

Journal:

Journal of Computational Biology

Year:

2008

Language:

english

File:

PDF, 601 KB

english, 2008

66

SPIE Proceedings [SPIE BiOS 2001 The International Symposium on Biomedical Optics - San Jose, CA (Saturday 20 January 2001)] Microarrays: Optical Technologies and Informatics - Genetic network models: a comparative study

van Someren, Eugene P., Wessels, Lodewyk F. A., Reinders, Marcel J. T., Bittner, Michael L., Chen, Yidong, Dorsel, Andreas N., Dougherty, Edward R.

Year:

2001

Language:

english

File:

PDF, 1.12 MB

english, 2001

67

Comparative Network Reconstruction using mixed integer programming

Bosdriesz, Evert, Prahallad, Anirudh, Klinger, Bertram, Sieber, Anja, Bosma, Astrid, Bernards, René, Blüthgen, Nils, Wessels, Lodewyk F A

Journal:

Year:

2018

Language:

english

File:

PDF, 799 KB

english, 2018

68

Integrative analysis of genomic amplification-dependent expression and loss-of-function screen identifies ASAP1 as a driver gene in triple-negative breast cancer progression

He, Jichao, McLaughlin, Ronan P., van der Beek, Lambert, Canisius, Sander, Wessels, Lodewyk, Smid, Marcel, Martens, John W. M., Foekens, John A., Zhang, Yinghui, van de Water, Bob

Journal:

Year:

2020

Language:

english

File:

PDF, 3.93 MB

english, 2020

69

Cross-species comparison of aCGH data from mouse and humanBRCA1- andBRCA2-mutated breast cancers

Henne Holstege, Erik van Beers, Arno Velds, Xiaoling Liu, Simon A Joosse, Sjoerd Klarenbeek, Eva Schut, Ron Kerkhoven, Christiaan N Klijn, Lodewyk FA Wessels, Petra M Nederlof, Jos Jonkers

Journal:

Year:

2010

Language:

english

File:

PDF, 3.61 MB

english, 2010

70

Platform comparisons for identification of breast cancers with a BRCA-like copy number profile

Schouten, Philip C., Dyk, Ewald, Braaf, Linde M., Mulder, Lennart, Lips, Esther H., Ronde, Jorma J., Holtman, Laura, Wesseling, Jelle, Hauptmann, Michael, Wessels, Lodewyk F. A., Linn, Sabine C., Nede

Journal:

Breast Cancer Research and Treatment

Year:

2013

Language:

english

File:

PDF, 1.04 MB

english, 2013

71

ElevatedAPOBEC3BCorrelates with Poor Outcomes for Estrogen-Receptor-Positive Breast Cancers

Sieuwerts, Anieta M., Willis, Scooter, Burns, Michael B., Look, Maxime P., Gelder, Marion E. Meijer-Van, Schlicker, Andreas, Heideman, Marinus R., Jacobs, Heinz, Wessels, Lodewyk, Leyland-Jones, Brian

Journal:

Hormones and Cancer

Year:

2014

Language:

english

File:

PDF, 728 KB

english, 2014

72

Approximating multivariate posterior distribution functions from Monte Carlo samples for sequential Bayesian inference

Thijssen, Bram, Wessels, Lodewyk F. A., Hutson, Alan D

Journal:

Year:

2020

Language:

english

File:

PDF, 3.22 MB

english, 2020

73

Chromatin Landscapes of Retroviral and Transposon Integration Profiles

de Jong, Johann, Akhtar, Waseem, Badhai, Jitendra, Rust, Alistair G., Rad, Roland, Hilkens, John, Berns, Anton, van Lohuizen, Maarten, Wessels, Lodewyk F. A., de Ridder, Jeroen, Roth, Monica J.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.38 MB

english, 2014

74

CD4+ T cell help creates memory CD8+ T cells with innate and help-independent recall capacities

Ahrends, Tomasz, Busselaar, Julia, Severson, Tesa M., Bąbała, Nikolina, de Vries, Evert, Bovens, Astrid, Wessels, Lodewyk, van Leeuwen, Fred, Borst, Jannie

Journal:

Nature Communications

Year:

2019

File:

PDF, 2.68 MB

2019

75

KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data

Jorma J de Ronde, Christiaan Klijn, Arno Velds, Henne Holstege, Marcel JT Reinders, Jos Jonkers, Lodewyk FA Wessels

Journal:

BMC Research Notes

Year:

2010

Language:

english

File:

PDF, 945 KB

english, 2010

76

SERPINA6, BEX1, AGTR1, SLC26A3, and LAPTM4B are markers of resistance to neoadjuvant chemotherapy in HER2-negative breast cancer

Jorma J. de Ronde, Esther H. Lips, Lennart Mulder, Andrew D. Vincent, Jelle Wesseling, Marja Nieuwland, Ron Kerkhoven, Marie-Jeanne T. F. D. Vrancken Peeters, Gabe S. Sonke, Sjoerd Rodenhuis, Lodewyk

Journal:

Breast Cancer Research and Treatment

Year:

2013

Language:

english

File:

PDF, 614 KB

english, 2013

77

Genome-wide epigenetic profiling of breast cancer tumors treated with aromatase inhibitors

Nevedomskaya, Ekaterina, Wessels, Lodewyk, Zwart, Wilbert

Journal:

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

78

Do predictive signatures really predict response to cancer chemotherapy?

Borst, Piet, Wessels, Lodewyk

Journal:

Year:

2010

Language:

english

File:

PDF, 1.01 MB

english, 2010

79

Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer

Nevedomskaya, Ekaterina, Stelloo, Suzan, van der Poel, Henk G., de Jong, Jeroen, Wessels, Lodewyk F.A., Bergman, Andries M., Zwart, Wilbert

Journal:

Year:

2016

Language:

english

File:

PDF, 337 KB

english, 2016

80

A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence

Canisius, Sander, Martens, John W. M., Wessels, Lodewyk F. A.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.19 MB

english, 2016

81

A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers

Šuštić, Tonći, van Wageningen, Sake, Bosdriesz, Evert, Reid, Robert J. D., Dittmar, John, Lieftink, Cor, Beijersbergen, Roderick L., Wessels, Lodewyk F. A., Rothstein, Rodney, Bernards, René

Journal:

Genome Medicine

Year:

2018

Language:

english

File:

PDF, 3.63 MB

english, 2018

82

Genomic data integration by WON-PARAFAC identifies interpretable factors for predicting drug-sensitivity in vivo

Kim, Yongsoo, Bismeijer, Tycho, Zwart, Wilbert, Wessels, Lodewyk F. A., Vis, Daniel J.

Journal:

Nature Communications

Year:

2019

File:

PDF, 3.83 MB

2019

83

Selection of Patients for Hepatic Surgery of Colorectal Cancer Liver Metastasis Based on Genomic Aberrations

Bruin, Sjoerd C., Ronde, Jorma J., Wiering, Bas, Braaf, Linde M., Wilt, J. H. W., Vincent, Andrew D., Velthuysen, Marie-Louise F., Ruers, T. J., Wessels, Lodewyk F.A., Veer, Laura J.

Journal:

Annals of Surgical Oncology

Year:

2013

Language:

english

File:

PDF, 599 KB

english, 2013

84

Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets

Farazi, Thalia A, ten Hoeve, Jelle J, Brown, Miguel, Mihailovic, Aleksandra, Horlings, Hugo M, van de Vijver, Marc J, Tuschl, Thomas, Wessels, Lodewyk FA

Journal:

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

85

Integrative modeling identifies key determinants of inhibitor sensitivity in breast cancer cell lines

Jastrzebski, Katarzyna, Thijssen, Bram, Kluin, Roelof JC, de Lint, Klaas, Majewski, Ian J, Beijersbergen, Roderick L., Wessels, Lodewyk F.A.

Journal:

Cancer Research

Year:

2018

Language:

english

File:

PDF, 10.81 MB

english, 2018

86

Specific genomic aberrations in primary colorectal cancer are associated with liver metastases

Sjoerd C Bruin, Christiaan Klijn, Gerrit-Jan Liefers, Linde M Braaf, Simon A Joosse, Eric H van Beers, Victor J Verwaal, Hans Morreau, Lodewyk F Wessels, Marie-Louise F van Velthuysen, Rob AEM Tollena

Journal:

Year:

2010

Language:

english

File:

PDF, 682 KB

english, 2010

87

[Lecture Notes in Computer Science] Pattern Recognition in Bioinformatics Volume 7036 || A New Framework for Co-clustering of Gene Expression Data

Loog, Marco, Wessels, Lodewyk, Reinders, Marcel J. T., de Ridder, Dick

Year:

2011

Language:

english

File:

PDF, 839 KB

english, 2011

88

PROTEIN COMPLEX PREDICTION USING AN INTEGRATIVE BIOINFORMATICS APPROACH

VAN BERLO, ROGIER J. P., WESSELS, LODEWYK F. A., DE RIDDER, DICK, REINDERS, MARCEL J. T.

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2007

Language:

english

File:

PDF, 638 KB

english, 2007

89

PTEN Loss in E-Cadherin-Deficient Mouse Mammary Epithelial Cells Rescues Apoptosis and Results in Development of Classical Invasive Lobular Carcinoma

Boelens, Mirjam C., Nethe, Micha, Klarenbeek, Sjoerd, de Ruiter, Julian R., Schut, Eva, Bonzanni, Nicola, Zeeman, Amber L., Wientjens, Ellen, van der Burg, Eline, Wessels, Lodewyk, van Amerongen, René

Journal:

Year:

2016

Language:

english

File:

PDF, 9.15 MB

english, 2016

90

Radiogenomic Analysis of Breast Cancer by Linking MRI Phenotypes with Tumor Gene Expression

Bismeijer, Tycho, van der Velden, Bas H. M., Canisius, Sander, Lips, Esther H., Loo, Claudette E., Viergever, Max A., Wesseling, Jelle, Gilhuijs, Kenneth G. A., Wessels, Lodewyk F. A.

Journal:

Year:

2020

File:

PDF, 1.80 MB

2020

91

PKA-induced phosphorylation of ERα at serine 305 and high PAK1 levels is associated with sensitivity to tamoxifen in ER-positive breast cancer

Marleen Kok, Wilbert Zwart, Caroline Holm, Renske Fles, Michael Hauptmann, Laura J. Van’t Veer, Lodewyk F. A. Wessels, Jacques Neefjes, Olle Stål, Sabine C. Linn, Göran Landberg, Rob Michalides

Journal:

Breast Cancer Research and Treatment

Year:

2011

Language:

english

File:

PDF, 683 KB

english, 2011

92

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

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

Journal:

Year:

2007

Language:

english

File:

PDF, 570 KB

english, 2007

93

Quantitative imaging of focal adhesion dynamics and their regulation by HGF and Rap1 signaling

Spanjaard, Emma, Smal, Ihor, Angelopoulos, Nicos, Verlaan, Ingrid, Matov, Alexandre, Meijering, Erik, Wessels, Lodewyk, Bos, Hans, de Rooij, Johan

Journal:

Experimental Cell Research

Year:

2015

Language:

english

File:

PDF, 5.32 MB

english, 2015

94

SPIE Proceedings [SPIE International Symposium on Biomedical Optics - San Jose, CA (Saturday 19 January 2002)] Functional Monitoring and Drug-Tissue Interaction - Reverse engineering of genetic networks through multicriterion optimization

van Someren, Eugene P., Wessels, Lodewyk F. A., Reinders, Marcel J. T., Backer, Eric, Kessler, Manfred D., Mueller, Gerhard J.

Year:

2002

Language:

english

File:

PDF, 1.60 MB

english, 2002

95

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

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

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 678 KB

english, 2016

96

Lack of Genomic Heterogeneity at High-Resolution aCGH between Primary Breast Cancers and Their Paired Lymph Node Metastases

Vollebergh, Marieke A., Klijn, Christiaan, Schouten, Philip C., Wesseling, Jelle, Israeli, Danielle, Ylstra, Bauke, Wessels, Lodewyk F.A., Jonkers, Jos, Linn, Sabine C., van Diest, Paul J.

Journal:

Year:

2014

Language:

english

File:

PDF, 4.70 MB

english, 2014

97

Artifacts of Markov blanket filtering based on discretized features in small sample size applications

Theo A. Knijnenburg, Marcel J.T. Reinders, Lodewyk F.A. Wessels

Journal:

Pattern Recognition Letters

Year:

2006

Language:

english

File:

PDF, 153 KB

english, 2006

98

[Lecture Notes in Computer Science] Pattern Recognition in Bioinformatics Volume 7036 || PAAA: A Progressive Iterative Alignment Algorithm Based on Anchors

Loog, Marco, Wessels, Lodewyk, Reinders, Marcel J. T., de Ridder, Dick

Year:

2011

Language:

english

File:

PDF, 209 KB

english, 2011

99

Defining chromosomal translocation risks in cancer

Hogenbirk, Marc A., Heideman, Marinus R., de Rink, Iris, Velds, Arno, Kerkhoven, Ron M., Wessels, Lodewyk F. A., Jacobs, Heinz

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 769 KB

english, 2016

100

Module-Based Outcome Prediction Using Breast Cancer Compendia

van Vliet, Martin H., Klijn, Christiaan N., Wessels, Lodewyk F. A., Reinders, Marcel J. T., Wu, Xiaolin

Journal:

Year:

2007

Language:

english

File:

PDF, 409 KB

english, 2007

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